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Sample records for interactive identification key

  1. Illustrated Plant Identification Keys: An Interactive Tool to Learn Botany

    ERIC Educational Resources Information Center

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

    2011-01-01

    An Interactive Dichotomous Key (IDK) for 390 "taxa" of vascular plants from the Ria de Aveiro, available on a website, was developed to help teach botany to school and universitary students. This multimedia tool includes several links to Descriptive and Illustrated Glossaries. Questionnaires answered by high-school and undergraduate students about…

  2. Illustrated Plant Identification Keys: An Interactive Tool to Learn Botany

    ERIC Educational Resources Information Center

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

    2011-01-01

    An Interactive Dichotomous Key (IDK) for 390 "taxa" of vascular plants from the Ria de Aveiro, available on a website, was developed to help teach botany to school and universitary students. This multimedia tool includes several links to Descriptive and Illustrated Glossaries. Questionnaires answered by high-school and undergraduate students about

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

    PubMed Central

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

    2014-01-01

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

  4. Development and validation of IIKC: an interactive identification key for Culicoides (Diptera: Ceratopogonidae) females from the Western Palaearctic region

    PubMed Central

    2012-01-01

    Background and methods The appearance of bluetongue virus (BTV) in 2006 within northern Europe exposed a lack of expertise and resources available across this region to enable the accurate morphological identification of species of Culicoides Latreille biting midges, some of which are the major vectors of this pathogen. This work aims to organise extant Culicoides taxonomic knowledge into a database and to produce an interactive identification key for females of Culicoides in the Western Palaearctic (IIKC: Interactive identification key for Culicoides). We then validated IIKC using a trial carried out by six entomologists based in this region with variable degrees of experience in identifying Culicoides. Results The current version of the key includes 98 Culicoides species with 10 morphological variants, 61 descriptors and 837 pictures and schemes. Validation was carried out by six entomologists as a blind trial with two users allocated to three classes of expertise (beginner, intermediate and advanced). Slides were identified using a median of seven steps and seven minutes and user confidence in the identification varied from 60% for failed identifications to a maximum of 80% for successful ones. By user class, the beginner group successfully identified 44.6% of slides, the intermediate 56.8% and the advanced 74.3%. Conclusions Structured as a multi-entry key, IIKC is a powerful database for the morphological identification of female Culicoides from the Western Palaearctic region. First developed for use as an interactive identification key, it was revealed to be a powerful back-up tool for training new taxonomists and to maintain expertise level. The development of tools for arthropod involvement in pathogen transmission will allow clearer insights into the ecology and dynamics of Culicoides and in turn assist in understanding arbovirus epidemiology. PMID:22776566

  5. New distribution records for the rare genus Afrotremex Pasteels (Siricidae: Hymenoptera) and provision of interactive Lucid identification keys to species

    PubMed Central

    Goulet, Henri

    2015-01-01

    Abstract Background Afrotremex Pasteels, 1951 is a rare genus of wasps endemic to the Afrotropical region, containing 6 species represented by 14 specimens. Specimens were previously only recorded from central Africa: Cameroon, Congo, Democratic Republic of Congo, Gabon and Uganda. New information Here we record two additional specimens housed in the Natural History Museum in London (BMNH), one of which is a male of A. xylophagus Goulet, 2014 collected in Ghana (previously Gold Coast). This record extends the known distribution of the genus into west Africa, and represents the second known male specimen for the genus. The other BMNH specimen is a female paratype of A. violaceus Pasteels, 1951 collected in the Democratic Republic of Congo. We provide high quality photographs of these additional two specimens. Images of all six known species are openly available online on WaspWeb. In addition we have developed interactive online Lucid Matrix and Lucid Phoenix identification keys to the species, which are openly available on WaspWeb at: http://www.waspweb.org/Siricoidea/Siricidae/Keys/index.htm PMID:26696771

  6. Afrotropical Ophioninae (Hymenoptera, Ichneumonidae): an update of Gauld and Mitchell’s revision, including two new species and an interactive matrix identification key

    PubMed Central

    Rousse, Pascal; van Noort, Simon

    2014-01-01

    Abstract The revision of the Afrotropical Ophioninae is updated, based on the examination of about 800–900 individuals in the South African and European museum collections. A robust interactive matrix key was built to provide quick and reliable identifications. The key is available online at http://www.waspweb.org. Two new species are described: Dicamptus maxipol sp. n. and Enicospilus gauldetmitchellorum sp. n. Numerous new distribution and biological records are provided, and noticeable morphological intra-specific variations are detailed. Enicospilus batus Gauld & Mitchell, syn. n. is considered as a junior synonym of Enicospilus luebberti (Enderlein). PMID:25709521

  7. Identification of Key Barriers in Workforce Development

    SciTech Connect

    2008-03-31

    This report documents the identification of key barriers in the development of an adequate national security workforce as part of the National Security Preparedness Project, being performed under a Department of Energy/National Nuclear Security Administration grant. Many barriers exist that prevent the development of an adequate number of propertly trained national security personnel. Some barriers can be eliminated in a short-term manner, whereas others will involve a long-term strategy that takes into account public policy.

  8. Species Identification Key of Korean Mammal Hair

    PubMed Central

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

    2014-01-01

    ABSTRACT The hair microstructures of Korean terrestrial mammals from 23 species (22 wild and one domestic) were analyzed using light and scanning electron microscopy (SEM) to construct a hair identification key. The hairs were examined using the medulla structures and cuticular scales of guard hairs from the dorsal regions of mature adult animals. All cuticular scale structures in the hair of Rodentia, Lagomorpha, Carnivora and Insectivora showed the petal pattern, and those of Artiodactyla and Chiroptera showed the wave pattern and coronal pattern, respectively. Rodentia, Lagomorpha and Carnivora showed multicellular, and Insectivora and Artiodactyla showed unicellular regular, mesh or columnar in the medulla structures, respectively. Chiroptera did not show the medulla structures in their hair. We found that it is possible to distinguish between species and order based on general appearance, medulla structures and cuticular scales. Thus, we constructed a hair identification key with morphological characteristics from each species. This study suggests that hair identification keys could be useful in fields, such as forensic science, food safety and foraging ecology. PMID:24451929

  9. Molecular identification key of the family Streptococcaceae.

    PubMed

    Kany, Istvn; Nagy, Dnes

    2014-03-01

    The gene order conservation (GOC) between the species of family Streptococcaceae was analysed. The rate of GOC in the strains belonging to the same species is 70% or more. When we compared different species belonging to the same genus, the rate of GOC was 30-47% while it was below 20% when the species were from different genera. A molecular identification key was established for identifying those genera and species within the family Streptococcaceae which have an already known full genome sequence (24 Streptococcus and 2 Lactococcus species). Identical genome parts of the species belonging to the same genus were used for determination of genera. These are the sections surrounding the replication origin dnaA, the sequence from gene phaB to the gene accA, and the sequence of alr acpS secA. Sections around the genes pepX, leuS and rplM were used for identifying the species. The gene order analysis and data in molecular identification key showed that S. uberis and S. parauberis also belong to the same species, and our suggestion for their new names is S. uberis subsp. uberis and S uberis subsp. parauberis. Based on this data, a new definition of bacterial species is proposed: two isolates belong to the same species if the order of the genes in their genomes is almost identical. PMID:24631752

  10. Simple Web-based interactive key development software (WEBiKEY) and an example key for Kuruna (Poaceae: Bambusoideae)1

    PubMed Central

    Attigala, Lakshmi; De Silva, Nuwan I.; Clark, Lynn G.

    2016-01-01

    Premise of the study: Programs that are user-friendly and freely available for developing Web-based interactive keys are scarce and most of the well-structured applications are relatively expensive. WEBiKEY was developed to enable researchers to easily develop their own Web-based interactive keys with fewer resources. Methods and Results: A Web-based multiaccess identification tool (WEBiKEY) was developed that uses freely available Microsoft ASP.NET technologies and an SQL Server database for Windows-based hosting environments. WEBiKEY was tested for its usability with a sample data set, the temperate woody bamboo genus Kuruna (Poaceae). Conclusions: WEBiKEY is freely available to the public and can be used to develop Web-based interactive keys for any group of species. The interactive key we developed for Kuruna using WEBiKEY enables users to visually inspect characteristics of Kuruna and identify an unknown specimen as one of seven possible species in the genus. PMID:27144109

  11. Identification of key residues in rabbit liver microsomal cytochrome P450 2B4: importance in interactions with NADPH-cytochrome P450 reductase.

    PubMed

    Lehnerer, M; Schulze, J; Achterhold, K; Lewis, D F; Hlavica, P

    2000-01-01

    A cytochrome P450 2B4 (CYP2B4) model was used to select key residues supposed to serve in interactions with NADPH-cytochrome P450 reductase (P450R). Eight amino acid residues located on the surface of the hemoprotein were chosen for mutagenesis experiments with CYP2B4(Delta2-27) lacking the NH(2)-terminal signal anchor sequence. The mutated proteins were expressed in Escherichia coli, purified, and characterized by EPR- and CD-spectral analysis. Replacement of histidine 226 with alanine caused a 3.8-fold fall in the affinity for P450R with undisturbed reductive capacity of the system. Similarly, the K225A, R232A, and R253A variants exhibited P450R-directed activity that was depressed to about half that of the control enzyme, suggesting that the deletion of positive charges on the surface of CYP2B4(Delta2-27) resulted in impaired electrostatic contacts with complementary amino acids on the P450R protein. While the Y235A mutant did not show appreciably perturbed reduction activity, the conservative substitution with alanine of the phenylalanine residues at positions 223 and 227 gave a 2.1- to 6. 1-fold increase in the K(m) values with unchanged V(max); this was attributed to the disruption of hydrophobic forces rather than to global structural rearrangement(s) of the engineered pigments. Measurement of the stoichiometry of aerobic NADPH consumption and H(2)O(2) formation revealed the oxyferrous forms of the F223A, H226A, and F227A mutants to autoxidize more readily owing to less efficient coupling of the systems. Noteworthy, the F244A enzyme did not exhibit significant reduction activity, suggesting a pivotal role of Phe-244 in the functional coupling of P450R. The residue was predicted to constitute part of an obligatory electron transfer conduit through pi-stacking with Phe-296 located close to the heme unit. All of the residues examined reside in the putative G helix of CYP2B4, so that this domain obviously defines part of the binding site for P450R. PMID:10731679

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

    PubMed Central

    2013-01-01

    Abstract Images are a critical part of the identification process because they enable direct, immediate and relatively unmediated comparisons between a specimen being identified and one or more reference specimens. The Carices Interactive Visual Identification Key (CIVIK) is a novel tool for identification of North American Carex species, the largest vascular plant genus in North America, and two less numerous closely-related genera, Cymophyllus and Kobresia. CIVIK incorporates 1288 high-resolution tiled image sets that allow users to zoom in to view minute structures that are crucial at times for identification in these genera. Morphological data are derived from the earlier Carex Interactive Identification Key (CIIK) which in turn used data from the Flora of North America treatments. In this new iteration, images can be viewed in a grid or histogram format, allowing multiple representations of data. In both formats the images are fully zoomable. PMID:24723777

  13. Keys to Biological Identification: Their Role and Construction.

    ERIC Educational Resources Information Center

    Tilling, Steve

    1984-01-01

    Argues that the decreasing priority given to training in identification skills has hampered the development of several biological disciplines. The importance of taxonomic keys in acquiring the necessary skills is stressed and a range of such aids (with methods for their construction) is described and discussed. (Author/JN)

  14. Temporal Dynamics and the Identification of Musical Key

    PubMed Central

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

    2013-01-01

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

  15. Interaction: The Key to Successful Distance Learning.

    ERIC Educational Resources Information Center

    Byers, Al

    This paper discusses the impediments to distance education (DE) programs and the critical value of interaction and dialog in DE learning environments. The types of interaction to be considered when designing a DE program are listed, including interaction to increase learning, to increase participation, to develop communication, to receive…

  16. Key Results of Interaction Models with Centering

    ERIC Educational Resources Information Center

    Afshartous, David; Preston, Richard A.

    2011-01-01

    We consider the effect on estimation of simultaneous variable centering and interaction effects in linear regression. We technically define, review, and amplify many of the statistical issues for interaction models with centering in order to create a useful and compact reference for teachers, students, and applied researchers. In addition, we

  17. Identification key for coryneform bacteria derived by numerical taxonomic studies.

    PubMed

    Seiler, H

    1983-05-01

    Six main groups were formed from a complete linkage dendrogram on 557 bacteria tested for 53 physiological features. The organisms were obtained from culture collections and included representatives of the following genera: Arthrobacter, Brevibacterium, Caseobacter, Cellulomonas, Corynebacterium, Curtobacterium, Micrococcus, Microbacterium, Mycobacterium, Nocardia, Oerskovia and Rhodococcus. The six groups were individually subjected to a numerical taxonomic analysis based on linkage maps, which resulted in a total of 33 subclusters. An identification key to determine the affiliation of the bacteria to the six main clusters and five group-specific schemes is presented. Reference strains are proposed for the 33 subclusters. PMID:6413644

  18. Hyperfine interactions, the key to multiquark physics

    SciTech Connect

    Likpink, H.J.

    1988-08-08

    Clues in the search for a fundamental description of hadron physics based on QCD may be obtained from a phenomenological constituent quark model in which the color-electric force binds quarks into saturated color-singlet hadrons, and finer details of the spectrum and multiquark physics are dominated by the color-magnetic hyperfine interaction. 47 refs.

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

    PubMed

    Scharf, Sara T

    2009-01-01

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

  20. Identification of key recombinants in multiplex SMA families

    SciTech Connect

    Van Der Steege, G.; Cobben, J.M.; Osinga, J.

    1994-07-01

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

  1. Decoding time for the identification of musical key.

    PubMed

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

    2015-01-01

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

  2. Classification and the Dichotomous Key: Tools for Teaching Identification

    ERIC Educational Resources Information Center

    Watson, Sandy; Miller, Ted

    2009-01-01

    Classification is a vital science-process skill for all students to master. Understanding dichotomous keys as a means of classification enables students to better comprehend large amounts of information and understand how to organize, compare and contrast, and analyze that information. To biology students, mastering the dichotomous key provides an…

  3. Identification of the Key Fields and Their Key Technical Points of Oncology by Patent Analysis

    PubMed Central

    Zhang, Ting; Chen, Juan; Jia, Xiaofeng

    2015-01-01

    Background This paper aims to identify the key fields and their key technical points of oncology by patent analysis. Methodology/Principal Findings Patents of oncology applied from 2006 to 2012 were searched in the Thomson Innovation database. The key fields and their key technical points were determined by analyzing the Derwent Classification (DC) and the International Patent Classification (IPC), respectively. Patent applications in the top ten DC occupied 80% of all the patent applications of oncology, which were the ten fields of oncology to be analyzed. The number of patent applications in these ten fields of oncology was standardized based on patent applications of oncology from 2006 to 2012. For each field, standardization was conducted separately for each of the seven years (2006–2012) and the mean of the seven standardized values was calculated to reflect the relative amount of patent applications in that field; meanwhile, regression analysis using time (year) and the standardized values of patent applications in seven years (2006–2012) was conducted so as to evaluate the trend of patent applications in each field. Two-dimensional quadrant analysis, together with the professional knowledge of oncology, was taken into consideration in determining the key fields of oncology. The fields located in the quadrant with high relative amount or increasing trend of patent applications are identified as key ones. By using the same method, the key technical points in each key field were identified. Altogether 116,820 patents of oncology applied from 2006 to 2012 were retrieved, and four key fields with twenty-nine key technical points were identified, including “natural products and polymers” with nine key technical points, “fermentation industry” with twelve ones, “electrical medical equipment” with four ones, and “diagnosis, surgery” with four ones. Conclusions/Significance The results of this study could provide guidance on the development direction of oncology, and also help researchers broaden innovative ideas and discover new technological opportunities. PMID:26599967

  4. Statistical mechanics approach to lock-key supramolecular chemistry interactions.

    PubMed

    Odriozola, Gerardo; Lozada-Cassou, Marcelo

    2013-03-01

    In the supramolecular chemistry field, intuitive concepts such as molecular complementarity and molecular recognition are used to explain the mechanism of lock-key associations. However, these concepts lack a precise definition, and consequently this mechanism is not well defined and understood. Here we address the physical basis of this mechanism, based on formal statistical mechanics, through Monte Carlo simulation and compare our results with recent experimental data for charged or uncharged lock-key colloids. We find that, given the size range of the molecules involved in these associations, the entropy contribution, driven by the solvent, rules the interaction, over that of the enthalpy. A universal behavior for the uncharged lock-key association is found. Based on our results, we propose a supramolecular chemistry definition. PMID:23521272

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

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

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

  6. A Key for the Identification of Eighteen Common Timbers.

    ERIC Educational Resources Information Center

    Thomas, P. A.

    1991-01-01

    Dichotomous key for 18 woods in common domestic and architectural use in Britain is provided. It is based upon structures visible with the naked eye and a hand-lens. Descriptions of the necessary anatomy and terminology are given. Timbers include yew, pine, spruce, oak, sweet chestnut, elm, ash, teak, cherry, walnut, mahogany, box, beech,

  7. A Key for the Identification of Eighteen Common Timbers.

    ERIC Educational Resources Information Center

    Thomas, P. A.

    1991-01-01

    Dichotomous key for 18 woods in common domestic and architectural use in Britain is provided. It is based upon structures visible with the naked eye and a hand-lens. Descriptions of the necessary anatomy and terminology are given. Timbers include yew, pine, spruce, oak, sweet chestnut, elm, ash, teak, cherry, walnut, mahogany, box, beech,…

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

    ERIC Educational Resources Information Center

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

    2013-01-01

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

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

    ERIC Educational Resources Information Center

    Wood, Piers

    2004-01-01

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

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

    ERIC Educational Resources Information Center

    Sorgo, Andrej

    2006-01-01

    We tried to enrich teaching human anatomy in high school biology lessons. Students construct dichotomous identification keys to the cells, tissues, organs, or body parts. By doing this, students have achieved higher-order cognitive levels of knowledge because construction of such keys is based on analysis, synthesis, and evaluation. Students found

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

    ERIC Educational Resources Information Center

    Sorgo, Andrej

    2006-01-01

    We tried to enrich teaching human anatomy in high school biology lessons. Students construct dichotomous identification keys to the cells, tissues, organs, or body parts. By doing this, students have achieved higher-order cognitive levels of knowledge because construction of such keys is based on analysis, synthesis, and evaluation. Students found…

  12. Functional module identification in protein interaction networks by interaction patterns

    PubMed Central

    Wang, Yijie; Qian, Xiaoning

    2014-01-01

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

  13. Identification of the Key Enzyme of Roseoflavin Biosynthesis.

    PubMed

    Schwarz, Julia; Konjik, Valentino; Jankowitsch, Frank; Sandhoff, Roger; Mack, Matthias

    2016-05-10

    The bacteria Streptomyces davawensis and Streptomyces cinnabarinus produce roseoflavin, the only known natural riboflavin (vitamin B2 ) analogue with antibiotic activity. Roseoflavin can be considered a natural antimetabolite and has been postulated to be biosynthesized from riboflavin via the key intermediate 8-demethyl-8-aminoriboflavin (AF). The required site-specific substitution of one of the methyl groups on the dimethylbenzene ring of riboflavin by an amino group (to give AF) is challenging. The pathway from riboflavin to AF has remained elusive, and the corresponding enzyme/s was/were unknown. Herein, we show by systematic gene deletion, heterologous gene expression, and biochemical studies that the enzyme specified by the gene BN159_7989 from S. davawensis is able to carry out a whole set of chemical reactions starting from riboflavin-5'-phosphate to give the final product 8-demethyl-8-aminoriboflavin-5'-phosphate (AFP). PMID:27062037

  14. Macroscopic hotspots identification: A Bayesian spatio-temporal interaction approach.

    PubMed

    Dong, Ni; Huang, Helai; Lee, Jaeyoung; Gao, Mingyun; Abdel-Aty, Mohamed

    2016-07-01

    This study proposes a Bayesian spatio-temporal interaction approach for hotspot identification by applying the full Bayesian (FB) technique in the context of macroscopic safety analysis. Compared with the emerging Bayesian spatial and temporal approach, the Bayesian spatio-temporal interaction model contributes to a detailed understanding of differential trends through analyzing and mapping probabilities of area-specific crash trends as differing from the mean trend and highlights specific locations where crash occurrence is deteriorating or improving over time. With traffic analysis zones (TAZs) crash data collected in Florida, an empirical analysis was conducted to evaluate the following three approaches for hotspot identification: FB ranking using a Poisson-lognormal (PLN) model, FB ranking using a Bayesian spatial and temporal (B-ST) model and FB ranking using a Bayesian spatio-temporal interaction (B-ST-I) model. The results show that (a) the models accounting for space-time effects perform better in safety ranking than does the PLN model, and (b) the FB approach using the B-ST-I model significantly outperforms the B-ST approach in correctly identifying hotspots by explicitly accounting for the space-time variation in addition to the stable spatial/temporal patterns of crash occurrence. In practice, the B-ST-I approach plays key roles in addressing two issues: (a) how the identified hotspots have evolved over time and (b) the identification of areas that, whilst not yet hotspots, show a tendency to become hotspots. Finally, it can provide guidance to policy decision makers to efficiently improve zonal-level safety. PMID:27110645

  15. Multi-shot person re-identification approach based key frame selection

    NASA Astrophysics Data System (ADS)

    Hadj Hassen, Yousra; Ayedi, Walid; Ouni, Tarek; Jallouli, Mohamed

    2015-12-01

    This paper presents a novel approach to solve the problem of person re-identification in non-overlapping camera views. We propose an appearance based method for person re-identification that condenses a set of frames of the same individual into the multi-class classifier SVM (Support Vector Machine). Still, the choice of different and most expressive frames for each target is very challenging. Besides, efficient person re-identification algorithms are computationally expensive due to the big amount of data used. One of the originalities of our method is how to select different shots during person tracking within each camera to guaranty efficient person re-identification. We evaluate our approach on the publicly available PRID 2011 multi-shot re-identification dataset and demonstrate some performance in comparison with the elimination of the proposed key frames selection.

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

    PubMed Central

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

    2012-01-01

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

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

    USGS Publications Warehouse

    Robbins, E.I.

    2000-01-01

    Natural and anthropogenic acidic environments are dominated by bacteria and Archaea. As many as 86 genera or species have been identified or isolated from pH <4.5 environments. This paper reviews the worldwide literature and provide tables of morphological characteristics, habitat information and a key for light microscope identification for the non-microbiologist.

  18. A Molecular Key for the Identification of Blow Flies in Southeastern Nebraska

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The identification of blow flies (Calliphoridae) (typically the first colonizers of cadavers) is difficult, especially in the earlier instars because of their small size, similarity and simplicity in external morphology. We consider how taxonomic keys based on molecular genetic data facilitate accur...

  19. Bioactive nanofibers enable the identification of thrombospondin 2 as a key player in enamel regeneration.

    PubMed

    Huang, Zhan; Newcomb, Christina J; Lei, Yaping; Zhou, Yan; Bornstein, Paul; Amendt, Brad A; Stupp, Samuel I; Snead, Malcolm L

    2015-08-01

    Tissue regeneration and development involves highly synchronized signals both between cells and with the extracellular environment. Biomaterials can be tuned to mimic specific biological signals and control cell response(s). As a result, these materials can be used as tools to elucidate cell signaling pathways and candidate molecules involved with cellular processes. In this work, we explore enamel-forming cells, ameloblasts, which have a limited regenerative capacity. By exposing undifferentiated cells to a self-assembling matrix bearing RGDS epitopes, we elicited a regenerative signal at will that subsequently led to the identification of thrombospondin 2 (TSP2), an extracellular matrix protein that has not been previously recognized as a key player in enamel development and regeneration. Targeted disruption of the thrombospondin 2 gene (Thbs2) resulted in enamel formation with a disordered architecture that was highly susceptible to wear compared to their wild-type counterparts. To test the regenerative capacity, we injected the bioactive matrix into the enamel organ and discovered that the enamel organic epithelial cells in TSP-null mice failed to polarize on the surface of the artificial matrix, greatly reducing integrin β1 and Notch1 expression levels, which represent signaling pathways known to be associated with TSP2. These results suggest TSP2 plays an important role in regulating cell-matrix interactions during enamel formation. Exploiting the signaling pathways activated by biomaterials can provide insight into native signaling mechanisms crucial for tooth development and cell-based strategies for enamel regeneration. PMID:26004236

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

    PubMed Central

    Leggett, Roxanne; Kirchoff, Bruce K.

    2011-01-01

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

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

    PubMed

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

    2015-01-01

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

  2. Bryophytes for Beginners: The Usability of a Printed Dichotomous Key versus a Multi-Access Computer-Based Key for Bryophyte Identification

    ERIC Educational Resources Information Center

    Stagg, Bethan C.; Donkin, Maria E.; Smith, Alison M.

    2015-01-01

    Bryophytes are a rewarding study group in field biology and the UK bryophyte flora has international importance to biodiversity conservation. We designed an identification key to common woodland moss species and compared the usability of two formats, web-based multi-access and printed dichotomous key, with undergraduate students. The rate of

  3. Bryophytes for Beginners: The Usability of a Printed Dichotomous Key versus a Multi-Access Computer-Based Key for Bryophyte Identification

    ERIC Educational Resources Information Center

    Stagg, Bethan C.; Donkin, Maria E.; Smith, Alison M.

    2015-01-01

    Bryophytes are a rewarding study group in field biology and the UK bryophyte flora has international importance to biodiversity conservation. We designed an identification key to common woodland moss species and compared the usability of two formats, web-based multi-access and printed dichotomous key, with undergraduate students. The rate of…

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

    PubMed Central

    Lopes-Andrade, Cristiano; Lawrence, John F.

    2011-01-01

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

  5. Identification of Inhibitors of Biological Interactions Involving Intrinsically Disordered Proteins

    PubMed Central

    Marasco, Daniela; Scognamiglio, Pasqualina Liana

    2015-01-01

    Proteinprotein interactions involving disordered partners have unique features and represent prominent targets in drug discovery processes. Intrinsically Disordered Proteins (IDPs) are involved in cellular regulation, signaling and control: they bind to multiple partners and these high-specificity/low-affinity interactions play crucial roles in many human diseases. Disordered regions, terminal tails and flexible linkers are particularly abundant in DNA-binding proteins and play crucial roles in the affinity and specificity of DNA recognizing processes. Protein complexes involving IDPs are short-lived and typically involve short amino acid stretches bearing few hot spots, thus the identification of molecules able to modulate them can produce important lead compounds: in this scenario peptides and/or peptidomimetics, deriving from structure-based, combinatorial or protein dissection approaches, can play a key role as hit compounds. Here, we propose a panoramic review of the structural features of IDPs and how they regulate molecular recognition mechanisms focusing attention on recently reported drug-design strategies in the field of IDPs. PMID:25849651

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

    PubMed

    Chen, Jing; Proctor, Robert W

    2014-10-01

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

  7. Communication via Interactive Media: Communication in a New Key?

    ERIC Educational Resources Information Center

    Carveth, Rod

    1996-01-01

    Explores the use of the World Wide Web as an advertising medium--many companies are having difficulties seeing exactly how the Web will fit into their media strategies. Argues that media decision makers need to realize that interactive media are different from traditional media in terms of form and content. (PA)

  8. Understanding Dengue Virus Capsid Protein Interaction with Key Biological Targets

    PubMed Central

    Faustino, André F.; Martins, Ivo C.; Carvalho, Filomena A.; Castanho, Miguel A. R. B.; Maurer-Stroh, Sebastian; Santos, Nuno C.

    2015-01-01

    Dengue virus (DENV) causes over 500,000 hospitalizations and 20,000 deaths worldwide every year. Dengue epidemics now reach temperate regions due to globalization of trade and travel and climate changes. Currently, there are no successful therapeutic or preventive approaches. We previously developed a peptide drug lead, pep14-23, that inhibits the biologically relevant interaction of DENV capsid (C) protein with lipid droplets (LDs). Surprisingly, pep14-23 also inhibits DENV C interaction with very low-density lipoproteins (VLDL). We thus investigated the similarity between the proposed DENV C molecular targets in LDs and VLDL, respectively, the proteins perilipin 3 (PLIN3) and apolipoprotein E (APOE). APOE N-terminal and PLIN3 C-terminal regions are remarkably similar, namely APOE α-helix 4 (APOEα4) and PLIN3 α-helix 5 (PLIN3α5) sequences, which are also highly superimposable structurally. Interestingly, APOE α-helical N-terminal sequence and structure superimposes with DENV C α-helices α1 and α2. Moreover, the DENV C hydrophobic cleft can accommodate the structurally analogous APOEα4 and PLIN3α5 helical regions. Mirroring DENV C-LDs interaction (previously shown experimentally to require PLIN3), we experimentally demonstrated that DENV C-VLDL interaction requires APOE. Thus, the results fit well with previous data and suggest future drug development strategies targeting the above mentioned α-helical structures. PMID:26161501

  9. Interaction of key pathways in sorafenib-treated hepatocellular carcinoma based on a PCR-array

    PubMed Central

    Liu, Yan; Wang, Ping; Li, Shijie; Yin, Linan; Shen, Haiyang; Liu, Ruibao

    2015-01-01

    This study aimed to identify the key pathways and to explore the mechanism of sorafenib in inhibiting hepatocellular carcinoma (HCC). The gene expression profile of GSE33621, including 6 sorafenib treated group and 6 control samples, was downloaded from the GEO (Gene Expression Omnibus) database. The differentially expressed genes (DEGs) in HCC samples were screened using the ΔΔCt method with the homogenized internal GAPDH. Also, the functions and pathways of DEGs were analyzed using the DAVID. Moreover, the significant pathways of DEGs that involved in HCC were analyzed based on the Latent pathway identification analysis (LPIA). A total of 44 down-regulated DEGs were selected in HCC samples. Also, there were 84 biological pathways that these 44 DEGs involved in. Also, LPIA showed that Osteoclast differentiation and hsa04664-Fc epsilon RI signaling pathway was the most significant interaction pathways. Moreover, Apoptosis, Toll-like receptor signaling pathway, Chagas disease, and T cell receptor signaling pathway were the significant pathways that interacted with hsa04664. In addition, DEGs such as AKT1 (v-akt murine thymoma viral oncogene homolog 1), TNF (tumor necrosis factor), SYK (spleen tyrosine kinase), and PIK3R1 (phosphoinositide-3-kinase, regulatory subunit 1 (alpha)) were the common genes that involved in the significant pathways. Several pathway interaction pairs that caused by several downregulated genes such as SYK, PI3K, AKT1, and TNF, were identified play curial role in sorafenib treated HCC. Sorafenib played important inhibition roles in HCC by affecting a complicate pathway interaction network. PMID:26045814

  10. THE IDENTIFICATION AND TESTING OF INTERACTION PATTERNS

    EPA Science Inventory

    This paper presents a method for identifying and assessing the significance of interaction patterns among various chemicals and chemical classes of importance to regulatory toxicologists. To this end, efforts were made to assemble and evaluate experimental data on toxicologically...

  11. Key interactions of surfactants in therapeutic protein formulations: A review.

    PubMed

    Khan, Tarik A; Mahler, Hanns-Christian; Kishore, Ravuri S K

    2015-11-01

    Proteins as amphiphilic, surface-active macromolecules, demonstrate substantial interfacial activity, which causes considerable impact on their multifarious applications. A commonly adapted measure to prevent interfacial damage to proteins is the use of nonionic surfactants. Particularly in biotherapeutic formulations, the use of nonionic surfactants is ubiquitous in order to prevent the impact of interfacial stress on drug product stability. The scope of this review is to convey the current understanding of interactions of nonionic surfactants with proteins both at the interface and in solution, with specific focus to their effects on biotherapeutic formulations. PMID:26435336

  12. Identification of miRNA-Target RNA Interactions Using CLASH.

    PubMed

    Helwak, Aleksandra; Tollervey, David

    2016-01-01

    We present a detailed protocol for the experimental identification of miRNA-target RNA interaction sites using cross-linking, ligation, and sequencing of hybrids (CLASH). The basis of the technique is the purification of UV-stabilized Argonaute (AGO)-RNA complexes assembled in living cells, with subsequent ligation of AGO-associated RNA-RNA duplexes to form chimeric RNAs. Following cDNA synthesis, DNA library preparation and high-throughput sequencing, interacting RNA molecules are unambiguously identified as chimeric reads in bioinformatic analysis of sequencing data. CLASH potentially recovers any RNA duplex that is bound by RNA-binding protein, so modified approaches would be suitable for the identification of many other inter- and intramolecular RNA-RNA interactions. Since CLASH analysis is independent of bioinformatic predictions it allows the identification and analysis of RNA targeting rules in an unbiased way. PMID:26463387

  13. Recent analysis of key plasma wall interactions issues for ITER

    NASA Astrophysics Data System (ADS)

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

    2009-06-01

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

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

    ERIC Educational Resources Information Center

    Hoffner, Cynthia

    1996-01-01

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

  15. Emotional Identification with Teacher Identities in Student Teachers' Narrative Interaction

    ERIC Educational Resources Information Center

    Karlsson, Marie

    2013-01-01

    The paper suggests that narrative interaction in student teacher peer groups is an important context for emotional identification with culturally available teacher identities. It addresses issues pointed out as problematic in research on teacher identity formation: focus on the individual and the underestimation of context. A positioning analysis…

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

    ERIC Educational Resources Information Center

    Hoffner, Cynthia

    1996-01-01

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

  17. Emotional Identification with Teacher Identities in Student Teachers' Narrative Interaction

    ERIC Educational Resources Information Center

    Karlsson, Marie

    2013-01-01

    The paper suggests that narrative interaction in student teacher peer groups is an important context for emotional identification with culturally available teacher identities. It addresses issues pointed out as problematic in research on teacher identity formation: focus on the individual and the underestimation of context. A positioning analysis

  18. New records of Protura (Entognatha, Arthropoda) from Romania, with an identification key to the Romanian species.

    PubMed

    Shrubovych, Julia; Fiera, Cristina

    2016-01-01

    The Romanian Protura were studied based on 175 specimens collected from Romania, along with bibliographic data. The main publication on the Romanian proturans was written by M.A. Ionescu (1951), who described 13 species mainly from soil and forest litter from 15 collecting points. The current paper represents the first study at a national level. Faunal data on Protura were obtained from 22 sites, mostly from forests of the Romanian Carpathians and also from a peri-urban area of Bucharest, which had not been studied before. As a result, the Romanian Protura fauna now consists of 27 known taxa in 6 genera and 4 families. Of the 27 taxa, 15 species are new records for Romanian fauna. An identification key to the Romanian Protura species is provided. PMID:26865814

  19. New records of Protura (Entognatha, Arthropoda) from Romania, with an identification key to the Romanian species

    PubMed Central

    Shrubovych, Julia; Fiera, Cristina

    2016-01-01

    Abstract The Romanian Protura were studied based on 175 specimens collected from Romania, along with bibliographic data. The main publication on the Romanian proturans was written by M.A. Ionescu (1951), who described 13 species mainly from soil and forest litter from 15 collecting points. The current paper represents the first study at a national level. Faunal data on Protura were obtained from 22 sites, mostly from forests of the Romanian Carpathians and also from a peri-urban area of Bucharest, which had not been studied before. As a result, the Romanian Protura fauna now consists of 27 known taxa in 6 genera and 4 families. Of the 27 taxa, 15 species are new records for Romanian fauna. An identification key to the Romanian Protura species is provided. PMID:26865814

  20. A new species of Spelaeogammarus (Amphipoda: Bogidielloidea: Artesiidae) with an identification key for the genus.

    PubMed

    Bastos-Pereira, Rafaela; Ferreira, Rodrigo L

    2015-01-01

    There are five described species of the cave-dwelling amphipods of the genus Spelaeogammarus, all of them inhabiting caves on the Brazilian state of Bahia. A new species of this genus is here described, which is closely related to the already known species S. santanensis and S. titan. Spelaeogammarus sanctus sp. nov. differs from its congeneric species basically by the presence of more than 18 bifid setae on the dorsal margin of uropod 3 outer ramus and telson with one apical and two subapical stout setae, while the other species generally present less setae on the third uropod and more setae on telson. An identification key and an updated table of the Spelaeogammarus species diagnosis are provided, as well as a multivariate statistical approach of morphological variations among the species. PMID:26624139

  1. Easier detection of invertebrate "identification-key characters" with light of different wavelengths

    PubMed Central

    2011-01-01

    The marine α-taxonomist often encounters two problems. Firstly, the "environmental dirt" that is frequently present on the specimens and secondly the difficulty in distinguishing key-features due to the uniform colours which fixed animals often adopt. Here we show that illuminating animals with deep-blue or ultraviolet light instead of the normal white-light abrogates both difficulties; dirt disappears and important details become clearly visible. This light regime has also two other advantages. It allows easy detection of very small, normally invisible, animals (0.1 μm range). And as these light wavelengths can induce fluorescence, new identification markers may be discovered by this approach. PMID:22040277

  2. Quantum Key Distribution Based on Interferometry and Interaction-Free Measurement

    NASA Astrophysics Data System (ADS)

    Li, Yan-Bing; Xu, Sheng-Wei; Wang, Qing-Le; Liu, Fang; Wan, Zong-Jie

    2016-01-01

    We propose a quantum key distribution based on Mach-Zehnder (MZ) interferometry and interaction-free measurement on single photon. The raw key comes from the photons on which MZ interferometry happened. And the interaction-free measurements are used to detect eavesdroppers. The analysis indicates that the protocol is secure, and can prevent some familiar attacks, such as photon number splitting (PNS) attack. This scheme is easy to be realized in current experiments.

  3. Data publication and dissemination of interactive keys under the open access model

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The concepts of publication, citation and dissemination of interactive keys and other online keys are discussed and illustrated by a sample paper published in the present issue (doi: 10.3897/zookeys.21.271). The present model is based on previous experience with several existing examples of publishi...

  4. The Keys to Interactive Parenting Scale: A Window into Many Facets of Parenting

    ERIC Educational Resources Information Center

    Comfort, Marilee; Gordon, Philip R.; Unger, Donald G.

    2006-01-01

    The Keys to Interactive Parenting Scale (KIPS) is a brief practical tool to assess the quality of parenting interactions across 12 parenting behaviors. Family service providers from a variety of education, health, and social service settings can use KIPS to identify parenting strengths and needs. In this article, the authors describe the rating…

  5. A non-interactive and efficient key agreement protocol for ASNs

    NASA Astrophysics Data System (ADS)

    Yang, Deming; Mu, Dejun; Xu, Zhong

    2007-11-01

    Ad hoc space networks (ASNs) are implemented using flexible, distributed architecture consisting of constellations of dynamically deployed space, airborne and mobile platforms. The nodes within ASNs operate both as communication end-points as well as routers, enabling multi-hop wireless communication and dynamic network topology. Secure and efficient key agreement scheme is the crucial mechanism to construct secure ASNs. Previous ID-based cryptosystem is not feasible in ASNs because of the interaction process in key agreement. A novel non-interactive and efficient ID-based two-party key agreement protocol is proposed for ASNs. Based on the security analysis of IDNIKS proposed by Tso et al., the feasibility of adopting non-interactive key agreement for multi-party in ASNs is analyzed and a conclusion is given.

  6. Raman spectroscopic identification of scytonemin and its derivatives as key biomarkers in stressed environments.

    PubMed

    Varnali, Tereza; Edwards, Howell G M

    2014-12-13

    Raman spectroscopy has been identified as an important first-pass analytical technique for deployment on planetary surfaces as part of a suite of instrumentation in projected remote space exploration missions to detect extant or extinct extraterrestrial life signatures. Aside from the demonstrable advantages of a non-destructive sampling procedure and an ability to record simultaneously the molecular signatures of biological, geobiological and geological components in admixture in the geological record, the interrogation and subsequent interpretation of spectroscopic data from these experiments will be critically dependent upon the recognition of key biomolecular markers indicative of life existing or having once existed in extreme habitats. A comparison made with the characteristic Raman spectral wavenumbers obtained from standards is not acceptable because of shifts that can occur in the presence of other biomolecules and their host mineral matrices. In this paper, we identify the major sources of difficulty experienced in the interpretation of spectroscopic data centring on a key family of biomarker molecules, namely scytonemin and its derivatives; the parent scytonemin has been characterized spectroscopically in cyanobacterial colonies inhabiting some of the most extreme terrestrial environments and, with the support of theoretical calculations, spectra have been predicted for the characterization of several of its derivatives which could occur in novel extraterrestrial environments. This work will form the foundation for the identification of novel biomarkers and for their Raman spectroscopic discrimination, an essential step in the interpretation of potentially complex and hitherto unknown biological radiation protectants based on the scytoneman and scytonin molecular skeletons which may exist in niche geological scenarios in the surface and subsurface of planets and their satellites in our Solar System. PMID:25368346

  7. Identification of Key Proteins in Human Epithelial Cells Responding to Bystander Signals From Irradiated Trout Skin

    PubMed Central

    Smith, Richard; Wang, Jiaxi; Seymour, Colin; Mothersill, Carmel; Howe, Orla

    2015-01-01

    Radiation-induced bystander signaling has been found to occur in live rainbow trout fish (Oncorhynchus mykiss). This article reports identification of key proteomic changes in a bystander reporter cell line (HaCaT) grown in low-dose irradiated tissue-conditioned media (ITCM) from rainbow trout fish. In vitro explant cultures were generated from the skin of fish previously exposed to low doses (0.1 and 0.5 Gy) of X-ray radiation in vivo. The ITCM was harvested from all donor explant cultures and placed on recipient HaCaT cells to observe any change in protein expression caused by the bystander signals. Proteomic methods using 2-dimensional (2D) gel electrophoresis and mass spectroscopy were employed to screen for novel proteins expressed. The proteomic changes measured in HaCaT cells receiving the ITCM revealed that exposure to 0.5 Gy induced an upregulation of annexin A2 and cingulin and a downregulation of Rho-GDI2, F-actin-capping protein subunit beta, microtubule-associated protein RP/EB family member, and 14-3-3 proteins. The 0.1 Gy dose also induced a downregulation of Rho-GDI2, hMMS19, F-actin-capping protein subunit beta, and microtubule-associated protein RP/EB family member proteins. The proteins reported may influence apoptotic signaling, as the results were suggestive of an induction of cell communication, repair mechanisms, and dysregulation of growth signals. PMID:26673684

  8. Identification of Key Proteins in Human Epithelial Cells Responding to Bystander Signals From Irradiated Trout Skin.

    PubMed

    Furlong, Hayley; Smith, Richard; Wang, Jiaxi; Seymour, Colin; Mothersill, Carmel; Howe, Orla

    2015-01-01

    Radiation-induced bystander signaling has been found to occur in live rainbow trout fish (Oncorhynchus mykiss). This article reports identification of key proteomic changes in a bystander reporter cell line (HaCaT) grown in low-dose irradiated tissue-conditioned media (ITCM) from rainbow trout fish. In vitro explant cultures were generated from the skin of fish previously exposed to low doses (0.1 and 0.5 Gy) of X-ray radiation in vivo. The ITCM was harvested from all donor explant cultures and placed on recipient HaCaT cells to observe any change in protein expression caused by the bystander signals. Proteomic methods using 2-dimensional (2D) gel electrophoresis and mass spectroscopy were employed to screen for novel proteins expressed. The proteomic changes measured in HaCaT cells receiving the ITCM revealed that exposure to 0.5 Gy induced an upregulation of annexin A2 and cingulin and a downregulation of Rho-GDI2, F-actin-capping protein subunit beta, microtubule-associated protein RP/EB family member, and 14-3-3 proteins. The 0.1 Gy dose also induced a downregulation of Rho-GDI2, hMMS19, F-actin-capping protein subunit beta, and microtubule-associated protein RP/EB family member proteins. The proteins reported may influence apoptotic signaling, as the results were suggestive of an induction of cell communication, repair mechanisms, and dysregulation of growth signals. PMID:26673684

  9. The scorpions of Yunnan (China): updated identification key, new record and redescriptions of Euscorpiops kubani and E. shidian (Arachnida, Scorpiones)

    PubMed Central

    Di, Zhiyong; He, Yawen; Wu, Yingliang; Cao, Zhijian; Liu, Hui; Jiang, Dahe; Li, Wenxin

    2011-01-01

    Abstract We present an identification key to the scorpion species of Yunnan (China) with notes on the distribution and ecology. Euscorpiops kubani is recorded for the first time for China. The redescriptions of Euscorpiops shidian and Euscorpiops kubani are provided. The number of known scorpion species from Yunnan is raised to nine. PMID:21594054

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

    ERIC Educational Resources Information Center

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

    2009-01-01

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

  11. Comparative proteomic analysis of Lactobacillus plantarum for the identification of key proteins in bile tolerance

    PubMed Central

    2011-01-01

    Background Lactic acid bacteria are commonly marketed as probiotics based on their putative or proven health-promoting effects. These effects are known to be strain specific but the underlying molecular mechanisms remain poorly understood. Therefore, unravelling the determinants behind probiotic features is of particular interest since it would help select strains that stand the best chance of success in clinical trials. Bile tolerance is one of the most crucial properties as it determines the ability of bacteria to survive in the small intestine, and consequently their capacity to play their functional role as probiotics. In this context, the objective of this study was to investigate the natural protein diversity within the Lactobacillus plantarum species with relation to bile tolerance, using comparative proteomics. Results Bile tolerance properties of nine L. plantarum strains were studied in vitro. Three of them presenting different bile tolerance levels were selected for comparative proteomic analysis: L. plantarum 299 V (resistant), L. plantarum LC 804 (intermediate) and L. plantarum LC 56 (sensitive). Qualitative and quantitative differences in proteomes were analyzed using two-dimensional electrophoresis (2-DE), tryptic digestion, liquid chromatography-mass spectrometry analysis and database search for protein identification. Among the proteins correlated with differences in the 2-DE patterns of the bacterial strains, 15 have previously been reported to be involved in bile tolerance processes. The effect of a bile exposure on these patterns was investigated, which led to the identification of six proteins that may be key in the bile salt response and adaptation in L. plantarum: two glutathione reductases involved in protection against oxidative injury caused by bile salts, a cyclopropane-fatty-acyl-phospholipid synthase implicated in maintenance of cell envelope integrity, a bile salt hydrolase, an ABC transporter and a F0F1-ATP synthase which participate in the active removal of bile-related stress factors. Conclusions These results showed that comparative proteomic analysis can help understand the differential bacterial properties of lactobacilli. In the field of probiotic studies, characteristic proteomic profiles can be identified for individual properties that may serve as bacterial biomarkers for the preliminary selection of strains with the best probiotic potential. PMID:21447177

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

    PubMed Central

    2012-01-01

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

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

    PubMed

    Kim, Hyunsung

    2014-01-01

    The digitization of patient health information (PHI) for wireless health monitoring systems (WHMSs) has brought many benefits and challenges for both patients and physicians. However, security, privacy and robustness have remained important challenges for WHMSs. Since the patient's PHI is sensitive and the communication channel, i.e., the Internet, is insecure, it is important to protect them against unauthorized entities, i.e., attackers. Otherwise, failure to do so will not only lead to the compromise of a patient's privacy, but will also put his/her life at risk. This paper proposes a freshness-preserving non-interactive hierarchical key agreement protocol (FNKAP) for WHMSs. The FNKAP is based on the concept of the non-interactive identity-based key agreement for communication efficiency. It achieves patient anonymity between a patient and physician, session key secrecy and resistance against various security attacks, especially including replay attacks. PMID:25513824

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

    PubMed Central

    Kim, Hyunsung

    2014-01-01

    The digitization of patient health information (PHI) for wireless health monitoring systems (WHMSs) has brought many benefits and challenges for both patients and physicians. However, security, privacy and robustness have remained important challenges for WHMSs. Since the patient's PHI is sensitive and the communication channel, i.e., the Internet, is insecure, it is important to protect them against unauthorized entities, i.e., attackers. Otherwise, failure to do so will not only lead to the compromise of a patient's privacy, but will also put his/her life at risk. This paper proposes a freshness-preserving non-interactive hierarchical key agreement protocol (FNKAP) for WHMSs. The FNKAP is based on the concept of the non-interactive identity-based key agreement for communication efficiency. It achieves patient anonymity between a patient and physician, session key secrecy and resistance against various security attacks, especially including replay attacks. PMID:25513824

  15. Identification of key genes associated with colorectal cancer based on the transcriptional network.

    PubMed

    Chen, Guoting; Li, Hengping; Niu, Xianping; Li, Guofeng; Han, Ning; Li, Xin; Li, Guang; Liu, Yangzhou; Sun, Guixin; Wang, Yong; Li, Zengchun; Li, Qinchuan

    2015-07-01

    Colorectal cancer (CRC) is among the most lethal human cancers, but the mechanism of the cancer is still unclear enough. We aimed to explore the key genes in CRC progression. The gene expression profile (GSE4183) of CRC was obtained from Gene Expression Omnibus database which included 8 normal samples, 15 adenoma samples, 15 CRC samples and 15 inflammatory bowel disease (IBD) samples. Thereinto, 8 normal, 15 adenoma, and 15 CRC samples were chosen for our research. The differentially expressed genes (DEGs) in normal vs. adenoma, normal vs. CRC, and adenoma vs. CRC, were identified using the Wilcoxon test method in R respectively. The interactive network of DEGs was constructed to select the significant modules using the Pearson's correlation. Meanwhile, transcriptional network of DEGs was also constructed using the g: Profiler. Totally, 2,741 DEGs in normal vs. adenoma, 1,484 DEGs in normal vs. CRC, and 396 DEGs in adenoma vs. CRC were identified. Moreover, function analysis of DEGs in each group showed FcR-mediated phagocytosis pathway in module 1, cardiac muscle contraction pathway in module 6, and Jak-STAT signaling pathway in module 19 were also enriched. Furthermore, MZF1 and AP2 were the transcription factor in module 6, with the target SP1, while SP1 was also a transcription in module 20. DEGs like NCF1, AKT, SP1, AP2, MZF1, and TPM might be used as specific biomarkers in CRC development. Therapy targeting on the functions of these key genes might provide novel perspective for CRC treatment. PMID:25613817

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

    PubMed Central

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

    2012-01-01

    The Takagi-Sugeno (TS) fuzzy rule system is a widely used data mining technique, and is of particular use in the identification of non-linear interactions between variables. However the number of rules increases dramatically when applied to high dimensional data sets (the curse of dimensionality). Few robust methods are available to identify important rules while removing redundant ones, and this results in limited applicability in fields such as epidemiology or bioinformatics where the interaction of many variables must be considered. Here, we develop a new parsimonious TS rule system. We propose three statistics: R, L, and ω-values, to rank the importance of each TS rule, and a forward selection procedure to construct a final model. We use our method to predict how key components of childhood deprivation combine to influence educational achievement outcome. We show that a parsimonious TS model can be constructed, based on a small subset of rules, that provides an accurate description of the relationship between deprivation indices and educational outcomes. The selected rules shed light on the synergistic relationships between the variables, and reveal that the effect of targeting specific domains of deprivation is crucially dependent on the state of the other domains. Policy decisions need to incorporate these interactions, and deprivation indices should not be considered in isolation. The TS rule system provides a basis for such decision making, and has wide applicability for the identification of non-linear interactions in complex biomedical data. PMID:23272108

  17. Constructing compact Takagi-Sugeno rule systems: identification of complex interactions in epidemiological data.

    PubMed

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

    2012-01-01

    The Takagi-Sugeno (TS) fuzzy rule system is a widely used data mining technique, and is of particular use in the identification of non-linear interactions between variables. However the number of rules increases dramatically when applied to high dimensional data sets (the curse of dimensionality). Few robust methods are available to identify important rules while removing redundant ones, and this results in limited applicability in fields such as epidemiology or bioinformatics where the interaction of many variables must be considered. Here, we develop a new parsimonious TS rule system. We propose three statistics: R, L, and ω-values, to rank the importance of each TS rule, and a forward selection procedure to construct a final model. We use our method to predict how key components of childhood deprivation combine to influence educational achievement outcome. We show that a parsimonious TS model can be constructed, based on a small subset of rules, that provides an accurate description of the relationship between deprivation indices and educational outcomes. The selected rules shed light on the synergistic relationships between the variables, and reveal that the effect of targeting specific domains of deprivation is crucially dependent on the state of the other domains. Policy decisions need to incorporate these interactions, and deprivation indices should not be considered in isolation. The TS rule system provides a basis for such decision making, and has wide applicability for the identification of non-linear interactions in complex biomedical data. PMID:23272108

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

    ERIC Educational Resources Information Center

    Bryant, Trevor N.; Smith, John E.

    1979-01-01

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

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

    PubMed

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

    2013-12-01

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

  20. Identification of key neoculin residues responsible for the binding and activation of the sweet taste receptor

    PubMed Central

    Koizumi, Taichi; Terada, Tohru; Nakajima, Ken-ichiro; Kojima, Masaki; Koshiba, Seizo; Matsumura, Yoshitaka; Kaneda, Kohei; Asakura, Tomiko; Shimizu-Ibuka, Akiko; Abe, Keiko; Misaka, Takumi

    2015-01-01

    Neoculin (NCL) is a heterodimeric protein isolated from the edible fruit of Curculigo latifolia. It exerts a taste-modifying activity by converting sourness to sweetness. We previously demonstrated that NCL changes its action on the human sweet receptor hT1R2-hT1R3 from antagonism to agonism as the pH changes from neutral to acidic values, and that the histidine residues of NCL molecule play critical roles in this pH-dependent functional change. Here, we comprehensively screened key amino acid residues of NCL using nuclear magnetic resonance (NMR) spectroscopy and alanine scanning mutagenesis. We found that the mutations of Arg48, Tyr65, Val72 and Phe94 of NCL basic subunit increased or decreased both the antagonist and agonist activities. The mutations had only a slight effect on the pH-dependent functional change. These residues should determine the affinity of NCL for the receptor regardless of pH. Their locations were separated from the histidine residues responsible for the pH-dependent functional change in the tertiary structure. From these results, we concluded that NCL interacts with hT1R2-hT1R3 through a pH-independent affinity interface including the four residues and a pH-dependent activation interface including the histidine residues. Thus, the receptor activation is induced by local structural changes in the pH-dependent interface. PMID:26263392

  1. Computational Identification of Key Regulators in Two Different Colorectal Cancer Cell Lines

    PubMed Central

    Wlochowitz, Darius; Haubrock, Martin; Arackal, Jetcy; Bleckmann, Annalen; Wolff, Alexander; Beißbarth, Tim; Wingender, Edgar; Gültas, Mehmet

    2016-01-01

    Transcription factors (TFs) are gene regulatory proteins that are essential for an effective regulation of the transcriptional machinery. Today, it is known that their expression plays an important role in several types of cancer. Computational identification of key players in specific cancer cell lines is still an open challenge in cancer research. In this study, we present a systematic approach which combines colorectal cancer (CRC) cell lines, namely 1638N-T1 and CMT-93, and well-established computational methods in order to compare these cell lines on the level of transcriptional regulation as well as on a pathway level, i.e., the cancer cell-intrinsic pathway repertoire. For this purpose, we firstly applied the Trinity platform to detect signature genes, and then applied analyses of the geneXplain platform to these for detection of upstream transcriptional regulators and their regulatory networks. We created a CRC-specific position weight matrix (PWM) library based on the TRANSFAC database (release 2014.1) to minimize the rate of false predictions in the promoter analyses. Using our proposed workflow, we specifically focused on revealing the similarities and differences in transcriptional regulation between the two CRC cell lines, and report a number of well-known, cancer-associated TFs with significantly enriched binding sites in the promoter regions of the signature genes. We show that, although the signature genes of both cell lines show no overlap, they may still be regulated by common TFs in CRC. Based on our findings, we suggest that canonical Wnt signaling is activated in 1638N-T1, but inhibited in CMT-93 through cross-talks of Wnt signaling with the VDR signaling pathway and/or LXR-related pathways. Furthermore, our findings provide indication of several master regulators being present such as MLK3 and Mapk1 (ERK2) which might be important in cell proliferation, migration, and invasion of 1638N-T1 and CMT-93, respectively. Taken together, we provide new insights into the invasive potential of these cell lines, which can be used for development of effective cancer therapy. PMID:27092172

  2. A Linnaeus NG TM interactive key to the Lithocolletinae of North-West Europe aimed at accelerating the accumulation of reliable biodiversity data (Lepidoptera, Gracillariidae)

    PubMed Central

    Doorenweerd, Camiel; van Haren, Merel M.; Schermer, Maarten; Pieterse, Sander; van Nieukerken, Erik J.

    2014-01-01

    Abstract We present an interactive key that is available online through any web browser without the need to install any additional software, making it an easily accessible tool for the larger public. The key can be found at http://identify.naturalis.nl/lithocolletinae. The key includes all 86 North-West European Lithocolletinae, a subfamily of smaller moths (“micro-moths”) that is commonly not treated in field guides. The user can input data on several external morphological character systems in addition to distribution, host plant and even characteristics of the larval feeding traces to reach an identification. We expect that this will enable more people to contribute with reliable observation data on this group of moths and alleviate the workload of taxonomic specialists, allowing them to focus on other new keys or taxonomic work. PMID:25061390

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

    PubMed

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

    2015-02-19

    'Key biodiversity areas' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgró et al. (2011 Evol. Appl. 4, 326-337. (doi:10.1111/j.1752-4571.2010.00157.x)) to extend a framework for how components of genetic diversity might be considered in the identification of key biodiversity areas. We make three recommendations to inform the ongoing process of consolidating a key biodiversity areas standard: (i) thresholds for the threatened species criterion currently consider a site's share of a threatened species' population; expand these to include the proportion of the species' genetic diversity unique to a site; (ii) expand criterion for 'threatened species' to consider 'threatened taxa' and (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the compositional or phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism. We also recommend consideration of occurrence of EDGE species (i.e. threatened phylogenetic diversity) in key biodiversity areas to prioritize species-specific conservation actions among sites. PMID:25561678

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

    PubMed Central

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

    2015-01-01

    Key biodiversity areas' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgró et al. (2011 Evol. Appl. 4, 326–337. (doi:10.1111/j.1752-4571.2010.00157.x)) to extend a framework for how components of genetic diversity might be considered in the identification of key biodiversity areas. We make three recommendations to inform the ongoing process of consolidating a key biodiversity areas standard: (i) thresholds for the threatened species criterion currently consider a site's share of a threatened species' population; expand these to include the proportion of the species' genetic diversity unique to a site; (ii) expand criterion for ‘threatened species' to consider ‘threatened taxa’ and (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the compositional or phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism. We also recommend consideration of occurrence of EDGE species (i.e. threatened phylogenetic diversity) in key biodiversity areas to prioritize species-specific conservation actions among sites. PMID:25561678

  5. Identification of novel CBP interacting proteins in embryonic orofacial tissue

    SciTech Connect

    Yin Xiaolong; Warner, Dennis R.; Roberts, Emily A.; Pisano, M. Michele; Greene, Robert M. . E-mail: greene@louisville.edu

    2005-04-15

    cAMP response element-binding protein (CREB)-binding protein (CBP) plays an important role as a general co-integrator of multiple signaling pathways and interacts with a large number of transcription factors and co-factors, through its numerous protein-binding domains. To identify nuclear factors associated with CBP in developing orofacial tissue, a yeast two-hybrid screen of a cDNA library derived from orofacial tissue from gestational day 11 to 13 mouse embryos was conducted. Using the carboxy terminus (amino acid residues 1676-2441) of CBP as bait, several novel proteins that bind CBP were identified, including an Msx-interacting-zinc finger protein, CDC42 interaction protein 4/thyroid hormone receptor interactor 10, SH3-domain GRB2-like 1, CCR4-NOT transcription complex subunit 3, adaptor protein complex AP-1 {beta}1 subunit, eukaryotic translation initiation factor 2B subunit 1 ({alpha}), and cyclin G-associated kinase. Results of the yeast two-hybrid screen were confirmed by glutathione S-transferase pull-down assays. The identification of these proteins as novel CBP-binding partners allows exploration of new mechanisms by which CBP regulates and integrates diverse cell signaling pathways.

  6. Modeling and analysis of PM2.5 generation for key factors identification in China

    NASA Astrophysics Data System (ADS)

    Xia, Dehong; Jiang, Binfan; Xie, Yulei

    2016-06-01

    Recently, the PM2.5 pollution in China has occurred frequently and caused widely concern. In order to identify the key factors for PM2.5 generation, the formation characteristics of PM2.5 would be revealed. A property of electric neutrality of PM2.5 was proposed under the least-energy principle and verified through electricity-charge calculation in this paper. It indicated that PM2.5 is formed by the effect of electromagnetic force, including the effect of ionic bond, hydrogen bond and polarization. According to the analysis of interactive forces among different chemical components, a simulation model is developed for describing the random process of PM2.5 generation. In addition, an orthogonal test with two levels and four factors has been designed and carried out through the proposed model. From the text analysis, PM2.5 would be looser and suspend longer in atmosphere due to Organic Compound (OC) existing (OC can reduce about 67% of PM2.5 density). Considering that NH4+ is the only cation in the main chemical components of PM2.5, it would be vital for anions (such as SO42- and NO3-) to aggregate together for facilitating PM2.5 growing. Therefore, in order to relieve PM2.5 pollution, control strategies for OC and NH4+ would be enhanced by government through improving the quality of oils and solvent products, decreasing the amount of nitrogenous fertilizer utilization, or changing the fertilizing environment from dry condition to wet condition.

  7. Identification of protein interacting partners using tandem affinity purification.

    PubMed

    Bailey, Dalan; Urena, Luis; Thorne, Lucy; Goodfellow, Ian

    2012-01-01

    A critical and often limiting step in understanding the function of host and viral proteins is the identification of interacting cellular or viral protein partners. There are many approaches that allow the identification of interacting partners, including the yeast two hybrid system, as well as pull down assays using recombinant proteins and immunoprecipitation of endogenous proteins followed by mass spectrometry identification(1). Recent studies have highlighted the utility of double-affinity tag mediated purification, coupled with two specific elution steps in the identification of interacting proteins. This approach, termed Tandem Affinity Purification (TAP), was initially used in yeast(2,3) but more recently has been adapted to use in mammalian cells(4-8). As proof-of-concept we have established a tandem affinity purification (TAP) method using the well-characterized eukaryotic translation initiation factor eIF4E(9,10).The cellular translation factor eIF4E is a critical component of the cellular eIF4F complex involved in cap-dependent translation initiation(10). The TAP tag used in the current study is composed of two Protein G units and a streptavidin binding peptide separated by a Tobacco Etch Virus (TEV) protease cleavage sequence. The TAP tag used in the current study is composed of two Protein G units and a streptavidin binding peptide separated by a Tobacco Etch Virus (TEV) protease cleavage sequence(8). To forgo the need for the generation of clonal cell lines, we developed a rapid system that relies on the expression of the TAP-tagged bait protein from an episomally maintained plasmid based on pMEP4 (Invitrogen). Expression of tagged murine eIF4E from this plasmid was controlled using the cadmium chloride inducible metallothionein promoter. Lysis of the expressing cells and subsequent affinity purification via binding to rabbit IgG agarose, TEV protease cleavage, binding to streptavidin linked agarose and subsequent biotin elution identified numerous proteins apparently specific to the eIF4E pull-down (when compared to control cell lines expressing the TAP tag alone). The identities of the proteins were obtained by excision of the bands from 1D SDS-PAGE and subsequent tandem mass spectrometry. The identified components included the known eIF4E binding proteins eIF4G and 4EBP-1. In addition, other components of the eIF4F complex, of which eIF4E is a component were identified, namely eIF4A and Poly-A binding protein. The ability to identify not only known direct binding partners as well as secondary interacting proteins, further highlights the utility of this approach in the characterization of proteins of unknown function. PMID:22395237

  8. Key role for Bak activation and Bak-Bax interaction in the apoptotic response to vinblastine.

    PubMed

    Upreti, Meenakshi; Chu, Rong; Galitovskaya, Elena; Smart, Sherri K; Chambers, Timothy C

    2008-07-01

    Microtubule inhibitors such as vinblastine cause mitotic arrest and subsequent apoptosis through the intrinsic mitochondrial pathway. However, although Bcl-2 family proteins have been implicated as distal mediators, their precise role is largely unknown. In this study, we investigated the role of Bak in vinblastine-induced apoptosis. Bak was mainly monomeric in untreated KB-3 cells, and multimers corresponding to dimer, trimer, and higher oligomers were observed after vinblastine treatment. The oligomeric Bak species were strongly diminished in cells stably overexpressing Bcl-xL. Immunoprecipitation with a conformation-dependent Bak antibody revealed that vinblastine induced Bak activation. Reciprocal immunoprecipitations indicated that vinblastine induced the interaction of active Bak with active Bax. Furthermore, Bcl-xL overexpression prevented Bak and Bax interaction and strongly inhibited apoptosis, whereas Bcl-2 overexpression did not prevent Bak-Bax interaction and only weakly inhibited apoptosis. The relative contributions of Bak and Bax were investigated using fibroblasts deficient in one or both of these proteins; double knockouts were highly resistant compared with single knockouts, with vinblastine sensitivities in the order of Bak(+)/Bax(+) > Bak(+)/Bax(-) > Bak(-)/Bax(+) > Bak(-)/Bax(-). These results highlight Bak as a key mediator of vinblastine-induced apoptosis and show for the first time activation and oligomerization of Bak by an antimitotic agent. In addition, our results suggest that the interaction of the activated forms of Bak and Bax represents a key distal step in the apoptotic response to this important chemotherapeutic drug. PMID:18645031

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

    ERIC Educational Resources Information Center

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

    2008-01-01

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

  10. Guide and keys for the identification of Syllidae (Annelida, Phyllodocida) from the British Isles (reported and expected species)

    PubMed Central

    San Martín, Guillermo; Worsfold, Tim M.

    2015-01-01

    Abstract In November 2012, a workshop was carried out on the taxonomy and systematics of the family Syllidae (Annelida: Phyllodocida) at the Dove Marine Laboratory, Cullercoats, Tynemouth, UK for the National Marine Biological Analytical Quality Control (NMBAQC) Scheme. Illustrated keys for subfamilies, genera and species found in British and Irish waters were provided for participants from the major national agencies and consultancies involved in benthic sample processing. After the workshop, we prepared updates to these keys, to include some additional species provided by participants, and some species reported from nearby areas. In this paper, we provide the revised keys to enable rapid identification of Syllidae from the seas around Britain and Ireland. One new combination, Palposyllis propeweismanni, is proposed. PMID:25878521

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

    PubMed Central

    Agrain, Federico A.

    2014-01-01

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

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

    PubMed

    Agrain, Federico A

    2014-01-01

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

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

    ERIC Educational Resources Information Center

    Ragan, Lawrence C.

    1991-01-01

    In cooperation with a university educational technology unit, an agronomy professor used hypercard and videodisk technology to develop a computer program for identification of 181 weed species based on user-selected characteristics. This solution was found during a search for a way to organize course content in a concise, manageable system. (MSE)

  14. MOLECULAR TAXONOMIC KEYS – ARE THEY THE SOLUTION FOR SPECIES IDENTIFICATION IN FORENSIC ENTOMOLOGY?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A functional diagnostic technique must have the ability to unambiguously identify and differentiate insect species. Insect species developing in cadavers are often used to estimate the time since death or postmortem interval (PMI). Accurate identification of the species involved is essential, but ex...

  15. Identification of key transcription factors in caerulein-induced pancreatitis through expression profiling data.

    PubMed

    Qi, Dachuan; Wu, Bo; Tong, Danian; Pan, Ye; Chen, Wei

    2015-08-01

    The current study aimed to isolate key transcription factors (TFs) in caerulein-induced pancreatitis, and to identify the difference between wild type and Mist1 knockout (KO) mice, in order to elucidate the contribution of Mist1 to pancreatitis. The gene profile of GSE3644 was downloaded from the Gene Expression Omnibus database then analyzed using the t-test. The isolated differentially expressed genes (DEGs) were mapped into a transcriptional regulatory network derived from the Integrated Transcription Factor Platform database and in the network, the interaction pairs involving at least one DEG were screened. Fisher's exact test was used to analyze the functional enrichment of the target genes. A total of 1,555 and 3,057 DEGs were identified in the wild type and Mist1KO mice treated with caerulein, respectively. DEGs screened in Mist1KO mice were predominantly enriched in apoptosis, mitogen-activated protein kinase signaling and other cancer-associated pathways. A total of 188 and 51 TFs associated with pathopoiesis were isolated in Mist1KO and wild type mice, respectively. Out of the top 10 TFs (ranked by P-value), 7 TFs, including S-phase kinase-associated protein 2 (Skp2); minichromosome maintenance complex component 3 (Mcm3); cell division cycle 6 (Cdc6); cyclin B1 (Ccnb1); mutS homolog 6 (Msh6); cyclin A2 (Ccna2); and cyclin B2 (Ccnb2), were expressed in the two types of mouse. These TFs were predominantly involved in phosphorylation, DNA replication, cell division and DNA mismatch repair. In addition, specific TFs, including minichromosome maintenance complex component 7 (Mcm7); lymphoid-specific helicase (Hells); and minichromosome maintenance complex component 6 (Mcm6), that function in the unwinding of DNA were identified to participate in Mist1KO pancreatitis. The DEGs, including Cdc6, Mcm6, Msh6 and Wdr1 are closely associated with the regulation of caerulein-induced pancreatitis. Furthermore, other identified TFs were also involved in this type of regulation. PMID:25975747

  16. Rapid identification of chemical genetic interactions in Saccharomyces cerevisiae.

    PubMed

    Dilworth, David; Nelson, Christopher J

    2015-01-01

    Determining the mode of action of bioactive chemicals is of interest to a broad range of academic, pharmaceutical, and industrial scientists. Saccharomyces cerevisiae, or budding yeast, is a model eukaryote for which a complete collection of ~6,000 gene deletion mutants and hypomorphic essential gene mutants are commercially available. These collections of mutants can be used to systematically detect chemical-gene interactions, i.e. genes necessary to tolerate a chemical. This information, in turn, reports on the likely mode of action of the compound. Here we describe a protocol for the rapid identification of chemical-genetic interactions in budding yeast. We demonstrate the method using the chemotherapeutic agent 5-fluorouracil (5-FU), which has a well-defined mechanism of action. Our results show that the nuclear TRAMP RNA exosome and DNA repair enzymes are needed for proliferation in the presence of 5-FU, which is consistent with previous microarray based bar-coding chemical genetic approaches and the knowledge that 5-FU adversely affects both RNA and DNA metabolism. The required validation protocols of these high-throughput screens are also described. PMID:25867090

  17. A systems biology approach to detect key pathways and interaction networks in gastric cancer on the basis of microarray analysis.

    PubMed

    Guo, Leilei; Song, Chunhua; Wang, Peng; Dai, Liping; Zhang, Jianying; Wang, Kaijuan

    2015-11-01

    The aim of the present study was to explore key molecular pathways contributing to gastric cancer (GC) and to construct an interaction network between significant pathways and potential biomarkers. Publicly available gene expression profiles of GSE29272 for GC, and data for the corresponding normal tissue, were downloaded from Gene Expression Omnibus. Pre‑processing and differential analysis were performed with R statistical software packages, and a number of differentially expressed genes (DEGs) were obtained. A functional enrichment analysis was performed for all the DEGs with a BiNGO plug‑in in Cytoscape. Their correlation was analyzed in order to construct a network. The modularity analysis and pathway identification operations were used to identify graph clusters and associated pathways. The underlying molecular mechanisms involving these DEGs were also assessed by data mining. A total of 249 DEGs, which were markedly upregulated and downregulated, were identified. The extracellular region contained the most significantly over‑represented functional terms, with respect to upregulated and downregulated genes, and the closest topological matches were identified for taste transduction and regulation of autophagy. In addition, extracellular matrix‑receptor interactions were identified as the most relevant pathway associated with the progression of GC. The genes for fibronectin 1, secreted phosphoprotein 1, collagen type 4 variant α‑1/2 and thrombospondin 1, which are involved in the pathways, may be considered as potential therapeutic targets for GC. A series of associations between candidate genes and key pathways were also identified for GC, and their correlation may provide novel insights into the pathogenesis of GC. PMID:26324226

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

    ERIC Educational Resources Information Center

    Hager, Stephen B.; Cosentino, Bradley J.

    2006-01-01

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

  19. DETECTION AND IDENTIFICATION THRESHOLD VALUES FOR KEY FLAVOR COMPONENTS IN AN ORANGE JUICE MATRIX

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Due to the complex nature of orange juice, threshold values for key flavor components could differ significantly from those values reported in simpler systems, like water. In order to provide the citrus industry with reference values closer to the real situation in orange juice, different orange ju...

  20. Identification of key residues for protein conformational transition using elastic network model

    NASA Astrophysics Data System (ADS)

    Su, Ji Guo; Jin Xu, Xian; Hua Li, Chun; Chen, Wei Zu; Wang, Cun Xin

    2011-11-01

    Proteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The large-scale allosteric conformational transitions are believed to involve some key residues that mediate the conformational movements between different regions of the protein. In the present work, a thermodynamic method based on the elastic network model is proposed to predict the key residues involved in protein conformational transitions. In our method, the key functional sites are identified as the residues whose perturbations largely influence the free energy difference between the protein states before and after transition. Two proteins, nucleotide binding domain of the heat shock protein 70 and human/rat DNA polymerase β, are used as case studies to identify the critical residues responsible for their open-closed conformational transitions. The results show that the functionally important residues mainly locate at the following regions for these two proteins: (1) the bridging point at the interface between the subdomains that control the opening and closure of the binding cleft; (2) the hinge region between different subdomains, which mediates the cooperative motions between the corresponding subdomains; and (3) the substrate binding sites. The similarity in the positions of the key residues for these two proteins may indicate a common mechanism in their conformational transitions.

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

    PubMed Central

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

    2013-01-01

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

  2. Identification of key pathways and genes in psoriasis via gene microarray analysis.

    PubMed

    Chen, Wei; Xie, Kuixia; Liu, Xinhua; Chen, Hong

    2016-03-01

    Psoriasis is a common chronic inflammatory, immune-mediated skin disease with a high incidence worldwide. It is a multifactorial disease and its exact pathogenesis has remained largely elusive. The purpose of the present study was to uncover the key pathways and genes associated with the incidence of psoriasis. Gene expression profiles (dataset no. GSE13355) were downloaded from Gene Expression Omnibus. Differentially expressed genes between skin samples from patients with lesional psoriasis or non‑lesional psoriasis and those of normal healthy controls were identified using Bioconductor version 2.13 based in R. Kyoto Encyclopedia of Genes and genomes (KEGG) pathways significantly enriched in patients with lesional psoriasis were identified using gene set enrichment analysis (GSEA). Key KEGG pathways were then identified using leading-edge analysis of the results of GSEA. Differentially expressed genes involved in the significantly enriched KEGG pathways were considered as key genes. Several KEGG pathways which are known to be associated with lesional psoriasis, including autoimmune thyroid disease signaling, natural killer cell-mediated cytotoxicity signaling, as well as several novel pathways, including FCγR-mediated phagocytosis and neurotrophin signaling pathway, were identified. Several verified and novel genes were also got. The present study revealed key pathways and genes associated with psoriasis, which may serve as important biomarkers for the diagnosis and treatment of psoriasis. PMID:26781069

  3. The neotropical flower-living genus Lenkothrips (Thysanoptera, Heterothripidae): three new species and an identification key.

    PubMed

    Cavalleri, Adriano; Mound, Laurence A

    2014-01-01

    Three new species are described in the South American genus of flower-feeding thrips, Lenkothrips De Santis & Sureda: L. mollinediae sp. n. from four species of Mollinedia (Monimiaceae) in Brazil and Ecuador; L. guaraniticus sp. n. and L. kaminskii sp. n. from Malpighiaceae in Brazil. An illustrated key to the five Lenkothrips species now recognized is provided. PMID:24943450

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

    PubMed

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

    2011-01-01

    The family Elmidae Curtis, 1830 has cosmopolitan distribution and most species inhabit riffles on streams and rivers, hence the name "riffle beetle". In recent years, this family has been featured in papers addressing the assessment and environmental monitoring of water quality. In Brazil, studies on the family remain scarce and the present investigation is a pioneering study in the state of São Paulo. This study aims to propose a taxonomic key for the identification of larvae of Elmidae genera known to occur in the State, as well as to report new records and the distribution of these genera. The material analyzed was collected from various locations in each of 15 drainage basins from 2005 to 2010. The identification key includes 12 genera (Austrolimnius Carter & Zeck, 1929, Heterelmis Sharp, 1882, Hexacylloepus Hinton, 1940, Hexanchorus Sharp, 1882, Huleechius Brown, 1981, Macrelmis Motschulsky, 1859, Microcylloepus Hinton, 1935, Neoelmis Musgrave, 1935, Phanocerus Sharp, 1882, Potamophilops Grouvelle, 1896, Stegoelmis Hinton, 1939 and Xenelmis Hinton, 1936) known in Brazil as well as three morphotypes designated herein as Genus A, Genus M and Genus X. The genus Hexanchorus is recorded for the first time in the state of São Paulo. PMID:22368452

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

    PubMed Central

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

    2011-01-01

    Abstract The family Elmidae Curtis, 1830 has cosmopolitan distribution and most species inhabit riffles on streams and rivers, hence the name “riffle beetle”. In recent years, this family has been featured in papers addressing the assessment and environmental monitoring of water quality. In Brazil, studies on the family remain scarce and the present investigation is a pioneering study in the state of São Paulo. This study aims to propose a taxonomic key for the identification of larvae of Elmidae genera known to occur in the State, as well as to report new records and the distribution of these genera. The material analyzed was collected from various locations in each of 15 drainage basins from 2005 to 2010. The identification key includes 12 genera (Austrolimnius Carter & Zeck, 1929, Heterelmis Sharp, 1882, Hexacylloepus Hinton, 1940, Hexanchorus Sharp, 1882, Huleechius Brown, 1981, Macrelmis Motschulsky, 1859, Microcylloepus Hinton, 1935, Neoelmis Musgrave, 1935, Phanocerus Sharp, 1882, Potamophilops Grouvelle, 1896, Stegoelmis Hinton, 1939 and Xenelmis Hinton, 1936) known in Brazil as well as three morphotypes designated herein as Genus A, Genus M and Genus X. The genus Hexanchorus is recorded for the first time in the state of São Paulo. PMID:22368452

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

    NASA Astrophysics Data System (ADS)

    Mizukami, Yuzo; Yamaguchi, Yuichi

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

  7. Identification and expression of isoflavone synthase, the key enzyme for biosynthesis of isoflavones in legumes.

    PubMed

    Jung, W; Yu, O; Lau, S M; O'Keefe, D P; Odell, J; Fader, G; McGonigle, B

    2000-02-01

    Isoflavones have drawn much attention because of their benefits to human health. These compounds, which are produced almost exclusively in legumes, have natural roles in plant defense and root nodulation. Isoflavone synthase catalyzes the first committed step of isoflavone biosynthesis, a branch of the phenylpropanoid pathway. To identify the gene encoding this enzyme, we used a yeast expression assay to screen soybean ESTs encoding cytochrome P450 proteins. We identified two soybean genes encoding isoflavone synthase, and used them to isolate homologous genes from other leguminous species including red clover, white clover, hairy vetch, mung bean, alfalfa, lentil, snow pea, and lupine, as well as from the nonleguminous sugarbeet. We expressed soybean isoflavone synthase in Arabidopsis thaliana, which led to production of the isoflavone genistein in this nonlegume plant. Identification of the isoflavone synthase gene should allow manipulation of the phenylpropanoid pathway for agronomic and nutritional purposes. PMID:10657130

  8. Interaction Studies of Withania Somnifera's Key Metabolite Withaferin A with Different Receptors Assoociated with Cardiovascular Disease.

    PubMed

    Ravindran, Rekha; Sharma, Nitika; Roy, Sujata; Thakur, Ashoke R; Ganesh, Subhadra; Kumar, Sriram; Devi, Jamuna; Rajkumar, Johanna

    2015-01-01

    Withania somnifera commonly known as Ashwagandha in India is used in many herbal formulations to treat various cardiovascular diseases. The key metabolite of this plant, Withaferin A was analyzed for its molecular mechanism through docking studies on different targets of cardiovascular disease. Six receptor proteins associated with cardiovascular disease were selected and interaction studies were performed with Withaferin A using AutoDock Vina. CORINA was used to model the small molecules and HBAT to compute the hydrogen bonding. Among the six targets, β1- adrenergic receptors, HMG-CoA and Angiotensinogen-converting enzyme showed significant interaction with Withaferin A. Pharmacophore modeling was done using PharmaGist to understand the pharmacophoric potential of Withaferin A. Clustering of Withaferin A with different existing drug molecules for cardiovascular disease was performed with ChemMine based on structural similarity and physicochemical properties. The ability of natural active component, Withaferin A to interact with different receptors associated with cardiovascular disease was elucidated with various modeling techniques. These studies conclusively revealed Withaferin A as a potent lead compound against multiple targets associated with cardiovascular disease. PMID:26548552

  9. The Undecided Have the Key: Interaction-Driven Opinion Dynamics in a Three State Model.

    PubMed

    Balenzuela, Pablo; Pinasco, Juan Pablo; Semeshenko, Viktoriya

    2015-01-01

    The effects of interpersonal interactions on individual's agreements result in a social aggregation process which is reflected in the formation of collective states, as for instance, groups of individuals with a similar opinion about a given issue. This field, which has been a longstanding concern of sociologists and psychologists, has been extended into an area of experimental social psychology, and even has attracted the attention of physicists and mathematicians. In this article, we present a novel model of opinion formation in which agents may either have a strict preference for a choice, or be undecided. The opinion shift emerges, in a threshold process, as a consequence of a cumulative persuasion for either one of the two opinions in repeated interactions. There are two main ingredients which play key roles in determining the steady states: the initial fraction of undecided agents and the change in agents' persuasion after each interaction. As a function of these two parameters, the model presents a wide range of solutions, among which there are consensus of each opinion and bi-polarization. We found that a minimum fraction of undecided agents is not crucial for reaching consensus only, but also to determine a dominant opinion in a polarized situation. In order to gain a deeper comprehension of the dynamics, we also present the theoretical framework of the model. The master equations are of special interest for their nontrivial properties and difficulties in being solved analytically. PMID:26436421

  10. The Undecided Have the Key: Interaction-Driven Opinion Dynamics in a Three State Model

    PubMed Central

    2015-01-01

    The effects of interpersonal interactions on individual’s agreements result in a social aggregation process which is reflected in the formation of collective states, as for instance, groups of individuals with a similar opinion about a given issue. This field, which has been a longstanding concern of sociologists and psychologists, has been extended into an area of experimental social psychology, and even has attracted the attention of physicists and mathematicians. In this article, we present a novel model of opinion formation in which agents may either have a strict preference for a choice, or be undecided. The opinion shift emerges, in a threshold process, as a consequence of a cumulative persuasion for either one of the two opinions in repeated interactions. There are two main ingredients which play key roles in determining the steady states: the initial fraction of undecided agents and the change in agents’ persuasion after each interaction. As a function of these two parameters, the model presents a wide range of solutions, among which there are consensus of each opinion and bi-polarization. We found that a minimum fraction of undecided agents is not crucial for reaching consensus only, but also to determine a dominant opinion in a polarized situation. In order to gain a deeper comprehension of the dynamics, we also present the theoretical framework of the model. The master equations are of special interest for their nontrivial properties and difficulties in being solved analytically. PMID:26436421

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

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

  12. Identification of key taxa that favor intestinal colonization of Clostridium difficile in an adult Chinese population.

    PubMed

    Gu, Silan; Chen, Yunbo; Zhang, Xuewu; Lu, Haifeng; Lv, Tao; Shen, Ping; Lv, Longxian; Zheng, Beiwen; Jiang, Xiawei; Li, Lanjuan

    2016-01-01

    Fecal microbial transplantation provides a high curative rate for recurrent Clostridium difficile infection (CDI). However, limitations associated with FMT drive the need to identify key taxa for selective probiotic therapy for prevention, treatment and cure of human CDI. CDI-associated changes in gut microbiota were investigated in adult patients in the Western countries and among infant population in China. However, there has been no such study involving adult patients in China. Therefore, using high throughput sequencing of the 16S ribosomal RNA V3 region and real-time quantitative polymerase chain reaction, we identified CDI-associated key taxa by comparing the fecal microbiota composition of 15 adult patients with CDI with those of 18 individuals with C. difficile-negative nosocomial diarrhea (CDN) and 25 healthy control subjects. Reduced fecal bacterial diversity and dramatic shifts of intestinal microbial composition in CDI and CDN groups were observed compared with healthy controls. Putative butyrate-producing anaerobic bacteria were significantly depleted whereas endotoxin-producing opportunistic pathogens and lactate-producing phylotypes increased dramatically in patients with CDI compared with healthy controls. Further screening of specific microbes causing diarrheal diseases and resistance against CDI is necessary. PMID:26383014

  13. Lipidomics as an important key for the identification of beer-spoilage bacteria.

    PubMed

    Řezanka, T; Matoulková, D; Benada, O; Sigler, K

    2015-06-01

    Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was used for characterizing intact plasmalogen phospholipid molecules in beer-spoilage bacteria. Identification of intact plasmalogens was carried out using collision-induced dissociation and the presence of suitable marker molecular species, both qualitative and quantitative, was determined in samples containing the anaerobic bacteria Megasphaera and Pectinatus. Using selected ion monitoring (SIM), this method had a limit of detection at 1 pg for the standard, i.e. 1-(1Z-octadecenyl)-2-oleoyl-sn-glycero-3-phosphoethanolamine and be linear in the range of four orders of magnitude from 2 pg to 20 ng. This technique was applied to intact plasmalogen extracts from the samples of contaminated and uncontaminated beer without derivatization and resulted in the identification of contamination of beer by Megasphaera and Pectinatus bacteria. The limit of detection was about 830 cells of anaerobic bacteria, i.e. bacteria containing natural cyclopropane plasmalogenes (c-p-19:0/15:0), which is the majority plasmalogen located in both Megasphaera and Pectinatus. The SIM ESI-MS method has been shown to be useful for the analysis of low concentration of plasmalogens in all biological samples, which were contaminated with anaerobic bacteria, e.g. juice, not only in beer. Significance and impact of the study: Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) using collision-induced dissociation was used to characterize intact plasmalogen phospholipid molecules in beer-spoilage anaerobic bacteria Megasphaera and Pectinatus. Using selected ion monitoring (SIM), this method has a detection limit of 1 pg for the standard 1-(1Z-octadecenyl)-2-oleoyl-sn-glycero-3-phosphoethanolamine and is linear within four orders of magnitude (2 pg to 20 ng). The limit of detection was about 830 cells of bacteria containing natural cyclopropane plasmalogen (c-p-19:0/15:0). SIM ESI-MS method is useful for analyzing low concentrations of plasmalogens in biological samples contaminated with anaerobic bacteria, e.g. beer or juice. PMID:25773514

  14. Interactions between Intracellular Domains as Key Determinants of the Quaternary Structure and Function of Receptor Heteromers*

    PubMed Central

    Navarro, Gemma; Ferré, Sergi; Cordomi, Arnau; Moreno, Estefania; Mallol, Josefa; Casadó, Vicent; Cortés, Antoni; Hoffmann, Hanne; Ortiz, Jordi; Canela, Enric I.; Lluís, Carme; Pardo, Leonardo; Franco, Rafael; Woods, Amina S.

    2010-01-01

    G protein-coupled receptor (GPCR) heteromers are macromolecular complexes with unique functional properties different from those of its individual protomers. Little is known about what determines the quaternary structure of GPCR heteromers resulting in their unique functional properties. In this study, using resonance energy transfer techniques in experiments with mutated receptors, we provide for the first time clear evidence for a key role of intracellular domains in the determination of the quaternary structure of GPCR heteromers between adenosine A2A, cannabinoid CB1, and dopamine D2 receptors. In these interactions, arginine-rich epitopes form salt bridges with phosphorylated serine or threonine residues from CK1/2 consensus sites. Each receptor (A2A, CB1, and D2) was found to include two evolutionarily conserved intracellular domains to establish selective electrostatic interactions with intracellular domains of the other two receptors, indicating that these particular electrostatic interactions constitute a general mechanism for receptor heteromerization. Mutation experiments indicated that the interactions of the intracellular domains of the CB1 receptor with A2A and D2 receptors are fundamental for the correct formation of the quaternary structure needed for the function (MAPK signaling) of the A2A-CB1-D2 receptor heteromers. Analysis of MAPK signaling in striatal slices of CB1 receptor KO mice and wild-type littermates supported the existence of A1-CB1-D2 receptor heteromer in the brain. These findings allowed us to propose the first molecular model of the quaternary structure of a receptor heteromultimer. PMID:20562103

  15. Key role of Dkk3 protein in inhibition of cancer cell proliferation: An in silico identification.

    PubMed

    Mohammadpour, Hemn; Pourfathollah, Ali Akbar; Nikougoftar Zarif, Mahin; Khalili, Saeed

    2016-03-21

    Dkk3 is a member of Dkk family proteins, regulating Wnt signaling. Dkk3 plays different roles in human and mouse tumors. Dkk3 predominantly act as a tumor suppressor, however several reports revealed that Dkk3 could accelerate cancer cell proliferation. Herein, we aimed at launching an in silico study to determine Dkk3 structure and its interactions with Kremen and LRP as Wnt signaling receptors as well as EGF receptor. Using various softwares a model was built for Dkk3 molecule. Different protein modeling approaches along with model refinement processes were employed to arrive at the final model. To achieve the final complex of Dkk3 with Kremen, LRP and EGFR molecules protein-protein docking servers were employed. Model assessment softwares indicated the high quality of the finally refined Dkk3 3D structure, indicating the accuracy of modeling and refinement process. Our results revealed that Dkk3 is capable of interacting with Kremen, LRP and EGFR with comparable binding energies. Dkk3 efficiently interacts with LRP, Kremen and EGF receptor and may be a promising protein in cancer therapy by blocking Wnt and EGFR downstream signaling. PMID:26780644

  16. Identification of key genes involved in root development of tomato using expressed sequence tag analysis.

    PubMed

    Kalidhasan, N; Joshi, Deepti; Bhatt, Tarun Kumar; Gupta, Aditya Kumar

    2015-10-01

    Root system of plants are actually fascinating structures, not only critical for plant development, but also important for storage and conduction. Due to its agronomic importance, identification of genes involved in root development has been a subject of intense study. Tomato is the one of the most consumed vegetables in the world. Tomato has been used as model system for dicot plants because of its small genome, well-established transformation techniques and well-constructed physical map. The present study is targeted to identify of root specific genes expressed temporally and also gene(s) involved in lateral root and profuse root development. A total of 890 ESTs were identified from five EST libraries constructed using SSH approach which included temporal gene regulation (early and late) and genes involved in morphogenetic traits (lateral and profuse rooting). One hundred sixty-one unique ESTs identified from various libraries were categorized based on their putative functions and deposited in NCBI-dbEST database. In addition, 36 ESTs were selected for validation of their expression by RT-PCR. The present findings will help in shedding light to the unexplored developmental process of root growth in tomato and plant in general. PMID:26600676

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

    NASA Technical Reports Server (NTRS)

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

    2010-01-01

    This report identifies key human-performance-related issues associated with Next Generation Air Transportation System (NextGen) research in the NASA NextGen-Airspace Project. Four Research Focus Areas (RFAs) in the NextGen-Airspace Project - namely Separation Assurance (SA), Airspace Super Density Operations (ASDO), Traffic Flow Management (TFM), and Dynamic Airspace Configuration (DAC) - were examined closely. In the course of the research, it was determined that the identified human performance issues needed to be analyzed in the context of NextGen operations rather than through basic human factors research. The main gaps in human factors research in NextGen were found in the need for accurate identification of key human-systems related issues within the context of specific NextGen concepts and better design of the operational requirements for those concepts. By focusing on human-system related issues for individual concepts, key human performance issues for the four RFAs were identified and described in this report. In addition, mixed equipage airspace with components of two RFAs were characterized to illustrate potential human performance issues that arise from the integration of multiple concepts.

  18. Identification of key odorants related to the typical aroma of oxidation-spoiled white wines.

    PubMed

    Silva Ferreira, Antonio César; Hogg, Timothy; Guedes de Pinho, Paula

    2003-02-26

    The oxidative degradation of white wines rapidly leads to a loss of their sensorial qualities. The identification of the most important descriptors related with oxidation-spoiled wine was performed by a trained sensory panel. The terms selected were "honey-like", "farm-feed", "hay", and "woody-like". By gas chromatography-olfactometry analysis three aromatic zones related to these descriptors in the oxidation-spoiled white wines could be determined. Comparison of the aroma extract dilution analysis aromagrams of oxidation-spoiled white wines and a nonspoiled wine showed the highest values of dilution factors were attributed to 3-(methylthio)propionaldehyde, phenylacetaldehyde, 1,1,6-trimethyl-1,2-dihydronaphthalene (TDN), and 4,5-dimethyl-3-hydroxy-2(5H)-furanone (sotolon). A "forced aging" experiment was implemented to simulate the typical oxidation-spoiled aroma. Samples rated with the highest score in the ranking test were also those that presented the highest concentration of these four molecules. To test the sensory impact of these substances, a normal wine (unspoiled) was spiked with these molecules (with the exception of TDN) singly and in combination, and the similarity value (SV) between samples and the oxidation-spoiled white wines was then determined. The highest value from the similarity tests was 5.4 when the three compounds were added simultaneously; 3-(methylthio)propionaldehyde alone was found to be responsible for 3.6, suggesting that, among the molecules studied, it is the most important contributor to the typical aroma of an oxidation-spoiled white wine. PMID:12590484

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

    NASA Technical Reports Server (NTRS)

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

    2000-01-01

    The mineralogic signatures of past aqueous alteration of a basaltic Martian crust may include iron oxides and oxyhydroxides, zeolites, carbonates, phyllosilicates, and silica. The identities, relative abundances, and crystallinities of the phases formed in a particular environment depend on physicochemical conditions. At one extreme, hot spring environments may be characterized by smectite-chlorite to talc-kaolinite silicate assemblages, plus crystalline ferric oxides dominated by hematite. However, most environments, including cold springs, pedogenic layers, and ponded surface water, are expected to deposit iron oxides and oxyhydroxides, carbonates, and smectite-dominated phyllosilicates. A substantial fraction of the ferric iron is expected to occur in nanophase form, with the exact mineralogy strongly influenced by Eh-pH conditions. Detection of these phases has been an objective of a large body of terrestrial telescopic, Mars orbital, and landed spectral investigations and in situ compositional measurements. However, clear identifications of many of these phases is lacking. Neither carbonate nor silica has been unequivocally detected by any method. Although phyllosilicates may occur near the limit of detection by remote sensing, in general they appear to occur in only poorly crystalline form. In contrast, compelling evidence for ferric iron minerals has been gathered by recent telescopic investigations, the Imager for Mars Pathfinder (IMP), and the Thermal Emission Spectrometer (TES) on the Mars Global Surveyor (MGS). These data yield two crucial findings: (1) In the global, high spatial resolution TES data set, highly crystalline ferric iron (as coarse-grained 'gray' hematite) has been recognized but with only very limited spatial occurrence and (2) Low-resolution telescopic reflectance spectroscopy, very limited orbital reflectance spectroscopy, and landed multispectral imaging provide strong indications that at least two broad classes of ferric iron minerals are commonplace in non-dust covered regions.

  20. The Arabidopsis NRG2 Protein Mediates Nitrate Signaling and Interacts with and Regulates Key Nitrate Regulators.

    PubMed

    Xu, Na; Wang, Rongchen; Zhao, Lufei; Zhang, Chengfei; Li, Zehui; Lei, Zhao; Liu, Fei; Guan, Peizhu; Chu, Zhaohui; Crawford, Nigel M; Wang, Yong

    2016-02-01

    We show that NITRATE REGULATORY GENE2 (NRG2), which we identified using forward genetics, mediates nitrate signaling in Arabidopsis thaliana. A mutation in NRG2 disrupted the induction of nitrate-responsive genes after nitrate treatment by an ammonium-independent mechanism. The nitrate content in roots was lower in the mutants than in the wild type, which may have resulted from reduced expression of NRT1.1 (also called NPF6.3, encoding a nitrate transporter/receptor) and upregulation of NRT1.8 (also called NPF7.2, encoding a xylem nitrate transporter). Genetic and molecular data suggest that NRG2 functions upstream of NRT1.1 in nitrate signaling. Furthermore, NRG2 directly interacts with the nitrate regulator NLP7 in the nucleus, but nuclear retention of NLP7 in response to nitrate is not dependent on NRG2. Transcriptomic analysis revealed that genes involved in four nitrogen-related clusters including nitrate transport and response to nitrate were differentially expressed in the nrg2 mutants. A nitrogen compound transport cluster containing some members of the NRT/PTR family was regulated by both NRG2 and NRT1.1, while no nitrogen-related clusters showed regulation by both NRG2 and NLP7. Thus, NRG2 plays a key role in nitrate regulation in part through modulating NRT1.1 expression and may function with NLP7 via their physical interaction. PMID:26744214

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

    PubMed

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

    2013-02-01

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

  2. Checklist and Simple Identification Key for Frogs and Toads from District IV of The MADA Scheme, Kedah, Malaysia

    PubMed Central

    Jaafar, Ibrahim; Chai, Teoh Chia; Sah, Shahrul Anuar Mohd; Akil, Mohd Abdul Muin Md.

    2009-01-01

    A survey was conducted to catalogue the diversity of anurans in District IV of the Muda Agriculture Development Authority Scheme (MADA) in Kedah Darul Aman, Malaysia, from July 1996 to January 1997. Eight species of anurans from three families were present in the study area. Of these, the Common Grass Frog (Fejevarya limnocharis) was the most abundant, followed by Mangrove Frog (Fejevarya cancrivora), Long-legged Frog (Hylarana macrodactyla), and Common Toad (Duttaphrynus melanostictus). Puddle Frog (Occidozyga lima), Taiwanese Giant Frog (Hoplobatrachus rugulosus), and Banded Bullfrog (Kaluola pulchra) were rare during the sampling period, and only one Paddy Frog (Hylarana erythraea) was captured. A simple identification key for the anurans of this area is included for use by scientists and laymen alike. PMID:24575178

  3. Identification of the key stages for sex determination in the silkworm, Bombyx mori.

    PubMed

    Sakai, Hiroki; Aoki, Fugaku; Suzuki, Masataka G

    2014-03-01

    In general, the master switch gene for sex determination is expressed for a limited period during the early embryonic stage. To increase our understanding of the sex determination mechanism in Bombyx mori, it is important to understand when sex determination takes place. To examine the key stages for sex determination in this insect, we focused on the expression patterns of Bmdsx (a double-switch gene in the sex determination cascade of B. mori) and BmIMP (a gene expressed specifically in males involved in male-specific splicing of Bmdsx). Reverse transcription PCR (RT-PCR) analysis revealed that male-type Bmdsx expression was observed in females at 27 and 29 h after oviposition (hao), and finally disappeared at 32 hao. Moreover, BmIMP mRNA was also expressed in these females, and its expression level was comparable to that of the male-type Bmdsx mRNA. These results demonstrated that female embryos before 32 hao can show male-type expression of Bmdsx and BmIMP, suggesting that sex determination occurs between 29 and 32 hao, which correspond to the developmental stages from the head lobe differentiation to spoon-shaped embryo stages. This also suggests that the master switch gene for sex determination of B. mori is expressed in females during this period and represses the male-specific mode of expression in sex-determining genes. PMID:24346480

  4. Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities

    PubMed Central

    Narayanasamy, Shaman; Muller, Emilie E L; Sheik, Abdul R; Wilmes, Paul

    2015-01-01

    Biological wastewater treatment plants harbour diverse and complex microbial communities which prominently serve as models for microbial ecology and mixed culture biotechnological processes. Integrated omic analyses (combined metagenomics, metatranscriptomics, metaproteomics and metabolomics) are currently gaining momentum towards providing enhanced understanding of community structure, function and dynamics in situ as well as offering the potential to discover novel biological functionalities within the framework of Eco-Systems Biology. The integration of information from genome to metabolome allows the establishment of associations between genetic potential and final phenotype, a feature not realizable by only considering single ‘omes’. Therefore, in our opinion, integrated omics will become the future standard for large-scale characterization of microbial consortia including those underpinning biological wastewater treatment processes. Systematically obtained time and space-resolved omic datasets will allow deconvolution of structure–function relationships by identifying key members and functions. Such knowledge will form the foundation for discovering novel genes on a much larger scale compared with previous efforts. In general, these insights will allow us to optimize microbial biotechnological processes either through better control of mixed culture processes or by use of more efficient enzymes in bioengineering applications. PMID:25678254

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

    PubMed Central

    Parsa, Soroush; Kondo, Takumasa; Winotai, Amporn

    2012-01-01

    Phenacoccus manihoti Matile-Ferrero (Hemiptera: Pseudococcidae), one of the most serious pests of cassava worldwide, has recently reached Asia, raising significant concern over its potential spread throughout the region. To support management decisions, this article reports recent distribution records, and estimates the climatic suitability for its regional spread using a CLIMEX distribution model. The article also presents a taxonomic key that separates P. manihoti from all other mealybug species associated with the genus Manihot. Model predictions suggest P. manihoti imposes an important, yet differential, threat to cassava production in Asia. Predicted risk is most acute in the southern end of Karnataka in India, the eastern end of the Ninh Thuan province in Vietnam, and in most of West Timor in Indonesia. The model also suggests P. manihoti is likely to be limited by cold stress across Vietnam's northern regions and in the entire Guangxi province in China, and by high rainfall across the wet tropics in Indonesia and the Philippines. Predictions should be particularly important to guide management decisions for high risk areas where P. manihoti is absent (e.g., India), or where it has established but populations remain small and localized (e.g., South Vietnam). Results from this article should help decision-makers assess site-specific risk of invasion, and develop proportional prevention and surveillance programs for early detection and rapid response. PMID:23077659

  6. Anaerobic digestion of biowaste under extreme ammonia concentration: Identification of key microbial phylotypes.

    PubMed

    Poirier, Simon; Desmond-Le Quéméner, Elie; Madigou, Céline; Bouchez, Théodore; Chapleur, Olivier

    2016-05-01

    Ammonia inhibition represents a major operational issue for anaerobic digestion (AD). In order to get more insights into AD microbiota resistance, anaerobic batch reactors performances were investigated under a wide range of Total Ammonia Nitrogen (TAN) concentrations up to 50.0g/L at 35°C. The half maximal inhibitory concentration (IC50) value was determined to be 19.0g/L. Microbial community dynamics revealed that above a TAN concentration of 10.0g/L, remarkable modifications within archaeal and bacterial communities occurred. 16S rRNA gene sequencing analysis showed a gradual methanogenic shift between two OTUs from genus Methanosarcina when TAN concentration increased up to 25.0g/L. Proportion of potential syntrophic microorganisms such as Methanoculleus and Treponema progressively raised with increasing TAN up to 10.0 and 25.0g/L respectively, while Syntrophomonas and Ruminococcus groups declined. In 25.0g/L assays, Caldicoprobacter were dominant. This study highlights the emergence of AD key phylotypes at extreme ammonia concentrations. PMID:26874221

  7. Obstructive Lung Diseases in HIV: A Clinical Review and Identification of Key Future Research Needs.

    PubMed

    Drummond, M Bradley; Kunisaki, Ken M; Huang, Laurence

    2016-04-01

    HIV infection has shifted from what was once a disease directly impacting short-term mortality to what is now a chronic illness controllable in the era of effective combination antiretroviral therapy (ART). In this setting, life expectancy for HIV-infected individual is nearly comparable to that of individuals without HIV. Subsequent to this increase in life expectancy, there has been recognition of increased multimorbidity among HIV-infected persons, with prevalence of comorbid chronic illnesses now approaching 65%. Obstructive lung diseases, including chronic obstructive pulmonary disease (COPD) and asthma, are prevalent conditions associated with substantial morbidity and mortality in the United States. There is overlap in risk factors for HIV acquisition and chronic lung diseases, including lower socioeconomic status and the use of tobacco and illicit drugs. Objectives of this review are to (1) summarize the current state of knowledge regarding COPD and asthma among HIV-infected persons, (2) highlight implications for clinicians caring for patients with these combined comorbidities, and (3) identify key research initiatives to reduce the burden of obstructive lung diseases among HIV-infected persons. PMID:26974304

  8. Identification of the NF-?B inhibitor A20 as a key regulator for human adipogenesis

    PubMed Central

    Dorronsoro, A; Lang, V; Jakobsson, E; Ferrin, I; Salcedo, J M; Fernndez-Rueda, J; Fechter, K; Rodriguez, M S; Trigueros, C

    2013-01-01

    The zinc-finger protein A20 is a key player in the negative feedback regulation of the nuclear factor kappa-light-chain-enhancer of activated B-cell (NF-?B) pathway in response to multiple stimuli. Tumor necrosis factor alpha (TNF?), a cytokine with pleiotropic effects on cellular proliferation and differentiation, dramatically increases A20 expression in all tissues. As TNF? inhibits adipocyte differentiation, we have determined the contribution of A20 to the adipogenic capacity of human mesenchymal stromal cells (MSCs). Here we show that A20 is constitutively expressed in MSCs, which previously has been observed only in cells that are either tumor or immune cells (T/B lymphocytes). TNF? stimulation induced a rapid degradation of A20 protein mediated exclusively by the proteasome in MSCs and not by caspases. This degradation is concomitant to the induction of its own mRNA, which suggests that a tight regulation of NF-?B signaling in MSCs is fundamental. On one hand, we demonstrate that the knockdown of A20-mediated transcript dramatically decreases the adipogenic capacity of MSCs, which correlates with the phenotype observed in the presence of TNF?. On the other hand, A20 overexpression blocks NF-?B activation and drives to increased adipogenesis, even in the presence of TNF? treatment. In conclusion, our data demonstrate that the presence of A20 allows MSCs to differentiate into adipocytes by maintaining NF-?B signaling at a basal state. PMID:24357803

  9. Reduced and oxidised scytonemin: Theoretical protocol for Raman spectroscopic identification of potential key biomolecules for astrobiology

    NASA Astrophysics Data System (ADS)

    Varnali, Tereza; Edwards, Howell G. M.

    2014-01-01

    Scytonemin is an important UV-radiation protective biomolecule synthesised by extremophilic cyanobacteria in stressed terrestrial environments. Scytonemin and its reduced form have been both isolated experimentally and the Raman spectrum for scytonemin has been assigned and characterised experimentally both in extracts and in living extremophilic cyanobacterial colonies. Scytonemin is recognised as a key biomarker molecule for terrestrial organisms in stressed environments. We propose a new, theoretically plausible structure for oxidised scytonemin which has not been mentioned in the literature hitherto. DFT calculations for scytonemin, reduced scytonemin and the new structure modelled and proposed for oxidised scytonemin are reported along with their Raman spectroscopic data and λmax UV-absorption data obtained theoretically. Comparison of the vibrational spectroscopic assignments allows the three forms of scytonemin to be detected and identified and assist not only in the clarification of the major features in the experimentally observed Raman spectral data for the parent scytonemin but also support a protocol proposed for their analytical discrimination. The results of this study provide a basis for the search for molecules of this type in future astrobiological missions of exploration and the search for extinct and extant life terrestrially.

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

    PubMed

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

    1998-05-01

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

  11. Identification of key drought stress-related genes in the hyacinth bean.

    PubMed

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

    2013-01-01

    Hyacinth bean (Lablab purpureus [Linn.] Sweet) possesses excellent characteristics for field production, but the response of this plant to drought stress has not been described at the molecular level. Suppression subtraction hybridization (SSH) is an effective way to exploit key factors for plant responses to drought stress that are involved in transcriptional and metabolic activities. In this study, forward and reverse SSH libraries were generated from root tissues of the drought-tolerant hyacinth bean genotype MEIDOU 2012 under water-stress conditions. A total of 1,287 unigenes (94 contigs and 1,193 singletons) were derived from sequence alignment and cluster assembly of 1400 ESTs, and 80.6% of those hit against NCBI non-redundant (nr) database with E value <1E-06. BLASTX analysis revealed that the majority top matches were proteins form Glycine max (L.) Merrill. (61.5%). According to a gene ontology (GO) functional classification, 816 functionally annotated unigenes were assigned to the biological process category (74.1%), and 83.9% of them classified into molecular function and 69.2% involved in cellular component. A total of 168 sequences were further annotated with 207 Enzyme Commission (EC) codes and mapped to 83 different KEGG pathways. Seventeen functionally relevant genes were found to be overrepresented under drought stress using enrichment analysis. Differential expression of unigenes were confirmed by quantitative real-time PCR assays, and their transcript profiles generally divided into three patterns, depending on the expression peaked levels after 6, 8 or 10 days dehydration, which indicated that these genes are functionally associated in the drought-stress response. PMID:23472143

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

    PubMed Central

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

    2013-01-01

    Poor endometrial perfusion during implantation window is reported to be one of the possible causes of idiopathic recurrent spontaneous miscarriage (IRSM). We have tested the hypothesis that certain angiogenic and vasoactive factors are associated with vascular dysfunction during implantation window in IRSM and, therefore, could play a contributory role in making the endometrium unreceptive in these women. This is a prospective case-controlled study carried out on 66 women with IRSM and age and BMI matched 50 fertile women serving as controls. Endometrial expression of pro-inflammatory (IL-1β, TNF-α, IFN-γ, TGF-β1), anti-inflammatory (IL-4, -10), angiogenesis-associated cytokines (IL-2, -6, -8), angiogenic and vasoactive factors including prostaglandin E2 (PGE2), vascular endothelial growth factor (VEGF), endothelial nitric oxide synthase (eNOS), nitric oxide (NO) and adrenomedullin (ADM) were measured during implantation window by ELISA. Subendometrial blood flow (SEBF) was assessed by color Doppler ultrasonography. Multivariate analysis was used to identify the significant factor(s) responsible for vascular dysfunction in IRSM women during window of implantation and further correlated with vascular dysfunction. Endometrial expression of pro-inflammatory cytokines and PGE2 were up-regulated and anti-inflammatory and angiogenesis-associated cytokines down-regulated in IRSM women as compared with controls. Further, the angiogenic and vasoactive factors including VEGF, eNOS, NO and ADM were found to be down-regulated and SEBF grossly affected in these women. Multivariate analysis identified IL-10, followed by VEGF and eNOS as the major factors contributing towards vascular dysfunction in IRSM women. Moreover, these factors strongly correlated with blood flow impairment. This study provides an understanding that IL-10, VEGF and eNOS are the principal key components having a contributory role in endometrial vascular dysfunction in women with IRSM. Down-regulation of these factors is also associated with impaired endometrial perfusion which possibly makes the endometrium unreceptive that may eventually cause early pregnancy loss. PMID:24260517

  13. Identification of Transcriptional Factors and Key Genes in Primary Osteoporosis by DNA Microarray

    PubMed Central

    Xie, Wengui; Ji, Lixin; Zhao, Teng; Gao, Pengfei

    2015-01-01

    Background A number of genes have been identified to be related with primary osteoporosis while less is known about the comprehensive interactions between regulating genes and proteins. We aimed to identify the differentially expressed genes (DEGs) and regulatory effects of transcription factors (TFs) involved in primary osteoporosis. Material/Methods The gene expression profile GSE35958 was obtained from Gene Expression Omnibus database, including 5 primary osteoporosis and 4 normal bone tissues. The differentially expressed genes between primary osteoporosis and normal bone tissues were identified by the same package in R language. The TFs of these DEGs were predicted with the Essaghir A method. DAVID (The Database for Annotation, Visualization and Integrated Discovery) was applied to perform the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis of DEGs. After analyzing regulatory effects, a regulatory network was built between TFs and the related DEGs. Results A total of 579 DEGs was screened, including 310 up-regulated genes and 269 down-regulated genes in primary osteoporosis samples. In GO terms, more up-regulated genes were enriched in transcription regulator activity, and secondly in transcription factor activity. A total 10 significant pathways were enriched in KEGG analysis, including colorectal cancer, Wnt signaling pathway, Focal adhesion, and MAPK signaling pathway. Moreover, total 7 TFs were enriched, of which CTNNB1, SP1, and TP53 regulated most up-regulated DEGs. Conclusions The discovery of the enriched TFs might contribute to the understanding of the mechanism of primary osteoporosis. Further research on genes and TFs related to the WNT signaling pathway and MAPK pathway is urgent for clinical diagnosis and directing treatment of primary osteoporosis. PMID:25957414

  14. Identification of key genes associated with gastric cancer based on DNA microarray data

    PubMed Central

    SUN, HUI

    2016-01-01

    The present study aimed to identify genes with a differential pattern of expression in gastric cancer (GC), and to find novel molecular biomarkers for GC diagnosis and therapeutic treatment. The gene expression profile of GSE19826, including 12 GC samples and 15 normal controls, was downloaded from the Gene Expression Omnibus database. Differentially-expressed genes (DEGs) were screened in the GC samples compared with the normal controls. Two-way hierarchical clustering of DEGs was performed to distinguish the normal controls from the GC samples. The co-expression coefficient was analyzed among the DEGs using the data from COXPRESdb. The gene co-expression network was constructed based on the DEGs using Cytoscape software, and modules in the network were analyzed by ClusterOne and Bingo. Furthermore, enrichment analysis of the DEGs in the modules was performed using the Database for Annotation, Visualization and Integrated Discovery. In total, 596 DEGs in the GC samples and 57 co-expression gene pairs were identified. A total of 7 genes were enriched in the same module, for which the function was phosphate transport and which was annotated to participate in the extracellular matrix-receptor interaction pathway. These genes were collagen, type VI, α3 (COL6A3), COL1A2, COL1A1, COL5A2, thrombospondin 2, COL11A1 and COL5A1. Overall, the present study identified several biomarkers for GC using the gene expression profiling of human GC samples. The COL family is a promising prognostic marker for GC. Gene expression products represent candidate biomarkers endowed with great potential for the early screening and therapy of GC patients. PMID:26870242

  15. Identification of key genes for laryngeal squamous cell carcinoma using weighted co-expression network analysis

    PubMed Central

    LI, XIAO-TIAN

    2016-01-01

    Laryngeal squamous cell carcinoma (LSCC) is the most common malignant tumor in the head and neck, and can seriously affect the daily life of patients. To study the mechanisms of LSCC, the microarray of GSE51958 was analyzed in the present study. GSE51958 was downloaded from Gene Expression Omnibus, and included a collection of LSCC tissue samples and matched adjacent non-cancerous tissue samples from 10 patients. Differentially-expressed genes (DEGs) were identified using limma package. Next, a weighted co-expression network was constructed for the DEGs by WGCNA package in R. Modules of the weighted co-expression network were obtained through constructing a hierarchical clustering tree using the hybrid dynamic shear tree method. Using the clusterProfiler package, the potential functions of DEGs in the modules correlated with LSCC were predicted by pathway enrichment analysis. In total, 959 DEGs were screened from the LSCC samples compared with the adjacent non-cancerous samples, including 553 upregulated and 406 downregulated genes. The appointed black, brown, gray, pink and yellow modules were screened for the DEGs in the weighted co-expression network. For the DEGs in the brown and yellow modules, the enriched pathways were cytokine-cytokine receptor interaction and metabolic pathways, respectively. The DEGs in the pink module were involved in the majority of pathways. With high connectivity degrees in the pink module, TPX2, microtubule-associated (TPX2; degree, 25), minichromosome maintenance complex component 2 (MCM2; degree, 25), ubiquitin-like with PHD and ring finger domains 1 (UHRF1; degree, 22), cyclin-dependent kinase 2 (CDK2; degree, 20) and protein regulator of cytokinesis 1 (PRC1; degree, 20) may be involved in LSCC. Overall, In conclusion, from the integrated bioinformatics analysis of genes that may be associated with LSCC, 959 DEGs were obtained from LSCC samples compared with adjacent non-cancerous samples, and TPX2, MCM2, UHRF1, CDK2 and PRC1 were found to hold a possible association with the disease.

  16. Molecular Identification of Atlantic Bluefin Tuna (Thunnus thynnus, Scombridae) Larvae and Development of a DNA Character-Based Identification Key for Mediterranean Scombrids

    PubMed Central

    Puncher, Gregory Neils; Arrizabalaga, Haritz; Alemany, Francisco; Cariani, Alessia; Oray, Isik K.; Karakulak, F. Saadet; Basilone, Gualtiero; Cuttitta, Angela; Mazzola, Salvatore; Tinti, Fausto

    2015-01-01

    The Atlantic bluefin tuna, Thunnus thynnus, is a commercially important species that has been severely over-exploited in the recent past. Although the eastern Atlantic and Mediterranean stock is now showing signs of recovery, its current status remains very uncertain and as a consequence their recovery is dependent upon severe management informed by rigorous scientific research. Monitoring of early life history stages can inform decision makers about the health of the species based upon recruitment and survival rates. Misidentification of fish larvae and eggs can lead to inaccurate estimates of stock biomass and productivity which can trigger demands for increased quotas and unsound management conclusions. Herein we used a molecular approach employing mitochondrial and nuclear genes (CO1 and ITS1, respectively) to identify larvae (n = 188) collected from three spawning areas in the Mediterranean Sea by different institutions working with a regional fisheries management organization. Several techniques were used to analyze the genetic sequences (sequence alignments using search algorithms, neighbour joining trees, and a genetic character-based identification key) and an extensive comparison of the results is presented. During this process various inaccuracies in related publications and online databases were uncovered. Our results reveal important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology-based methods. While less than half of larvae provided were bluefin tuna, other dominant taxa were bullet tuna (Auxis rochei), albacore (Thunnus alalunga) and little tunny (Euthynnus alletteratus). We advocate an expansion of expertise for a new generation of morphology-based taxonomists, increased dialogue between morphology-based and molecular taxonomists and increased scrutiny of public sequence databases. PMID:26147931

  17. Molecular Identification of Atlantic Bluefin Tuna (Thunnus thynnus, Scombridae) Larvae and Development of a DNA Character-Based Identification Key for Mediterranean Scombrids.

    PubMed

    Puncher, Gregory Neils; Arrizabalaga, Haritz; Alemany, Francisco; Cariani, Alessia; Oray, Isik K; Karakulak, F Saadet; Basilone, Gualtiero; Cuttitta, Angela; Mazzola, Salvatore; Tinti, Fausto

    2015-01-01

    The Atlantic bluefin tuna, Thunnus thynnus, is a commercially important species that has been severely over-exploited in the recent past. Although the eastern Atlantic and Mediterranean stock is now showing signs of recovery, its current status remains very uncertain and as a consequence their recovery is dependent upon severe management informed by rigorous scientific research. Monitoring of early life history stages can inform decision makers about the health of the species based upon recruitment and survival rates. Misidentification of fish larvae and eggs can lead to inaccurate estimates of stock biomass and productivity which can trigger demands for increased quotas and unsound management conclusions. Herein we used a molecular approach employing mitochondrial and nuclear genes (CO1 and ITS1, respectively) to identify larvae (n = 188) collected from three spawning areas in the Mediterranean Sea by different institutions working with a regional fisheries management organization. Several techniques were used to analyze the genetic sequences (sequence alignments using search algorithms, neighbour joining trees, and a genetic character-based identification key) and an extensive comparison of the results is presented. During this process various inaccuracies in related publications and online databases were uncovered. Our results reveal important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology-based methods. While less than half of larvae provided were bluefin tuna, other dominant taxa were bullet tuna (Auxis rochei), albacore (Thunnus alalunga) and little tunny (Euthynnus alletteratus). We advocate an expansion of expertise for a new generation of morphology-based taxonomists, increased dialogue between morphology-based and molecular taxonomists and increased scrutiny of public sequence databases. PMID:26147931

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

    PubMed

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

    2014-04-22

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  1. Automated identification of social interaction criteria in Drosophila melanogaster.

    PubMed

    Schneider, J; Levine, J D

    2014-10-01

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

  2. Large-Scale Identification and Analysis of Suppressive Drug Interactions

    PubMed Central

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

    2014-01-01

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

  3. Pathway-guided Identification of Gene-Gene Interactions

    PubMed Central

    Wang, Xin; Zhang, Daowen; Tzeng, Jung-Ying

    2014-01-01

    Summary Assessing gene-gene interactions (GxG) at the gene level can permit examination of epistasis at biologically functional units with amplified interaction signals from marker-marker pairs. Current gene-based GxG methods tend to be designed for studying interactions among two or a few genes. For complex traits, it is often common to have a list of many candidate genes to explore GxG. In this work, we propose a pathway-guided approach based on penalized regression for detecting interactions among genes. Specifically, we apply the principal component analysis to summarize the multi-SNP genotypes and SNP-SNP interaction between a gene pair, and to identify important main and interaction effects using an L1 penalty, which incorporates adaptive weights based on biological guidance and trait supervision. Our approach aims to combine the advantages of biological guidance and data adaptiveness, and yields credible findings that have both biological and statistical support and may be likely to shed insights in order to formulate biological hypotheses for further cellular and molecular studies. The proposed approach can be used to explore the gene-gene interactions with a list of many candidate genes and is applicable even when sample size is smaller than the number of predictors studied. We evaluate the utility of the pathway-guided penalized GxG regression using simulation and real data analysis. The numerical studies suggest improved performance over methods not utilizing pathway and trait guidance. PMID:25227508

  4. Improved symbol rate identification method for on-off keying and advanced modulation format signals based on asynchronous delayed sampling

    NASA Astrophysics Data System (ADS)

    Cui, Sheng; Jin, Shang; Xia, Wenjuan; Ke, Changjian; Liu, Deming

    2015-11-01

    Symbol rate identification (SRI) based on asynchronous delayed sampling is accurate, cost-effective and robust to impairments. For on-off keying (OOK) signals the symbol rate can be derived from the periodicity of the second-order autocorrelation function (ACF2) of the delay tap samples. But it is found that when applied this method to advanced modulation format signals with auxiliary amplitude modulation (AAM), incorrect results may be produced because AAM has significant impact on ACF2 periodicity, which makes the symbol period harder or even unable to be correctly identified. In this paper it is demonstrated that for these signals the first order autocorrelation function (ACF1) has stronger periodicity and can be used to replace ACF2 to produce more accurate and robust results. Utilizing the characteristics of the ACFs, an improved SRI method is proposed to accommodate both OOK and advanced modulation formant signals in a transparent manner. Furthermore it is proposed that by minimizing the peak to average ratio (PAPR) of the delay tap samples with an additional tunable dispersion compensator (TDC) the limited dispersion tolerance can be expanded to desired values.

  5. 7α-Hydroxypregnenolone, a New Key Regulator of Locomotor Activity of Vertebrates: Identification, Mode of Action, and Functional Significance

    PubMed Central

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Noël, J. P.; Renson, L.; Kerschen, G.

    2014-06-01

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

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

    PubMed

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

    2013-01-01

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

  8. Host associations and incidence of Diuraphis spp. in the Rocky Mountain region of the United States, and pictorial key for their identification.

    PubMed

    Puterka, Gary J; Hammon, Robert W; Burd, John D; Peairs, Frank B; Randolph, Terri; Cooper, W Rodney

    2010-10-01

    The Russian wheat aphid, Diuraphis noxia Kurdjumov, is an introduced species first identified in 1986 into the United States. It has since become a major pest of wheat, Triticum aestivum L., and other small grains in the western United States. Three other Diuraphis species, Diuraphis frequens (Walker), Diuraphis mexicana (McVicar Baker), and Diuraphis tritici (Gillette), were already endemic to the United States before the introduction of D. noxia. The objective of this study was to determine the occurrence and host associations of these four Diuraphis spp. in the Rocky Mountain region that borders the western Great Plains to better understand their distribution and ecological interactions. In addition, a key to these species with photographs of live or fresh preparations of specimens is presented to aid in their identification. D. noxia was the most widely distributed species in the study area spanning the Rocky Mountain areas of Wyoming, New Mexico, Utah, and Colorado. This species was most common in the cereal-producing areas of the Colorado Plateau ecoregion. D. frequens was found to be the predominant species in the Alpine/Aspen Mountain areas of the South Central Rockies and Colorado Rockies ecoregions. The other Diuraphis species were rarely encountered even though their plant hosts occurred in the ecoregions sampled. D. noxia shared common hosts and was found co-infesting grasses with other Diuraphis species. Therefore, the potential exists for D. noxia to impact the other native Diuraphis species. PMID:21061992

  9. Identification of key genes associated with the human abdominal aortic aneurysm based on the gene expression profile.

    PubMed

    Chen, Xudong; Zheng, Chengfei; He, Yunjun; Tian, Lu; Li, Jianhui; Li, Donglin; Jin, Wei; Li, Ming; Zheng, Shusen

    2015-12-01

    The present study was aimed at screening the key genes associated with abdominal aortic aneurysm (AAA) in the neck, and to investigate the molecular mechanism underlying the development of AAA. The gene expression profile, GSE47472, including 14 AAA neck samples and eight donor controls, was downloaded from the Gene Expression Omnibus database. The total AAA samples were grouped into two types to avoid bias. Differentially expressed genes (DEGs) were screened in patients with AAA and subsequently compared with donor controls using linear models for microarray data, or the Limma package in R, followed by gene ontology enrichment analysis. Furthermore, a protein‑protein interaction (PPI) network based on the DEGs was constructed to detect highly connected regions using a Cytoscape plugin. In total, 388 DEGs in the AAA samples were identified. These DEGs were predominantly associated with limb development, including embryonic limb development and appendage development. Nuclear receptor co‑repressor 1 (NCOR1), histone 4 (H4), E2F transcription factor 4 (E2F4) and hepatocyte nuclear factor 4α (HNF4A) were the four transcription factors associated with AAA. Furthermore, HNF4A indirectly interacted with the other three transcription factors. Additionally, six clusters were selected from the PPI network. The DEG screening process and the construction of an interaction network enabled an understanding of the mechanism of AAA to be gleaned. HNF4A may exert an important role in AAA development through its interactions with the three other transcription factors (E2F4, NCOR1 and H4), and the mechanism of this coordinated regulation of the transcription factors in AAA may provide a suitable target for the development of therapeutic intervention strategies. PMID:26498477

  10. Identification of key genes associated with the human abdominal aortic aneurysm based on the gene expression profile

    PubMed Central

    CHEN, XUDONG; ZHENG, CHENGFEI; HE, YUNJUN; TIAN, LU; LI, JIANHUI; LI, DONGLIN; JIN, WEI; LI, MING; ZHENG, SHUSEN

    2015-01-01

    The present study was aimed at screening the key genes associated with abdominal aortic aneurysm (AAA) in the neck, and to investigate the molecular mechanism underlying the development of AAA. The gene expression profile, GSE47472, including 14 AAA neck samples and eight donor controls, was downloaded from the Gene Expression Omnibus database. The total AAA samples were grouped into two types to avoid bias. Differentially expressed genes (DEGs) were screened in patients with AAA and subsequently compared with donor controls using linear models for microarray data, or the Limma package in R, followed by gene ontology enrichment analysis. Furthermore, a protein-protein interaction (PPI) network based on the DEGs was constructed to detect highly connected regions using a Cytoscape plugin. In total, 388 DEGs in the AAA samples were identified. These DEGs were predominantly associated with limb development, including embryonic limb development and appendage development. Nuclear receptor co-repressor 1 (NCOR1), histone 4 (H4), E2F transcription factor 4 (E2F4) and hepatocyte nuclear factor 4α (HNF4A) were the four transcription factors associated with AAA. Furthermore, HNF4A indirectly interacted with the other three transcription factors. Additionally, six clusters were selected from the PPI network. The DEG screening process and the construction of an interaction network enabled an understanding of the mechanism of AAA to be gleaned. HNF4A may exert an important role in AAA development through its interactions with the three other transcription factors (E2F4, NCOR1 and H4), and the mechanism of this coordinated regulation of the transcription factors in AAA may provide a suitable target for the development of therapeutic intervention strategies. PMID:26498477

  11. "Key Interactions" as Agency and Empowerment: Providing a Sense of the Possible to Marginalized, Mexican-Descent Students

    ERIC Educational Resources Information Center

    Reyes, Reynaldo, III

    2009-01-01

    This article discusses how key interactions between community members, teachers, and Latino counselors and advisers were integral in providing support, knowledge, and agency to marginalized, Mexican-descent students in their 1st year of college. Findings show that particular types of discourse and narrative exchanged between integral adult figures…

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

    PubMed Central

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

    2009-01-01

    The NIAID (National Institute for Allergy and Infectious Diseases) Biodefense Proteomics program aims to identify targets for potential vaccines, therapeutics, and diagnostics for agents of concern in bioterrorism, including bacterial, parasitic, and viral pathogens. The program includes seven Proteomics Research Centers, generating diverse types of pathogen-host data, including mass spectrometry, microarray transcriptional profiles, protein interactions, protein structures and biological reagents. The Biodefense Resource Center (www.proteomicsresource.org) has developed a bioinformatics framework, employing a protein-centric approach to integrate and support mining and analysis of the large and heterogeneous data. Underlying this approach is a data warehouse with comprehensive protein + gene identifier and name mappings and annotations extracted from over 100 molecular databases. Value-added annotations are provided for key proteins from experimental findings using controlled vocabulary. The availability of pathogen and host omics data in an integrated framework allows global analysis of the data and comparisons across different experiments and organisms, as illustrated in several case studies presented here. (1) The identification of a hypothetical protein with differential gene and protein expressions in two host systems (mouse macrophage and human HeLa cells) infected by different bacterial (Bacillus anthracis and Salmonella typhimurium) and viral (orthopox) pathogens suggesting that this protein can be prioritized for additional analysis and functional characterization. (2) The analysis of a vaccinia-human protein interaction network supplemented with protein accumulation levels led to the identification of human Keratin, type II cytoskeletal 4 protein as a potential therapeutic target. (3) Comparison of complete genomes from pathogenic variants coupled with experimental information on complete proteomes allowed the identification and prioritization of ten potential diagnostic targets from Bacillus anthracis. The integrative analysis across data sets from multiple centers can reveal potential functional significance and hidden relationships between pathogen and host proteins, thereby providing a systems approach to basic understanding of pathogenicity and target identification. PMID:19779614

  13. Identification of Key Factors Involved in the Biosorption of Patulin by Inactivated Lactic Acid Bacteria (LAB) Cells.

    PubMed

    Wang, Ling; Wang, Zhouli; Yuan, Yahong; Cai, Rui; Niu, Chen; Yue, Tianli

    2015-01-01

    The purpose of this study was to identify the key factors involved in patulin adsorption by heat-inactivated lactic acid bacteria (LAB) cells. For preventing bacterial contamination, a sterilization process was involved in the adsorption process. The effects of various physical, chemical, and enzymatic pre-treatments, simultaneous treatments, and post-treatments on the patulin adsorption performances of six LAB strains were evaluated. The pre-treated cells were characterized by scanning electron microscopy (SEM). Results showed that the removal of patulin by viable cells was mainly based on adsorption or degradation, depending on the specific strain. The adsorption abilities were widely increased by NaOH and esterification pre-treatments, and reduced by trypsin, lipase, iodate, and periodate pre-treatments. Additionally, the adsorption abilities were almost maintained at pH 2.2-4.0, and enhanced significantly at pH 4.0-6.0. The effects of sodium and magnesium ions on the adsorption abilities at pH 4 were slight and strain-specific. A lower proportion of patulin was released from the strain with higher adsorption ability. Analyses revealed that the physical structure of peptidoglycan was not a principal factor. Vicinal OH and carboxyl groups were not involved in patulin adsorption, while alkaline amino acids, thiol and ester compounds were important for patulin adsorption. Additionally, besides hydrophobic interaction, electrostatic interaction also participated in patulin adsorption, which was enhanced with the increase in pH (4.0-6.0). PMID:26581099

  14. Stochastic Identification of Stability of Competitive Interactions in Ecosystems

    PubMed Central

    Vach, Marek; Vachová, Pavla

    2016-01-01

    The problem of finding an optimum within a set of possibilities that represent the varying successfulness of numerous subjects competing with one another is highly relevant in the field of ecosystem interactions. We propose a method for solving this problem by the application of the Nash equilibrium concept, which is frequently used in ecology. The proposed model is based on the transformation of the initial payoff vectors of subjects that interact in different situations into a statistical set of symmetrical game matrices that consist of permutations of payoff values. The equilibrium solution is expressed as values of the probability of Nash equilibrium occurrence with uniform distribution over all possible permutations based on uncertainty of positions of payoff values in the matrix. We assume that this equilibrium solution provides information on the distribution of the degree of stability among individual situations and interacting subjects. In this paper, we validate this assumption and demonstrate its application to a dataset that represents interspecies interactions in plant ecology. We propose that the use of the Nash equilibrium in the analysis of datasets formalized according to the Pareto optimality scheme is applicable in numerous other contexts. PMID:27171283

  15. Revisiting cobalt chloride preconditioning to prevent hypobaric hypoxia-induced damage: identification of global proteomic alteration and key networks.

    PubMed

    Ahmad, Yasmin; Mishra, Shalini; Arya, Adtiya; Paul, Subhojit; Sharma, Manish; Prasad, Jyotsna; Bhargava, Kalpana

    2016-05-01

    Several studies have supported the hypoxia mimetic roles and cytoprotective properties of cobalt chloride in vitro and in vivo. However, a clear understanding of biological process-based mechanism that integrates the available information remains unknown. This study was aimed to explore the potential mechanism of cobalt chloride deciphering its benefits and well-known physiological challenge caused by hypobaric hypoxia that reportedly affects nearly 24 % of the global population. In order to explore the mechanism of CoCl2, we used global proteomic and systems biology approach in rat model to provide a deeper insight into molecular mechanisms of preconditioning. Furthermore, key conclusions were drawn based on biological network analysis and their enrichment with ontological overlaps. The study was further strengthened by consistent identification of validation of proteins using immunoblotting. CoCl2-pretreated animals exposed to hypoxia showed two significant networks, one lipid metabolism and other cell cycle associated, with a total score of 23 and eight focus molecules. In this study, we delineated two primary routes: one, by direct modulation of reactive oxygen species metabolism and, second, by regulation of lipid metabolism which was not known until now. The previously known benefits of cobalt chloride during physiological challenge by hypobaric hypoxia are convincing and could be explained by some basic set of metabolic and molecular reorganization within the hypoxia model. Interestingly, we also observed some of the completely unknown roles of cobalt chloride such as regulation of lipid that could undulate the translational roles of cobalt chloride supplementation beyond hypoxia preconditioning. PMID:26882918

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

    ERIC Educational Resources Information Center

    Kohut, Connie K.; And Others

    1993-01-01

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

  17. Key interactions in integrin ectodomain responsible for global conformational change detected by elastic network normal-mode analysis.

    PubMed

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

    2008-09-15

    Integrin, a membrane protein with a huge extracellular domain, participates in cell-cell and cell-extracellular-matrix interactions for metazoan. A group of integrins is known to perform a large-scale structural change when the protein is activated, but the activation mechanism and generality of the conformational change remain to be elucidated. We performed normal-mode analysis of the elastic network model on integrin alpha(V)beta(3) ectodomain in the bent form and identified key residues that influenced molecular motions. Iterative normal-mode calculations demonstrated that the specific nonbonded interactions involving the key residues work as a snap to keep integrin in the bent form. The importance of the key residues for the conformational change was further verified by mutation experiments, in which integrin alpha(IIb)beta(3) was used. The conservation pattern of amino acid residues among the integrin family showed that the characteristic pattern of residues seen around these key residues is found in the limited groups of integrin beta-chains. This conservation pattern suggests that the molecular mechanism of the conformational change relying on the interactions found in integrin alpha(V)beta(3) is unique to the limited types of integrins. PMID:18515366

  18. Proteome identification of proteins interacting with histone methyltransferase SET8.

    PubMed

    Qin, Yi; Ouyang, Huafang; Liu, Jing; Xie, Youhua

    2013-04-01

    SET8 (also known as PR-Set7/9, SETD8, KMT5A), a member of the SET domain containing methyltransferase family, which specifically catalyzes mono-methylation of K20 on histone H4 (H4K20me1), has been implicated in multiple biological processes, such as gene transcriptional regulation, cell cycle control, genomic integrity maintenance and development. In this study, we used GST-SET8 fusion protein as bait to search for SET8 interaction partners to elucidate physiological functions of SET8. In combination with mass spectrometry, we identified 40 proteins that potentially interact with SET8. DDX21, a nucleolar protein, was further confirmed to associate with SET8. Furthermore, we discovered a novel function of SET8 in the regulation of rRNA transcription. PMID:23419719

  19. Identification of interspecies interactions affecting Porphyromonas gingivalis virulence phenotypes

    PubMed Central

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

    2011-01-01

    Background Periodontitis is recognized as a complex polymicrobial disease, however, the impact of the bacterial interactions among the 7001,000 different species of the oral microbiota remains poorly understood. We conducted an in vitro screen for oral bacteria that mitigate selected virulence phenotypes of the important periodontal pathogen, Porphyromonas gingivalis. Method We isolated and identified oral anaerobic bacteria from subgingival plaque of dental patients. When cocultured with P. gingivalis W83, specific isolates reduced the cytopathogenic effects of P. gingivalis on oral epithelial cells. Result In an initial screen of 103 subgingival isolates, we identified 19 distinct strains from nine species of bacteria (including Actinomyces naeslundii, Streptococcus oralis, Streptococcus mitis, and Veilonella dispar) that protect oral epithelial cells from P. gingivalis-induced cytotoxicity. We found that some of these strains inhibited P. gingivalis growth in plate assays through the production of organic acids, whereas some decreased the gingipain activity of P. gingivalis in coculture or mixing experiments. Conclusion In summary, we identified 19 strains isolated from human subgingival plaque that interacted with P. gingivalis, resulting in mitigation of its cytotoxicity to oral epithelial cells, inhibition of growth, and/or reduction of gingipain activity. Understanding the mechanisms of interaction between bacteria in the oral microbial community may lead to the development of new probiotic agents and new strategies for interrupting the development of periodontal disease. PMID:22022641

  20. Identification of Global Ferredoxin Interaction Networks in Chlamydomonas reinhardtii*

    PubMed Central

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

    2013-01-01

    Ferredoxins (FDXs) can distribute electrons originating from photosynthetic water oxidation, fermentation, and other reductant-generating pathways to specific redox enzymes in different organisms. The six FDXs identified in Chlamydomonas reinhardtii are not fully characterized in terms of their biological function. In this report, we present data from the following: (a) yeast two-hybrid screens, identifying interaction partners for each Chlamydomonas FDX; (b) pairwise yeast two-hybrid assays measuring FDX interactions with proteins from selected biochemical pathways; (c) affinity pulldown assays that, in some cases, confirm and even expand the interaction network for FDX1 and FDX2; and (d) in vitro NADP+ reduction and H2 photo-production assays mediated by each FDX that verify their role in these two pathways. Our results demonstrate new potential roles for FDX1 in redox metabolism and carbohydrate and fatty acid biosynthesis, for FDX2 in anaerobic metabolism, and possibly in state transition. Our data also suggest that FDX3 is involved in nitrogen assimilation, FDX4 in glycolysis and response to reactive oxygen species, and FDX5 in hydrogenase maturation. Finally, we provide experimental evidence that FDX1 serves as the primary electron donor to two important biological pathways, NADPH and H2 photo-production, whereas FDX2 is capable of driving these reactions at less than half the rate observed for FDX1. PMID:24100040

  1. Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network model.

    PubMed

    Su, Ji Guo; Han, Xiao Ming; Zhang, Xiao; Hou, Yan Xue; Zhu, Jian Zhuo; Wu, Yi Dong

    2016-03-01

    Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK2) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified. PMID:25909329

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

    PubMed Central

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  4. Identification of Key Factors Involved in the Biosorption of Patulin by Inactivated Lactic Acid Bacteria (LAB) Cells

    PubMed Central

    Wang, Ling; Wang, Zhouli; Yuan, Yahong; Cai, Rui; Niu, Chen; Yue, Tianli

    2015-01-01

    The purpose of this study was to identify the key factors involved in patulin adsorption by heat-inactivated lactic acid bacteria (LAB) cells. For preventing bacterial contamination, a sterilization process was involved in the adsorption process. The effects of various physical, chemical, and enzymatic pre-treatments, simultaneous treatments, and post-treatments on the patulin adsorption performances of six LAB strains were evaluated. The pre-treated cells were characterized by scanning electron microscopy (SEM). Results showed that the removal of patulin by viable cells was mainly based on adsorption or degradation, depending on the specific strain. The adsorption abilities were widely increased by NaOH and esterification pre-treatments, and reduced by trypsin, lipase, iodate, and periodate pre-treatments. Additionally, the adsorption abilities were almost maintained at pH 2.2–4.0, and enhanced significantly at pH 4.0–6.0. The effects of sodium and magnesium ions on the adsorption abilities at pH 4 were slight and strain-specific. A lower proportion of patulin was released from the strain with higher adsorption ability. Analyses revealed that the physical structure of peptidoglycan was not a principal factor. Vicinal OH and carboxyl groups were not involved in patulin adsorption, while alkaline amino acids, thiol and ester compounds were important for patulin adsorption. Additionally, besides hydrophobic interaction, electrostatic interaction also participated in patulin adsorption, which was enhanced with the increase in pH (4.0–6.0). PMID:26581099

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

    PubMed Central

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

    2014-01-01

    Clathrin-mediated endocytosis is a highly conserved intracellular trafficking pathway that depends on dynamic protein–protein interactions between up to 60 different proteins. However, little is known about the spatio-temporal regulation of these interactions. Using fluorescence (cross)-correlation spectroscopy in yeast, we tested 41 previously reported interactions in vivo and found 16 to exist in the cytoplasm. These detected cytoplasmic interactions included the self-interaction of Ede1, homolog of mammalian Eps15. Ede1 is the crucial scaffold for the organization of the early stages of endocytosis. We show that oligomerization of Ede1 through its central coiled coil domain is necessary for its localization to the endocytic site and we link the oligomerization of Ede1 to its function in locally concentrating endocytic adaptors and organizing the endocytic machinery. Our study sheds light on the importance of the regulation of protein–protein interactions in the cytoplasm for the assembly of the endocytic machinery in vivo. PMID:25366307

  6. Identification of Crew-Systems Interactions and Decision Related Trends

    NASA Technical Reports Server (NTRS)

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

    2013-01-01

    NASA Vehicle System Safety Technology (VSST) project management uses systems analysis to identify key issues and maintain a portfolio of research leading to potential solutions to its three identified technical challenges. Statistical data and published safety priority lists from academic, industry and other government agencies were reviewed and analyzed by NASA Aviation Safety Program (AvSP) systems analysis personnel to identify issues and future research needs related to one of VSST's technical challenges, Crew Decision Making (CDM). The data examined in the study were obtained from the National Transportation Safety Board (NTSB) Aviation Accident and Incident Data System, Federal Aviation Administration (FAA) Accident/Incident Data System and the NASA Aviation Safety Reporting System (ASRS). In addition, this report contains the results of a review of safety priority lists, information databases and other documented references pertaining to aviation crew systems issues and future research needs. The specific sources examined were: Commercial Aviation Safety Team (CAST) Safety Enhancements Reserved for Future Implementation (SERFIs), Flight Deck Automation Issues (FDAI) and NTSB Most Wanted List and Open Recommendations. Various automation issues taxonomies and priority lists pertaining to human factors, automation and flight design were combined to create a list of automation issues related to CDM.

  7. Systematic Identification of Protein-Metabolite Interactions in Complex Metabolite Mixtures by Ligand-Detected Nuclear Magnetic Resonance Spectroscopy.

    PubMed

    Nikolaev, Yaroslav V; Kochanowski, Karl; Link, Hannes; Sauer, Uwe; Allain, Frederic H-T

    2016-05-10

    Protein-metabolite interactions play a vital role in the regulation of numerous cellular processes. Consequently, identifying such interactions is a key prerequisite for understanding cellular regulation. However, the noncovalent nature of the binding between proteins and metabolites has so far hampered the development of methods for systematically mapping protein-metabolite interactions. The few available, largely mass spectrometry-based, approaches are restricted to specific metabolite classes, such as lipids. In this study, we address this issue and show the potential of ligand-detected nuclear magnetic resonance (NMR) spectroscopy, which is routinely used in drug development, to systematically identify protein-metabolite interactions. As a proof of concept, we selected four well-characterized bacterial and mammalian proteins (AroG, Eno, PfkA, and bovine serum albumin) and identified metabolite binders in complex mixes of up to 33 metabolites. Ligand-detected NMR captured all of the reported protein-metabolite interactions, spanning a full range of physiologically relevant Kd values (low micromolar to low millimolar). We also detected a number of novel interactions, such as promiscuous binding of the negatively charged metabolites citrate, AMP, and ATP, as well as binding of aromatic amino acids to AroG protein. Using in vitro enzyme activity assays, we assessed the functional relevance of these novel interactions in the case of AroG and show that l-tryptophan, l-tyrosine, and l-histidine act as novel inhibitors of AroG activity. Thus, we conclude that ligand-detected NMR is suitable for the systematic identification of functionally relevant protein-metabolite interactions. PMID:27065204

  8. Identification of Posttranslational Modification-Dependent Protein Interactions Using Yeast Surface Displayed Human Proteome Libraries

    PubMed Central

    Bidlingmaier, Scott; Liu, Bin

    2016-01-01

    The identification of proteins that interact specifically with posttranslational modifications such as phosphorylation is often necessary to understand cellular signaling pathways. Numerous methods for identifying proteins that interact with posttranslational modifications have been utilized, including affinity-based purification and analysis, protein microarrays, phage display, and tethered catalysis. Although these techniques have been used successfully, each has limitations. Recently, yeast surface-displayed human proteome libraries have been utilized to identify protein fragments with affinity for various target molecules, including phosphorylated peptides. When coupled with fluorescently activated cell sorting and high throughput methods for the analysis of selection outputs, yeast surface-displayed human proteome libraries can rapidly and efficiently identify protein fragments with affinity for any soluble ligand that can be fluorescently detected, including posttranslational modifications. In this review we compare the use of yeast surface display libraries to other methods for the identification of interactions between proteins and posttranslational modifications and discuss future applications of the technology. PMID:26060076

  9. Key role of asymmetric interactions in low-dimensional heat transport

    NASA Astrophysics Data System (ADS)

    Chen, Shunda; Zhang, Yong; Wang, Jiao; Zhao, Hong

    2016-03-01

    We study the heat current autocorrelation function (HCAF) in one-dimensional, momentum-conserving lattices. In particular, we explore if there is any link between the decaying characteristics of the HCAF and asymmetric interparticle interactions. The Lennard-Jones model is investigated intensively in view of its significance to applications. It is found that, in the time range accessible to numerical simulations, the HCAF decays faster than power-law manners, and in some cases it decays even exponentially. Following the Green-Kubo formula, fast decay of the HCAF implies convergence of the heat conductivity, which is also corroborated by simulations. In addition, with a comparison to the Fermi-Pasta-Ulam-β model of symmetric interactions, the HCAF of the Fermi-Pasta-Ulam-α-β model of asymmetric interactions is also investigated. The results of all these studies lead to that, in certain ranges of parameters, fast decaying of the HCAF can be observed and correlated to the asymmetry degree of interactions.

  10. Hydrophobic Interactions Are Key To Drive the Association of Tapasin with Peptide Transporter Subunit TAP2.

    PubMed

    Rufer, Elke; Kägebein, Danny; Leonhardt, Ralf M; Knittler, Michael R

    2015-12-01

    The transporter associated with Ag processing (TAP) translocates proteasomally derived cytosolic peptides into the endoplasmic reticulum. TAP is a central component of the peptide-loading complex (PLC), to which tapasin (TPN) recruits MHC class I (MHC I) and accessory chaperones. The PLC functions to facilitate and optimize MHC I-mediated Ag presentation. The heterodimeric peptide transporter consists of two homologous subunits, TAP1 and TAP2, each of which contains an N-terminal domain (N-domain) in addition to a conserved transmembrane (TM) core segment. Each N-domain binds to the TM region of a single TPN molecule, which recruits one MHC I molecule to TAP1 and/or TAP2. Although both N-domains act as TPN-docking sites, various studies suggest a functional asymmetry within the PLC resulting in greater significance of the TAP2/TPN interaction for MHC loading. In this study, we demonstrate that the leucine-rich hydrophobic sequence stretches (with the central leucine residues L20 and L66) in the first and second TM helix of TAP2 form a functional unit acting as a docking site for optimal TPN/MHC I recruitment, whereas three distinct highly conserved arginine and/or aspartate residues inside or flanking these TM helices are dispensable. Moreover, we show that the physical interaction between TAP2 and TPN is disrupted by benzene, a compound known to interfere with hydrophobic interactions, such as those between pairing leucine zippers. No such effects were observed for the TAP1/TAP2 interaction or the complex formation between TPN and MHC I. We propose that TAP/TPN complex formation is driven by hydrophobic interactions via leucine zipper-like motifs. PMID:26519531

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

    PubMed Central

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

    2015-01-01

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

  12. Identification of HNF-4α as a key transcription factor to promote ChREBP expression in response to glucose

    PubMed Central

    Meng, Jian; Feng, Ming; Dong, Weibing; Zhu, Yemin; Li, Yakui; Zhang, Ping; Wu, Lifang; Li, Minle; Lu, Ying; Chen, Hanbei; Liu, Xing; Lu, Yan; Sun, Haipeng; Tong, Xuemei

    2016-01-01

    Transcription factor carbohydrate responsive element binding protein (ChREBP) promotes glycolysis and lipogenesis in metabolic tissues and cancer cells. ChREBP-α and ChREBP-β, two isoforms of ChREBP transcribed from different promoters, are both transcriptionally induced by glucose. However, the mechanism by which glucose increases ChREBP mRNA levels remains unclear. Here we report that hepatocyte nuclear factor 4 alpha (HNF-4α) is a key transcription factor for glucose-induced ChREBP-α and ChREBP-β expression. Ectopic HNF-4α expression increased ChREBP transcription while knockdown of HNF-4α greatly reduced ChREBP mRNA levels in liver cancer cells and mouse primary hepatocytes. HNF-4α not only directly bound to an E-box-containing region in intron 12 of the ChREBP gene, but also promoted ChREBP-β transcription by directly binding to two DR1 sites and one E-box-containing site of the ChREBP-β promoter. Moreover, HNF-4α interacted with ChREBP-α and synergistically promoted ChREBP-β transcription. Functionally, HNF-4α suppression reduced glucose-dependent ChREBP induction. Increased nuclear abundance of HNF-4α and its binding to cis-elements of ChREBP gene in response to glucose contributed to glucose-responsive ChREBP transcription. Taken together, our results not only revealed the novel mechanism by which HNF-4α promoted ChREBP transcription in response to glucose, but also demonstrated that ChREBP-α and HNF-4α synergistically increased ChREBP-β transcription. PMID:27029511

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

    PubMed Central

    Gao, Hui-Ming; Hong, Jau-shyong

    2011-01-01

    Parkinson’s disease (PD) is the second most common neurodegenerative disease. The gradual, irreversible loss of dopamine neurons in the substantia nigra isthe signature lesion of PD. Clinical symptoms of PD become apparent when 50–60% of nigral dopamine neurons are lost. PD progresses insidiously for 5–7 years (preclinical period) and then continues to worsen even under the symptomatic treatment. To determine what triggers the disease onset and what drives the chronic, self-propelling neurodegenerative process becomes critical and urgent, since lack of such knowledge impedes the discovery of effective treatments to retard PD progression. At present, available therapeutics only temporarily relieve PD symptoms. While the identification of causative gene defects in familial PD uncovers important genetic influences in this disease, the majority of PD cases are sporadic and idiopathic. The current consensus suggests that PD develops from multiple risk factors including aging, genetic predisposition, and environmental exposure. Here, we briefly review research on the genetic and environmental causes of PD. We also summarize very recent genome-wide association studies on risk gene polymorphisms in the emergence of PD. We highlight the new converging evidence on gene-environment interplay in the development of PD with an emphasis on newly developed multiple-hit PD models involving both genetic lesions and environmental triggers. PMID:21439347

  14. Catecholamines and acetylcholine are key regulators of the interaction between microbes and the immune system.

    PubMed

    Weinstein, Leon Islas; Revuelta, Alberto; Pando, Rogelio Hernandez

    2015-09-01

    Recent studies suggest that catecholamines (CAs) and acetylcholine (ACh) play essential roles in the crosstalk between microbes and the immune system. Host cholinergic afferent fibers sense pathogen-associated molecular patterns and trigger efferent cholinergic and catecholaminergic pathways that alter immune cell proliferation, differentiation, and cytokine production. On the other hand, microbes have the ability to produce and degrade ACh and also regulate autogenous functions in response to CAs. Understanding the role played by these neurotransmitters in host-microbe interactions may provide valuable information for the development of novel therapies. PMID:26378438

  15. Thermodynamics of Distinguishable Particles: A Key to High-Energy Strong Interactions?

    NASA Astrophysics Data System (ADS)

    Hagedorn, Rolf

    A new kind of thermodynamical model for strong interactions at high energies is proposed. We start from the fact that strong interactions produce so many possible particle states (from \\uppi over its resonances to nucleons, strange particles and their resonances, up to highly excited `fireballs') that in an actual process each of these states practically never occurs more than once. We use this in order to treat the very first instant of a high-energy collision by statistical thermodynamics of a system of an illimited number of distinguishable particles. The model shows surprising properties: there exists a universal highest possible temperature T 0 of the order of 150-200 MeV (corresponding to ≈ 1012 K) which governs all high-energy processes of strongly interacting particles, independently of the actual energy and independently of the particle number, from cosmic ray jets down to elastic scattering. If a Lorentz contracted volume is introduced, the transverse momentum distribution in jets as well as in elastic scattering is described in agreement with experimental results. Paradoxically, this distribution is independent of whether or not `thermal equilibrium' is reached. If it is not reached—in the majority of cases it is not reached—then the jet structure for production processes is the consequence. If the model turns out to be as good as present experiments indicated, then the existence of a highest temperature is very likely; it implies that, from higher and higher energy experiments, not much new can be learnt about the structure of strong interactions, since the mode of excitation (which depends on the dynamical details we would like to know) has no influence on what is finally observed. The situation would then be similar to that in ordinary thermodynamics, where no experiment could possibly reveal how a certain system was brought into its thermodynamical state. In astrophysics, the method of thermodynamics of distinguishable particles may have important consequences for the treatment of the highly compressed interior of heavy stars (`neutron stars') where Fermi statistics would have to be replaced by the one used here.

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

    PubMed

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

    2014-04-01

    EIIA(Ntr) is a member of a truncated phosphotransferase (PTS) system that serves regulatory functions and exists in many Proteobacteria in addition to the sugar transport PTS. In Escherichia coli, EIIA(Ntr) regulates K(+) homeostasis through interaction with the K(+) transporter TrkA and sensor kinase KdpD. In the β-Proteobacterium Ralstonia eutropha H16, EIIA(Ntr) influences formation of the industrially important bioplastic poly(3-hydroxybutyrate) (PHB). PHB accumulation is controlled by the stringent response and induced under conditions of nitrogen deprivation. Knockout of EIIA(Ntr) increases the PHB content. In contrast, absence of enzyme I or HPr, which deliver phosphoryl groups to EIIA(Ntr), has the opposite effect. To clarify the role of EIIA(Ntr) in PHB formation, we screened for interacting proteins that co-purify with Strep-tagged EIIA(Ntr) from R. eutropha cells. This approach identified the bifunctional ppGpp synthase/hydrolase SpoT1, a key enzyme of the stringent response. Two-hybrid and far-Western analyses confirmed the interaction and indicated that only non-phosphorylated EIIA(Ntr) interacts with SpoT1. Interestingly, this interaction does not occur between the corresponding proteins of E. coli. Vice versa, interaction of EIIA(Ntr) with KdpD appears to be absent in R. eutropha, although R. eutropha EIIA(Ntr) can perfectly substitute its homologue in E. coli in regulation of KdpD activity. Thus, interaction with KdpD might be an evolutionary 'ancient' task of EIIA(Ntr) that was subsequently replaced by interaction with SpoT1 in R. eutropha. In conclusion, EIIA(Ntr) might integrate information about nutritional status, as reflected by its phosphorylation state, into the stringent response, thereby controlling cellular PHB content in R. eutropha. PMID:24515609

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

    SciTech Connect

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

    2011-08-12

    Highlights: {yields} Brain-specific angiogenesis inhibitor 2 (BAI2) is a new partner protein for GIP. {yields} BAI2 interaction with GIP was revealed by yeast two-hybrid assay. {yields} Binding of BAI2 to GIP was characterized by NMR, CD and fluorescence. {yields} BAI2 and GIP binding was mediated through the C-terminus of BAI2. -- Abstract: The vast majority of physiological processes in living cells are mediated by protein-protein interactions often specified by particular protein sequence motifs. PDZ domains, composed of 80-100 amino acid residues, are an important class of interaction motif. Among the PDZ-containing proteins, glutaminase interacting protein (GIP), also known as Tax Interacting Protein TIP-1, is unique in being composed almost exclusively of a single PDZ domain. GIP has important roles in cellular signaling, protein scaffolding and modulation of tumor growth and interacts with a number of physiological partner proteins, including Glutaminase L, {beta}-Catenin, FAS, HTLV-1 Tax, HPV16 E6, Rhotekin and Kir 2.3. To identify the network of proteins that interact with GIP, a human fetal brain cDNA library was screened using a yeast two-hybrid assay with GIP as bait. We identified brain-specific angiogenesis inhibitor 2 (BAI2), a member of the adhesion-G protein-coupled receptors (GPCRs), as a new partner of GIP. BAI2 is expressed primarily in neurons, further expanding GIP cellular functions. The interaction between GIP and the carboxy-terminus of BAI2 was characterized using fluorescence, circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy assays. These biophysical analyses support the interaction identified in the yeast two-hybrid assay. This is the first study reporting BAI2 as an interaction partner of GIP.

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

    NASA Astrophysics Data System (ADS)

    Counsell, G. F.

    2002-08-01

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

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

    PubMed

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

    2012-06-01

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

  20. BMRF-MI: integrative identification of protein interaction network by modeling the gene dependency

    PubMed Central

    2015-01-01

    Background Identification of protein interaction network is a very important step for understanding the molecular mechanisms in cancer. Several methods have been developed to integrate protein-protein interaction (PPI) data with gene expression data for network identification. However, they often fail to model the dependency between genes in the network, which makes many important genes, especially the upstream genes, unidentified. It is necessary to develop a method to improve the network identification performance by incorporating the dependency between genes. Results We proposed an approach for identifying protein interaction network by incorporating mutual information (MI) into a Markov random field (MRF) based framework to model the dependency between genes. MI is widely used in information theory to measure the uncertainty between random variables. Different from traditional Pearson correlation test, MI is capable of capturing both linear and non-linear relationship between random variables. Among all the existing MI estimators, we choose to use k-nearest neighbor MI (kNN-MI) estimator which is proved to have minimum bias. The estimated MI is integrated with an MRF framework to model the gene dependency in the context of network. The maximum a posterior (MAP) estimation is applied on the MRF-based model to estimate the network score. In order to reduce the computational complexity of finding the optimal network, a probabilistic searching algorithm is implemented. We further increase the robustness and reproducibility of the results by applying a non-parametric bootstrapping method to measure the confidence level of the identified genes. To evaluate the performance of the proposed method, we test the method on simulation data under different conditions. The experimental results show an improved accuracy in terms of subnetwork identification compared to existing methods. Furthermore, we applied our method onto real breast cancer patient data; the identified protein interaction network shows a close association with the recurrence of breast cancer, which is supported by functional annotation. We also show that the identified subnetworks can be used to predict the recurrence status of cancer patients by survival analysis. Conclusions We have developed an integrated approach for protein interaction network identification, which combines Markov random field framework and mutual information to model the gene dependency in PPI network. Improvements in subnetwork identification have been demonstrated with simulation datasets compared to existing methods. We then apply our method onto breast cancer patient data to identify recurrence related subnetworks. The experiment results show that the identified genes are enriched in the pathway and functional categories relevant to progression and recurrence of breast cancer. Finally, the survival analysis based on identified subnetworks achieves a good result of classifying the recurrence status of cancer patients. PMID:26099273

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

    PubMed Central

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

    2010-01-01

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

  2. Large-scale identification of potential drug targets based on the topological features of human protein-protein interaction network.

    PubMed

    Li, Zhan-Chao; Zhong, Wen-Qian; Liu, Zhi-Qing; Huang, Meng-Hua; Xie, Yun; Dai, Zong; Zou, Xiao-Yong

    2015-04-29

    Identifying potential drug target proteins is a crucial step in the process of drug discovery and plays a key role in the study of the molecular mechanisms of disease. Based on the fact that the majority of proteins exert their functions through interacting with each other, we propose a method to recognize target proteins by using the human protein-protein interaction network and graph theory. In the network, vertexes and edges are weighted by using the confidence scores of interactions and descriptors of protein primary structure, respectively. The novel network topological features are defined and employed to characterize protein using existing databases. A widely used minimum redundancy maximum relevance and random forests algorithm are utilized to select the optimal feature subset and construct model for the identification of potential drug target proteins at the proteome scale. The accuracies of training set and test set are 89.55% and 85.23%. Using the constructed model, 2127 potential drug target proteins have been recognized and 156 drug target proteins have been validated in the database of drug target. In addition, some new drug target proteins can be considered as targets for treating diseases of mucopolysaccharidosis, non-arteritic anterior ischemic optic neuropathy, Bernard-Soulier syndrome and pseudo-von Willebrand, etc. It is anticipated that the proposed method may became a powerful high-throughput virtual screening tool of drug target. PMID:25847157

  3. Microbial Glycan Microarrays Define Key Features of Host-Microbial Interactions

    PubMed Central

    Stowell, Sean R.; Arthur, Connie M.; McBride, Ryan; Berger, Oren; Razi, Nahid; Heimburg-Molinaro, Jamie; Rodrigues, Lilian C.; Gourdine, Jean-Philippe; Noll, Alexander J.; von Gunten, Stephan; Smith, David F.; Knirel, Yuriy A.; Paulson, James C.; Cummings, Richard D.

    2014-01-01

    Genomic approaches continue to provide unprecedented insight into the microbiome, yet host immune interactions with diverse microbiota can be difficult to study. We therefore generated a microbial microarray containing defined antigens isolated from a broad range of microbial flora to examine adaptive and innate immunity. Serological studies with this microarray show that immunoglobulins from multiple mammalian species exhibit unique patterns of reactivity, while exposure of animals to distinct microbes induces specific serological recognition. While adaptive immunity exhibited plasticity toward microbial antigens, immunological tolerance limits reactivity toward self. We discovered that several innate immune galectins exhibit specific recognition of microbes that express self-like antigens, leading to direct killing of a broad range of gram negative and positive microbes. Thus, host protection against microbes appears to represent a balance between adaptive and innate immunity to defend against evolving antigenic determinants while protecting against molecular mimicry. PMID:24814672

  4. Interactive voice response systems for medication identification requests: poison or cure?

    PubMed

    Benson, Blaine E

    2011-11-01

    Interactive voice response systems (IVR) have traditionally been used by banking and credit card industries to rapidly process information requests for their customers. Today IVR technology is being used in clinical medicine to randomize patients in clinical studies, to collect patient data, and to follow-up on recently discharged patients. Use of IVR systems by poison centers is relatively new. This commentary explores the advantages and disadvantages of applying IVR technology to the medication identification requests in poison centers. PMID:22077245

  5. Dynamic Transcription Factor Activity Profiles Reveal Key Regulatory Interactions During Megakaryocytic and Erythroid Differentiation

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Roehner, Bertrand M.

    2005-03-01

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

  8. The phospholipid code: a key component of dying cell recognition, tumor progression and host-microbe interactions.

    PubMed

    Baxter, A A; Hulett, M D; Poon, I K H

    2015-12-01

    A significant effort is made by the cell to maintain certain phospholipids at specific sites. It is well described that proteins involved in intracellular signaling can be targeted to the plasma membrane and organelles through phospholipid-binding domains. Thus, the accumulation of a specific combination of phospholipids, denoted here as the 'phospholipid code', is key in initiating cellular processes. Interestingly, a variety of extracellular proteins and pathogen-derived proteins can also recognize or modify phospholipids to facilitate the recognition of dying cells, tumorigenesis and host-microbe interactions. In this article, we discuss the importance of the phospholipid code in a range of physiological and pathological processes. PMID:26450453

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

    PubMed

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

    2013-07-01

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

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

    PubMed Central

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

    2011-01-01

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

  11. Topological robustness analysis of protein interaction networks reveals key targets for overcoming chemotherapy resistance in glioma

    NASA Astrophysics Data System (ADS)

    Azevedo, Hátylas; Moreira-Filho, Carlos Alberto

    2015-11-01

    Biological networks display high robustness against random failures but are vulnerable to targeted attacks on central nodes. Thus, network topology analysis represents a powerful tool for investigating network susceptibility against targeted node removal. Here, we built protein interaction networks associated with chemoresistance to temozolomide, an alkylating agent used in glioma therapy, and analyzed their modular structure and robustness against intentional attack. These networks showed functional modules related to DNA repair, immunity, apoptosis, cell stress, proliferation and migration. Subsequently, network vulnerability was assessed by means of centrality-based attacks based on the removal of node fractions in descending orders of degree, betweenness, or the product of degree and betweenness. This analysis revealed that removing nodes with high degree and high betweenness was more effective in altering networks’ robustness parameters, suggesting that their corresponding proteins may be particularly relevant to target temozolomide resistance. In silico data was used for validation and confirmed that central nodes are more relevant for altering proliferation rates in temozolomide-resistant glioma cell lines and for predicting survival in glioma patients. Altogether, these results demonstrate how the analysis of network vulnerability to topological attack facilitates target prioritization for overcoming cancer chemoresistance.

  12. Topological robustness analysis of protein interaction networks reveals key targets for overcoming chemotherapy resistance in glioma

    PubMed Central

    Azevedo, Hátylas; Moreira-Filho, Carlos Alberto

    2015-01-01

    Biological networks display high robustness against random failures but are vulnerable to targeted attacks on central nodes. Thus, network topology analysis represents a powerful tool for investigating network susceptibility against targeted node removal. Here, we built protein interaction networks associated with chemoresistance to temozolomide, an alkylating agent used in glioma therapy, and analyzed their modular structure and robustness against intentional attack. These networks showed functional modules related to DNA repair, immunity, apoptosis, cell stress, proliferation and migration. Subsequently, network vulnerability was assessed by means of centrality-based attacks based on the removal of node fractions in descending orders of degree, betweenness, or the product of degree and betweenness. This analysis revealed that removing nodes with high degree and high betweenness was more effective in altering networks’ robustness parameters, suggesting that their corresponding proteins may be particularly relevant to target temozolomide resistance. In silico data was used for validation and confirmed that central nodes are more relevant for altering proliferation rates in temozolomide-resistant glioma cell lines and for predicting survival in glioma patients. Altogether, these results demonstrate how the analysis of network vulnerability to topological attack facilitates target prioritization for overcoming cancer chemoresistance. PMID:26582089

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  15. Blind identification of the Millikan Library from earthquake data considering soil–structure interaction

    USGS Publications Warehouse

    Ghahari, S. F.; Abazarsa, F.; Avci, O.; Celebi, Mehmet; Taciroglu, E.

    2016-01-01

    The Robert A. Millikan Library is a reinforced concrete building with a basement level and nine stories above the ground. Located on the campus of California Institute of Technology (Caltech) in Pasadena California, it is among the most densely instrumented buildings in the U.S. From the early dates of its construction, it has been the subject of many investigations, especially regarding soil–structure interaction effects. It is well accepted that the structure is significantly interacting with the surrounding soil, which implies that the true foundation input motions cannot be directly recorded during earthquakes because of inertial effects. Based on this limitation, input–output modal identification methods are not applicable to this soil–structure system. On the other hand, conventional output-only methods are typically based on the unknown input signals to be stationary whitenoise, which is not the case for earthquake excitations. Through the use of recently developed blind identification (i.e. output-only) methods, it has become possible to extract such information from only the response signals because of earthquake excitations. In the present study, we employ such a blind identification method to extract the modal properties of the Millikan Library. We present some modes that have not been identified from force vibration tests in several studies to date. Then, to quantify the contribution of soil–structure interaction effects, we first create a detailed Finite Element (FE) model using available information about the superstructure; and subsequently update the soil–foundation system's dynamic stiffnesses at each mode such that the modal properties of the entire soil–structure system agree well with those obtained via output-only modal identification.

  16. The diaphanous Gene of Drosophila Interacts Antagonistically with multiple wing hairs and Plays a Key Role in Wing Hair Morphogenesis

    PubMed Central

    Lu, Qiuheng; Adler, Paul N.

    2015-01-01

    The Drosophila wing is covered by an array of distally pointing hairs that has served as a key model system for studying planar cell polarity (PCP). The adult cuticular hairs are formed in the pupae from cell extensions that contain extensive actin filaments and microtubules. The importance of the actin cytoskeleton for hair growth and morphogenesis is clear from the wide range of phenotypes seen in mutations in well-known actin regulators. Formin proteins promote the formation of long actin filaments of the sort thought to be important for hair growth. We report here that the formin encoding diaphanous (dia) gene plays a key role in hair morphogenesis. Both loss of function mutations and the expression of a constitutively active Dia led to cells forming both morphologically abnormal hairs and multiple hairs. The conserved frizzled (fz)/starry night (stan) PCP pathway functions to restrict hair initiation and activation of the cytoskeleton to the distal most part of wing cells. It also ensures the formation of a single hair per cell. Our data suggest that the localized inhibition of Dia activity may be part of this mechanism. We found the expression of constitutively active Dia greatly expands the region for activation of the cytoskeleton and that dia functions antagonistically with multiple wing hairs (mwh), the most downstream member of the fz/stan pathway. Further we established that purified fragments of Dia and Mwh could be co-immunoprecipitated suggesting the genetic interaction could reflect a direct physical interaction. PMID:25730111

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

    PubMed

    Hofmann, Thomas

    2009-07-01

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

  18. Three New Bat Ectoparasite Species of the Genus Macronyssus from Western Siberia (with an Identification Key for Females of the Genus Macronyssus from the Palearctic Boreal Zone).

    PubMed

    Orlova, M V; Zhigalin, A V

    2015-06-01

    Three new gamasid mite species belonging to the genus Macronyssus Kolenati, 1858 (Acari: Macronyssidae), namely, Macronyssus sibiricus n. sp., Macronyssus stanyukovichi n. sp., and Macronyssus tigirecus n. sp., are described (females only; males, protonymphs, and larvae remain unknown). All species are known from Western Siberia and belong to the Siberian-Far Eastern bat ectoparasite fauna complex. The parasite hosts are the eastern water bat Myotis petax Hollister, 1912, and Hilgendorf's tube-nosed bat Murina hilgendorfi Peters, 1880 (Chiroptera: Vespertilionidae). An identification key for females of the genus Macronyssus Kolenati, 1858, in the boreal Palearctic region is presented. PMID:25674831

  19. Information flow between interacting human brains: Identification, validation, and relationship to social expertise.

    PubMed

    Bilek, Edda; Ruf, Matthias; Schäfer, Axel; Akdeniz, Ceren; Calhoun, Vince D; Schmahl, Christian; Demanuele, Charmaine; Tost, Heike; Kirsch, Peter; Meyer-Lindenberg, Andreas

    2015-04-21

    Social interactions are fundamental for human behavior, but the quantification of their neural underpinnings remains challenging. Here, we used hyperscanning functional MRI (fMRI) to study information flow between brains of human dyads during real-time social interaction in a joint attention paradigm. In a hardware setup enabling immersive audiovisual interaction of subjects in linked fMRI scanners, we characterize cross-brain connectivity components that are unique to interacting individuals, identifying information flow between the sender's and receiver's temporoparietal junction. We replicate these findings in an independent sample and validate our methods by demonstrating that cross-brain connectivity relates to a key real-world measure of social behavior. Together, our findings support a central role of human-specific cortical areas in the brain dynamics of dyadic interactions and provide an approach for the noninvasive examination of the neural basis of healthy and disturbed human social behavior with minimal a priori assumptions. PMID:25848050

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

    PubMed

    Muzón, Javier; Pessacq, Pablo; Lozano, Federico

    2014-01-01

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

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

    PubMed Central

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

    2011-01-01

    Abstract A key to species and descriptions are presented for 14 species of the New World genus Crassomicrodus Ashmead. Seven new species, Crassomicrodus azteca, Crassomicrodus clypealis, Crassomicrodus costaricensis, Crassomicrodus jalisciensis, Crassomicrodus mariae, Crassomicrodus oaxaquensis,and Crassomicrodus olgae are described. Crassomicrodus fenestratus (Viereck) is synonymized with Crassomicrodus nigriceps (Cresson). Crassomicrodus melanopleurus (Ashmead) is recognized as a valid species. PMID:22144862

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

    PubMed Central

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

    2014-01-01

    Analysis consisting of numerical simulations along with lab experiments of interaction effects between key parameters on the electromagnetic force based on response surface methodology (RSM) has been also proposed to optimize the design of high-speed solenoid valve (HSV) and improve its performance. Numerical simulation model of HSV has been developed in Ansoft Maxwell environment and its accuracy has been validated through lab experiments. Effect of change of core structure, coil structure, armature structure, working air gap, and drive current on the electromagnetic force of HSV has been analyzed through simulation model and influence rules of various parameters on the electromagnetic force have been established. The response surface model of the electromagnetic force has been utilized to analyze the interaction effect between major parameters. It has been concluded that six interaction factors including working air gap with armature radius, drive current with armature thickness, coil turns with side pole radius, armature thickness with its radius, armature thickness with side pole radius, and armature radius with side pole radius have significant influence on the electromagnetic force. Optimal match values between coil turns and side pole radius; armature thickness and side pole radius; and armature radius and side pole radius have also been determined. PMID:25243217

  3. A proof-of-concept model for the identification of the key events in the infection process with specific reference to Pseudomonas aeruginosa in corneal infections

    PubMed Central

    Soumpasis, Ilias; Knapp, Laura; Pitt, Tyrone

    2015-01-01

    Background It is a common medical practice to characterise an infection based on the causative agent and to adopt therapeutic and prevention strategies targeting the agent itself. However, from an epidemiological perspective, exposure to a microbe can be harmless to a host as a result of low-level exposure or due to host immune response, with opportunistic infection only occurring as a result of changes in the host, pathogen, or surrounding environment. Methods We have attempted to review systematically the key host, pathogen, and environmental factors that may significantly impact clinical outcomes of exposure to a pathogen, using Pseudomonas aeruginosa eye infection as a case study. Results and discussion Extended contact lens wearing and compromised hygiene may predispose users to microbial keratitis, which can be a severe and vision-threatening infection. P. aeruginosa has a wide array of virulence-associated genes and sensing systems to initiate and maintain cell populations at the corneal surface and beyond. We have adapted the well-known concept of the epidemiological triangle in combination with the classic risk assessment framework (hazard identification, characterisation, and exposure) to develop a conceptual pathway-based model that demonstrates the overlapping relationships between the host, the pathogen, and the environment; and to illustrate the key events in P. aeruginosa eye infection. Conclusion This strategy differs from traditional approaches that consider potential risk factors in isolation, and hopefully will aid the identification of data and models to inform preventive and therapeutic measures in addition to risk assessment. Furthermore, this may facilitate the identification of knowledge gaps to direct research in areas of greatest impact to avert or mitigate adverse outcomes of infection. PMID:26546946

  4. A gallery of the key characters to ease identification of Dermanyssus gallinae (Acari: Gamasida: Dermanyssidae) and allow differentiation from Ornithonyssus sylviarum (Acari: Gamasida: Macronyssidae)

    PubMed Central

    2012-01-01

    Background Dermanyssus gallinae (poultry red mite) is a major threat for the poultry industry and is of significant interest for public health. Identification of D. gallinae can be difficult for scientists not familiar with mite morphology and terminology especially when trying to use identification keys. Moreover, this species may easily be confused with another dermanyssoid mite, Ornithonyssus sylviarum (northern fowl mite), which often shares the same hosts and environment. Methods Specimens of D. gallinae were collected at poultry farms in the Puglia and performed for light and scanning electron microscopy observations, identification and micrographs. Moreover specimens of O. sylviarum were collected separately macerated and mounted on slides for light microscopy observations, identification and pictures. Results The micrographs used in this study, based on LM and SEM observations, highlight the following important identifying characters of D. gallinae: the prominent shoulders of the dorsal shield and the jagged edges of the shield reticulations, the position of setae j1, s1 and the epigynal pores, and the presence on tibia IV pl of one seta. Additional micrographs highlighting the shape of the dorsal (abruptly narrowed posteriorly) and epigynal (narrowly rounded posteriorly) shields and the chelicera (elongate, with distinct digits) of O. sylviarum enable its differentiation from D.gallinae. Conclusion The photographic support provided here (both LM and SEM pictures) can be considered a practical tool for scientists who are not well acquainted with the morphology of D.gallinae, and who are involved with classical and molecular systematics, veterinary and human health aspects of poultry red mites. PMID:22647594

  5. Identification of AFB1-interacting proteins and interactions between RPSA and AFB1.

    PubMed

    Zhuang, Zhenhong; Huang, Yaling; Yang, Yanling; Wang, Shihua

    2016-01-15

    A method using immobilized affinity chromatography (IAC) was developed to screen for aflatoxin B1 (AFB1)-binding proteins. AFB1 and bovine serum albumin (BSA) coupled protein (BSA-AFB1) was prepared using 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride. The resulting coupled compound was immobilized onto PVDF transfer membranes, which were then incubated with total protein from mouse liver. AFB1-binding proteins were eluted, after non-specific washing, by specific elution, and the eluted proteins were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Two candidate AFB1-binding proteins were identified by liquid chromatography-tandem mass spectrometry as the 40S ribosomal protein SA (RPSA) and a putative uncharacterized protein. RPSA and AFB1 interactions were further analyzed by ELISA in vitro and laser confocal immunofluorescence analysis in vivo. The results from ELISA and immunofluorescence showed that RPSA efficiently bound AFB1 in vitro and in vivo. This study's conclusion laid the foundation for further exploration of the role of AFB1-binding proteins in AFB1 toxicology towards hepatocytes and the entry pathway of AFB1 into hepatocytes. PMID:26372695

  6. Identification of key peptide-specific CD4+ T cell responses to human cytomegalovirus: implications for tracking antiviral populations.

    PubMed

    Harcourt, G C; Scriba, T J; Semmo, N; Bounds, S; Taylor, E; Klenerman, P

    2006-11-01

    Human cytomegalovirus (CMV) infection is normally controlled effectively by the immune response, including CD4(+) T cells. Large numbers of these cells are present in healthy seropositive individuals but their loss in immunosuppression leads to reactivation and disease. Tracking such responses in vivo is hampered by poor definition of their peptide targets. In this study, we defined the key targets of the peptide-specific CD4(+) T cell responses to the CMV pp65 protein using functional assays and a peptide library. Despite a good deal of interindividual variation in the numbers of peptides recognized, responses to CMV pp65 were strikingly targeted at three key epitopes. A response to one or more of these three key peptides was seen in all individuals tested (P < 0.0001) and this finding was tested and reproduced in a second independent population. The most common response identified was that to a DR53 restricted epitope, aa281-295. HLA-DR1 restricted CMV pp65-specific populations, although reproducibly detected, were of low frequency ex vivo. However, it was possible to detect and phenotype these cells using an enrichment protocol and this revealed them to have 'effector memory' status although, in contrast to CD8(+) T cell responses, these were CD45RA(-). These data suggest that CD4(+) T cell responses to CMV can be identified reliably using a pool of just three peptides. This simple approach will provide a robust and reliable as well as economic method for tracking peptide specific populations in health and disease. PMID:17034571

  7. Spectrin-ankyrin interaction mechanics: A key force balance factor in the red blood cell membrane skeleton.

    PubMed

    Saito, Masakazu; Watanabe-Nakayama, Takahiro; Machida, Shinichi; Osada, Toshiya; Afrin, Rehana; Ikai, Atsushi

    2015-01-01

    As major components of red blood cell (RBC) cytoskeleton, spectrin and F-actin form a network that covers the entire cytoplasmic surface of the plasma membrane. The cross-linked two layered structure, called the membrane skeleton, keeps the structural integrity of RBC under drastically changing mechanical environment during circulation. We performed force spectroscopy experiments on the atomic force microscope (AFM) as a means to clarify the mechanical characteristics of spectrin-ankyrin interaction, a key factor in the force balance of the RBC cytoskeletal structure. An AFM tip was functionalized with ANK1-62k and used to probe spectrin crosslinked to mica surface. A force spectroscopy study gave a mean unbinding force of ~30 pN under our experimental conditions. Two energy barriers were identified in the unbinding process. The result was related to the well-known flexibility of spectrin tetramer and participation of ankyrin 1-spectrin interaction in the overall balance of membrane skeleton dynamics. PMID:25866912

  8. The Arabidopsis NRG2 Protein Mediates Nitrate Signaling and Interacts with and Regulates Key Nitrate Regulators[OPEN

    PubMed Central

    Zhao, Lufei; Zhang, Chengfei; Li, Zehui; Lei, Zhao; Liu, Fei; Guan, Peizhu; Crawford, Nigel M.

    2016-01-01

    We show that NITRATE REGULATORY GENE2 (NRG2), which we identified using forward genetics, mediates nitrate signaling in Arabidopsis thaliana. A mutation in NRG2 disrupted the induction of nitrate-responsive genes after nitrate treatment by an ammonium-independent mechanism. The nitrate content in roots was lower in the mutants than in the wild type, which may have resulted from reduced expression of NRT1.1 (also called NPF6.3, encoding a nitrate transporter/receptor) and upregulation of NRT1.8 (also called NPF7.2, encoding a xylem nitrate transporter). Genetic and molecular data suggest that NRG2 functions upstream of NRT1.1 in nitrate signaling. Furthermore, NRG2 directly interacts with the nitrate regulator NLP7 in the nucleus, but nuclear retention of NLP7 in response to nitrate is not dependent on NRG2. Transcriptomic analysis revealed that genes involved in four nitrogen-related clusters including nitrate transport and response to nitrate were differentially expressed in the nrg2 mutants. A nitrogen compound transport cluster containing some members of the NRT/PTR family was regulated by both NRG2 and NRT1.1, while no nitrogen-related clusters showed regulation by both NRG2 and NLP7. Thus, NRG2 plays a key role in nitrate regulation in part through modulating NRT1.1 expression and may function with NLP7 via their physical interaction. PMID:26744214

  9. New species and new records of freshwater Heterolepidoderma (Gastrotricha: Chaetonotidae) from Brazil with an identification key to the genus.

    PubMed

    Garraffoni, André R S; Melchior, Marina P

    2015-01-01

    A new species of freshwater Heterolepidoderma (Gastrotricha) was found in Brazil. Heterolepidoderma mariae sp. nov. is unique in possessing a three-lobed head, three types of dorsal keeled scales, a thin band of cilia on the head, connecting the two bands of ventral cilia, and an interciliary area with elliptical keeled scales with short spines. Heterolepidoderma famaillense Grosso & Drahg, 1991 is reported for the first time outside the type locality in Argentina, and we make some initial remarks on H. aff. majus Remane, 1927, a possible undescribed species. A dichotomous key for all freshwater species of Heterolepidoderma , with distributional data, is also provided. PMID:26701498

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

    PubMed Central

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

    2012-01-01

    Abstract The parasitoid complex associated with Monochamus galloprovincialis (Olivier), vector of the pine wood nematode, is discussed. Four species of the family Braconidae and one Ichneumonidae were found associated with Monochamus galloprovincialis in Portugal, namely Atanycolus denigrator (Linnaeus), Atanycolus ivanowi (Kokujev), Cyanopterus flavator (Fabricius), Doryctes striatellus (Nees) (Braconidae), and Xorides depressus (Holmgren) (Ichneumonidae). Atanycolus ivanowi, Atanycolus denigrator, Doryctes striatellus and Xorides depressus are new species for Portugal fauna, and Monochamus galloprovincialis is recorded as a new host of Xorides depressus. A key for determination of the ichneumonoid parasitoids of the pine sawyer is provided for the Palaearctic fauna. PMID:23378807

  11. Uncertainties in Biologically-Based Modeling of Formaldehyde-Induced Respiratory Cancer Risk: Identification of Key Issues

    PubMed Central

    Subramaniam, Ravi P.; Chen, Chao; Crump, Kenny S.; DeVoney, Danielle; Fox, John F.; Portier, Christopher J.; Schlosser, Paul M.; Thompson, Chad M.; White, Paul

    2009-01-01

    In a series of articles and a health-risk assessment report, scientists at the CIIT Hamner Institutes developed a model (CIIT model) for estimating respiratory cancer risk due to inhaled formaldehyde within a conceptual framework incorporating extensive mechanistic information and advanced computational methods at the toxicokinetic and toxicodynamic levels. Several regulatory bodies have utilized predictions from this model; on the other hand, upon detailed evaluation the California EPA has decided against doing so. In this article, we study the CIIT model to identify key biological and statistical uncertainties that need careful evaluation if such two-stage clonal expansion models are to be used for extrapolation of cancer risk from animal bioassays to human exposure. Broadly, these issues pertain to the use and interpretation of experimental labeling index and tumor data, the evaluation and biological interpretation of estimated parameters, and uncertainties in model specification, in particular that of initiated cells. We also identify key uncertainties in the scale-up of the CIIT model to humans, focusing on assumptions underlying model parameters for cell replication rates and formaldehyde-induced mutation. We discuss uncertainties in identifying parameter values in the model used to estimate and extrapolate DNA protein cross-link levels. The authors of the CIIT modeling endeavor characterized their human risk estimates as “conservative in the face of modeling uncertainties.” The uncertainties discussed in this article indicate that such a claim is premature. PMID:18564991

  12. A proximity based general method for identification of ligand and receptor interactions in living cells.

    PubMed

    Zhang, Hongkai; Xie, Jia; Lerner, Richard A

    2014-11-01

    Autocrine based selections from intracellular combinatorial antibody and peptide libraries have proven to be a powerful method for selection of agonists and identification of new therapeutic targets. However, success requires a case-by-case construction of a robust selection system which is a process that can be time consuming and expensive. Here we report a general system that takes advantage of the chemical rate acceleration caused by approximation of a membrane tethered ligand and its receptor. The system uses an artificial signal transduction and is, thus, agnostic to the endogenous signal transduction of the receptor-ligand system. This method allows analysis of receptor-ligand interactions and selection of molecules from large libraries that interact with receptors when they are in their natural milieu. PMID:25451250

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

    PubMed

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

    2012-01-15

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

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2010-06-01

    Wetland tree species are of importance for economic and restoration purposes. We describe the germination process and seedling morphology of six arboreal native species typical of Southeastern Mexico: Annona glabra, Ceiba pentandra, Pachira aquatica, Haematoxylum campechianum, Coccoloba barbadensis and Crataeva tapia. A total of 300 seeds per species were planted in a mixture of sand, cocoa plant husk and black soil (1:1:1), and maintained in a tree nursery with 30% artificial shade, from February to November of 2007. We carried out the morphological characterization, and elaborated a key to seedlings based on: 1) germination type 2) seedling axis and 3) leaf elements. P. aquatica has cryptocotylar hypogeal germination, the others have phanerocotylar epigeal germination. Germination rates were high (>86%), except for C. barbadensis (69%). PMID:20527471

  16. A new species of jumping spider Neonella Gertsch, with notes on the genus and male identification key (Araneae, Salticidae)

    PubMed Central

    Rubio, Gonzalo D.; Argañaraz, Carina I.; Gleiser, Raquel M.

    2015-01-01

    Abstract The American genus Neonella Gertsch, 1936 consists of very small jumping spiders whose biology is not well known. The genus currently includes eleven valid species, of which eight are known from both sexes and two are only known from one sex. This paper describes and illustrates a new species Neonella acostae sp. n., demonstrates male palpal variation in Neonella montana Galiano, 1988, and provides some information on the ecology of three sympatric species. New records of Neonella montana and Neonella minuta Galiano, 1965 are reported. Because the previously described species of Neonella were well illustrated and diagnosed, a dichotomous key to males is given along with genital illustrations of both sexes for all known species. PMID:26692804

  17. Identification of a key residue for oligomerisation and pore-formation of Clostridium perfringens NetB.

    PubMed

    Fernandes da Costa, Sérgio P; Savva, Christos G; Bokori-Brown, Monika; Naylor, Claire E; Moss, David S; Basak, Ajit K; Titball, Richard W

    2014-03-01

    Necrotic enteritis toxin B (NetB) is a β-pore-forming toxin produced by Clostridium perfringens and has been identified as a key virulence factor in the pathogenesis of avian necrotic enteritis, a disease causing significant economic damage to the poultry industry worldwide. In this study, site-directed mutagenesis was used to identify amino acids that play a role in NetB oligomerisation and pore-formation. NetB K41H showed significantly reduced toxicity towards LMH cells and human red blood cells relative to wild type toxin. NetB K41H was unable to oligomerise and form pores in liposomes. These findings suggest that NetB K41H could be developed as a genetic toxoid vaccine to protect against necrotic enteritis. PMID:24625763

  18. Pairwise alignment of interaction networks by fast identification of maximal conserved patterns.

    PubMed

    Tian, Wenhong; Samatova, Nagiza F

    2009-01-01

    A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. They typically find conserved interaction patterns by various local or global search algorithms, and then validate the results using genome annotation. The improvement of the speed, scalability and accuracy of network alignment is still the target of ongoing research. In view of this, we introduce a connected-components based algorithm, called HopeMap for pairwise network alignment with the focus on fast identification of maximal conserved patterns across species. Observing that the number of true homologs across species is relatively small compared to the total number of proteins in all species, we start with highly homologous groups across species, find maximal conserved interaction patterns globally with a generic scoring system, and validate the results across multiple known functional annotations. The results are evaluated in terms of statistical enrichment of gene ontology (GO) terms and KEGG ortholog groups (KO) within conserved interaction patters. HopeMap is fast, with linear computational cost, accurate in terms of KO groups and GO terms specificity and sensitivity, and extensible to multiple network alignment. PMID:19209698

  19. Identification of the interaction between vimentin and nucleocapsid protein of transmissible gastroenteritis virus.

    PubMed

    Zhang, Xin; Shi, HongYan; Chen, JianFei; Shi, Da; Dong, Hui; Feng, Li

    2015-03-16

    Nucleocapsid (N) protein of transmissible gastroenteritis virus (TGEV) packages viral RNA genome to form a ribonucleoprotein complex. In addition to its function as a structural protein, N protein is involved in cell apoptosis or cell-cycle regulation. N protein possibly interacts with host factors to modulate cellular functions. To identify cellular proteins that interacted with N protein of TGEV, methods of GST pull-down and Co-IP were utilized to precipitate cellular proteins of swine testicular (ST). Bound cellular proteins were resolved by SDS-PAGE. Analysis of interacting proteins by mass spectrometry allowed identification of 15 cellular protein bands representative of 12 cellular proteins including vimentin that bound to N protein. Furthermore, the function of vimentin cytoskeleton in ST cells during TGEV infection was examined. Vimentin cytoskeleton was required for virus replication. The present study thus provides protein-related information about interaction of TGEV N protein with host cell that should be useful for understanding host cell response to coronavirus pathogenesis infection and the underlying mechanism of coronavirus replication. PMID:25533531

  20. Revision of the genus Soricinia Spassky & Spasskaja, 1954 (Cestoda: Cyclophyllidea: Hymenolepididae) with redescriptions of three species, an amended generic diagnosis and an identification key to species.

    PubMed

    Kornienko, Svetlana; Binkienė, Rasa; Tkach, Vasyl V

    2016-06-01

    Redescriptions of three species of Soricinia Spassky & Spasskaja, 1954 are provided. The type-species of the genus, Soricinia soricis (Baer, 1925), is redescribed on the basis of the holotype from the Alpine shrew Sorex alpinus Schinz collected in Salève Mountain, France. Since the type-material of Soricinia infirma (Żarnowski, 1955) has apparently been lost, a neotype from the type-host Sorex araneus L. and from a region reasonably close to the type-locality (Poltavska Oblast' in the Ukraine), is designated. The type-material of Soricinia quarta (Karpenko, 1983) Karpenko, 1999 from Sorex isodon Turov in Khabarovsk Kray (Russia) is redescribed. A taxonomic revision and an overview of the geographical distribution of species of the genus Soricinia are presented. An amended generic diagnosis and a key to identification of Soricinia spp. are also presented. PMID:27220999

  1. An annotated key to the identification of commonly occurring and dominant genera of algae observed in the phytoplankton of the United States

    USGS Publications Warehouse

    Greeson, Phillip E.

    1982-01-01

    In early 1979, a retrieval was made for all phytoplankton data contained in the computerized data file of the U. S. Geological Survey. The retrieval revealed the analytical results of 17,959 samples collected and processed between October 1973 and October 1978. Of the approximately 500 genera of freshwater algae reported in the United States, the U.S. Geological Survey observed 321 genera in the phytoplankton. Fifty-two genera were considered to be commonly occurring and 42 genera were considered to be community dominants. The report lists, describes, and provides a detailed taxonomic key to the identification of 58 genera of algae considered either commonly occurring or dominant. Also included is a summary of environmental conditions under which each algal genus was observed, as well as a glossary and an extensive list of selected references.

  2. A key gene of the small RNA pathway in the flounder, Paralichthys olivaceus: identification and functional characterization of dicer.

    PubMed

    Fu, Yuanshuai; Zhang, Junling; Shi, Zhiyi; Wang, Guyue; Li, Wejuan; Jia, Liang

    2015-10-01

    Dicer is critical for producing mature microRNAs (miRNAs) from precursor molecules and small interfering RNAs and plays an important role in controlling development and metabolism. In the present study, we cloned the flounder dicer gene, which is 6585 nucleotides (nt), including a 5'-untranslated region (UTR) of 231 nt, a 3'-UTR of 663 nt and an open reading frame of 5691 nt encoding a polypeptide of 1897 amino acids, and analyzed the conservation and expression pattern of dicer. The tissue distribution analysis indicated that dicer is abundantly expressed in the brain, heart, liver, spleen, stomach, kidney, gill, muscle, intestine and gonad of adult fish. Temporal expression analysis indicated that dicer mRNA is highly expressed during the embryonic and early larval stages, and exhibits low expression during the metamorphic stages. Treatment with thyroid hormone (TH) or thiourea indirectly or directly up-regulated dicer mRNA levels at 17 and 23 dph, whereas treatment with TH down-regulated dicer mRNA levels at 36 dph. The dicer-specific siRNA significantly down-regulated dicer mRNA and pol-let-7d levels, while pol-let-7d precursor levels were not differentially changed compared with the control (NC). These results demonstrated that dicer plays a key role in development and metabolism through the production of mature miRNAs, providing basic information for further studies concerning the role of dicer in Paralichthys olivaceus development. PMID:26045159

  3. Phalangopsidae crickets from Tropical Africa (Orthoptera, Grylloidea), with descriptions of new taxa and an identification key for African genera.

    PubMed

    Desutter-Grandcolas, Laure

    2015-01-01

    New Phalangopsidae crickets are described from tropical Africa, including three new genera and ten new species: Afrophaloria Desutter-Grandcolas, n.gen., Afrophaloria amani Desutter-Grandcolas, n. sp., type species, Afrophaloria apiariensis Desutter-Grandcolas, n. sp., Afrophaloria hempae Desutter-Grandcolas, n. sp., Kameruloria gabonensis Desutter-Grandcolas, n. sp., Kameruloria nigricornis Desutter-Grandcolas, n. sp., Kameruloria trimaculata Desutter-Grandcolas, n. sp., Paragryllodes amani Desutter-Grandcolas, n. sp., Phasmagryllus Desutter-Grandcolas, n.gen., Phasmagryllus elegans Desutter-Grandcolas, n. sp., type species, Upupagryllus Desutter-Grandcolas, n.gen., Upupagryllus subalatus Desutter-Grandcolas, n. sp., type species, and Upupagryllus alatus Desutter-Grandcolas, n. sp. All these taxa, except Paragryllodes amani Desutter-Grandcolas, n. sp., belong to the subfamily Phaloriinae. The subfamily is redefined, to take into account their morphological (apterous taxa) and ecological (straminicolous taxa) diversity. A key for phalangopsid African genera is proposed, and the status of Larandeicus Chopard, 1937 briefly discussed. PMID:25947784

  4. Ruguo key genes and tumor driving factors identification of bladder cancer based on the RNA-seq profile

    PubMed Central

    Zhang, Minglei; Li, Hongyan; Zou, Di; Gao, Ji

    2016-01-01

    Aim This study aimed to select several signature genes associated with bladder cancer, thus to investigate the possible mechanism in bladder cancer. Methods The mRNA expression profile data of GSE31614, including ten bladder tissues and ten control samples, was downloaded from the Gene Expression Omnibus. The differentially expressed genes (DEGs) in bladder cancer samples compared with the control samples were screened using the Student’s t-test method. Functional analysis for the DEGs was analyzed using the Database for Annotation, Visualization, and Integrated Discovery from the Gene Ontology database, followed by the transcription function annotation of DEGs from Tumor-Associated Gene database. Motifs of genes that had transcription functions in promoter region were analyzed using the Seqpos. Results A total of 1,571 upregulated and 1,507 downregulated DEGs in the bladder cancer samples were screened. ELF3 and MYBL2 involved in cell cycle and DNA replication were tumor suppressors. MEG3, APEX1, and EZH2 were related with the cell epigenetic regulation in bladder cancer. Moreover, HOXB9 and EN1 that have their own motif were the transcription factors. Conclusion Our study has identified several key genes involved in bladder cancer. ELF3 and MYBL2 are tumor suppressers, HOXB9 and EN1 are the main regulators, while MEG3, APEX1, and EZH2 are driving factors for bladder cancer progression. PMID:27217782

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

    PubMed

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

    2006-03-23

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

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

    PubMed Central

    2011-01-01

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

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

    PubMed Central

    2013-01-01

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

  8. Identification of Cys255 in HIF-1? as a novel site for development of covalent inhibitors of HIF-1?/ARNT PasB domain proteinprotein interaction

    PubMed Central

    Cardoso, Rosa; Love, Robert; Nilsson, Carol L; Bergqvist, Simon; Nowlin, Dawn; Yan, Jiangli; Liu, Kevin K-C; Zhu, Jing; Chen, Ping; Deng, Ya-Li; Dyson, H Jane; Greig, Michael J; Brooun, Alexei

    2012-01-01

    The heterodimer HIF-1? (hypoxia inducible factor)/HIF-? (also known as ARNT-aryl hydrocarbon nuclear translocator) is a key mediator of cellular response to hypoxia. The interaction between these monomer units can be modified by the action of small molecules in the binding interface between their C-terminal heterodimerization (PasB) domains. Taking advantage of the presence of several cysteine residues located in the allosteric cavity of HIF-1? PasB domain, we applied a cysteine-based reactomics hotspot identification strategy to locate regions of HIF-1? PasB domain critical for its interaction with ARNT. COMPOUND 5 was identified using a mass spectrometry-based primary screening strategy and was shown to react specifically with Cys255 of the HIF-1? PasB domain. Biophysical characterization of the interaction between PasB domains of HIF-1? and ARNT revealed that covalent binding of COMPOUND 5 to Cys255 reduced binding affinity between HIF-1? and ARNT PasB domains approximately 10-fold. Detailed NMR structural analysis of HIF-1?-PasB-COMPOUND 5 conjugate showed significant local conformation changes in the HIF-1? associated with key residues involved in the HIF-1?/ARNT PasB domain interaction as revealed by the crystal structure of the HIF-1?/ARNT PasB heterodimer. Our screening strategy could be applied to other targets to identify pockets surrounding reactive cysteines suitable for development of small molecule modulators of protein function. PMID:23033253

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

    PubMed Central

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

    2013-01-01

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

  10. Functional identification of APIP as human mtnB, a key enzyme in the methionine salvage pathway.

    PubMed

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

    2012-01-01

    The methionine salvage pathway is widely distributed among some eubacteria, yeast, plants and animals and recycles the sulfur-containing metabolite 5-methylthioadenosine (MTA) to methionine. In eukaryotic cells, the methionine salvage pathway takes place in the cytosol and usually involves six enzymatic activities: MTA phosphorylase (MTAP, EC 2.4.2.28), 5'-methylthioribose-1-phosphate isomerase (mtnA, EC 5.3.1.23), 5'-methylthioribulose-1-phosphate dehydratase (mtnB, EC: 4.2.1.109), 2,3-dioxomethiopentane-1-phosphate enolase/phosphatase (mtnC, EC 3.1.3.77), aci-reductone dioxygenase (mtnD, EC 1.13.11.54) and 4-methylthio-2-oxo-butanoate (MTOB) transaminase (EC 2.6.1.-). The aim of this study was to complete the available information on the methionine salvage pathway in human by identifying the enzyme responsible for the dehydratase step. Using a bioinformatics approach, we propose that a protein called APIP could perform this role. The involvement of this protein in the methionine salvage pathway was investigated directly in HeLa cells by transient and stable short hairpin RNA interference. We show that APIP depletion specifically impaired the capacity of cells to grow in media where methionine is replaced by MTA. Using a Shigella mutant auxotroph for methionine, we confirm that the knockdown of APIP specifically affects the recycling of methionine. We also show that mutation of three potential phosphorylation sites does not affect APIP activity whereas mutation of the potential zinc binding site completely abrogates it. Finally, we show that the N-terminal region of APIP that is missing in the short isoform is required for activity. Together, these results confirm the involvement of APIP in the methionine salvage pathway, which plays a key role in many biological functions like cancer, apoptosis, microbial proliferation and inflammation. PMID:23285211

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

    PubMed Central

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

    2012-01-01

    The methionine salvage pathway is widely distributed among some eubacteria, yeast, plants and animals and recycles the sulfur-containing metabolite 5-methylthioadenosine (MTA) to methionine. In eukaryotic cells, the methionine salvage pathway takes place in the cytosol and usually involves six enzymatic activities: MTA phosphorylase (MTAP, EC 2.4.2.28), 5′-methylthioribose-1-phosphate isomerase (mtnA, EC 5.3.1.23), 5′-methylthioribulose-1-phosphate dehydratase (mtnB, EC: 4.2.1.109), 2,3-dioxomethiopentane-1-phosphate enolase/phosphatase (mtnC, EC 3.1.3.77), aci-reductone dioxygenase (mtnD, EC 1.13.11.54) and 4-methylthio-2-oxo-butanoate (MTOB) transaminase (EC 2.6.1.-). The aim of this study was to complete the available information on the methionine salvage pathway in human by identifying the enzyme responsible for the dehydratase step. Using a bioinformatics approach, we propose that a protein called APIP could perform this role. The involvement of this protein in the methionine salvage pathway was investigated directly in HeLa cells by transient and stable short hairpin RNA interference. We show that APIP depletion specifically impaired the capacity of cells to grow in media where methionine is replaced by MTA. Using a Shigella mutant auxotroph for methionine, we confirm that the knockdown of APIP specifically affects the recycling of methionine. We also show that mutation of three potential phosphorylation sites does not affect APIP activity whereas mutation of the potential zinc binding site completely abrogates it. Finally, we show that the N-terminal region of APIP that is missing in the short isoform is required for activity. Together, these results confirm the involvement of APIP in the methionine salvage pathway, which plays a key role in many biological functions like cancer, apoptosis, microbial proliferation and inflammation. PMID:23285211

  12. Design of optimal food-based complementary feeding recommendations and identification of key "problem nutrients" using goal programming.

    PubMed

    Ferguson, Elaine L; Darmon, Nicole; Fahmida, Umi; Fitriyanti, Suci; Harper, Timothy B; Premachandra, Inguruwatte M

    2006-09-01

    The WHO is urging countries to promote improved complementary feeding practices to ensure optimal health, growth, and development of young children. To help achieve this, a rigorous 4-phase approach for designing optimal population- specific food-based complementary feeding recommendations (CFRs) was developed and is illustrated here. In phase I, an optimized diet is selected, using goal programming (Model #1), which aims to provide a desired nutrient content with respect to habitual diet patterns and cost. Based on its food patterns, a set of draft CFRs is designed. In phase II, their success for ensuring a nutritionally adequate diet is assessed via linear programming (Model type #2) by sequentially minimizing and maximizing the level of each nutrient (i.e., worst and best-case scenarios) while respecting the CFRs. For nutrients that are <70% of desired levels, the best food sources are identified via linear programming in phase III (Model #3). Different combinations of these foods are incorporated into the original draft of the CFRs to produce alternative CFRs, which are then compared on the basis of their cost, flexibility, and "worst-case scenario" nutrient levels (Model type #2) to select, in phase IV, a final set of CFRs. A hypothetical example is used to illustrate this approach. Outcomes include a set of optimal, population-specific CFRs and practical information regarding key "problem nutrients" in the local diet. Such information is valuable for nutrition promotion, as well as nutrition program planning and advocacy, to help achieve global initiatives for improving the complementary feeding practices of young children living in disadvantaged environments. PMID:16920861

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

    PubMed Central

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

    2013-01-01

    Oleaginous microalgae are one of the promising resource of nonedible biodiesel fuel (BDF) feed stock alternatives. Now a challenge task is the decrease of the long-chain polyunsaturated fatty acids (PUFAs) content affecting on the BDF oxidative stability by using gene manipulation techniques. However, only the limited knowledge has been available concerning the fatty acid and PUFA synthesis pathways in microalgae. Especially, the function of Δ9 desaturase, which is a key enzyme in PUFA synthesis pathway, has not been determined in diatom. In this study, 4 Δ9 desaturase genes (fD9desA, fD9desB, fD9desC and fD9desD) from the oleaginous diatom Fistulifera were newly isolated and functionally characterized. The putative Δ9 acyl-CoA desaturases in the endoplasmic reticulum (ER) showed 3 histidine clusters that are well-conserved motifs in the typical Δ9 desaturase. Furthermore, the function of these Δ9 desaturases was confirmed in the Saccharomyces cerevisiae ole1 gene deletion mutant (Δole1). All the putative Δ9 acyl-CoA desaturases showed Δ9 desaturation activity for C16∶0 fatty acids; fD9desA and fD9desB also showed desaturation activity for C18∶0 fatty acids. This study represents the first functional analysis of Δ9 desaturases from oleaginous microalgae and from diatoms as the first enzyme to introduce a double bond in saturated fatty acids during PUFA synthesis. The findings will provide beneficial insights into applying metabolic engineering processes to suppressing PUFA synthesis in this oleaginous microalgal strain. PMID:24039966

  14. Key protection factors against tetanus: Anti-tetanus toxin antibody affinity and its ability to prevent tetanus toxin - ganglioside interaction.

    PubMed

    Lukić, Ivana; Marinković, Emilija; Filipović, Ana; Krnjaja, Ognjen; Kosanović, Dejana; Inić-Kanada, Aleksandra; Stojanović, Marijana

    2015-09-01

    Antibodies capable to neutralize tetanus toxin (TeNT) are key factors in protection against tetanus disease. Although antibody-based therapeutics for treatment of tetanus exist on the market its production is tedious. Hence, the tetanus-specific antibodies preparation that could be easily produced in large scale in vitro would be beneficial. Monoclonal antibodies (MAbs) are considered for a long time as a reagent of choice, but the core drawback is how to select a MAb that would be safe in providing efficacious protection. In this study we have investigated the parameters crucial for a single MAb to be assigned as protective. Eight murine MAbs were characterized in vitro for their reactivity toward TeNT and assessed in vivo for protectiveness against TeNT intoxication. Correlation of in vitro and in vivo data has revealed that in vitro selection of MAb that is protective in vivo could be performed by a combination of two assays: the measurement of MAb affinity toward TeNT taking Ka 1 × 10(8) M(-1) as a threshold level, and the evaluation of its capability to prevent TeNT-ganglioside interaction. Single MAb could be taken into consideration as a potential therapeutic only if it has a capacity to completely inhibits TeNT-ganglioside complex formation. PMID:26140841

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

    PubMed Central

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

    2011-01-01

    Ribonuclease H2 (RNase H2) is the major nuclear enzyme involved in the degradation of RNA/DNA hybrids and removal of ribonucleotides misincorporated in genomic DNA. Mutations in each of the three RNase H2 subunits have been implicated in a human auto-inflammatory disorder, Aicardi-Goutières Syndrome (AGS). To understand how mutations impact on RNase H2 function we determined the crystal structure of the human heterotrimer. In doing so, we correct several key regions of the previously reported murine RNase H2 atomic model and provide biochemical validation for our structural model. Our results provide new insights into how the subunits are arranged to form an enzymatically active complex. In particular, we establish that the RNASEH2A C terminus is a eukaryotic adaptation for binding the two accessory subunits, with residues within it required for enzymatic activity. This C-terminal extension interacts with the RNASEH2C C terminus and both are necessary to form a stable, enzymatically active heterotrimer. Disease mutations cluster at this interface between all three subunits, destabilizing the complex and/or impairing enzyme activity. Altogether, we locate 25 out of 29 residues mutated in AGS patients, establishing a firm basis for future investigations into disease pathogenesis and function of the RNase H2 enzyme. PMID:21177854

  16. Key Role of Local Regulation in Chemosensing Revealed by a New Molecular Interaction-Based Modeling Method

    PubMed Central

    Meier-Schellersheim, Martin; Xu, Xuehua; Angermann, Bastian; Kunkel, Eric J; Jin, Tian; Germain, Ronald N

    2006-01-01

    The signaling network underlying eukaryotic chemosensing is a complex combination of receptor-mediated transmembrane signals, lipid modifications, protein translocations, and differential activation/deactivation of membrane-bound and cytosolic components. As such, it provides particularly interesting challenges for a combined computational and experimental analysis. We developed a novel detailed molecular signaling model that, when used to simulate the response to the attractant cyclic adenosine monophosphate (cAMP), made nontrivial predictions about Dictyostelium chemosensing. These predictions, including the unexpected existence of spatially asymmetrical, multiphasic, cyclic adenosine monophosphate–induced PTEN translocation and phosphatidylinositol-(3,4,5)P3 generation, were experimentally verified by quantitative single-cell microscopy leading us to propose significant modifications to the current standard model for chemoattractant-induced biochemical polarization in this organism. Key to this successful modeling effort was the use of “Simmune,” a new software package that supports the facile development and testing of detailed computational representations of cellular behavior. An intuitive interface allows user definition of complex signaling networks based on the definition of specific molecular binding site interactions and the subcellular localization of molecules. It automatically translates such inputs into spatially resolved simulations and dynamic graphical representations of the resulting signaling network that can be explored in a manner that closely parallels wet lab experimental procedures. These features of Simmune were critical to the model development and analysis presented here and are likely to be useful in the computational investigation of many aspects of cell biology. PMID:16854213

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

    PubMed

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

    2015-06-01

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

  18. Information flow between interacting human brains: Identification, validation, and relationship to social expertise

    PubMed Central

    Bilek, Edda; Ruf, Matthias; Schäfer, Axel; Akdeniz, Ceren; Calhoun, Vince D.; Schmahl, Christian; Demanuele, Charmaine; Tost, Heike; Kirsch, Peter; Meyer-Lindenberg, Andreas

    2015-01-01

    Social interactions are fundamental for human behavior, but the quantification of their neural underpinnings remains challenging. Here, we used hyperscanning functional MRI (fMRI) to study information flow between brains of human dyads during real-time social interaction in a joint attention paradigm. In a hardware setup enabling immersive audiovisual interaction of subjects in linked fMRI scanners, we characterize cross-brain connectivity components that are unique to interacting individuals, identifying information flow between the sender’s and receiver’s temporoparietal junction. We replicate these findings in an independent sample and validate our methods by demonstrating that cross-brain connectivity relates to a key real-world measure of social behavior. Together, our findings support a central role of human-specific cortical areas in the brain dynamics of dyadic interactions and provide an approach for the noninvasive examination of the neural basis of healthy and disturbed human social behavior with minimal a priori assumptions. PMID:25848050

  19. Identification of Critical Paraoxonase 1 Residues Involved in High Density Lipoprotein Interaction.

    PubMed

    Gu, Xiaodong; Huang, Ying; Levison, Bruce S; Gerstenecker, Gary; DiDonato, Anthony J; Hazen, Leah B; Lee, Joonsue; Gogonea, Valentin; DiDonato, Joseph A; Hazen, Stanley L

    2016-01-22

    Paraoxonase 1 (PON1) is a high density lipoprotein (HDL)-associated protein with atherosclerosis-protective and systemic anti-oxidant functions. We recently showed that PON1, myeloperoxidase, and HDL bind to one another in vivo forming a functional ternary complex (Huang, Y., Wu, Z., Riwanto, M., Gao, S., Levison, B. S., Gu, X., Fu, X., Wagner, M. A., Besler, C., Gerstenecker, G., Zhang, R., Li, X. M., Didonato, A. J., Gogonea, V., Tang, W. H., et al. (2013) J. Clin. Invest. 123, 3815-3828). However, specific residues on PON1 involved in the HDL-PON1 interaction remain unclear. Unambiguous identification of protein residues involved in docking interactions to lipid surfaces poses considerable methodological challenges. Here we describe a new strategy that uses a novel synthetic photoactivatable and click chemistry-taggable phospholipid probe, which, when incorporated into HDL, was used to identify amino acid residues on PON1 that directly interact with the lipoprotein phospholipid surface. Several specific PON1 residues (Leu-9, Tyr-185, and Tyr-293) were identified through covalent cross-links with the lipid probes using affinity isolation coupled to liquid chromatography with on-line tandem mass spectrometry. Based upon the crystal structure for PON1, the identified residues are all localized in relatively close proximity on the surface of PON1, defining a domain that binds to the HDL lipid surface. Site-specific mutagenesis of the identified PON1 residues (Leu-9, Tyr-185, and Tyr-293), coupled with functional studies, reveals their importance in PON1 binding to HDL and both PON1 catalytic activity and stability. Specifically, the residues identified on PON1 provide important structural insights into the PON1-HDL interaction. More generally, the new photoactivatable and affinity-tagged lipid probe developed herein should prove to be a valuable tool for identifying contact sites supporting protein interactions with lipid interfaces such as found on cell membranes or lipoproteins. PMID:26567339

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

    PubMed

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

    2014-01-01

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

  1. Network Understanding of Herb Medicine via Rapid Identification of Ingredient-Target Interactions

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

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

    PubMed Central

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

    2015-01-01

    Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R2). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q ≤ 0.10), representing 38 SNPs from nine genes, and its average effect (R2 = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene–gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding. PMID:25428896

  3. Identification of tissue interaction of terahertz radiation toward functional tissue imaging

    NASA Astrophysics Data System (ADS)

    Yokus, Hamdullah; Baughman, William; Balci, Soner; Bolus, Michael; Wilbert, David; Kung, Patrick; Kim, Seongsin M.

    2013-02-01

    In recent years, many applications have been recognized for biomedical imaging techniques utilizing terahertz frequency radiation. This is largely due to the capability of unique tissue identification resulting from the nature of the interaction between THz radiation and the molecular structure of the cells. By THz identification methods, tissue changes in tooth enamel, cartilage, and malignant cancer cells have already been demonstrated. Terahertz Time-Domain Spectroscopy (THz-TDS) remains one of the most versatile methods for spectroscopic image acquisition for its ability to simultaneously determine amplitude and phase over a broad spectral range. In this study we investigate the use of THz imaging techniques to uniquely identify damage types in tissue samples for both forensic and treatment applications. Using THz-TDS imaging in both transmission and reflection schemes, we examine tissue samples which have been damaged using a variety of acids. Each method of damage causes structural deterioration to the tissue by a different mechanism, thus leaving the remaining tissue uniquely changed based on the damage type. We correlate the change in frequency spectra, phase shift for each damage type to the mechanisms and severity of injury.

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

    PubMed

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

    2013-02-01

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

  5. Leukocytes and endothelium interaction as rate limiting step in the inflammatory response and a key factor in the ischemia-reperfusion injury.

    PubMed

    Maroszy?ska, I; Fiedor, P

    2000-01-01

    Leukocyte-endothelium interactions play a key role in regulation of the inflammatory response, leukocytes migration and ischaemia-reperfusion injury. These adhesive reactions controlling the circulation of leukocytes, are key parts of immune surveillance arising from extravasation of neutrophils, and migration into tissue to eliminate invading microorganism. They also play important role in the generation of ischaemic-reperfusion injury of different organs including brain. Plasma levels of soluble adhesion molecules may be a diagnostic marker of the systemic endothelial injury. It is likely that the next few years bring new therapies to control leukocyte-endothelial interaction by directly inhibiting the adhesion molecules or by modulating their expression. PMID:11499361

  6. Discovery of novel interacting partners of PSMD9, a proteasomal chaperone: Role of an Atypical and versatile PDZ-domain motif interaction and identification of putative functional modules

    PubMed Central

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

    2014-01-01

    PSMD9 (Proteasome Macropain non-ATPase subunit 9), a proteasomal assembly chaperone, harbors an uncharacterized PDZ-like domain. Here we report the identification of five novel interacting partners of PSMD9 and provide the first glimpse at the structure of the PDZ-domain, including the molecular details of the interaction. We based our strategy on two propositions: (a) proteins with conserved C-termini may share common functions and (b) PDZ domains interact with C-terminal residues of proteins. Screening of C-terminal peptides followed by interactions using full-length recombinant proteins, we discovered hnRNPA1 (an RNA binding protein), S14 (a ribosomal protein), CSH1 (a growth hormone), E12 (a transcription factor) and IL6 receptor as novel PSMD9-interacting partners. Through multiple techniques and structural insights, we clearly demonstrate for the first time that human PDZ domain interacts with the predicted Short Linear Sequence Motif (SLIM) at the C-termini of the client proteins. These interactions are also recapitulated in mammalian cells. Together, these results are suggestive of the role of PSMD9 in transcriptional regulation, mRNA processing and editing, hormone and receptor activity and protein translation. Our proof-of-principle experiments endorse a novel and quick method for the identification of putative interacting partners of similar PDZ-domain proteins from the proteome and for discovering novel functions. PMID:25009770

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

    PubMed

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

    2015-01-01

    Simulation plays an essential role in the development of new computational and statistical methods for the genetic analysis of complex traits. Most simulations start with a statistical model using methods such as linear or logistic regression that specify the relationship between genotype and phenotype. This is appealing due to its simplicity and because these statistical methods are commonly used in genetic analysis. It is our working hypothesis that simulations need to move beyond simple statistical models to more realistically represent the biological complexity of genetic architecture. The goal of the present study was to develop a prototype genotype-phenotype simulation method and software that are capable of simulating complex genetic effects within the context of a hierarchical biology-based framework. Specifically, our goal is to simulate multilocus epistasis or gene-gene interaction where the genetic variants are organized within the framework of one or more genes, their regulatory regions and other regulatory loci. We introduce here the Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (HIBACHI) method and prototype software for simulating data in this manner. This approach combines a biological hierarchy, a flexible mathematical framework, a liability threshold model for defining disease endpoints, and a heuristic search strategy for identifying high-order epistatic models of disease susceptibility. We provide several simulation examples using genetic models exhibiting independent main effects and three-way epistatic effects. PMID:25395175

  8. Identification of unique SUN-interacting nuclear envelope proteins with diverse functions in plants

    PubMed Central

    Zhou, Xiao; Graumann, Katja; Wirthmueller, Lennart; Jones, Jonathan D.G.

    2014-01-01

    Although a plethora of nuclear envelope (NE) transmembrane proteins (NETs) have been identified in opisthokonts, plant NETs are largely unknown. The only known NET homologues in plants are Sad1/UNC-84 (SUN) proteins, which bind Klarsicht/ANC-1/Syne-1 homology (KASH) proteins. Therefore, de novo identification of plant NETs is necessary. Based on similarities between opisthokont KASH proteins and the only known plant KASH proteins, WPP domain–interacting proteins, we used a computational method to identify the KASH subset of plant NETs. Ten potential plant KASH protein families were identified, and five candidates from four of these families were verified for their NE localization, depending on SUN domain interaction. Of those, Arabidopsis thaliana SINE1 is involved in actin-dependent nuclear positioning in guard cells, whereas its paralogue SINE2 contributes to innate immunity against an oomycete pathogen. This study dramatically expands our knowledge of plant KASH proteins and suggests that plants and opisthokonts have recruited different KASH proteins to perform NE regulatory functions. PMID:24891605

  9. Identification of RNA-protein interaction networks involved in the norovirus life cycle.

    PubMed

    Vashist, Surender; Urena, Luis; Chaudhry, Yasmin; Goodfellow, Ian

    2012-11-01

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

  10. Heuristic Identification of Biological Architectures for Simulating Complex Hierarchical Genetic Interactions

    PubMed Central

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

    2015-01-01

    Simulation plays an essential role in the development of new computational and statistical methods for the genetic analysis of complex traits. Most simulations start with a statistical model using methods such as linear or logistic regression that specify the relationship between genotype and phenotype. This is appealing due to its simplicity and because these statistical methods are commonly used in genetic analysis. It is our working hypothesis that simulations need to move beyond simple statistical models to more realistically represent the biological complexity of genetic architecture. The goal of the present study was to develop a prototype genotype–phenotype simulation method and software that are capable of simulating complex genetic effects within the context of a hierarchical biology-based framework. Specifically, our goal is to simulate multilocus epistasis or gene–gene interaction where the genetic variants are organized within the framework of one or more genes, their regulatory regions and other regulatory loci. We introduce here the Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (HIBACHI) method and prototype software for simulating data in this manner. This approach combines a biological hierarchy, a flexible mathematical framework, a liability threshold model for defining disease endpoints, and a heuristic search strategy for identifying high-order epistatic models of disease susceptibility. We provide several simulation examples using genetic models exhibiting independent main effects and three-way epistatic effects. PMID:25395175

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

    PubMed Central

    Vashist, Surender; Urena, Luis; Chaudhry, Yasmin

    2012-01-01

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

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

    ERIC Educational Resources Information Center

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

    2011-01-01

    This article is a review of available interactive aids designed to enhance the identification and expression of feelings in children. These skills are part of the overall development of empathy. The development of empathy, in turn, is crucial for social competence, social relatedness, and prosocial behavior. Improving these skills is likely to…

  13. Identification of Cell Cycle Dependent Interaction Partners of the Septins by Quantitative Mass Spectrometry.

    PubMed

    Renz, Christian; Oeljeklaus, Silke; Grinhagens, Sören; Warscheid, Bettina; Johnsson, Nils; Gronemeyer, Thomas

    2016-01-01

    The septins are a conserved family of GTP-binding proteins that, in the baker's yeast, assemble into a highly ordered array of filaments at the mother bud neck. These filaments undergo significant structural rearrangements during the cell cycle. We aimed at identifying key components that are involved in or regulate the transitions of the septins. By combining cell synchronization and quantitative affinity-purification mass-spectrometry, we performed a screen for specific interaction partners of the septins at three distinct stages of the cell cycle. A total of 83 interaction partners of the septins were assigned. Surprisingly, we detected DNA-interacting/nuclear proteins and proteins involved in ribosome biogenesis and protein synthesis predominantly present in alpha-factor arrested that do not display an assembled septin structure. Furthermore, two distinct sets of regulatory proteins that are specific for cells at S-phase with a stable septin collar or at mitosis with split septin rings were identified. Complementary methods like SPLIFF and immunoprecipitation allowed us to more exactly define the spatial and temporal characteristics of selected hits of the AP-MS screen. PMID:26871441

  14. Identification of Cell Cycle Dependent Interaction Partners of the Septins by Quantitative Mass Spectrometry

    PubMed Central

    Renz, Christian; Oeljeklaus, Silke; Grinhagens, Sören; Warscheid, Bettina; Johnsson, Nils; Gronemeyer, Thomas

    2016-01-01

    The septins are a conserved family of GTP-binding proteins that, in the baker's yeast, assemble into a highly ordered array of filaments at the mother bud neck. These filaments undergo significant structural rearrangements during the cell cycle. We aimed at identifying key components that are involved in or regulate the transitions of the septins. By combining cell synchronization and quantitative affinity-purification mass-spectrometry, we performed a screen for specific interaction partners of the septins at three distinct stages of the cell cycle. A total of 83 interaction partners of the septins were assigned. Surprisingly, we detected DNA-interacting/nuclear proteins and proteins involved in ribosome biogenesis and protein synthesis predominantly present in alpha-factor arrested that do not display an assembled septin structure. Furthermore, two distinct sets of regulatory proteins that are specific for cells at S-phase with a stable septin collar or at mitosis with split septin rings were identified. Complementary methods like SPLIFF and immunoprecipitation allowed us to more exactly define the spatial and temporal characteristics of selected hits of the AP-MS screen. PMID:26871441

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

    PubMed Central

    2013-01-01

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

  16. Identification of key active constituents of Buchang Naoxintong capsules with therapeutic effects against ischemic stroke by using an integrative pharmacology-based approach.

    PubMed

    Haiyu, Xu; Yang, Shi; Yanqiong, Zhang; Qiang, Jia; Defeng, Li; Yi, Zhang; Feng, Liu; Hongjun, Yang

    2015-12-15

    Integrative pharmacology has been used to identify the key active constituents (KACs) of Buchang Naoxintong capsules (BNCs), a traditional Chinese medical preparation; this approach involves the evaluation of the content profiles and drug-like properties of the BNC constituents and development of an ingredient-target network. In this study, we used a sensitive analytical method to simultaneously identify and quantify 16 constituents of BNCs. Metabolism of these constituents by gut microbiota and human oral bioavailability were predicted using an in silico approach, followed by construction of networks to analyze the interactions between BNC constituents, their molecular targets, and proteins known to be the molecular targets for Food and Drug Administration-approved colitis medication. Finally, an animal model of ischemic stroke was used to verify the therapeutic effects of the KACs of BNCs. Amygdalin and paeoniflorin were identified as the KACs because they were the 2 most abundant BNC constituents, having appropriate drug-like properties, and produced therapeutic effects against cerebral ischemia. Amygdalin produced an anti-cerebral ischemia effect, likely by interacting with the glucocorticoid receptor (NR3C1) and serpin peptidase inhibitor, clade C (antithrombin), member 1 (SERPINC1). These results form the basis for conducting studies to identify KACs in traditional medicinal preparations; such studies might improve quality control and allow the in vivo evaluation of synergistic interactions between the complex mixtures of compounds. PMID:26588440

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    USGS Publications Warehouse

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

    2002-01-01

    A method was developed for the quantitative detection of pathogenic human enteroviruses from surface waters in the Florida Keys using Taqman (R) one-step Reverse transcription (RT)-PCR with the Model 7700 ABI Prism (R) Sequence Detection System. Viruses were directly extracted from unconcentrated grab samples of seawater, from seawater concentrated by vortex flow filtration using a 100kD filter and from sponge tissue. Total RNA was extracted from the samples, purified and concentrated using spin-column chromatography. A 192-196 base pair portion of the 5??? untranscribed region was amplified from these extracts. Enterovirus concentrations were estimated using real-time RT-PCR technology. Nine of 15 sample sites or 60% were positive for the presence of pathogenic human enteroviruses. Considering only near-shore sites, 69% were positive with viral concentrations ranging from 9.3viruses/ml to 83viruses/g of sponge tissue (uncorrected for extraction efficiency). Certain amplicons were selected for cloning and sequencing for identification. Three strains of waterborne enteroviruses were identified as Coxsackievirus A9, Coxsackievirus A16, and Poliovirus Sabin type 1. Time and cost efficiency of this one-step real-time RT-PCR methodology makes this an ideal technique to detect, quantitate and identify pathogenic enteroviruses in recreational waters. Copyright ?? 2002 Elsevier Science Ltd.

  19. Three new species of Trigonospila Pokorny (Diptera: Tachinidae), from Area de Conservación Guanacaste, northwestern Costa Rica, with a key for their identification.

    PubMed

    Fleming, A J; Wood, D Monty; Janzen, Daniel H; Hallwachs, Winnie; Smith, M Alex

    2015-01-01

    We describe three new species of Trigonospila Pokorny (Tachinidae: Blondeliini) from Area de Conservación Guanacaste (ACG), northwestern Costa Rica. All were reared from -various species of ACG caterpillars during an ongoing inventory of caterpillars, their food plants and their parasitoids in dry forest, rain forest and cloud forest. By coupling morphology, photographic documentation, life history and molecular data, we provide a clear and concise description of each species. All species published as new, are known to be previously undescribed as a result of careful study of the genus by DMW. This study builds on the current knowledge of the genus by adding three new species to the current 7 described in the New World. Trigonospila edwinbermudezi sp. n., Trigonospila uniformis sp. n., and Trigonospila josemariamoragai sp. n. are all authored and described as new by Fleming and Wood, with a key to their identification. The authors also offer a new record and description of the previously unknown male of Trigonospila panamensis (Townsend), reared from ACG caterpillars. PMID:26379456

  20. Cebrennus Simon, 1880 (Araneae: Sparassidae): a revisionary up-date with the description of four new species and an updated identification key for all species.

    PubMed

    Jäger, Peter

    2014-01-01

    The spider genus Cebrennus Simon, 1880 is revised again after thirteen years. Four new species are described: Cebrennus atlas spec. nov. from Morocco (female), C. flagellatus spec. nov. from Afghanistan (male), C. laurae spec. nov. from Canary Islands (male), and C. rechenbergi spec. nov. from Morocco (male and female). Cebrennus clercki (Audouin, 1826) comb. nov. is transferred from Philodromidae to Sparassidae and considered a nomen dubium. The holotype of C. aethiopicus Simon, 1880 is illustrated for the first time. Cebrennus tunetanus Simon, 1885 is re-described by illustrating its copulatory organs and some somatic characters, the internal duct system is shown for the first time supporting its placement in Cebrennus. An updated identification key for all species is provided. New records of Cebrennus species are listed: C. wagae (Simon, 1874) is recorded from Libya and Malta for the first time, the latter representing the first record for the entire genus from Europe. C. kochi (O. Pickard-Cambridge, 1872) is recorded from Syria, C. aethiopicus from Sudan for the first time. Records from the Canary Islands and from Afghanistan extend the known generic distribution range further to the West and East. Behavioural aspects (burrowing, escaping, mating) of C. rechenbergi and partly of C. villosus (Jézéquel & Junqua, 1966) are described. Photographs of this behaviour as well as of the habitus of several species are provided. PMID:24869871

  1. Three new species of Trigonospila Pokorny (Diptera: Tachinidae), from Area de Conservación Guanacaste, northwestern Costa Rica, with a key for their identification

    PubMed Central

    Wood, D. Monty; Janzen, Daniel H; Hallwachs, Winnie; Smith, M. Alex

    2015-01-01

    Abstract We describe three new species of Trigonospila Pokorny (Tachinidae: Blondeliini) from Area de Conservación Guanacaste (ACG), northwestern Costa Rica. All were reared from ­various species of ACG caterpillars during an ongoing inventory of caterpillars, their food plants and their parasitoids in dry forest, rain forest and cloud forest. By coupling morphology, photographic documentation, life history and molecular data, we provide a clear and concise description of each species. All species published as new, are known to be previously undescribed as a result of careful study of the genus by DMW. This study builds on the current knowledge of the genus by adding three new species to the current 7 described in the New World. Trigonospila edwinbermudezi sp. n., Trigonospila uniformis sp. n., and Trigonospila josemariamoragai sp. n. are all authored and described as new by Fleming and Wood, with a key to their identification. The authors also offer a new record and description of the previously unknown male of Trigonospila panamensis (Townsend), reared from ACG caterpillars. PMID:26379456

  2. Crayfish fossil burrows, a key tool for identification of terrestrial environments in tide-dominated sequence, Upper Eocene, Sirt Basin, Libya

    NASA Astrophysics Data System (ADS)

    Abouessa, Ashour; Duringer, Philippe; Schuster, Mathieu; Pelletier, Jonathan

    2015-11-01

    The majority of decapod crustaceans are defined as marine organisms. Crayfish are one of the relatively few known exceptions. They are freshwater-environment adapted decapods that build characteristically large, simple and branched cylindrical morphotype traces in fluvial plains. Their burrows bear lots of special features that make them different from other burrows. Consequently, the identification of true crayfish burrows in the sedimentary record is crucial for the interpretation of depositional environment. The studied interval (45 m thick, exposed in the Dur At Talah escarpment southern Sirt Basin; Fig. 1) represents a case-study which is previously believed to be purely tidal. In this interval, the identification of the crayfish burrows provides a reliable tool for distinguishing terrestrial environments. The crayfish burrows of Dur At Talah are characterized by dimensional, morphological, and especially behavioral aspects that combined, cannot be ascribed to another burrow makers. Essential criteria used to attribute these burrows to the crayfish include: Their length (the depth of penetration into the sediments), their regularly circular cross-sectional area, the presence of mid-way enlargement chamber along the burrow vertical axis, as well as the subtle preservation of the burrow chimney. More importantly, these morphological features allow the recognition of some of the crayfish diagnostic behavioral habits. Most significant of these is the one deduced from the interaction of the burrow with the seasonal fluctuation of the paleo groundwater level. Supplementary indications that restrict the studied burrows to terrestrial organism include their occurrences within pedogenically altered strata that bear evident features of prolonged emersion. Of these features, mud cracks and burrows that are filled with continental fossil are the clearest. Few horizons with termite fungus comb are also distinguishable. Although other burrows of the classically known thalassinoide morphotypes are common in the studied outcrop, this article focuses essentially on the relatively (several orders of magnitude) larger cylindrical morphotypes. This study is based on comparing the field data concerning the studied burrows with those morphometrically similar modern and ancient documented cases.

  3. Identification and evolution of structurally dominant nodes in protein-protein interaction networks.

    PubMed

    Wang, Pei; Yu, Xinghuo; Lü, Jinhu

    2014-02-01

    It is well known that protein-protein interaction (PPI) networks are typical evolving complex networks. Identification of important nodes has been an emerging popular topic in complex networks. Many indexes have been proposed to measure the importance of nodes in complex networks, such as degree, closeness, betweenness, k-shell, clustering coefficient, semi-local centrality, eigenvector centrality. Based on multivariate statistical analysis, through integrating the above indexes and further considering the appearances of nodes in network motifs, this paper aims at developing a new measure to characterize the structurally dominant proteins (SDP) in PPI networks. Moreover, we will further investigate the evolution of the defined dominant nodes in temporal evolving real-world and artificial PPI networks. Our results indicate that the constructed artificial networks have some similar statistical properties as those of the real-world evolving networks. In this case, the artificial PPI networks can be used to further investigate the above evolution characteristics of the real-world evolving networks. Simulation results reveal that SDP in the yeast PPI networks are evolutionary conserved, however, the undominant nodes evolve rapidly. Furthermore, PPI networks are very robust against random mutations, while fragile yet with certain robustness to targeted mutations on SDP. Our investigations shed some light on the future applications of the evolving characteristics of bio-molecular networks, such as reengineering of particular networks for technological, synthetic or pharmacological purposes. PMID:24681922

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

    PubMed Central

    Wohlrab, Hartmut

    2010-01-01

    Transporter (carrier) proteins of the inner mitochondrial membrane link metabolic pathways within the matrix and the cytosol with transport/exchange of metabolites and inorganic ions. Their strict control of these fluxes is required for oxidative phosphorylation. Understanding the ternary complex transport mechanism with which most of these transporters function requires an accounting of the number and interactions of their subunits. The phosphate transporter (PTP, Mir1p) subunit readily forms homodimers with intersubunit affinities changeable by mutations. Cys28, likely at the subunit interface, is a site for mutations yielding transport inhibition or a channel-like transport mode. Such mutations yield a small increase or decrease in affinity between the subunits. The PTP inhibitor N-ethylmaleimide decreases subunit affinity by a small amount. PTP mutations that yield the highest (40%) and the lowest (2%) liposome incorporation efficiencies (LIE) are clustered near Cys28. Such mutant subunits show the lowest and highest subunit affinities respectively. The oxaloacetate transporter (Oac1p) subunit has an almost 2-fold lower affinity than the PTP subunit. The Oac1p, dicarboxylate (Dic1p) and PTP transporter subunits form heterodimers with even lower affinities. These results form a firm basis for detailed studies to establish the effect of subunit affinities on transport mode and activity and for the identification of the mechanism that prevents formation of heterodimers that surely will negatively impact oxidative phosphorylation and ATP levels with serious consequences for the cell. PMID:20171189

  5. A prototype framework for models of socio-hydrology: identification of key feedback loops with application to two Australian case-studies

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

    It is increasingly acknowledged that, in order to sustainably manage global freshwater resources, it is critical that we better understand the nature of human-hydrology interactions at the broader catchment system-scale. Yet to date, a generic conceptual framework for building models of catchment systems that include adequate representation of socioeconomic systems - and the dynamic feedbacks between human and natural systems - has remained elusive. In an attempt to work towards such a model, this paper outlines a generic framework for a model of socio-hydrology that posits a novel construct, a composite Community Sensitivity state variable, as a key link to elucidate the drivers of behavioural response in a hydrological context. The framework provides for both macro-scale contextual parameters, which allow it to be applied across climate, socioeconomic and political gradients, and catchment-specific conditions, by way of tailored "closure relationships", in order to ensure that site-specific and application-specific contexts of socio-hydrologic problems can be accommodated. To demonstrate how such a framework would be applied, two different socio-hydrological case studies, taken from the Australian experience, are presented and discussed. It is envisioned that the application of this framework across study sites and gradients will aid in developing our understanding of the fundamental interactions and feedbacks in such complex human-hydrology systems, and allow hydrologists to participate in the growing field of social-ecological systems modelling.

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

    NASA Astrophysics Data System (ADS)

    Al Azzawi, Dia

    Abnormal flight conditions play a major role in aircraft accidents frequently causing loss of control. To ensure aircraft operation safety in all situations, intelligent system monitoring and adaptation must rely on accurately detecting the presence of abnormal conditions as soon as they take place, identifying their root cause(s), estimating their nature and severity, and predicting their impact on the flight envelope. Due to the complexity and multidimensionality of the aircraft system under abnormal conditions, these requirements are extremely difficult to satisfy using existing analytical and/or statistical approaches. Moreover, current methodologies have addressed only isolated classes of abnormal conditions and a reduced number of aircraft dynamic parameters within a limited region of the flight envelope. This research effort aims at developing an integrated and comprehensive framework for the aircraft abnormal conditions detection, identification, and evaluation based on the artificial immune systems paradigm, which has the capability to address the complexity and multidimensionality issues related to aircraft systems. Within the proposed framework, a novel algorithm was developed for the abnormal conditions detection problem and extended to the abnormal conditions identification and evaluation. The algorithm and its extensions were inspired from the functionality of the biological dendritic cells (an important part of the innate immune system) and their interaction with the different components of the adaptive immune system. Immunity-based methodologies for re-assessing the flight envelope at post-failure and predicting the impact of the abnormal conditions on the performance and handling qualities are also proposed and investigated in this study. The generality of the approach makes it applicable to any system. Data for artificial immune system development were collected from flight tests of a supersonic research aircraft within a motion-based flight simulator. The abnormal conditions considered in this work include locked actuators (stabilator, aileron, rudder, and throttle), structural damage of the wing, horizontal tail, and vertical tail, malfunctioning sensors, and reduced engine effectiveness. The results of applying the proposed approach to this wide range of abnormal conditions show its high capability in detecting the abnormal conditions with zero false alarms and very high detection rates, correctly identifying the failed subsystem and evaluating the type and severity of the failure. The results also reveal that the post-failure flight envelope can be reasonably predicted within this framework.

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

    SciTech Connect

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

    2008-10-20

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

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

    PubMed Central

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

    2013-01-01

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

  9. A food-derived synergist of NGF signaling: identification of protein tyrosine phosphatase 1B as a key regulator of NGF receptor-initiated signal transduction.

    PubMed

    Shibata, Takahiro; Nakahara, Hiroko; Kita, Narumi; Matsubara, Yui; Han, Chunguang; Morimitsu, Yasujiro; Iwamoto, Noriko; Kumagai, Yoshito; Nishida, Motohiro; Kurose, Hitoshi; Aoki, Naohito; Ojika, Makoto; Uchida, Koji

    2008-12-01

    Neurotrophins, such as the nerve growth factor (NGF), play an essential role in the growth, development, survival and functional maintenance of neurons in the central and peripheral systems. They also prevent neuronal cell death under various stressful conditions, such as ischemia and neurodegenerative disorders. NGF induces cell differentiation and neurite outgrowth by binding with and activating the NGF receptor tyrosine kinase followed by activation of a variety of signaling cascades. We have investigated the NGF-dependent neuritogenesis enhancer potential of a food-derived small molecule contained in Brassica vegetables and identified the protein tyrosine phosphatase (PTP) 1B as a key regulator of the NGF receptor-initiated signal transduction. Based on an extensive screening of Brassica vegetable extracts for the neuritogenic-promoting activity in the rat pheochromocytoma cell line PC12, we found the Japanese horseradish, wasabi (Wasabia japonica, syn. Eutrema wasabi), as the richest source and identified 6-methylsulfinylhexyl isothiocyanate (6-HITC), an analogue of sulforaphane isolated from broccoli, as one of the major neuritogenic enhancers in the wasabi. 6-HITC strongly enhanced the neurite outgrowth and neurofilament expression elicited by a low-concentration of NGF that alone was insufficient to induce neuronal differentiation. 6-HITC also facilitated the sustained-phosphorylation of the extracellular signal-regulated kinase and the autophosphorylation of the NGF receptor TrkA. It was found that PTP1B act as a phosphatase capable of dephosphorylating Tyr-490 of TrkA and was inactivated by 6-HITC in a redox-dependent manner. The identification of PTP1B as a regulator of NGF signaling may provide new clues about the chemoprotective potential of food components, such as isothiocyanates. PMID:18796006

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

    PubMed

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

    2014-01-01

    Specimens of a new species of the non-marine ostracod genus, Tanycypris Triebel, 1959 were found in samples from water plant containers, displayed in a greenhouse of the botanical garden in Munich, Germany. Beside the ubiquitous species Cypridopsis vidua O.F. Müller, 1776, the samples contained four alien species of the subfamily Cypricercinae, namely Chlamydotheca arcuata Sars, 1901, Strandesia bicuspis Claus, 1892, Tanycypris centa Chang et al., 2012, and Tanycypris alfonsi n. sp.. The genus Tanycypris has mainly been reported (native) from Asia, and (invasive) from Italian rice fields. The Cypricercinae unite all species possessing a Triebel loop, a character of the caudal rami attachment. The subfamily is split into the tribes Cypricercini McKenzie, 1971, Bradleystrandesiini Savatenalinton & Martens, 2009 and Nealecypridini Savatenalinton & Martens, 2009, the latter of which comprises the genera Tanycypris Triebel, 1959, Astenocypris G.W. Müller, 1912, Diaphanocypris Würdig & Pinto, 1990 and Nealecypris Savatenalinton & Martens, 2009. During the process of describing the new species, a number of taxonomic uncertainties were detected within the genus Tanycypris, leading to a revision of the nine species currently ascribed to it: Tanycypris camaguinensis (Tressler, 1937), Tanycypris centa Chang et al., 2012 Tanycypris clavigera (G.W. Müller, 1898) (now: Nealecypris clavigera nov. comb.), Tanycypris madagascarensis (G.W. Müller, 1898), Tanycypris marina (Hartmann, 1965) (now: Dolerocypris marina nov. comb.), Tanycypris pedroensis (Tressler, 1950) (now: Diaphanocypris pedroensis nov. comb.), Tanycypris pellucida (Klie, 1932), Tanycypris siamensis Savatenalinton & Martens, 2009a, and Tanycypris telavivensis (Krampner, 1928) (now: Herpetocypris telavivensis). An identification key has been developed to the species of the genus Tanycypris. PMID:24989755

  11. An annotated list of the species of Gangesia Woodland, 1924 (Cestoda: Proteocephalidea), parasites of catfishes in Asia, with new synonyms and a key to their identification.

    PubMed

    Ash, Anirban; de Chambrier, Alain; Shimazu, Takeshi; Ermolenko, Alexey; Scholz, Tomáš

    2015-05-01

    An annotated list of tapeworms of the genus Gangesia Woodland, 1924 (Cestoda: Proteocephalidea), parasites of siluriform fishes in Asia, is provided. Based on the morphological examination of museum specimens and newly collected material from China, Japan and Russia, as well as the results of a previous revision of the Indomalayan species, only eight of more than 50 nominal taxa are considered to be valid. These are: from India and neighbouring countries, Gangesia bengalensis (Southwell, 1913) (type-species), G. agraensis Verma, 1928, both from Wallago attu (Bloch & Schneider) (Siluridae), G. macrones Woodland, 1924 from Sperata seenghala (Sykes) (Bagridae) and G. vachai (Gupta & Parmar, 1988) from different catfishes (type-host Eutropiichthys vacha (Hamilton); Schilbeidae), and, from the Palaearctic, G. margolisi Shimazu, 1994, a parasite of Silurus biwaensis (Tomoda) (Siluridae) in Japan, G. oligonchis Roitman & Freze, 1964 from Tachysurus fulvidraco (Richardson) (Bagridae) in Russia, and G. parasiluri Yamaguti, 1934 and G. polyonchis Roitman & Freze, 1964, both from Silurus asotus L. (Siluridae) in Japan and Russia, respectively. The poorly known G. oligonchis is redescribed. Seven new synonyms are proposed: G. chauhani Mathur & Srivastav, 2000, G. wallaguae Pradhan, Kulkarni, Kale & Wakle, 2010 and G. shivajiraoi Dhole, Waghmare & Chavan, 2012 are synonymised with G. agraensis; G. striatusii Bhure & Nanaware, 2012 and Silurotaenia govindii Sawarkar, 2013 with G. macrones; G. spasskajae Demshin, 1987 with G. polyonchis; and Silurotaenia spinula Chen, 1984 with Postgangesia orientalis Akhmerov, 1969. Gangesia pseudobagrae Chen, 1962 is considered to be a species inquirenda, whereas G. chauhani Mathur, 1992 and G. dineshei Jaysingpure, 2002 are recognised as unavailable names. An amended generic diagnosis of Gangesia and a key to the identification of its recognised species are also provided. PMID:25862030

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

    PubMed Central

    Biondi, Maurizio; D’Alessandro, Paola

    2012-01-01

    Abstract A revision of the Alticini genera from the Afrotropical region is reported. The paper includes the following for the flea beetle fauna occurring in Sub-Saharan Africa and Madagascar: a key to their identification; habitus photos of all the genera; microscope and scanning electron micrographs of many diagnostic morphological characters; and an updated annotated catalogue with biogeographical notes that include new distributional data. The following new synonymies are proposed: Aphthona Chevrolat, 1836 = Ethiopia Scherer, 1972 syn. n.; Sanckia Duvivier, 1891 = Eugonotes Jacoby, 1897 syn. n.; Eurylegna Weise, 1910a = Eurylegniella Scherer, 1972 syn. n.; Kimongona Bechyné, 1959a = Mesocrepis Scherer, 1963 syn. n.; Diphaulacosoma Jacoby, 1892a = Neoderina Bechyné, 1952 syn. n.; Sesquiphaera Bechyné, 1958a = Paropsiderma Bechyné, 1958a syn. n.; Podagrica Chevrolat, 1836 = Podagricina Csiki in Heikertinger and Csiki 1940 syn. n.; Amphimela Chapuis, 1875 = Sphaerophysa Baly, 1876a syn. n. The following new combinations are proposed: Blepharida insignis Brancsik, 1897 = Xanthophysca insignis (Brancsik, 1897) comb. n.; Blepharida multiguttata Duvivier, 1891 = Xanthophysca multiguttata (Duvivier, 1891) comb. n.; Hemipyxis balyana (Csiki in Heikertinger and Csiki 1940) = Pseudadorium balyanum (Csiki in Heikertinger and Csiki, 1940) comb. n.; Hemipyxis brevicornis (Jacoby, 1892a) = Pseudadorium brevicornis (Jacoby, 1892a) comb. n.; Hemipyxis cyanea (Weise, 1910b) = Pseudadorium cyaneum (Weise, 1910b) comb. n.; Hemipyxis gynandromorpha Bechyné, 1958c = Pseudadorium gynandromorphum (Bechyné, 1958c) comb. n.; Hemipyxis latiuscula Bechyné, 1958c = Pseudadorium latiusculum (Bechyné, 1958c) comb. n.; Hemipyxis soror (Weise, 1910b) = Pseudadorium soror (Weise, 1910b) comb. n. The genera Buphonella Jacoby, 1903aand Halticopsis Fairmaire, 1883a are transferred to the tribe Galerucini; the genus Biodontocnema Biondi, 2000 stat. prom. is considered to be valid and reinstated at generic level. Finally, a zoogeographical analysis of the flea beetle fauna in the Afrotropical region is provided. PMID:23378812

  13. A guide to the Simulium damnosum complex (Diptera: Simuliidae) in Nigeria, with a cytotaxonomic key for the identification of the sibling species

    PubMed Central

    Post, R J; Onyenwe, E; Somiari, S A E; Mafuyai, H B; Crainey, J L; Ubachukwu, P O

    2011-01-01

    Although approximately 40% of all the people blinded by Onchocerca volvulus are Nigerians, almost nothing was known about the various cytospecies of the blackfly vectors present in Nigeria until 1981. The activation of the Nigerian National Onchocerciasis Control Programme in 1986 (and that programme’s initiation of mass distributions of ivermectin in 1991) provided a significant stimulus to understand the biology of the Nigerian vectors but the exploration of any possible differences between the cytospecies has been hampered by a lack of accessible taxonomic information. This review attempts to satisfy that need. There are nine different cytoforms reliably recorded from Nigeria (Simulium damnosum s.s. Nile form, S. damnosum s.s. Volta form, S. sirbanum Sirba form, S. sirbanum Sudanense form, S. soubrense Beffa form, S. squamosum A, S. squamosum B, S. squamosum C and S. yahense typical form), and three more are known from surrounding countries and might be reasonably expected to occur in Nigeria. All of these cytospecies are presumed to be vectors, although there have been almost no identifications of the vectors of O. volvulus in Nigeria. The biogeographical distribution of the cytoforms is broadly similar to that known in other parts of West Africa (although many of the cytoforms remain insufficiently studied). The physico–chemical hydrology of the Nigerian breeding sites of the cytospecies does not, however, correspond to that seen elsewhere in West Africa, and it is not clear whether this might be related to differences in the cytoforms. An illustrated cytotaxonomic key is presented to facilitate and encourage future studies. PMID:21871165

  14. Insights into the key interactions between human protein phosphatase 5 and cantharidin using molecular dynamics and site-directed mutagenesis bioassays

    PubMed Central

    Liu, Ji-Yuan; Chen, Xi-En; Zhang, Ya-Lin

    2015-01-01

    Serine/threonine protein phosphatase 5 (PP5) is a promising novel target for anticancer therapies. This work aims to uncover the key interactions at the atomic level between PP5 and three inhibitors (cantharidin, norcantharidin and endothall). We found that, unlike previous report, Arg 100 contributes less to PP5-inhibitor binding, and the residues His 69, Asn 128, His 129, Arg 225, His 252 and Arg 250 are of importance to PP5-inhibitor binding. The hydrophobic interactions established between the residues Val 254, Phe 271 and Tyr 276, especially Glu 253, are very important to enhance the inhibitive interaction. We suggested that, to increase the inhibitory activity, the interactions of inhibitor with three negatively charged unfavorable interaction residues, Asp 99, Glu 130 and Asp 213, should be avoided. However, the interactions of inhibitor with favorable interaction residue Arg 250 could enhance the inhibitory activity. The Manganese ion 2 (MN2) unfavorably contribute to the total interaction free energies. The coordination between MN2 and chemical group of inhibitor should be eliminated. This work provides insight into how cantharidin and its analogs bind to PP5c at the atomic level and will facilitate modification of cantharidin-like chemicals to rationally develop more specific and less cytotoxic anti-cancer drugs. PMID:26190207

  15. Insights into the key interactions between human protein phosphatase 5 and cantharidin using molecular dynamics and site-directed mutagenesis bioassays.

    PubMed

    Liu, Ji-Yuan; Chen, Xi-En; Zhang, Ya-Lin

    2015-01-01

    Serine/threonine protein phosphatase 5 (PP5) is a promising novel target for anticancer therapies. This work aims to uncover the key interactions at the atomic level between PP5 and three inhibitors (cantharidin, norcantharidin and endothall). We found that, unlike previous report, Arg 100 contributes less to PP5-inhibitor binding, and the residues His 69, Asn 128, His 129, Arg 225, His 252 and Arg 250 are of importance to PP5-inhibitor binding. The hydrophobic interactions established between the residues Val 254, Phe 271 and Tyr 276, especially Glu 253, are very important to enhance the inhibitive interaction. We suggested that, to increase the inhibitory activity, the interactions of inhibitor with three negatively charged unfavorable interaction residues, Asp 99, Glu 130 and Asp 213, should be avoided. However, the interactions of inhibitor with favorable interaction residue Arg 250 could enhance the inhibitory activity. The Manganese ion 2 (MN2) unfavorably contribute to the total interaction free energies. The coordination between MN2 and chemical group of inhibitor should be eliminated. This work provides insight into how cantharidin and its analogs bind to PP5c at the atomic level and will facilitate modification of cantharidin-like chemicals to rationally develop more specific and less cytotoxic anti-cancer drugs. PMID:26190207

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

    PubMed

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

    2010-10-01

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

  17. Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital interfragment interaction energy analysis

    NASA Astrophysics Data System (ADS)

    Yamagishi, Kenji; Yamamoto, Keiko; Yamada, Sachiko; Tokiwa, Hiroaki

    2006-03-01

    Fragment molecular orbital-interfragment interaction energy calculations of the vitamin D receptor (VDR)/1α,25-dihydroxyvitamin D 3 complex were utilized to assign functions of key residues of the VDR. Only one residue forms a significant interaction with the corresponding hydroxy group of the ligand, although two residues are located around each hydroxy group. The degradation of binding affinity for derivatives upon removal of a hydroxy group is closely related to the trend in the strength of the hydrogen bonds. Type II hereditary rickets due to an Arg274 point mutation is caused by the lack of the strongest hydrogen bond.

  18. Identification of Small-Molecule Inhibitors of the HuR/RNA Interaction Using a Fluorescence Polarization Screening Assay Followed by NMR Validation

    PubMed Central

    Wang, Zhonghua; Bhattacharya, Akash; Ivanov, Dmitri N.

    2015-01-01

    The human antigen R (HuR) stabilizes many mRNAs of proto-oncogene, transcription factors, cytokines and growth factors by recognizing AU-rich elements (AREs) presented in their 3’ or 5’ untranslated region (UTR). Multiple lines of experimental evidence suggest that this process plays a key role in cancer development. Thus, destabilizing HuR/RNA interaction by small molecules presents an opportunity for cancer treatment/prevention. Here we present an integrated approach to identify inhibitors of HuR/RNA interaction using a combination of fluorescence-based and NMR-based high throughput screening (HTS). The HTS assay with fluorescence polarization readout and Z’-score of 0.8 was used to perform a screen of the NCI diversity set V library in a 384 well plate format. An NMR-based assay with saturation transfer difference (STD) detection was used for hits validation. Protein NMR spectroscopy was used to demonstrate that some hit compounds disrupt formation of HuR oligomer, whereas others block RNA binding. Thus, our integrated high throughput approach provides a new avenue for identification of small molecules targeting HuR/RNA interaction. PMID:26390015

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

    NASA Astrophysics Data System (ADS)

    Kim, Junhee; Lynch, Jerome P.

    2012-04-01

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

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

    PubMed Central

    Meng, Jun; Shi, Lin; Luan, Yushi

    2014-01-01

    Background Confident identification of microRNA-target interactions is significant for studying the function of microRNA (miRNA). Although some computational miRNA target prediction methods have been proposed for plants, results of various methods tend to be inconsistent and usually lead to more false positive. To address these issues, we developed an integrated model for identifying plant miRNA–target interactions. Results Three online miRNA target prediction toolkits and machine learning algorithms were integrated to identify and analyze Arabidopsis thaliana miRNA-target interactions. Principle component analysis (PCA) feature extraction and self-training technology were introduced to improve the performance. Results showed that the proposed model outperformed the previously existing methods. The results were validated by using degradome sequencing supported Arabidopsis thaliana miRNA-target interactions. The proposed model constructed on Arabidopsis thaliana was run over Oryza sativa and Vitis vinifera to demonstrate that our model is effective for other plant species. Conclusions The integrated model of online predictors and local PCA-SVM classifier gained credible and high quality miRNA-target interactions. The supervised learning algorithm of PCA-SVM classifier was employed in plant miRNA target identification for the first time. Its performance can be substantially improved if more experimentally proved training samples are provided. PMID:25051153

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

    SciTech Connect

    Leung, Cleo; Utokaparch, Soraya; Sharma, Arpeeta; Yu, Carol; Abraham, Thomas; Borchers, Christoph; University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia ; Bernatchez, Pascal; University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia

    2011-11-18

    Highlights: Black-Right-Pointing-Pointer Bi-directional (inward and outward) movement of GFP-dysferlin in COS-7 cells. Black-Right-Pointing-Pointer Dysferlin interacts with key signaling proteins for transcytosis in EC. Black-Right-Pointing-Pointer Dysferlin mediates trafficking of vesicles carrying protein cargos in EC. -- Abstract: Dysferlin is a membrane-anchored protein known to facilitate membrane repair in skeletal muscles following mechanical injury. Mutations of dysferlin gene impair sarcolemma integrity, a hallmark of certain forms of muscular dystrophy in patients. Dysferlin contains seven calcium-dependent C2 binding domains, which are required to promote fusion of intracellular membrane vesicles. Emerging evidence reveal the unexpected expression of dysferlin in non-muscle, non-mechanically active tissues, such as endothelial cells, which cast doubts over the belief that ferlin proteins act exclusively as membrane repair proteins. We and others have shown that deficient trafficking of membrane bound proteins in dysferlin-deficient cells, suggesting that dysferlin might mediate trafficking of client proteins. Herein, we describe the intracellular trafficking and movement of GFP-dysferlin positive vesicles in unfixed reconstituted cells using live microscopy. By performing GST pull-down assays followed by mass spectrometry, we identified dysferlin binding protein complexes in human vascular endothelial cells. Together, our data further support the claims that dysferlin not only mediates membrane repair but also trafficking of client proteins, ultimately, help bridging dysferlinopathies to aberrant membrane signaling.

  2. The Identification of Novel Protein-Protein Interactions in Liver that Affect Glucagon Receptor Activity

    PubMed Central

    Froese, Sean; Dai, Feihan F.; Robitaille, Mélanie; Bhattacharjee, Alpana; Huang, Xinyi; Jia, Weiping; Angers, Stéphane; Wheeler, Michael B.; Wei, Li

    2015-01-01

    Glucagon regulates glucose homeostasis by controlling glycogenolysis and gluconeogenesis in the liver. Exaggerated and dysregulated glucagon secretion can exacerbate hyperglycemia contributing to type 2 diabetes (T2D). Thus, it is important to understand how glucagon receptor (GCGR) activity and signaling is controlled in hepatocytes. To better understand this, we sought to identify proteins that interact with the GCGR to affect ligand-dependent receptor activation. A Flag-tagged human GCGR was recombinantly expressed in Chinese hamster ovary (CHO) cells, and GCGR complexes were isolated by affinity purification (AP). Complexes were then analyzed by mass spectrometry (MS), and protein-GCGR interactions were validated by co-immunoprecipitation (Co-IP) and Western blot. This was followed by studies in primary hepatocytes to assess the effects of each interactor on glucagon-dependent glucose production and intracellular cAMP accumulation, and then in immortalized CHO and liver cell lines to further examine cell signaling. Thirty-three unique interactors were identified from the AP-MS screening of GCGR expressing CHO cells in both glucagon liganded and unliganded states. These studies revealed a particularly robust interaction between GCGR and 5 proteins, further validated by Co-IP, Western blot and qPCR. Overexpression of selected interactors in mouse hepatocytes indicated that two interactors, LDLR and TMED2, significantly enhanced glucagon-stimulated glucose production, while YWHAB inhibited glucose production. This was mirrored with glucagon-stimulated cAMP production, with LDLR and TMED2 enhancing and YWHAB inhibiting cAMP accumulation. To further link these interactors to glucose production, key gluconeogenic genes were assessed. Both LDLR and TMED2 stimulated while YWHAB inhibited PEPCK and G6Pase gene expression. In the present study, we have probed the GCGR interactome and found three novel GCGR interactors that control glucagon-stimulated glucose production by modulating cAMP accumulation and genes that control gluconeogenesis. These interactors may be useful targets to control glucose homeostasis in T2D. PMID:26075596

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

    ERIC Educational Resources Information Center

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

    2005-01-01

    The article describes data emerging from a study of a group of language teachers integrating use of the interactive whiteboard (IWB) into their classroom practice. Data collection tools were developed which allowed participants freedom of action and expression whilst providing a framework for reflection designed to focus on pedagogy rather than…

  4. Enacting Teaching and Learning in the Interaction Process: "Keys" for Developing Skills in Piano Lessons through Four-Hand Improvisations

    ERIC Educational Resources Information Center

    Laroche, Julien; Kaddouch, Ilan

    2014-01-01

    Embodied mind theories underline the role of the body in the act of knowing. According to the enactive approach, we learn to perceive and to know through our bodily interactions with the world (Varela, Thompson & Rosch, 1991). However, such an approach remains incomplete as long as sociality is not taken into account (Froese & Di Paolo,…

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

    ERIC Educational Resources Information Center

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

    2005-01-01

    The article describes data emerging from a study of a group of language teachers integrating use of the interactive whiteboard (IWB) into their classroom practice. Data collection tools were developed which allowed participants freedom of action and expression whilst providing a framework for reflection designed to focus on pedagogy rather than

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

    ERIC Educational Resources Information Center

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

    2012-01-01

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

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

    PubMed

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

    2013-01-01

    A novel illustration technique based on scanning electron microscopy is used for the first time to enhance taxonomic descriptions. The male genitalia (gonopods) of six species of millipedes are used for construction of interactive imaging models. Each model is a compilation of a number of SEM images taken consecutively while rotating the SEM stage 360°, which allows the structure in question to be seen from all angles of view in one plane. Seven new species of the genus Ommatoiulus collected in Tunisia are described: Ommatoiulus chambiensis, Ommatoiulus crassinigripes, Ommatoiulus kefi, Ommatoiulus khroumiriensis, Ommatoiulus xerophilus, Ommatoiulus xenos, and Ommatoiulus zaghouani spp. n. Size differences between syntopic adult males of Ommatoiulus chambiensis and Ommatoiulus xerophilus spp. n. from Châambi Mountain are illustrated using scatter diagrams. A similar diagram is used to illustrate size differences in Ommatoiulus crassinigripes, Ommatoiulus khroumiriensis spp. n. and Ommatoiulus punicus (Brölemann, 1894). In addition to morphological differences, the latter three species display allopatric distribution and different habitat preferences. A dichotomous interactive key with a high visual impact and an intuitive user interface is presented to serve identification of the 12 Ommatoiulus species so far known from Tunisia. Updates on the North African Ommatoiulus fauna in general are presented. PMID:24146546

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

    PubMed Central

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

    2013-01-01

    Abstract A novel illustration technique based on scanning electron microscopy is used for the first time to enhance taxonomic descriptions. The male genitalia (gonopods) of six species of millipedes are used for construction of interactive imaging models. Each model is a compilation of a number of SEM images taken consecutively while rotating the SEM stage 360°, which allows the structure in question to be seen from all angles of view in one plane. Seven new species of the genus Ommatoiulus collected in Tunisia are described: Ommatoiulus chambiensis, Ommatoiulus crassinigripes, Ommatoiulus kefi, Ommatoiulus khroumiriensis, Ommatoiulus xerophilus, Ommatoiulus xenos, and Ommatoiulus zaghouani spp. n. Size differences between syntopic adult males of Ommatoiulus chambiensis and Ommatoiulus xerophilus spp. n. from Châambi Mountain are illustrated using scatter diagrams. A similar diagram is used to illustrate size differences in Ommatoiulus crassinigripes, Ommatoiulus khroumiriensis spp. n. and Ommatoiulus punicus (Brölemann, 1894). In addition to morphological differences, the latter three species display allopatric distribution and different habitat preferences. A dichotomous interactive key with a high visual impact and an intuitive user interface is presented to serve identification of the 12 Ommatoiulus species so far known from Tunisia. Updates on the North African Ommatoiulus fauna in general are presented. PMID:24146546

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

    ERIC Educational Resources Information Center

    Shayler, Hannah A.; Siver, Peter A.

    2006-01-01

    The Freshwater Ecology Laboratory at Connecticut College has developed an interactive, Web-based identification key to freshwater algal genera using the Lucid Professional and Lucid 3 software developed by the Centre for Biological Information Technology at the University of Queensland, Brisbane, Australia. The "Key to Freshwater Algae" was funded…

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

    ERIC Educational Resources Information Center

    Shayler, Hannah A.; Siver, Peter A.

    2006-01-01

    The Freshwater Ecology Laboratory at Connecticut College has developed an interactive, Web-based identification key to freshwater algal genera using the Lucid Professional and Lucid 3 software developed by the Centre for Biological Information Technology at the University of Queensland, Brisbane, Australia. The "Key to Freshwater Algae" was funded

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

    ERIC Educational Resources Information Center

    Ginter, Earl J.; Bonney, Warren

    1993-01-01

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

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

    PubMed

    Hueston, Cara M; Deak, Terrence

    2014-01-30

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

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

    PubMed Central

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

    2009-01-01

    RNA triphosphatases (RTPases) are involved in the addition of the distinctive cap structure found at the 5′ ends of eukaryotic mRNAs. Fungi, protozoa and some DNA viruses possess an RTPase that belongs to the triphosphate tunnel metalloenzyme family of enzymes that can also hydrolyze nucleoside triphosphates. Previous crystallization studies revealed that the phosphohydrolase catalytic core is located in a hydrophilic tunnel composed of antiparallel β-strands. However, all past efforts to obtain structural information on the interaction between RTPases and their substrates were unsuccessful. In the present study, we used computational molecular docking to model the binding of a nucleotide substrate into the yeast RTPase active site. In order to confirm the docking model and to gain additional insights into the molecular determinants involved in substrate recognition, we also evaluated both the phosphohydrolysis and the inhibitory potential of an important number of nucleotide analogs. Our study highlights the importance of specific amino acids for the binding of the sugar, base and triphosphate moieties of the nucleotide substrate, and reveals both the structural flexibility and complexity of the active site. These data illustrate the functional features required for the interaction of an RTPase with a ligand and pave the way to the use of nucleotide analogs as potential inhibitors of RTPases of pathogenic importance. PMID:19372271

  14. Interactions between phytoplankton organisms and key carbonate system properties in the southern Adriatic Sea: seasonal variability within an annual cycle

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    Although the impact of CO2 uptake on ocean chemistry has been recognizing for the last decades, ocean acidification has emerged as a key issue of global concern in less than a decade. Studies of the impacts on marine organisms, ecosystems and biogeochemical processes are only at the beginning and the results are still contrasting. In open sea, the pool of particulate organic carbon is mainly determined by phytoplankton production (controlled by light and nutrient availabilities). However pH and key carbonate system properties (AT, DIC, calcium carbonate saturation states), influencing phytoplankton population and communities can play a fundamental role in determining the autothrophic production and its cycle. In the perspective of lighting possible impacts of climatic changes on natural phytoplankton communities of the Southern Adriatic open sea region, this contribute describes the relationships between pH/carbonate system and the phytoplankton during almost one year (Sept 2007-June 2008), with particular regard to calcareous phytoplankton. A few seasonal campaigns were conducted within the frame of the Italian VECTOR project, on a repeated section from Bari to Dubrovnik. The dynamics of phytoplankton community have been analyzed considering the export of particulate organic matter from the photic layer (collected in sediment traps at 150 m). The phytoplankton cycle from September 07 to late June 08 was determined analysing samples collected from CTD bottles. It appears to be characterized by short time blooms of different groups: in autumn the main component (62%) was represented by siliceous plankton (diatoms), in late winter calcareous plankton (coccolithophores) reached 31% of total biomass, whereas flagellates appeared the dominant group (84%) during summer. Downward fluxes of organic carbon (at 150 m), strictly depending on the upper layer autotrophic activity, were well correlated with carbonate fluxes. A succession of different dominant productive groups was observed through the year (confirming the very dynamic seasonal pattern of species composition). Blooms were relatively short time events (less than 15 days): diatoms showed peaks in late winter-spring, while coccolithophores showed an evident bloom in February. Biogeochemical conditions (nutrients, dissolved oxygen, AT, DIC, pH) fitted well to the described phytoplankton biomass abundances and species composition; in particular the decrease of both AT and DIC between February and June suggest the occurrence of calcification process, in good agreement with calcareous plankton bloom observed as a peak in the sediment traps. The relevance of calcareous community in Southern Adriatic Sea is evidenced by the BSi /CaCO3 ratio in sediment trap samples. Regarding the export of particles, the southern Adriatic can be considered a carbonate system with short-time, silica-dominated events (mainly occurring in the period March-April).

  15. Mechanism of conformational coupling in SecA: Key role of hydrogen-bonding networks and water interactions.

    PubMed

    Milenkovic, Stefan; Bondar, Ana-Nicoleta

    2016-02-01

    SecA uses the energy yielded by the binding and hydrolysis of adenosine triphosphate (ATP) to push secretory pre-proteins across the plasma membrane in bacteria. Hydrolysis of ATP occurs at the nucleotide-binding site, which contains the conserved carboxylate groups of the DEAD-box helicases. Although crystal structures provide valuable snapshots of SecA along its reaction cycle, the mechanism that ensures conformational coupling between the nucleotide-binding site and the other domains of SecA remains unclear. The observation that SecA contains numerous hydrogen-bonding groups raises important questions about the role of hydrogen-bonding networks and hydrogen-bond dynamics in long-distance conformational couplings. To address these questions, we explored the molecular dynamics of SecA from three different organisms, with and without bound nucleotide, in water. By computing two-dimensional hydrogen-bonding maps we identify networks of hydrogen bonds that connect the nucleotide-binding site to remote regions of the protein, and sites in the protein that respond to specific perturbations. We find that the nucleotide-binding site of ADP-bound SecA has a preferred geometry whereby the first two carboxylates of the DEAD motif bridge via hydrogen-bonding water. Simulations of a mutant with perturbed ATP hydrolysis highlight the water-bridged geometry as a key structural element of the reaction path. PMID:26607006

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

  17. Identification of key binding site residues of MCT1 for AR-C155858 reveals the molecular basis of its isoform selectivity.

    PubMed

    Nancolas, Bethany; Sessions, Richard B; Halestrap, Andrew P

    2015-02-15

    The proton-linked monocarboxylate transporters (MCTs) are required for lactic acid transport into and out of all mammalian cells. Thus, they play an essential role in tumour cells that are usually highly glycolytic and are promising targets for anti-cancer drugs. AR-C155858 is a potent MCT1 inhibitor (Ki ~2 nM) that also inhibits MCT2 when associated with basigin but not MCT4. Previous work [Ovens, M.J. et al. (2010) Biochem. J. 425, 523-530] revealed that AR-C155858 binding to MCT1 occurs from the intracellular side and involves transmembrane helices (TMs) 7-10. In the present paper, we generate a molecular model of MCT4 based on our previous models of MCT1 and identify residues in the intracellular substrate-binding cavity that differ significantly between MCT4 and MCT1/MCT2 and so might account for differences in inhibitor binding. We tested their involvement using site-directed mutagenesis (SDM) of MCT1 to change residues individually or in combination with their MCT4 equivalent and determined inhibitor sensitivity following expression in Xenopus oocytes. Phe360 and Ser364 were identified as important for AR-C155858 binding with the F360Y/S364G mutant exhibiting >100-fold reduction in inhibitor sensitivity. To refine the binding site further, we used molecular dynamics (MD) simulations and additional SDM. This approach implicated six more residues whose involvement was confirmed by both transport studies and [3H]-AR-C155858 binding to oocyte membranes. Taken together, our data imply that Asn147, Arg306 and Ser364 are important for directing AR-C155858 to its final binding site which involves interaction of the inhibitor with Lys38, Asp302 and Phe360 (residues that also play key roles in the translocation cycle) and also Leu274 and Ser278. PMID:25437897

  18. Identification of key binding site residues of MCT1 for AR-C155858 reveals the molecular basis of its isoform selectivity

    PubMed Central

    Nancolas, Bethany; Sessions, Richard B.; Halestrap, Andrew P.

    2014-01-01

    The proton-linked monocarboxylate transporters (MCTs) are required for lactic acid transport into and out of all mammalian cells. Thus, they play an essential role in tumour cells that are usually highly glycolytic and are promising targets for anti-cancer drugs. AR-C155858 is a potent MCT1 inhibitor (Ki ~2 nM) that also inhibits MCT2 when associated with basigin but not MCT4. Previous work [Ovens, M.J. et al. (2010) Biochem. J. 425, 523–530] revealed that AR-C155858 binding to MCT1 occurs from the intracellular side and involves transmembrane helices (TMs) 7–10. In the present paper, we generate a molecular model of MCT4 based on our previous models of MCT1 and identify residues in the intracellular substrate-binding cavity that differ significantly between MCT4 and MCT1/MCT2 and so might account for differences in inhibitor binding. We tested their involvement using site-directed mutagenesis (SDM) of MCT1 to change residues individually or in combination with their MCT4 equivalent and determined inhibitor sensitivity following expression in Xenopus oocytes. Phe360 and Ser364 were identified as important for AR-C155858 binding with the F360Y/S364G mutant exhibiting >100-fold reduction in inhibitor sensitivity. To refine the binding site further, we used molecular dynamics (MD) simulations and additional SDM. This approach implicated six more residues whose involvement was confirmed by both transport studies and [3H]-AR-C155858 binding to oocyte membranes. Taken together, our data imply that Asn147, Arg306 and Ser364 are important for directing AR-C155858 to its final binding site which involves interaction of the inhibitor with Lys38, Asp302 and Phe360 (residues that also play key roles in the translocation cycle) and also Leu274 and Ser278. PMID:25437897

  19. Conformations, conformational preferences, and conformational exchange of N'-substituted N-acylguanidines: intermolecular interactions hold the key.

    PubMed

    Kleinmaier, Roland; Keller, Max; Igel, Patrick; Buschauer, Armin; Gschwind, Ruth M

    2010-08-18

    Guanidine and acylguanidine groups are crucial structural features of numerous biologically active compounds. Depending on the biological target, acylguanidines may be considered as considerably less basic bioisosteres of guanidines with improved pharmacokinetics and pharmacodynamics, as recently reported for N'-monoalkylated N-acylguanidines as ligands of G-protein-coupled receptors (GPCRs). The molecular basis for enhanced ligand-receptor interactions of acylguanidines is far from being understood. So far, only a few and contradictory results about their conformational preferences have been reported. In this study, the conformations, conformational preferences, and conformational exchange of four unprotonated and seven protonated monoalkylated acylguanidines with up to six anions and with bisphosphonate tweezers are investigated by NMR. Furthermore, the effects of the acceptor properties in acylguanidine salts, of microsolvation by dimethylsulfoxide, and of varying acyl and alkyl substituents are studied. Throughout the whole study, exclusively two out of eight possible acylguanidine conformations were detected, independent of the compound, the anion, or the solvent used. For the first time, it is shown that the strength and number of intermolecular interactions with anions, solvent molecules, or biomimetic receptors decide the conformational preferences and exchange rates. One recently presented and two new crystal structures resemble the conformational preferences observed in solution. Thus, consistent conformational trends are found throughout the structurally diverse compound pool, including two potent GPCR ligands, different anions, and receptors. The presented results may contribute to a better understanding of the mechanism of action at the molecular level and to the prediction and rational design of these biologically active compounds. PMID:20698689

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

    PubMed Central

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

    2012-01-01

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

  1. Analysis and Identification of Aptamer-Compound Interactions with a Maximum Relevance Minimum Redundancy and Nearest Neighbor Algorithm.

    PubMed

    Wang, ShaoPeng; Zhang, Yu-Hang; Lu, Jing; Cui, Weiren; Hu, Jerry; Cai, Yu-Dong

    2016-01-01

    The development of biochemistry and molecular biology has revealed an increasingly important role of compounds in several biological processes. Like the aptamer-protein interaction, aptamer-compound interaction attracts increasing attention. However, it is time-consuming to select proper aptamers against compounds using traditional methods, such as exponential enrichment. Thus, there is an urgent need to design effective computational methods for searching effective aptamers against compounds. This study attempted to extract important features for aptamer-compound interactions using feature selection methods, such as Maximum Relevance Minimum Redundancy, as well as incremental feature selection. Each aptamer-compound pair was represented by properties derived from the aptamer and compound, including frequencies of single nucleotides and dinucleotides for the aptamer, as well as the constitutional, electrostatic, quantum-chemical, and space conformational descriptors of the compounds. As a result, some important features were obtained. To confirm the importance of the obtained features, we further discussed the associations between them and aptamer-compound interactions. Simultaneously, an optimal prediction model based on the nearest neighbor algorithm was built to identify aptamer-compound interactions, which has the potential to be a useful tool for the identification of novel aptamer-compound interactions. The program is available upon the request. PMID:26955638

  2. Analysis and Identification of Aptamer-Compound Interactions with a Maximum Relevance Minimum Redundancy and Nearest Neighbor Algorithm

    PubMed Central

    Wang, ShaoPeng; Zhang, Yu-Hang; Lu, Jing; Cui, Weiren; Hu, Jerry; Cai, Yu-Dong

    2016-01-01

    The development of biochemistry and molecular biology has revealed an increasingly important role of compounds in several biological processes. Like the aptamer-protein interaction, aptamer-compound interaction attracts increasing attention. However, it is time-consuming to select proper aptamers against compounds using traditional methods, such as exponential enrichment. Thus, there is an urgent need to design effective computational methods for searching effective aptamers against compounds. This study attempted to extract important features for aptamer-compound interactions using feature selection methods, such as Maximum Relevance Minimum Redundancy, as well as incremental feature selection. Each aptamer-compound pair was represented by properties derived from the aptamer and compound, including frequencies of single nucleotides and dinucleotides for the aptamer, as well as the constitutional, electrostatic, quantum-chemical, and space conformational descriptors of the compounds. As a result, some important features were obtained. To confirm the importance of the obtained features, we further discussed the associations between them and aptamer-compound interactions. Simultaneously, an optimal prediction model based on the nearest neighbor algorithm was built to identify aptamer-compound interactions, which has the potential to be a useful tool for the identification of novel aptamer-compound interactions. The program is available upon the request. PMID:26955638

  3. Homotypic interaction and multimerization of nucleocapsid protein of tomato spotted wilt tospovirus: Identification and characterization of two interacting domains

    PubMed Central

    Uhrig, J. F.; Soellick, T.-R.; Minke, C. J.; Philipp, C.; Kellmann, J.-W.; Schreier, P. H.

    1999-01-01

    The nucleocapsid protein (N) of tomato spotted wilt tospovirus (TSWV) plays a central role in the viral life cycle. With the aid of the yeast two-hybrid system and surface plasmon resonance analysis, homotypic interaction and multimerization of the N protein was detected. Analysis of deletion mutants identified two binding regions in the protein, located at the N terminus (amino acids 139) and the C terminus (amino acids 233248), respectively, implying a head-to-tail interaction of the N terminus with the C terminus to form a multimeric chain. Further characterization of the binding domains was performed by site-directed mutagenesis. Two phenylalanines (F242 and F246) highly conserved in the N proteins within the Tospovirus genus were shown to play a crucial role in the interaction. PMID:9874771

  4. Interactions with M cells and macrophages as key steps in the pathogenesis of enterohemorrhagic Escherichia coli infections.

    PubMed

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

    2011-01-01

    Enterohemorrhagic Escherichia coli (EHEC) are food-borne pathogens that can cause serious infections ranging from diarrhea to hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS). Translocation of Shiga-toxins (Stx) from the gut lumen to underlying tissues is a decisive step in the development of the infection, but the mechanisms involved remain unclear. Many bacterial pathogens target the follicle-associated epithelium, which overlies Peyer's patches (PPs), cross the intestinal barrier through M cells and are captured by mucosal macrophages. Here, translocation across M cells, as well as survival and proliferation of EHEC strains within THP-1 macrophages were investigated using EHEC O157:H7 reference strains, isogenic mutants, and 15 EHEC strains isolated from HC/HUS patients. We showed for the first time that E. coli O157:H7 strains are able to interact in vivo with murine PPs, to translocate ex vivo through murine ileal mucosa with PPs and across an in vitro human M cell model. EHEC strains are also able to survive and to produce Stx in macrophages, which induce cell apoptosis and Stx release. In conclusion, our results suggest that the uptake of EHEC by M cells and underlying macrophages in the PP may be a critical step in Stx translocation and release in vivo. A new model for EHEC infection in humans is proposed that could help in a fuller understanding of EHEC-associated diseases. PMID:21858177

  5. Identification of Metarhizium anisopliae transcripts expressed during the fungus- insect interaction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The identification of genes contributing to the establishment and disease progression of entomopathogenic fungi within their insect hosts has been conducted to date largely using in vitro systems mimicking specific phases of the infection. We are exploring the use of in vivo techniques to identify f...

  6. Attentional Resource Emancipation: Toward Understanding the Interaction of Word Identification and Comprehension Processes in Reading.

    ERIC Educational Resources Information Center

    Reynolds, Ralph E.

    2000-01-01

    Addresses lack of overlap and intercommunication between research on early reading and reading comprehension. Discusses metacognitive control in reading and learning processes. Suggests the emancipation of attentional resources by the automatization of lower level word identification and higher level basic comprehension skills. Concludes with…

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

    PubMed

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

    2011-03-01

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

  8. Identification of vancomycin interaction with Enterococcus faecalis within 30 min of interaction time using Raman spectroscopy.

    PubMed

    Assmann, Cora; Kirchhoff, Johanna; Beleites, Claudia; Hey, Jessica; Kostudis, Sophia; Pfister, Wolfgang; Schlattmann, Peter; Popp, Jürgen; Neugebauer, Ute

    2015-11-01

    Vancomycin is an important glycopeptide antibiotic which is used to treat serious infections caused by Gram-positive bacteria. However, during the last years, a tremendous rise in vancomycin resistances, especially among Enterococci, was reported, making fast diagnostic methods inevitable. In this contribution, we apply Raman spectroscopy to systematically characterize vancomycin-enterococci interactions over a time span of 90 min using a sensitive Enterococcus faecalis strain and two different vancomycin concentrations above the minimal inhibitory concentration (MIC). Successful action of the drug on the pathogen could be observed already after 30 min of interaction time. Characteristic spectral changes are visualized with the help of multivariate statistical analysis (linear discriminant analysis and partial least squares regressions). Those changes were employed to train a statistical model to predict vancomycin treatment based on the Raman spectra. The robustness of the model was tested using data recorded by an independent operator. Classification accuracies of >90 % were obtained for vancomycin concentrations in the lower range of a typical trough serum concentration recommended for most patients during appropriate vancomycin therapy. Characterization of drug-pathogen interactions by means of label-free spectroscopic methods, such as Raman spectroscopy, can provide the knowledge base for innovative and fast susceptibility tests which could speed up microbiological analysis as well as finding applications in novel antibiotic screenings assays. Graphical Abstract E. faecalis is incubated with vancomycin and characterized by means of Raman spectroscopy after different time points. Characteristic spectral changes reveal efficient vancomycin-enterococci-interaction. PMID:26231687

  9. Alkoxide coordination of iron(III) protoporphyrin IX by antimalarial quinoline methanols: a key interaction observed in the solid-state and solution.

    PubMed

    Gildenhuys, Johandie; Sammy, Chandre J; Müller, Ronel; Streltsov, Victor A; le Roex, Tanya; Kuter, David; de Villiers, Katherine A

    2015-10-14

    The quinoline methanol antimalarial drug mefloquine is a structural analogue of the Cinchona alkaloids, quinine and quinidine. We have elucidated the single crystal X-ray diffraction structure of the complexes formed between racemic erythro mefloquine and ferriprotoporphyrin IX (Fe(iii)PPIX) and show that alkoxide coordination is a key interaction in the solid-state. Mass spectrometry confirms the existence of coordination complexes of quinine, quinidine and mefloquine to Fe(iii)PPIX in acetonitrile. The length of the iron(iii)-O bond in the quinine and quinidine complexes as determined by Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy unequivocally confirms that coordination of the quinoline methanol compounds to Fe(iii)PPIX occurs in non-aqueous aprotic solution via their benzylic alkoxide functional group. UV-visible spectrophotometric titrations of the low-spin bis-pyridyl-Fe(iii)PPIX complex with each of the quinoline methanol compounds results in the displacement of a single pyridine molecule and subsequent formation of a six-coordinate pyridine-Fe(iii)PPIX-drug complex. We propose that formation of the drug-Fe(iii)PPIX coordination complexes is favoured in a non-aqueous environment, such as that found in lipid bodies or membranes in the malaria parasite, and that their existence may contribute to the mechanism of haemozoin inhibition or other toxicity effects that lead ultimately to parasite death. In either case, coordination is a key interaction to be considered in the design of novel antimalarial drug candidates. PMID:26335948

  10. Identification of a key recombinant narrows the CADASIL gene region to 8 cM and argues against allelism of CADASIL and familial hemiplegic migraine

    SciTech Connect

    Dichgans, M.; Mayer, M.; Straube, A.

    1996-02-15

    This article reports on new information regarding the genetic mapping of the human CADASIL gene region. Previously, the gene had been mapped to human chromosome 19q12. Using the identification of a chromosomal crossover, the region has been refined to an 8-cM interval. 11 refs., 2 figs., 1 tab.

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

    PubMed Central

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

    2009-01-01

    We present results from a novel strategy that enables concurrent identification of protein-protein interactions and topologies in living cells without specific antibodies or genetic manipulations for immuno-/affinity purifications. The strategy consists of (i) a chemical cross-linking reaction: intact cell labeling with a novel class of chemical cross-linkers, protein interaction reporters (PIRs); (ii) two-stage mass spectrometric analysis: stage 1 identification of PIR-labeled proteins and construction of a restricted database by two-dimensional LC/MSMS and stage 2 analysis of PIR-labeled peptides by multiplexed LC/FTICR-MS; and (iii) data analysis: identification of cross-linked peptides and proteins of origin using accurate mass and other constraints. The primary advantage of the PIR approach and distinction from current technology is that protein interactions together with topologies are detected in native biological systems by stabilizing protein complexes with new covalent bonds while the proteins are present in the original cellular environment. Thus, weak or transient interactions or interactions that require properly folded, localized, or membrane-bound proteins can be labeled and identified through the PIR approach. This strategy was applied to Shewanella oneidensis bacterial cells, and initial studies resulted in identification of a set of protein-protein interactions and their contact/binding regions. Furthermore most identified interactions involved membrane proteins, suggesting that the PIR approach is particularly suited for studies of membrane protein-protein interactions, an area under-represented with current widely used approaches. PMID:18936057

  12. Identification of a novel protein interaction between Elmo1 and Cdc27.

    PubMed

    Lee, Juyeon; Moon, Byeongjin; Lee, Dae-Hee; Lee, Gwangrog; Park, Daeho

    2016-03-18

    Elmo has no intrinsic catalytic activity but coordinate multiple cellular processes via their interactions with other proteins. Studies thus have been focused on identifying Elmo binding partners, but the number of characterized Elmo-interacting proteins remains limited. Here, we report Cdc27 as a novel Elmo1-interacting protein. In yeast and mammalian cells, Cdc27 specifically interacted with the C-terminal region of Elmo1 essential for Dock1 association and function. The interaction of Elmo1 with Dock1 abrogated binding between Elmo1 and Cdc27, but the Dock1-Elmo1 interaction was unaffected by Cdc27. Similarly, cellular phagocytotic functions mediated by the Elmo1-Dock1-Rac module were unaffected by Cdc27 levels. In summary, a novel binding partner, Cdc27, was identified for Elmo1 and they appear to be independent of Elmo-Dock1-Rac-mediated processes. PMID:26882976

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

    PubMed Central

    2014-01-01

    Background There is a need to evaluate complex interaction effects on human health, such as those induced by mixtures of environmental contaminants. The usual approach is to formulate an additive statistical model and check for departures using product terms between the variables of interest. In this paper, we present an approach to search for interaction effects among several variables using boosted regression trees. Methods We simulate a continuous outcome from real data on 27 environmental contaminants, some of which are correlated, and test the method’s ability to uncover the simulated interactions. The simulated outcome contains one four-way interaction, one non-linear effect and one interaction between a continuous variable and a binary variable. Four scenarios reflecting different strengths of association are simulated. We illustrate the method using real data. Results The method succeeded in identifying the true interactions in all scenarios except where the association was weakest. Some spurious interactions were also found, however. The method was also capable to identify interactions in the real data set. Conclusions We conclude that boosted regression trees can be used to uncover complex interaction effects in epidemiological studies. PMID:24993424

  14. Identification of subunits of acetylcholine receptor that interact with a cholesterol photoaffinity probe

    SciTech Connect

    Middlemas, D.S.; Raftery, M.A.

    1987-03-10

    All four subunits of the acetylcholine receptor in membrane vesicles isolated from Torpedo californica have been labeled with (/sup 3/H)cholesteryl diazoacetate. As this probe incorporates into lipid bilayers analogously to cholesterol, this result indicates that acetylcholine receptor interacts with cholesterol. This investigation also demonstrates that this probe is a useful reagent for studying the interaction of cholesterol with membrane proteins.

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

    PubMed Central

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

    2011-01-01

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

  16. Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae

    PubMed Central

    Atias, Nir; Kupiec, Martin; Sharan, Roded

    2016-01-01

    The yeast mutant collections are a fundamental tool in deciphering genomic organization and function. Over the last decade, they have been used for the systematic exploration of ∼6 000 000 double gene mutants, identifying and cataloging genetic interactions among them. Here we studied the extent to which these data are prone to neighboring gene effects (NGEs), a phenomenon by which the deletion of a gene affects the expression of adjacent genes along the genome. Analyzing ∼90,000 negative genetic interactions observed to date, we found that more than 10% of them are incorrectly annotated due to NGEs. We developed a novel algorithm, GINGER, to identify and correct erroneous interaction annotations. We validated the algorithm using a comparative analysis of interactions from Schizosaccharomyces pombe. We further showed that our predictions are significantly more concordant with diverse biological data compared to their mis-annotated counterparts. Our work uncovered about 9500 new genetic interactions in yeast. PMID:26602688

  17. Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae.

    PubMed

    Atias, Nir; Kupiec, Martin; Sharan, Roded

    2016-03-18

    The yeast mutant collections are a fundamental tool in deciphering genomic organization and function. Over the last decade, they have been used for the systematic exploration of ∼6 000 000 double gene mutants, identifying and cataloging genetic interactions among them. Here we studied the extent to which these data are prone to neighboring gene effects (NGEs), a phenomenon by which the deletion of a gene affects the expression of adjacent genes along the genome. Analyzing ∼90,000 negative genetic interactions observed to date, we found that more than 10% of them are incorrectly annotated due to NGEs. We developed a novel algorithm, GINGER, to identify and correct erroneous interaction annotations. We validated the algorithm using a comparative analysis of interactions from Schizosaccharomyces pombe. We further showed that our predictions are significantly more concordant with diverse biological data compared to their mis-annotated counterparts. Our work uncovered about 9500 new genetic interactions in yeast. PMID:26602688

  18. Identification of a redox-modulatory interaction between selenoprotein W and 14-3-3 protein.

    PubMed

    Jeon, Yeong Ha; Ko, Kwan Young; Lee, Jea Hwang; Park, Ki Jun; Jang, Jun Ki; Kim, Ick Young

    2016-01-01

    Selenoprotein W (SelW) contains a selenocysteine (Sec, U) in a conserved CXXU motif corresponding to the CXXC redox motif of thioredoxin, suggesting a putative redox function of SelW. We have previously reported that the binding of 14-3-3 protein to its target proteins, including CDC25B, Rictor and TAZ, is inhibited by the interaction of 14-3-3 protein with SelW. However, the binding mechanism is unclear. In this study, we sought to determine the binding site of SelW to understand the regulatory mechanism of the interaction between SelW and 14-3-3 and its biological effects. Phosphorylated Ser(pS) or Thr(pT) residues in RSXpSXP or RXXXp(S/T)XP motifs are well-known common 14-3-3-binding sites, but Thr41, Ser59, and T69 of SelW, which are computationally predicted to serve are phosphorylation sites, were neither phosphorylation sites nor sites involved in the interaction. A mutant SelW in which Sec13 is changed to Ser (U13S) was unable to interact with 14-3-3 protein and thus did not inhibit the interaction of 14-3-3 to other target proteins. However, other Cys mutants of SelW(C10S, C33S and C37S) normally interacted with 14-3-3 protein. The interaction of SelW to 14-3-3 protein was enhanced by diamide or H2O2 and decreased by dithiothreitol (DTT). Taken together, these findings demonstrate that the Sec of SelW is involved in its interaction with 14-3-3 protein and that this interaction is increased under oxidative stress conditions. Thus, SelW may have a regulatory function in redox cell signaling by interacting with 14-3-3 protein. PMID:26474786

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

    PubMed Central

    2014-01-01

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

  20. Tumor-extracellular matrix interactions: Identification of tools associated with breast cancer progression.

    PubMed

    Giussani, Marta; Merlino, Giuseppe; Cappelletti, Vera; Tagliabue, Elda; Daidone, Maria Grazia

    2015-12-01

    Several evidences support the concept that cancer development and progression are not entirely cancer cell-autonomous processes, but may be influenced, and possibly driven, by cross-talk between cancer cells and the surrounding microenvironment in which, besides immune cells, stromal cells and extracellular matrix (ECM) play a major role in regulating distinct biologic processes. Stroma and ECM-related signatures proved to influence breast cancer progression, and to contribute to the identification of tumor phenotypes resistant to cytotoxic and hormonal treatments. The possible clinical implications of the interplay between tumor cells and the microenvironment, with special reference to ECM remodelling, will be discussed in this review. PMID:26416466

  1. Identification of key factors affecting the water pollutant concentration in the sluice-controlled river reaches of the Shaying River in China via statistical analysis methods.

    PubMed

    Dou, Ming; Zhang, Yan; Zuo, Qiting; Mi, Qingbin

    2015-08-01

    The construction of sluices creates a strong disturbance in water environmental factors within a river. The change in water pollutant concentrations of sluice-controlled river reaches (SCRRs) is more complex than that of natural river segments. To determine the key factors affecting water pollutant concentration changes in SCRRs, river reaches near the Huaidian Sluice in the Shaying River of China were selected as a case study, and water quality monitoring experiments based on different regulating modes were implemented in 2009 and 2010. To identify the key factors affecting the change rates for the chemical oxygen demand of permanganate (CODMn) and ammonia nitrogen (NH3-N) concentrations in the SCRRs of the Huaidian Sluice, partial correlation analysis, principal component analysis and principal factor analysis were used. The results indicate four factors, i.e., the inflow quantity from upper reaches, opening size of sluice gates, water pollutant concentration from upper reaches, and turbidity before the sluice, which are the common key factors for the CODMn and NH3-N concentration change rates. Moreover, the dissolved oxygen before a sluice is a key factor for the permanganate concentration from CODMn change rate, and the water depth before a sluice is a key factor for the NH3-N concentration change rate. Multiple linear regressions between the water pollutant concentration change rate and key factors were established via multiple linear regression analyses, and the quantitative relationship between the CODMn and NH3-N concentration change rates and key affecting factors was analyzed. Finally, the mechanism of action for the key factors affecting the water pollutant concentration changes was analyzed. The results reveal that the inflow quantity from upper reaches, opening size of sluice gates, permanganate concentration from CODMn from upper reaches and dissolved oxygen before the sluice have a negative influence and the turbidity before the sluice has a positive influence on the permanganate concentration from CODMn change rates and that the opening size of sluice gates, NH3-N concentration from upper reaches, and water depth before the sluice have a negative influence and the inflow quantity from upper reaches and turbidity before the sluice have a positive influence on the NH3-N concentration change rates, which provides a scientific grounding for pollution control and sluice operations in SCRRs. PMID:26194187

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

    PubMed Central

    Emmott, Edward; Goodfellow, Ian

    2014-01-01

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

  3. Identification of the Interaction Sites of Inhibitor-3 for Protein Phosphatase-1

    PubMed Central

    Zhang, Lifang; Qi, Zhiqing; Gao, Yan; Lee, Ernest Y.C.

    2008-01-01

    Inhibitor-3 is a potent inhibitor of protein phosphatase-1, with an IC50 in the nanomolar range for the inhibition of the dephosphorylation of phosphorylase a. Human Inhibitor-3 possesses a putative protein phosphatase-1 binding motif, 39KKVEW43. We provide direct evidence that this sequence is involved in PP1 interaction by examining the effects of site-directed mutations of Inhibitor-3 on its ability to inhibit protein phosphatase-1. A second interaction site whose deletion led to loss of inhibitory potency was identified between residues 65–77. The existence of two interaction sites is consistent with the high inhibitory potency of Inhibitor-3, and with current models for other inhibitor and targeting proteins that interact with protein phosphatase-1 with high affinity. PMID:18951879

  4. Identification and measurement of intermolecular interaction in polyester/polystyrene blends by FTIR-photoacoustic spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fourier transform infrared photoacoustic spectrometry was used to reveal and identify n-p type intermolecular interaction formed in plastic comprising binary blends of polystyrene and a biodegradable polymer, either polylactic acid, polycaprolactone or poly(tetramethyleneadipate-co-terephthalate)....

  5. Detection and Identification of Mars Analogue Volcano — Ice Interaction Environments

    NASA Astrophysics Data System (ADS)

    Cousins, C. R.; Crawford, I.; Gunn, M.; Harris, J. K.; Steele, A.

    2012-03-01

    Volcano-ice interaction produces many environments available to microbial colonisation. Similar processes are likely to have occurred on Mars, and are prime exobiology targets. Multi-instrument analyses of volcano-ice deposits are presented.

  6. ChIP-based methods for the identification of long-range chromatin interactions.

    PubMed

    Fullwood, Melissa J; Ruan, Yijun

    2009-05-01

    Chromatin immunoprecipitation (ChIP) is an important technique for studying protein-DNA interactions. Whole genome ChIP methods have enjoyed much success, but are limited in that they cannot uncover important long-range chromatin interactions. Chromosome conformation capture (3C) and related methods are capable of detecting remote chromatin interactions, but are tedious, have low signal-to-noise ratios, and are not genome-wide. Although the addition of ChIP to 3C (ChIP-3C) would conceivably reduce noise and increase specificity for chromatin interaction detection, there are concerns that simple mixing of the ChIP and 3C protocols would lead to high levels of false positives. In this essay, we dissect current ChIP- and 3C-based methodologies, discuss the models of specific as opposed to non-specific chromatin interactions, and suggest approaches to separate specific chromatin complexes from non-specific chromatin fragments. We conclude that the combination of sonication-based chromatin fragmentation, ChIP-based enrichment, chromatin proximity ligation and Paired-End Tag ultra-high-throughput sequencing will be a winning implementation for genome-wide, unbiased and de novo discovery of long-range chromatin interactions, which will help to establish an emerging field for studying human chromatin interactomes and genome regulation networks in three-dimensional spaces. PMID:19247990

  7. Identification of neuroglobin-interacting proteins using yeast two-hybrid screening.

    PubMed

    Yu, Z; Liu, N; Wang, Y; Li, X; Wang, X

    2012-01-01

    Neuroglobin (Ngb) is a globin protein that is highly and specifically expressed in brain neurons. A large volume of evidence has proven that Ngb is a neuroprotective molecule against hypoxic/ischemic brain injury and other related neurological disorder; however, the underlying mechanisms remain poorly understood. Aiming to provide more clues in understanding the molecular mechanisms of Ngb's neuroprotection, we performed yeast two-hybrid screening to search for proteins that interact with Ngb. From a mouse brain cDNA library, we found totally 36 proteins that potentially interact with Ngb, and 10 of them were each identified in multiple positive clones. The shared sequences within these multiple clones are more likely to be Ngb-interacting domains. In primary cultured mouse cortical neurons, immuno-precipitation was performed to confirm the interactions of selected proteins with Ngb. The discovered Ngb-interacting proteins in this study include those involved in energy metabolism, mitochondria function, and signaling pathways for cell survival and proliferation. Our findings provide molecular targets for investigating protein interaction-based biological functions and neuroprotective mechanisms of Ngb. PMID:22079573

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

    PubMed Central

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

    2011-01-01

    Neuroglobin (Ngb) is a globin protein that is highly and specifically expressed in brain neurons. A large volume of evidence has proven that Ngb is a neuroprotective molecule against hypoxic/ischemic brain injury and other related neurological disorder; however, the underlying mechanisms remain poorly understood. Aiming to provide more clues in understanding the molecular mechanisms of Ngb’s neuroprotection, we performed yeast two-hybrid screening to search for proteins that interact with Ngb. From a mouse brain cDNA library, we found totally 36 proteins that potentially interact with Ngb, and 10 of them were each identified in multiple positive clones. The shared sequences within these multiple clones are more likely to be Ngb-interacting domains. In primary cultured mouse cortical neurons, immuno-precipitation was performed to confirm the interactions of selected proteins with Ngb. The discovered Ngb-interacting proteins in this study include those involved in energy metabolism, mitochondria function and signaling pathways for cell survival and proliferation. Our findings provide molecular targets for investigating protein interaction-based biological functions and neuroprotective mechanisms of Ngb. PMID:22079573

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

    Schoeps, Anja; Rudolph, Anja; Seibold, Petra; Dunning, Alison M.; Milne, Roger L.; Bojesen, Stig E.; Swerdlow, Anthony; Andrulis, Irene; Brenner, Hermann; Behrens, Sabine; Orr, Nicholas; Jones, Michael; Ashworth, Alan; Li, Jingmei; Cramp, Helen; Connley, Dan; Czene, Kamila; Darabi, Hatef; Chanock, Stephen J.; Lissowska, Jolanta; Figueroa, Jonine D.; Knight, Julia; Glendon, Gord; Mulligan, Anna M.; Dumont, Martine; Severi, Gianluca; Baglietto, Laura; Olson, Janet; Vachon, Celine; Purrington, Kristen; Moisse, Matthieu; Neven, Patrick; Wildiers, Hans; Spurdle, Amanda; Kosma, Veli-Matti; Kataja, Vesa; Hartikainen, Jaana M.; Hamann, Ute; Ko, Yon-Dschun; Dieffenbach, Aida K.; Arndt, Volker; Stegmaier, Christa; Malats, Núria; Arias Perez, JoséI.; Benítez, Javier; Flyger, Henrik; Nordestgaard, Børge G.; Truong, Théresè; Cordina-Duverger, Emilie; Menegaux, Florence; Silva, Isabel dos Santos; Fletcher, Olivia; Johnson, Nichola; Häberle, Lothar; Beckmann, Matthias W.; Ekici, Arif B.; Braaf, Linde; Atsma, Femke; van den Broek, Alexandra J.; Makalic, Enes; Schmidt, Daniel F.; Southey, Melissa C.; Cox, Angela; Simard, Jacques; Giles, Graham G.; Lambrechts, Diether; Mannermaa, Arto; Brauch, Hiltrud; Guénel, Pascal; Peto, Julian; Fasching, Peter A.; Hopper, John; Flesch-Janys, Dieter; Couch, Fergus; Chenevix-Trench, Georgia; Pharoah, Paul D. P.; Garcia-Closas, Montserrat; Schmidt, Marjanka K.; Hall, Per; Easton, Douglas F.; Chang-Claude, Jenny

    2014-01-01

    Genes that alter disease risk only in combination with certain environmental exposures may not be detected in genetic association analysis. By using methods accounting for gene-environment (G × E) interaction, we aimed to identify novel genetic loci associated with breast cancer risk. Up to 34,475 cases and 34,786 controls of European ancestry from up to 23 studies in the Breast Cancer Association Consortium were included. Overall, 71,527 single nucleotide polymorphisms (SNPs), enriched for association with breast cancer, were tested for interaction with 10 environmental risk factors using three recently proposed hybrid methods and a joint test of association and interaction. Analyses were adjusted for age, study, population stratification, and confounding factors as applicable. Three SNPs in two independent loci showed statistically significant association: SNPs rs10483028 and rs2242714 in perfect linkage disequilibrium on chromosome 21 and rs12197388 in ARID1B on chromosome 6. While rs12197388 was identified using the joint test with parity and with age at menarche (P-values = 3 × 10−07), the variants on chromosome 21 q22.12, which showed interaction with adult body mass index (BMI) in 8,891 postmenopausal women, were identified by all methods applied. SNP rs10483028 was associated with breast cancer in women with a BMI below 25 kg/m2 (OR = 1.26, 95% CI 1.15–1.38) but not in women with a BMI of 30 kg/m2 or higher (OR = 0.89, 95% CI 0.72–1.11, P for interaction = 3.2 × 10−05). Our findings confirm comparable power of the recent methods for detecting G × E interaction and the utility of using G × E interaction analyses to identify new susceptibility loci. PMID:24248812

  11. CH3-π interaction of explosives with cavity of a TPE macrocycle: the key cause for highly selective detection of TNT.

    PubMed

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

    2014-11-26

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

  12. Identification and Mechanistic Investigation of Drug-Drug Interactions Associated With Myopathy: A Translational Approach.

    PubMed

    Han, X; Quinney, S K; Wang, Z; Zhang, P; Duke, J; Desta, Z; Elmendorf, J S; Flockhart, D A; Li, L

    2015-09-01

    Myopathy is a group of muscle diseases that can be induced or exacerbated by drug-drug interactions (DDIs). We sought to identify clinically important myopathic DDIs and elucidate their underlying mechanisms. Five DDIs were found to increase the risk of myopathy based on analysis of observational data from the Indiana Network of Patient Care. Loratadine interacted with simvastatin (relative risk 95% confidence interval [CI] = [1.39, 2.06]), alprazolam (1.50, 2.31), ropinirole (2.06, 5.00), and omeprazole (1.15, 1.38). Promethazine interacted with tegaserod (1.94, 4.64). In vitro investigation showed that these DDIs were unlikely to result from inhibition of drug metabolism by CYP450 enzymes or from inhibition of hepatic uptake via the membrane transporter OATP1B1/1B3. However, we did observe in vitro synergistic myotoxicity of simvastatin and desloratadine, suggesting a role in loratadine-simvastatin interaction. This interaction was epidemiologically confirmed (odds ratio 95% CI = [2.02, 3.65]) using the data from the US Food and Drug Administration Adverse Event Reporting System. PMID:25975815

  13. Identification and Characterization of the Interaction Site between cFLIPL and Calmodulin

    PubMed Central

    Guo, Bingqian; Pellegrini, Maria; Mierke, Dale F.

    2015-01-01

    Overexpression of the cellular FLICE-like inhibitory protein (cFLIP) has been reported in a number of tumor types. As an inactive procaspase-8 homologue, cFLIP is recruited to the intracellular assembly known as the Death Inducing Signaling Complex (DISC) where it inhibits apoptosis, leading to cancer cell proliferation. Here we characterize the molecular details of the interaction between cFLIPL and calmodulin, a ubiquitous calcium sensing protein. By expressing the individual domains of cFLIPL, we demonstrate that the interaction with calmodulin is mediated by the N-terminal death effector domain (DED1) of cFLIPL. Additionally, we mapped the interaction to a specific region of the C-terminus of DED1, referred to as DED1 R4. By designing DED1/DED2 chimeric constructs in which the homologous R4 regions of the two domains were swapped, calmodulin binding properties were transferred to DED2 and removed from DED1. Furthermore, we show that the isolated DED1 R4 peptide binds to calmodulin and solve the structure of the peptide-protein complex using NMR and computational refinement. Finally, we demonstrate an interaction between cFLIPL and calmodulin in cancer cell lysates. In summary, our data implicate calmodulin as a potential player in DISC-mediated apoptosis and provide evidence for a specific interaction with the DED1 of cFLIPL. PMID:26529318

  14. Unambiguous Identification of miRNA:target site Interactions by Different Types of Ligation Reactions

    PubMed Central

    Manzano, Mark; Klironomos, Filippos; Schilling, Marcel; Herzog, Margareta; Gottwein, Eva; Rajewsky, Nikolaus

    2014-01-01

    SUMMARY To exert regulatory function, miRNAs guide Argonaute (AGO) proteins to partially complementary sites on target RNAs. Crosslinking and immunoprecipitation (“CLIP”) assays are state-of-the-art to map AGO binding sites, but assigning the targeting miRNA to these sites relies on bioinformatics predictions and is therefore indirect. To directly and unambiguously identify miRNA:target site interactions, we modified our CLIP methodology in C. elegans to experimentally ligate miRNAs to their target sites. Unexpectedly, ligation reactions also occurred in absence of the exogenous ligase. Our in vivo dataset and re-analysis of published mammalian AGO-CLIP data for miRNA-chimeras yielded ~17,000 miRNA:target site interactions. Analysis of interactions and extensive experimental validation of chimera-discovered targets of viral miRNAs suggest that our strategy identifies canonical, noncanonical, and nonconserved miRNA interactions. Our data suggest that ~80% of miRNA interactions have perfect or partial seed complementarity. In summary, analysis of miRNA:target chimeras enables the systematic, context-specific, in vivo discovery of miRNA binding. PMID:24857550

  15. Identification and Mechanistic Investigation of Drug-Drug Interactions Associated with Myopathy – A Translational Approach

    PubMed Central

    Han, Xu; Quinney, Sara K.; Wang, Zhiping; Zhang, Pengyue; Duke, Jon; Desta, Zeruesenay; Elmendorf, Jeffrey S.; Flockhart, David A.; Li, L

    2015-01-01

    Myopathy is a group of muscle diseases that can be induced or exacerbated by drug-drug interactions (DDIs). We sought to identify clinically important myopathic DDIs and elucidate their underlying mechanisms. Five DDIs were found to increase the risk of myopathy based on analysis of observational data from the Indiana Network of Patient Care. Loratadine interacted with simvastatin (relative risk 95% CI = [1.39, 2.06]), alprazolam (1.50, 2.31), ropinirole (2.06, 5.00) and omeprazole (1.15, 1.38). Promethazine interacted with tegaserod (1.94, 4.64). In vitro investigation showed that these DDIs were unlikely to result from inhibition of drug metabolism by CYP450 enzymes or from inhibition of hepatic uptake via the membrane transporter OATP1B1/1B3. However, we did observe in vitro synergistic myotoxicity of simvastatin and desloratadine, suggesting a role in loratadine-simvastatin interaction. This interaction was epidemiologically confirmed (odds ratio 95% CI = [2.02, 3.65]) using the data from the FDA Adverse Event Reporting System. PMID:25975815

  16. Fatty Acid-binding Proteins Interact with Comparative Gene Identification-58 Linking Lipolysis with Lipid Ligand Shuttling.

    PubMed

    Hofer, Peter; Boeszoermenyi, Andras; Jaeger, Doris; Feiler, Ursula; Arthanari, Haribabu; Mayer, Nicole; Zehender, Fabian; Rechberger, Gerald; Oberer, Monika; Zimmermann, Robert; Lass, Achim; Haemmerle, Guenter; Breinbauer, Rolf; Zechner, Rudolf; Preiss-Landl, Karina

    2015-07-24

    The coordinated breakdown of intracellular triglyceride (TG) stores requires the exquisitely regulated interaction of lipolytic enzymes with regulatory, accessory, and scaffolding proteins. Together they form a dynamic multiprotein network designated as the "lipolysome." Adipose triglyceride lipase (Atgl) catalyzes the initiating step of TG hydrolysis and requires comparative gene identification-58 (Cgi-58) as a potent activator of enzyme activity. Here, we identify adipocyte-type fatty acid-binding protein (A-Fabp) and other members of the fatty acid-binding protein (Fabp) family as interaction partners of Cgi-58. Co-immunoprecipitation, microscale thermophoresis, and solid phase assays proved direct protein/protein interaction between A-Fabp and Cgi-58. Using nuclear magnetic resonance titration experiments and site-directed mutagenesis, we located a potential contact region on A-Fabp. In functional terms, A-Fabp stimulates Atgl-catalyzed TG hydrolysis in a Cgi-58-dependent manner. Additionally, transcriptional transactivation assays with a luciferase reporter system revealed that Fabps enhance the ability of Atgl/Cgi-58-mediated lipolysis to induce the activity of peroxisome proliferator-activated receptors. Our studies identify Fabps as crucial structural and functional components of the lipolysome. PMID:25953897

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

    SciTech Connect

    Varela, C.L. Komar; Arico, S.F.; Mirandou, M.; Balart, S.N.; Gribaudo, L.M.

    2008-07-15

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

  18. Fatty Acid-binding Proteins Interact with Comparative Gene Identification-58 Linking Lipolysis with Lipid Ligand Shuttling*

    PubMed Central

    Hofer, Peter; Boeszoermenyi, Andras; Jaeger, Doris; Feiler, Ursula; Arthanari, Haribabu; Mayer, Nicole; Zehender, Fabian; Rechberger, Gerald; Oberer, Monika; Zimmermann, Robert; Lass, Achim; Haemmerle, Guenter; Breinbauer, Rolf; Zechner, Rudolf; Preiss-Landl, Karina

    2015-01-01

    The coordinated breakdown of intracellular triglyceride (TG) stores requires the exquisitely regulated interaction of lipolytic enzymes with regulatory, accessory, and scaffolding proteins. Together they form a dynamic multiprotein network designated as the “lipolysome.” Adipose triglyceride lipase (Atgl) catalyzes the initiating step of TG hydrolysis and requires comparative gene identification-58 (Cgi-58) as a potent activator of enzyme activity. Here, we identify adipocyte-type fatty acid-binding protein (A-Fabp) and other members of the fatty acid-binding protein (Fabp) family as interaction partners of Cgi-58. Co-immunoprecipitation, microscale thermophoresis, and solid phase assays proved direct protein/protein interaction between A-Fabp and Cgi-58. Using nuclear magnetic resonance titration experiments and site-directed mutagenesis, we located a potential contact region on A-Fabp. In functional terms, A-Fabp stimulates Atgl-catalyzed TG hydrolysis in a Cgi-58-dependent manner. Additionally, transcriptional transactivation assays with a luciferase reporter system revealed that Fabps enhance the ability of Atgl/Cgi-58-mediated lipolysis to induce the activity of peroxisome proliferator-activated receptors. Our studies identify Fabps as crucial structural and functional components of the lipolysome. PMID:25953897

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

    PubMed Central

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

    2014-01-01

    This work focuses on the identification of heterogeneous linear elastic moduli in the context of frequency-domain, coupled acoustic-structure interaction (ASI), using either solid displacement or fluid pressure measurement data. The approach postulates the inverse problem as an optimization problem where the solution is obtained by minimizing a modified error in constitutive equation (MECE) functional. The latter measures the discrepancy in the constitutive equations that connect kinematically admissible strains and dynamically admissible stresses, while incorporating the measurement data as additional quadratic error terms. We demonstrate two strategies for selecting the MECE weighting coefficient to produce regularized solutions to the ill-posed identification problem: 1) the discrepancy principle of Morozov, and 2) an error-balance approach that selects the weight parameter as the minimizer of another functional involving the ECE and the data misfit. Numerical results demonstrate that the proposed methodology can successfully recover elastic parameters in 2D and 3D ASI systems from response measurements taken in either the solid or fluid subdomains. Furthermore, both regularization strategies are shown to produce accurate reconstructions when the measurement data is polluted with noise. The discrepancy principle is shown to produce nearly optimal solutions, while the error-balance approach, although not optimal, remains effective and does not need a priori information on the noise level. PMID:25339790

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    We describe the use of the 13C-labeled artificial amino acid p-benzoyl-L-phenylalanine (Bpa) to improve the reliability of cross-linked product identification. Our strategy is exemplified for two protein-peptide complexes. These studies indicate that in many cases the identification of a cross-link without additional stable isotope labeling would result in an ambiguous assignment of cross-linked products. The use of a 13C-labeled photoreactive amino acid is considered to be preferred over the use of deuterated cross-linkers as retention time shifts in reversed phase chromatography can be ruled out. The observation of characteristic fragment ions additionally increases the reliability of cross-linked product assignment. Bpa possesses a broad reactivity towards different amino acids and the derived distance information allows mapping of spatially close amino acids and thus provides more solid structural information of proteins and protein complexes compared to the longer deuterated amine-reactive cross-linkers, which are commonly used for protein 3D-structure analysis and protein-protein interaction studies.

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    This work focuses on the identification of heterogeneous linear elastic moduli in the context of frequency-domain, coupled acoustic-structure interaction (ASI), using either solid displacement or fluid pressure measurement data. The approach postulates the inverse problem as an optimization problem where the solution is obtained by minimizing a modified error in constitutive equation (MECE) functional. The latter measures the discrepancy in the constitutive equations that connect kinematically admissible strains and dynamically admissible stresses, while incorporating the measurement data as additional quadratic error terms. We demonstrate two strategies for selecting the MECE weighting coefficient to produce regularized solutions to the ill-posed identification problem: 1) the discrepancy principle of Morozov, and 2) an error-balance approach that selects the weight parameter as the minimizer of another functional involving the ECE and the data misfit. Numerical results demonstrate that the proposed methodology can successfully recover elastic parameters in 2D and 3D ASI systems from response measurements taken in either the solid or fluid subdomains. Furthermore, both regularization strategies are shown to produce accurate reconstructions when the measurement data is polluted with noise. The discrepancy principle is shown to produce nearly optimal solutions, while the error-balance approach, although not optimal, remains effective and does not need a priori information on the noise level.

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

    SciTech Connect

    Richard L. Blanton

    2004-02-19

    OAK-B135 The major accomplishments of this project were: (1) the initial characterization of dcsA, the gene for the putative catalytic subunit of cellulose synthase in the cellular slime mold Dictyostelium discoideum; (2) the detection of a developmentally regulated event (unidentified, but perhaps a protein modification or association with a protein partner) that is required for cellulose synthase activity (i.e., the dcsA product is necessary, but not sufficient for cellulose synthesis); (3) the continued exploration of the developmental context of cellulose synthesis and DcsA; (4) the isolation of a GFP-DcsA-expressing strain (work in progress); and (5) the identification of Dictyostelium homologues for plant genes whose products play roles in cellulose biosynthesis. Although our progress was slow and many of our results negative, we did develop a number of promising avenues of investigation that can serve as the foundation for future projects.

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

    SciTech Connect

    Lupo, Julien; CHU de Grenoble, BP217, 38043 Grenoble Cedex 9 ; Conti, Audrey; Sueur, Charlotte; CHU de Grenoble, BP217, 38043 Grenoble Cedex 9 ; Coly, Pierre-Alain; Coute, Yohann; INSERM, U1038, F-38054 Grenoble; Universite Joseph Fourier, Grenoble 1, F-38000 Grenoble Cedex 09 ; Hunziker, Walter; Burmeister, Wim P.; Germi, Raphaelle; CHU de Grenoble, BP217, 38043 Grenoble Cedex 9 ; Manet, Evelyne; Gruffat, Henri; Ecole Normale Superieure de Lyon, F-69007 France; Universite Lyon1, F-69007, Lyon ; and others

    2012-03-10

    We have previously characterized ubinuclein (Ubn-1) as a NACos (Nuclear and Adherent junction Complex components) protein which interacts with viral or cellular transcription factors and the tight junction (TJ) protein ZO-1. The purpose of the present study was to get more insights on the binding partners of Ubn-1, notably those present in the epithelial junctions. Using an in vivo assay of fluorescent protein-complementation assay (PCA), we demonstrated that the N-terminal domains of the Ubn-1 and ZO-1 proteins triggered a functional interaction inside the cell. Indeed, expression of both complementary fragments of venus fused to the N-terminal parts of Ubn-1 and ZO-1 was able to reconstitute a fluorescent venus protein. Furthermore, nuclear expression of the chimeric Ubn-1 triggered nuclear localization of the chimeric ZO-1. We could localize this interaction to the PDZ2 domain of ZO-1 using an in vitro pull-down assay. More precisely, a 184-amino acid region (from amino acids 39 to 223) at the N-terminal region of Ubn-1 was responsible for the interaction with the PDZ2 domain of ZO-1. Co-imunoprecipitation and confocal microscopy experiments also revealed the tight junction protein cingulin as a new interacting partner of Ubn-1. A proteomic approach based on mass spectrometry analysis (MS) was then undertaken to identify further binding partners of GST-Ubn-1 fusion protein in different subcellular fractions of human epithelial HT29 cells. LYRIC (Lysine-rich CEACAM1-associated protein) and RACK-1 (receptor for activated C-kinase) proteins were validated as bona fide interacting partners of Ubn-1. Altogether, these results suggest that Ubn-1 is a scaffold protein influencing protein subcellular localization and is involved in several processes such as cell-cell contact signalling or modulation of gene activity.

  4. Identification of new candidate drugs for lung cancer using chemical-chemical interactions, chemical-protein interactions and a K-means clustering algorithm.

    PubMed

    Lu, Jing; Chen, Lei; Yin, Jun; Huang, Tao; Bi, Yi; Kong, Xiangyin; Zheng, Mingyue; Cai, Yu-Dong

    2016-04-01

    Lung cancer, characterized by uncontrolled cell growth in the lung tissue, is the leading cause of global cancer deaths. Until now, effective treatment of this disease is limited. Many synthetic compounds have emerged with the advancement of combinatorial chemistry. Identification of effective lung cancer candidate drug compounds among them is a great challenge. Thus, it is necessary to build effective computational methods that can assist us in selecting for potential lung cancer drug compounds. In this study, a computational method was proposed to tackle this problem. The chemical-chemical interactions and chemical-protein interactions were utilized to select candidate drug compounds that have close associations with approved lung cancer drugs and lung cancer-related genes. A permutation test and K-means clustering algorithm were employed to exclude candidate drugs with low possibilities to treat lung cancer. The final analysis suggests that the remaining drug compounds have potential anti-lung cancer activities and most of them have structural dissimilarity with approved drugs for lung cancer. PMID:26849843

  5. Identification of transcription factor-DNA interactions using chromatin immunoprecipitation assays.

    PubMed

    Nie, Liping; Vzquez, Ana E; Yamoah, Ebenezer N

    2009-01-01

    Expression of almost every gene is regulated at the transcription level. Therefore, transcriptional factor Transcription factors, consequently, have marked effects on the fate of a cell by establishing the gene expression patterns that determine biological processes. In the auditory and vestibular systems, transcription factors have been found to be responsible for development, cell growth, and apoptosis. It is vital to identify the transcription factor target genes and the mechanisms by which transcription factors control and guide gene expression and regulation pathways. Compared with earlier methods devised to study transcription factor-DNA interactions, the advantage of the chromatin immunoprecipitation (ChIP) assay is that the interaction of a transcription factor with its target genes is captured in the native context of chromatin in living cells. Therefore, ChIP base assays are powerful tools to identify the direct interaction of transcription factors and their target genes in vivo. More importantly, ChIP assays have been used in combination with molecular biology techniques, such as PCR and real time PCR, gene cloning, and DNA microarrays, to determine the interaction of transcription factor-DNA from a few potential individual targets to genome-wide surveys. PMID:18839356

  6. Identification and Characterization of a Novel Host-Toxin Interaction in the Wheat - Stagonospora Nodorum Pathosystem

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Stagonospora nodorum, casual agent of Stagonospora nodorum blotch (SNB) of wheat, produces a number of host-selective toxins (HSTs) known to be important in disease. To date, four HSTs and corresponding host sensitivity genes have been reported, and all four host-toxin interactions are significant f...

  7. Identification of Combat Unit Leader Skills and Leader-Group Interaction Processes.

    ERIC Educational Resources Information Center

    Henriksen, Kermit F.; And Others

    Research identified leader skills and leader-group interactive processes that have potential influence on unit performance in tactical situations. An historical review of the leader research literature was conducted, and leader models from leader research along with theory from industrial, managerial, and academic settings were reviewed. The…

  8. Identification of sequence motifs involved in Dengue virus-host interactions.

    PubMed

    Asnet Mary, J; Paramasivan, R; Shenbagarathai, R

    2016-03-01

    Dengue fever is a rapidly spreading mosquito-borne virus infection, which remains a serious global public health problem. As there is no specific treatment or commercial vaccine available for effective control of the disease, the attempts on developing novel control strategies are underway. Viruses utilize the surface receptor proteins of host to enter into the cells. Though various proteins were said to be receptors of Dengue virus (DENV) using Virus Overlay Protein Binding Assay, the precise interaction between DENV and host is not explored. Understanding the structural features of domain III envelope glycoprotein would help in developing efficient antiviral inhibitors. Therefore, an attempt was made to identify the sequence motifs present in domain III envelope glycoprotein of Dengue virus. Computational analysis revealed that the NGR motif is present in the domain III envelope glycoprotein of DENV-1 and DENV-3. Similarly, DENV-1, DENV-2 and DENV-4 were found to contain Yxxphi motif which is a tyrosine-based sorting signal responsible for the interaction with a mu subunit of adaptor protein complex. High-throughput virtual screening resulted in five compounds as lead molecules based on glide score, which ranges from -4.664 to -6.52 kcal/Mol. This computational prediction provides an additional tool for understanding the virus-host interactions and helps to identify potential targets in the host. Further, experimental evidence is warranted to confirm the virus-host interactions and also inhibitory activity of reported lead compounds. PMID:25905427

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

    PubMed

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

    2009-01-01

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

  10. Identification of Cellular Proteins That Interact with the Adeno-Associated Virus Rep Protein?

    PubMed Central

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

    2009-01-01

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

  11. Identification and characterization of two novel genes that may interact with neurofibromin

    SciTech Connect

    Murthy, A.E.; Bernards, A.; Gusella, I.F.

    1994-09-01

    Although it has been well documented that neurofibromin plays a role in RAS mediated signaling, its exact functions have not been established. However, clues to the roles of this protein may be obtained by identifying proteins with which it physically interacts. To identify gene products that can interact with a portion of the neurofibromin GAP related domain, we screened a HeLa cDNA library, using the {open_quotes}interaction trap{close_quotes} strategy. We have isolated 2 novel human genes encoding proteins that share a 34 amino acid repeating motif, the TPR motif. Here, we report their characterization. Sequence analysis has revealed that the B3-1 gene encodes 3 tandem TPR motifs, but is not related to any other known sequences outside this domain. B3-1 is present on chromosome 5 as a single copy gene and is ubiquitously expressed as a 1.6 kb transcript. The GRD gene encodes 7 TPR units and also shares a region of similarity with the {open_quotes}J region{close_quotes} of the DnaJ family. GRD maps to human chromosome 17 and is ubiquitously expressed as a 2.2 kb transcript. B3-1 and GRD are not related to one another outside of their TPR regions, suggesting that these motifs are responsible for the interaction with the neurofibromin bait in this assay. While it is uncertain whether a similar interaction occurs between the intact proteins in mammalian cells, a potential role for TPR proteins in the regulation of neurofibromin must now be explored.

  12. Identification of TgAtg8-TgAtg3 interaction in Toxoplasma gondii.

    PubMed

    Chen, Di; Lin, Jiaxin; Liu, Yangyang; Li, Xiangzhi; Chen, Gaozhi; Hua, Qianqian; Nie, Qinqin; Hu, Xin; Tan, Feng

    2016-01-01

    Autophagy is a catabolic process in eukaryotic cells involved in the targeted degradation of cellular organelles and the cytoplasm. Recent works in Toxoplasma gondii suggest that the autophagy processes may serve as an important pathway in modulating parasite survival or death. As an important modulator of Atg8 lipidation and autophagy, Atg8-Atg3 interaction has been attracting increasing attention. However, there is no direct evidence that TgAtg8-TgAtg3 interaction occurs in the parasite. In this study, we firstly found TgAtg8 partially colocalized with TgAtg3 in GFP-TgAtg8 transgenic strains using IFA. Then, lysates from GFP-TgAtg8 tachyzoites were directly subject to large-scale tandem affinity purification with anti-GFP antibody. Western blot and tandem mass spectrometry (MS/MS) analysis determined the interaction between TgAtg8 and TgAtg3. Additionally, we performed real-time interaction analysis with a surface plasmon resonance biosensor using BIAcore system. As expected, the result demonstrated a concentration-dependent increases in resonance signals and indicated the TgAtg8 could bind directly TgAtg3 in vitro. Noteworthily, A KD of 34.9nM obtained from TgAtg8-TgAtg3 interaction indicate a high-affinity between Atg8-Atg3 in Toxoplasma. Furthermore, homology modeling and sequence alignment showed that TgAtg8 has greatest sequence and structural conservation. Within TgAtg3, this protein possesses the core E2 enzymatic activity structure and a truncated handle region which may contain AIM sequence. Taken together, our findings would help elucidate the formation mechanism of autophagosome in Toxoplasma and provide a possibility for looking into parasitic drug targets. PMID:26407821

  13. Identification of Interaction Hot Spots in Structures of Drug Targets on the Basis of Three-Dimensional Activity Cliff Information.

    PubMed

    Furtmann, Norbert; Hu, Ye; Gtschow, Michael; Bajorath, Jrgen

    2015-12-01

    Activity cliffs are defined as pairs or groups of structurally similar or analogous compounds that share the same specific activity but have large differences in potency. Although activity cliffs are mostly studied in medicinal chemistry at the level of molecular graphs, they can also be assessed by comparing compound binding modes. If such three-dimensional activity cliffs (3D-cliffs) are studied on the basis of X-ray complex structures, experimental ligand-target interaction details can be taken into account. Rapid growth in the number of 3D-cliffs that can be derived from X-ray complex structures has made it possible to identify targets for which a substantial body of 3D-cliff information is available. Activity cliffs are typically studied to identify structure-activity relationship determinants and aid in compound optimization. However, 3D-cliff information can also be used to search for interaction hot spots and key residues, as reported herein. For six of seven drug targets for which more than 20 3D-cliffs were available, series of 3D-cliffs were identified that were consistently involved in interactions with different hot spots. These 3D-cliffs often encoded chemical modifications resulting in interactions that were characteristic of highly potent compounds but absent in weakly potent ones, thus providing information for structure-based design. PMID:26094578

  14. [Identification of C(2)M interacting proteins by yeast two-hybrid screening].

    PubMed

    Shanshan, Yue; Laixin, Xia

    2015-11-01

    The synaptonemal complex (SC) is a huge structure which assembles between the homologous chromosomes during meiotic prophase I. Drosophila germ cell-specific nucleoprotein C(2)M clustering at chromosomes can induce SC formation. To further study the molecular function and mechanism of C(2)M in meiosis, we constructed a bait vector for C(2)M and used the yeast two-hybrid system to identify C(2)M interacting proteins. Forty interacting proteins were obtained, including many DNA and histone binding proteins, ATP synthases and transcription factors. Gene silencing assays in Drosophila showed that two genes, wech and Psf1, may delay the disappearance of SC. These results indicate that Wech and Psf1 may form a complex with C(2)M to participate in the formation or stabilization of the SC complex. PMID:26582530

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

    PubMed Central

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

    2012-01-01

    The von Willebrand factor (VWF) A1-glycoprotein (GP) Ibα interaction is of major importance during thrombosis mainly at sites of high shear stress. Inhibitors of this interaction prevent platelet-dependent thrombus formation in vivo, without major bleeding complications. However, the size and/or protein nature of the inhibitors currently in development limit oral bioavailability and clinical development. We therefore aimed to search for a small molecule protein-protein interaction inhibitor interfering with the VWF-GPIbα binding. After determination of putative small molecule binding pockets on the surface of VWF-A1 and GPIbα using site-finding algorithms and molecular dynamics, high throughput molecular docking was performed on both binding partners. A selection of compounds showing good in silico docking scores into the predicted pockets was retained for testing their in vitro effect on VWF-GPIbα complex formation, by which we identified a compound that surprisingly stimulated the VWF-GPIbα binding in a ristocetin cofactor ELISA and increased platelet adhesion in whole blood to collagen under arterial shear rate but in contrast inhibited ristocetin-induced platelet aggregation. The selected compound adhering to the predicted binding partner GPIbα could be confirmed by saturation transfer difference NMR spectroscopy. We thus clearly identified a small molecule that modulates VWF-GPIbα binding and that will now serve as a starting point for further studies and chemical modifications to fully characterize the interaction and to manipulate specific activity of the compound. PMID:22232560

  16. Optical key system

    DOEpatents

    Hagans, Karla G.; Clough, Robert E.

    2000-01-01

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

  17. Crystal Structure and Identification of Two Key Amino Acids Involved in AI-2 Production and Biofilm Formation in Streptococcus suis LuxS

    PubMed Central

    Wang, Yang; Yi, Li; Wang, Shaohui; Fan, Hongjie; Ding, Chan; Mao, Xiang; Lu, Chengping

    2015-01-01

    Streptococcus suis has emerged as an important zoonotic pathogen that causes meningitis, arthritis, septicemia and even sudden death in pigs and humans. Quorum sensing is the signaling network for cell-to-cell communication that bacterial cells can use to monitor their own population density through production and exchange of signal molecules. S-Ribosylhomocysteinase (LuxS) is the key enzyme involved in the activated methyl cycle. Autoinducer 2 (AI-2) is the adduct of borate and a ribose derivative and is produced from S-adenosylhomocysteine (SAH). AI-2 can mediate interspecies communication and in some species facilitate the bacterial behavior regulation such as biofilm formation and virulence in both Gram-positive and Gram-negative bacteria. Here, we reported the overexpression, purification and crystallographic structure of LuxS from S. suis. Our results showed the catalytically active LuxS exists as a homodimer in solution. Inductively coupled plasma-mass spectrometry (ICP-MS) revealed the presence of Zn2+ in LuxS. Although the core structure shares the similar topology with LuxS proteins from other bacterial species, structural analyses and comparative amino acid sequence alignments identified two key amino acid differences in S. suis LuxS, Phe80 and His87, which are located near the substrate binding site. The results of site-directed mutagenesis and enzymology studies confirmed that these two residues affect the catalytic activity of the enzyme. These in vitro results were corroborated in vivo by expression of the LuxS variants in a S. suis ΔluxS strain. The single and two amino acid of LuxS variant decreased AI-2 production and biofilm formation significantly compared to that of the parent strain. Our findings highlight the importance of key LuxS residues that influence the AI-2 production and biofilm formation in S.suis. PMID:26484864

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

    PubMed

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

    2014-06-01

    This article proposes an approach to identify fractional-order systems with sparse interaction structures and high dimensions when observation data are supposed to be experimentally available. This approach includes two steps: first, it is to estimate the value of the fractional order by taking into account the solution properties of fractional-order systems; second, it is to identify the interaction coefficients among the system variables by employing the compressed sensing technique. An error analysis is provided analytically for this approach and a further improved approach is also proposed. Moreover, the applicability of the proposed approach is fully illustrated by two examples: one is to estimate the mutual interactions in a complex dynamical network described by fractional-order systems, and the other is to identify a high fractional-order and homogeneous sequential differential equation, which is frequently used to describe viscoelastic phenomena. All the results demonstrate the feasibility of figuring out the system mechanisms behind the data experimentally observed in physical or biological systems with viscoelastic evolution characters. PMID:24985433

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

    PubMed Central

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

    2013-01-01

    Background In their 2005 study, Adamic and Glance coined the memorable phrase ‘divided they blog’, referring to a trend of cyberbalkanization in the political blogosphere, with liberal and conservative blogs tending to link to other blogs with a similar political slant, and not to one another. As political discussion and activity increasingly moves online, the power of framing political discourses is shifting from mass media to social media. Methodology/Principal Findings Continued examination of political interactions online is critical, and we extend this line of research by examining the activities of political users within the Wikipedia community. First, we examined how users in Wikipedia choose to display their political affiliation. Next, we analyzed the patterns of cross-party interaction and community participation among those users proclaiming a political affiliation. In contrast to previous analyses of other social media, we did not find strong trends indicating a preference to interact with members of the same political party within the Wikipedia community. Conclusions/Significance Our results indicate that users who proclaim their political affiliation within the community tend to proclaim their identity as a ‘Wikipedian’ even more loudly. It seems that the shared identity of ‘being Wikipedian’ may be strong enough to triumph over other potentially divisive facets of personal identity, such as political affiliation. PMID:23573269

  20. The identification of novel PMADS3 interacting proteins indicates a role in post-transcriptional control.

    PubMed

    Li, Xin; Ning, Guogui; Han, Xueping; Liu, Caixian; Bao, Manzhu

    2015-06-10

    PMADS3, a known MADS-box transcriptional factor and a C-class gene for floral development, plays dual roles in controlling the identity of inner floral organs and the termination of flower meristems in petunia. In this study, it was confirmed by bimolecular fluorescence complementation (BiFC) assays that the PMADS3 protein can interact individually with E-class proteins FBP2, FBP5, FBP9 and PMADS12. A yeast two-hybrid cDNA library was screened using the entire PMADS3 as bait, and this identified further potential interaction candidates. Two novel genes, PheIF3f and PhAGO10, were isolated, and suggested to regulate mRNA and translational processes according to the analysis of protein functional domains and subcellular localization predictions. Notably, the PhAGO10 protein belongs to the Argonaute family, members of which are major players in small-RNA-guided gene silencing processes via mRNA cleavage or translational inhibition. The results of yeast two-hybrid and BiFC assays indicated that PheIF3f and PhAGO10 could interact with PMADS3. Our findings indicate that the C-class gene PMADS3 potentially participates in post-transcriptional control, as well as transcriptional regulation. PMID:25827715

  1. Identification of protein-RNA interaction sites using the information of spatial adjacent residues

    PubMed Central

    2011-01-01

    Background Protein-RNA interactions play an important role in numbers of fundamental cellular processes such as RNA splicing, transport and translation, protein synthesis and certain RNA-mediated enzymatic processes. The more knowledge of Protein-RNA recognition can not only help to understand the regulatory mechanism, the site-directed mutagenesis and regulation of RNA–protein complexes in biological systems, but also have a vitally effecting for rational drug design. Results Based on the information of spatial adjacent residues, novel feature extraction methods were proposed to predict protein-RNA interaction sites with SVM-KNN classifier. The total accuracies of spatial adjacent residue profile feature and spatial adjacent residues weighted accessibility solvent area feature are 78%, 67.07% respectively in 5-fold cross-validation test, which are 1.4%, 3.79% higher than that of sequence neighbour residue profile feature and sequence neighbour residue accessibility solvent area feature. Conclusions The results indicate that the performance of feature extraction method using the spatial adjacent information is superior to the sequence neighbour information approach. The performance of SVM-KNN classifier is little better than that of SVM. The feature extraction method of spatial adjacent information with SVM-KNN is very effective for identifying protein-RNA interaction sites and may at least play a complimentary role to the existing methods. PMID:22165911

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

    SciTech Connect

    Ji, Xiaoxi; Wu, Yu; Sheng, Wenbo; Lin, Wei; Shanghai Key Laboratory of Data Science, LMNS, and Shanghai Center for Mathematical Sciences, Shanghai 200433

    2014-06-15

    This article proposes an approach to identify fractional-order systems with sparse interaction structures and high dimensions when observation data are supposed to be experimentally available. This approach includes two steps: first, it is to estimate the value of the fractional order by taking into account the solution properties of fractional-order systems; second, it is to identify the interaction coefficients among the system variables by employing the compressed sensing technique. An error analysis is provided analytically for this approach and a further improved approach is also proposed. Moreover, the applicability of the proposed approach is fully illustrated by two examples: one is to estimate the mutual interactions in a complex dynamical network described by fractional-order systems, and the other is to identify a high fractional-order and homogeneous sequential differential equation, which is frequently used to describe viscoelastic phenomena. All the results demonstrate the feasibility of figuring out the system mechanisms behind the data experimentally observed in physical or biological systems with viscoelastic evolution characters.

  3. Identification of novel interacting protein partners of SMN using tandem affinity purification.

    PubMed

    Shafey, Dina; Boyer, Justin G; Bhanot, Kunal; Kothary, Rashmi

    2010-04-01

    Mutations in the survival motor neuron (SMN) gene cause spinal muscular atrophy (SMA), a neuromuscular disease associated with muscle weakness that progresses to paralysis, respiratory distress, and ultimately death. Both neurons and muscle are severely affected in this disease. Tandem affinity purification (TAP) has emerged as a useful tool for studying protein complexes in vitro. We have used this purification system to discover novel SMN interacting partners in C2C12 muscle and PC12 neuronal cells. To do so, we fused a TAP-tag, consisting of a HIS hexamer and FLAG epitope separated by the tobacco etch virus (TEV) protease cleavage site, to either the N- or C-terminal region of SMN. Interestingly, the profile of SMN interacting proteins varies depending on the cell type and stage. We have identified a number of novel SMN interacting proteins in both C2C12 and PC12 cells, and from among these we have validated Annexin II and myosin regulatory light chain (MRLC). The discovery of these proteins will lead to a better understanding of the mechanisms underlying the pathophysiology of SMA. PMID:20201562

  4. Comparative genome analysis and identification of competitive and cooperative interactions in a polymicrobial disease

    PubMed Central

    Endo, Akiko; Watanabe, Takayasu; Ogata, Nachiko; Nozawa, Takashi; Aikawa, Chihiro; Arakawa, Shinichi; Maruyama, Fumito; Izumi, Yuichi; Nakagawa, Ichiro

    2015-01-01

    Polymicrobial diseases are caused by combinations of multiple bacteria, which can lead to not only mild but also life-threatening illnesses. Periodontitis represents a polymicrobial disease; Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia, called the red complex', have been recognized as the causative agents of periodontitis. Although molecular interactions among the three species could be responsible for progression of periodontitis, the relevant genetic mechanisms are unknown. In this study, we uncovered novel interactions in comparative genome analysis among the red complex species. Clustered regularly interspaced short palindromic repeats (CRISPRs) of T. forsythia might attack the restriction modification system of P. gingivalis, and possibly work as a defense system against DNA invasion from P. gingivalis. On the other hand, gene deficiencies were mutually compensated in metabolic pathways when the genes of all the three species were taken into account, suggesting that there are cooperative relationships among the three species. This notion was supported by the observation that each of the three species had its own virulence factors, which might facilitate persistence and manifestations of virulence of the three species. Here, we propose new mechanisms of bacterial symbiosis in periodontitis; these mechanisms consist of competitive and cooperative interactions. Our results might shed light on the pathogenesis of periodontitis and of other polymicrobial diseases. PMID:25171331

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

    PubMed

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

    2011-04-15

    The Class I MAGE proteins are normally expressed only in developing germ cells but are often aberrantly expressed in malignancies, particularly melanoma, making them good therapeutic targets. MAGE proteins promote tumor survival by binding to the RBCC region of KAP-1 and suppressing p53. Although, suppression of MAGE expression, by RNA interference, relieves p53 suppression and inhibits tumor growth, its therapeutic uses are limited by lack of methods for systemic delivery of small interfering RNA. To overcome this barrier, we sought to discover chemical compounds that inhibit binding between MAGE and KAP-1 proteins. Based on previously published effects of MAGE suppression, we developed a strategy for screening a small molecule library based on selective death of MAGE positive cells, activation of p53 and lack of caspase activity. We screened the Maybridge HitFinder library of compounds and eight compounds fulfilled these criteria. Seven of these compounds interfered with co-precipitation of MAGE and KAP-1, and three interfered with binding of MAGE and KAP-1 in a mammalian two hybrid assay. We now report identification of three potential compounds that interfere with MAGE/KAP-1 binding and can be developed as novel chemo-therapeutic agents for treatment of advanced melanoma and other cancers. PMID:21277283

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

    PubMed

    Lambert, B; Joos, H; Dierickx, S; Vantomme, R; Swings, J; Kersters, K; Van Montagu, M

    1990-04-01

    The second most abundant bacterium on the root surface of young sugar beet plants was identified as a Phyllobacterium sp. (Rhizobiaceae) based on a comparison of the results of 39 conventional identification tests, 167 API tests, 30 antibiotic susceptibility tests, and sodium dodecyl sulfate-polyacrylamide gel electrophoretic fingerprints of total cellular proteins with type strains of Phyllobacterium myrsinacearum and Phyllobacterium rubiacearum. It was found on 198 of 1,100 investigated plants between the 2nd and 10th leaf stage on three different fields in Belgium and one field in Spain. Densities ranged from 2 x 10 to 2 x 10 CFU/g of root. Five isolates exerted a broad-spectrum in vitro antifungal activity. DNA-DNA hybridizations showed that Phyllobacterium sp. does not contain DNA sequences that are homologous with the attachment genes chvA, chvB, the transferred-DNA (T-DNA) hormone genes iaaH and ipt from Agrobacterium tumefaciens, iaaM from A. tumefaciens and Pseudomonas savastanoi, or the nitrogenase genes nifHDK from Klebsiella pneumoniae. Phyllobacterium sp. produces indolylacetic acid in in vitro cultures and induces auxinlike effects when cocultivated with callus tissue of tobacco. When Phyllobacterium sp. was transformed with a Ti plasmid derivative, it gained the capacity to induce tumors on Kalanchoe daigremontiana. The potential role of Phyllobacterium sp. in this newly recognized niche is discussed. PMID:16348158

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

    PubMed Central

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

    2005-01-01

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

  8. Identification of Evidence for Key Parameters in Decision-Analytic Models of Cost Effectiveness: A Description of Sources and a Recommended Minimum Search Requirement.

    PubMed

    Paisley, Suzy

    2016-06-01

    This paper proposes recommendations for a minimum level of searching for data for key parameters in decision-analytic models of cost effectiveness and describes sources of evidence relevant to each parameter type. Key parameters are defined as treatment effects, adverse effects, costs, resource use, health state utility values (HSUVs) and baseline risk of events. The recommended minimum requirement for treatment effects is comprehensive searching according to available methodological guidance. For other parameter types, the minimum is the searching of one bibliographic database plus, where appropriate, specialist sources and non-research-based and non-standard format sources. The recommendations draw on the search methods literature and on existing analyses of how evidence is used to support decision-analytic models. They take account of the range of research and non-research-based sources of evidence used in cost-effectiveness models and of the need for efficient searching. Consideration is given to what constitutes best evidence for the different parameter types in terms of design and scientific quality and to making transparent the judgments that underpin the selection of evidence from the options available. Methodological issues are discussed, including the differences between decision-analytic models of cost effectiveness and systematic reviews when searching and selecting evidence and comprehensive versus sufficient searching. Areas are highlighted where further methodological research is required. PMID:26861793

  9. A high-resolution atlas of the infrared spectrum of the Sun and the Earth atmosphere from space. Volume 3: Key to identification of solar features

    NASA Technical Reports Server (NTRS)

    Geller, Murray

    1992-01-01

    During the period April 29 through May 2, 1985, the Atmospheric Trace Molecule Spectroscopy (ATMOS) experiment was operated as part of the Spacelab-3 (SL-3) payload on the shuttle Challenger. The instrument, a Fourier transform spectrometer, recorded over 2000 infrared solar spectra from an altitude of 360 km. Although the majority of the spectra were taken through the limb of the Earth's atmosphere in order to better understand its composition, several hundred of the 'high-sun' spectra were completely free from telluric absorption. These high-sun spectra recorded from space are, at the present time, the only high-resolution infrared spectra ever taken of the Sun free from absorptions due to constituents in the Earth's atmosphere. Volumes 1 and 2 of this series provide a compilation of these spectra arranged in a format suitable for quick-look reference purposes and are the first record of the continuous high-resolution infrared spectrum of the Sun and the Earth's atmosphere from space. In the Table of Identifications, which constitutes the main body of this volume, each block of eight wavenumbers is given a separate heading and corresponds to a page of two panels in Volume 1 of this series. In addition, three separate blocks of data available from ATMOS from 622-630 cm(exp -1), 630-638 cm(exp -1) and 638-646 cm(exp -1), excluded from Volume 1 because of the low signal-to-noise ratio, have been included due to the certain identification of several OH and NH transitions. In the first column of the table, the corrected frequency is given. The second column identifies the molecular species. The third and fourth columns represent the assigned transition. The fifth column gives the depth of the molecular line in millimeters. Also included in this column is a notation to indicate whether the line is a blend or lies on the shoulder(s) of another line(s). The final column repeats a question mark if the line is unidentified.

  10. A homogeneous HTRF assay for the identification of inhibitors of the TWEAK-Fn14 protein interaction.

    PubMed

    Benicchi, Tiziana; Iozzi, Sara; Svahn, Andreas; Axelsson, Hanna; Mori, Elisa; Bernocco, Simonetta; Cappelli, Federico; Caramelli, Chiara; Fanti, Paola; Genesio, Eva; Maccari, Laura; Markova, Natalia; Micco, Iolanda; Porcari, Valentina; Schultz, Johan; Fecke, Wolfgang

    2012-08-01

    The TWEAK-Fn14 pathway is upregulated in models of inflammation, autoimmune diseases, and cancer. Both TWEAK and Fn14 show increased expression also in the CNS in response to different stimuli, particularly astrocytes, microglia, and neurons, leading to activation of NF-κB and release of proinflammatory cytokines. Although neutralizing antibodies against these proteins have been shown to have therapeutic efficacy in animal models of inflammation, no small-molecule therapeutics are yet available. Here, we describe the development of a novel homogeneous time-resolved fluorescence (HTRF)-based screening assay together with several counterassays for the identification of small-molecule inhibitors of this protein-protein interaction. Recombinant HIS-TWEAK and Fn14-Fc proteins as well as FLAG-TWEAK and Fn14-FLAG proteins and an anti-Fn14 antibody were used to establish and validate these assays and to screen a library of 60 000 compounds. Two HTRF counterassays with unrelated proteins in the same assay format, an antiaggregation assay and a redox assay, were applied to filter out potential false-positive compounds. The novel assay and associated screening cascade should be useful for the discovery of small-molecule inhibitors of the TWEAK-Fn14 protein interaction. PMID:22644269

  11. Identification of bovine sperm acrosomal proteins that interact with a 32-kDa acrosomal matrix protein.

    PubMed

    Nagdas, Subir K; Smith, Linda; Medina-Ortiz, Ilza; Hernandez-Encarnacion, Luisa; Raychoudhury, Samir

    2016-03-01

    Mammalian fertilization is accomplished by the interaction between sperm and egg. Previous studies from this laboratory have identified a stable acrosomal matrix assembly from the bovine sperm acrosome termed the outer acrosomal membrane-matrix complex (OMC). This stable matrix assembly exhibits precise binding activity for acrosin and N-acetylglucosaminidase. A highly purified OMC fraction comprises three major (54, 50, and 45 kDa) and several minor (38-19 kDa) polypeptides. The set of minor polypeptides (38-19 kDa) termed "OMCrpf polypeptides" is selectively solubilized by high-pH extraction (pH 10.5), while the three major polypeptides (55, 50, and 45 kDa) remain insoluble. Proteomic identification of the OMC32 polypeptide (32 kDa polypeptide isolated from high-pH soluble fraction of OMC) yielded two peptides that matched the NCBI database sequence of acrosin-binding protein. Anti-OMC32 recognized an antigenically related family of polypeptides (OMCrpf polypeptides) in the 38-19-kDa range with isoelectric points ranging between 4.0 and 5.1. Other than glycohydrolases, OMC32 may also be complexed to other acrosomal proteins. The present study was undertaken to identify and localize the OMC32 binding polypeptides and to elucidate the potential role of the acrosomal protein complex in sperm function. OMC32 affinity chromatography of a detergent-soluble fraction of bovine cauda sperm acrosome followed by mass spectrometry-based identification of bound proteins identified acrosin, lactadherin, SPACA3, and IZUMO1. Co-immunoprecipitation analysis also demonstrated the interaction of OMC32 with acrosin, lactadherin, SPACA3, and IZUMO1. Our immunofluorescence studies revealed the presence of SPACA3 and lactadherin over the apical segment, whereas IZUMO1 is localized over the equatorial segment of Triton X-100 permeabilized cauda sperm. Immunoblot analysis showed that a significant portion of SPACA3 was released after the lysophosphatidylcholine (LPC)-induced acrosome reaction, whereas the IZUMO1 and lactadherin polypeptides remain associated to the particulate fraction. Almost entire population of bovine sperm IZUMO1 relocates to the equatorial segment during the LPC-induced acrosome reaction. We propose that the interaction of OMC32 matrix polypeptide with detergent-soluble acrosomal proteins regulates the release of hydrolases/other acrosomal protein(s) during the acrosome reaction. PMID:26897631

  12. Interaction of CO with OH on Au(111): HCOO, CO3, and HOCO as Key Intermediates in the Water-Gas Shift Reaction

    SciTech Connect

    Senanayake, S.; Stacchiola, D; Liu, P; Mullins, C; Hrbek, J; Rodriguez, J

    2009-01-01

    We have investigated the role of formate (HCOO), carbonate (CO{sub 3}), and carboxyl (HOCO) species as possible intermediates in the OH{sub ads} + CO{sub gas} {yields} CO{sub 2,gas} + 0.5H{sub 2,gas} reaction on Au(111) using synchrotron-based core level photoemission, near-edge X-ray absorption fine structure (NEXAFS), and infrared absorption spectroscopy (IR). Adsorbed HCOO, CO{sub 3}, and OH species were prepared by adsorbing formic acid, carbon dioxide, and water on a Au(111) surface precovered with 0.2 ML of atomic oxygen, respectively. HCOOH interacts weakly with Au(111), but on O/Au(111) it dissociates its acidic H to yield adsorbed formate. The results of NEXAFS, IR, and density-functional calculations indicate that the formate adopts a bidentate configuration on Au(111). Since the HCOO groups are stable on Au(111) up to temperatures near 350 K, it is not likely that formate is a key intermediate for the OH{sub ads} + CO{sub gas} {yields} CO{sub 2,gas} + 0.5H{sub 2,gas} reaction at low temperatures. In fact, the formation of this species could lead eventually to surface poisoning. When compared to a formate species, a carbonate species formed by the reaction of CO{sub 2} with O/Au(111) has low stability, decomposing at temperatures between 100 and 125 K, and should not poison the gold surface. Neither HCOO nor CO{sub 3} was detected during the reaction of CO with OH on Au(111) at 90-120 K. The results of photoemission and IR spectroscopy point to HO {leftrightarrow} CO interactions, consistent with the formation of an unstable HOCO intermediate which has a very short lifetime on the gold surface. The possible mechanism for the low-temperature water-gas shift on gold catalysts is discussed in light of these results.

  13. Identification of AREG and PLK1 pathway modulation as a potential key of the response of intracranial 9L tumor to microbeam radiation therapy.

    PubMed

    Bouchet, Audrey; Sakakini, Nathalie; Atifi, Michèle El; Le Clec'h, Céline; Bräuer-Krisch, Elke; Rogalev, Léonid; Laissue, Jean Albert; Rihet, Pascal; Le Duc, Géraldine; Pelletier, Laurent

    2015-06-01

    Synchrotron microbeam radiation therapy (MRT) relies on the spatial fractionation of a synchrotron beam into parallel micron-wide beams allowing deposition of hectogray doses. MRT controls the intracranial tumor growth in rodent models while sparing normal brain tissues. Our aim was to identify the early biological processes underlying the differential effect of MRT on tumor and normal brain tissues. The expression of 28,000 transcripts was tested by microarray 6 hr after unidirectional MRT (400 Gy, 50 µm-wide microbeams, 200 µm spacing). The specific response of tumor tissues to MRT consisted in the significant transcriptomic modulation of 431 probesets (316 genes). Among them, 30 were not detected in normal brain tissues, neither before nor after MRT. Areg, Trib3 and Nppb were down-regulated, whereas all others were up-regulated. Twenty-two had similar expression profiles during the 2 weeks observed after MRT, including Ccnb1, Cdc20, Pttg1 and Plk1 related to the mitotic role of the Polo-like kinase (Plk) pathway. The up-regulation of Areg expression may indicate the emergence of survival processes in tumor cells triggered by the irradiation; while the modulation of the "mitotic role of Plk1" pathway, which relates to cytokinetic features of the tumor observed histologically after MRT, may partially explain the control of tumor growth by MRT. The identification of these tumor-specific responses permit to consider new strategies that might potentiate the antitumoral effect of MRT. PMID:25382544

  14. Identification of OmpR-Family Response Regulators Interacting with Thioredoxin in the Cyanobacterium Synechocystis sp. PCC 6803

    PubMed Central

    Kadowaki, Taro; Nishiyama, Yoshitaka; Hisabori, Toru; Hihara, Yukako

    2015-01-01

    The redox state of the photosynthetic electron transport chain is known to act as a signal to regulate the transcription of key genes involved in the acclimation responses to environmental changes. We hypothesized that the protein thioredoxin (Trx) acts as a mediator connecting the redox state of the photosynthetic electron transport chain and transcriptional regulation, and established a screening system to identify transcription factors (TFs) that interact with Trx. His-tagged TFs and S-tagged mutated form of Trx, TrxMC35S, whose active site cysteine 35 was substituted with serine to trap the target interacting protein, were co-expressed in E. coli cells and Trx-TF complexes were detected by immuno-blotting analysis. We examined the interaction between Trx and ten OmpR family TFs encoded in the chromosome of the cyanobacterium Synechocystis sp. PCC 6803 (S.6803). Although there is a highly conserved cysteine residue in the receiver domain of all OmpR family TFs, only three, RpaA (Slr0115), RpaB (Slr0946) and ManR (Slr1837), were identified as putative Trx targets. The recombinant forms of wild-type TrxM, RpaA, RpaB and ManR proteins from S.6803 were purified following over-expression in E. coli and their interaction was further assessed by monitoring changes in the number of cysteine residues with free thiol groups. An increase in the number of free thiols was observed after incubation of the oxidized TFs with Trx, indicating the reduction of cysteine residues as a consequence of interaction with Trx. Our results suggest, for the first time, the possible regulation of OmpR family TFs through the supply of reducing equivalents from Trx, as well as through the phospho-transfer from its cognate sensor histidine kinase. PMID:25774906

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

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

    Protein-protein interactions are key to most cellular processes. Tandem mass spectrometry (MS/MS)-based proteomics combined with co-immunoprecipitation (CO-IP) has emerged as a powerful approach for studying protein complexes. However, a majority of systematic proteomics studies on protein-protein interactions involve the use of protein overexpression and/or epitope-tagged bait proteins, which might affect binding stoichiometry and lead to higher false positives. Here, we report an application of a straightforward, label-free CO-IP-MS/MS method, without the use of protein overexpression or protein tags, to the investigation of changes in the abundance of endogenous proteins associated with a bait protein, which is in this case insulin receptor substrate-1 (IRS-1), under basal and insulin stimulated conditions. IRS-1 plays a central role in the insulin signaling cascade. Defects in the protein-protein interactions involving IRS-1 may lead to the development of insulin resistance and type 2 diabetes. HPLC-ESI-MS/MS analyses identified eleven novel endogenous insulin-stimulated IRS-1 interaction partners in L6 myotubes reproducibly, including proteins play an important role in protein dephosphorylation [protein phosphatase 1 regulatory subunit 12A, (PPP1R12A)], muscle contraction and actin cytoskeleton rearrangement, endoplasmic reticulum stress, and protein folding, as well as protein synthesis. This novel application of label-free CO-IP-MS/MS quantification to assess endogenous interaction partners of a specific protein will prove useful for understanding how various cell stimuli regulate insulin signal transduction.

  16. Florida Keys

    NASA Technical Reports Server (NTRS)

    2002-01-01

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

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

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

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

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

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

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

    SciTech Connect

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

    2008-04-01

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

  18. In Vivo Identification of Photosystem II Light Harvesting Complexes Interacting with PHOTOSYSTEM II SUBUNIT S.

    PubMed

    Gerotto, Caterina; Franchin, Cinzia; Arrigoni, Giorgio; Morosinotto, Tomas

    2015-08-01

    Light is the primary energy source for photosynthetic organisms, but in excess, it can generate reactive oxygen species and lead to cell damage. Plants evolved multiple mechanisms to modulate light use efficiency depending on illumination intensity to thrive in a highly dynamic natural environment. One of the main mechanisms for protection from intense illumination is the dissipation of excess excitation energy as heat, a process called nonphotochemical quenching. In plants, nonphotochemical quenching induction depends on the generation of a pH gradient across thylakoid membranes and on the presence of a protein called PHOTOSYSTEM II SUBUNIT S (PSBS). Here, we generated Physcomitrella patens lines expressing histidine-tagged PSBS that were exploited to purify the native protein by affinity chromatography. The mild conditions used in the purification allowed copurifying PSBS with its interactors, which were identified by mass spectrometry analysis to be mainly photosystem II antenna proteins, such as LIGHT-HARVESTING COMPLEX B (LHCB). PSBS interaction with other proteins appears to be promiscuous and not exclusive, although the major proteins copurified with PSBS were components of the LHCII trimers (LHCB3 and LHCBM). These results provide evidence of a physical interaction between specific photosystem II light-harvesting complexes and PSBS in the thylakoids, suggesting that these subunits are major players in heat dissipation of excess energy. PMID:26069151

  19. Identification and characterization of the interactive proteins with cytotoxic T-lymphocyte antigen-2α.

    PubMed

    Nga, Bui Thi To; Luziga, Claudius; Yamamoto, Misa; Kusakabe, Ken Takeshi; Yamamoto, Yoshimi

    2015-01-01

    Cytotoxic T-lymphocyte antigen-2α (CTLA-2α) is a potent inhibitor of cathepsin L-like cysteine proteases. Recombinant CTLA-2α is known to be a potent, competitive inhibitor of cathepsin L-like cysteine proteases. In this study, cathepsin L, cathepsin C, and tubulointerstitial nephritis antigen-related protein 1 (TINAGL1) were identified as novel interactive proteins of CTLA-2α by the yeast two-hybrid screening system. The direct interactions and co-localization of these proteins with CTLA-2α were confirmed using co-immunoprecipitation and immunofluorescence staining, respectively. The disulfide-bonded CTLA-2α/cathepsin L complex was isolated from mouse tissue. CTLA-2α was found to be specific and consistently expressed on the maternal side of the mouse placenta. Double immunofluorescence analysis showed that CTLA-2α was co-localized with cathepsin L, cathepsin C, and TINAGL1 in placenta. A simple cell-based fluorescence assay revealed that CTLA-2α exhibited inhibitory activity toward cathepsin C in live cells, which indicated that CTLA-2α is a novel endogenous inhibitor of cathepsin C. PMID:25514977

  20. Systematic identification of transcriptional regulatory modules from protein–protein interaction networks

    PubMed Central

    Diez, Diego; Hutchins, Andrew Paul; Miranda-Saavedra, Diego

    2014-01-01

    Transcription factors (TFs) combine with co-factors to form transcriptional regulatory modules (TRMs) that regulate gene expression programs with spatiotemporal specificity. Here we present a novel and generic method (rTRM) for the reconstruction of TRMs that integrates genomic information from TF binding, cell type-specific gene expression and protein–protein interactions. rTRM was applied to reconstruct the TRMs specific for embryonic stem cells (ESC) and hematopoietic stem cells (HSC), neural progenitor cells, trophoblast stem cells and distinct types of terminally differentiated CD4+ T cells. The ESC and HSC TRM predictions were highly precise, yielding 77 and 96 proteins, of which ∼75% have been independently shown to be involved in the regulation of these cell types. Furthermore, rTRM successfully identified a large number of bridging proteins with known roles in ESCs and HSCs, which could not have been identified using genomic approaches alone, as they lack the ability to bind specific DNA sequences. This highlights the advantage of rTRM over other methods that ignore PPI information, as proteins need to interact with other proteins to form complexes and perform specific functions. The prediction and experimental validation of the co-factors that endow master regulatory TFs with the capacity to select specific genomic sites, modulate the local epigenetic profile and integrate multiple signals will provide important mechanistic insights not only into how such TFs operate, but also into abnormal transcriptional states leading to disease. PMID:24137002

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

    SciTech Connect

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

    2012-05-04

    Most of an intravenous dose of species C adenovirus serotype 5 (Ad5) is destroyed by liver Kupffer cells. In contrast, another species C virus, Ad6, evades these cells to mediate more efficient liver gene delivery. Given that this difference in Kupffer cell interaction is mediated by the hypervariable (HVR) loops of the virus hexon protein, we genetically modified each of the seven HVRs of Ad5 with a cysteine residue to enable conditional blocking of these sites with polyethylene glycol (PEG). We show that these modifications do not affect in vitro virus transduction. In contrast, after intravenous injection, targeted PEGylation at HVRs 1, 2, 5, and 7 increased viral liver transduction up to 20-fold. Elimination or saturation of liver Kupffer cells did not significantly affect this increase in the liver transduction. In vitro, PEGylation blocked uptake of viruses via the Kupffer cell scavenger receptor SRA-II. These data suggest that HVRs 1, 2, 5, and 7 of Ad5 may be involved in Kupffer cell recognition and subsequent destruction. These data also demonstrate that this conditional genetic-chemical mutation strategy is a useful tool for investigating the interactions of viruses with host tissues.

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

    PubMed Central

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

    2014-01-01

    The human olfactory system recognizes a broad spectrum of odorants using approximately 400 different olfactory receptors (hORs). Although significant improvements of heterologous expression systems used to study interactions between ORs and odorant molecules have been made, screening the olfactory repertoire of hORs remains a tremendous challenge. We therefore developed a chemical systems level approach based on protein-protein association network to investigate novel hOR-odorant relationships. Using this new approach, we proposed and validated new bioactivities for odorant molecules and OR2W1, OR51E1 and OR5P3. As it remains largely unknown how human perception of odorants influence or prevent diseases, we also developed an odorant-protein matrix to explore global relationships between chemicals, biological targets and disease susceptibilities. We successfully experimentally demonstrated interactions between odorants and the cannabinoid receptor 1 (CB1) and the peroxisome proliferator-activated receptor gamma (PPARγ). Overall, these results illustrate the potential of integrative systems chemical biology to explore the impact of odorant molecules on human health, i.e. human odorome. PMID:24695519

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

    PubMed Central

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

    2010-01-01

    Activator of G protein Signaling 3 (AGS3) is a receptor-independent G protein activator that has been implicated in multiple biological events such as brain development, neuroplasticity and addiction, cardiac function, Golgi structure/function, macroautophagy and metabolism. However, how AGS3 is regulated is little known. We demonstrate here that AGS3 interacts with a ubiquitin specific protease USP9x, and this interaction is at least partially mediated through the C-terminal G protein regulatory domain of AGS3. Knockdown of USP9x causes a moderate reduction in the level of AGS3. In contrast, overexpression of either USP9x or its deubiquitinating domain UCH increases the amount of AGS3, whereas expression of the mutant UCH domain that lacks deubiquitinating activity does not have the same effect. As previously observed in AGS3 knockdown cells, the localization of several marker proteins of the late Golgi compartments is disturbed in cells depleted of USP9x. Taken together, our study suggests that USP9x can modulate the level of a subpopulation of AGS3, and this modulation plays a role in regulating the structure of the late Golgi compartments. Finally, we have found that levels of AGS3 and USP9x are co-regulated in the prefrontal cortex of rats withdrawn from repeated cocaine treatment. In conjunction with the above data, this observation indicates a potential role of USP9X in the regulation of the AGS3 level during cocaine-induced neuroplasticity. PMID:20305814

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

    PubMed

    Brailovsky, Harry

    2014-01-01

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

  5. First species of Leptochelia Dana, 1849 (Crustacea: Tanaidacea) from the Eastern Pacific, with an annotated checklist and identification keys for the genus.

    PubMed

    Jarquín-González, Jani; García-Madrigal, María Del Socorro; Carrera-Parra, Luis Fernando

    2015-01-01

    Forty three species of leptocheliids are known worldwide. In the American region only eight species have been described from the Western Atlantic, while for the Eastern Pacific none have been described, suggesting that the diversity of this family has been severely underestimated in this region. Here we describe the first species of Leptochelia from the Eastern Pacific, Leptochelia mexicana n. sp., which is characterized by the males having a spiniform seta on the second segment of uropodal endopod, a novel feature for the genus. In addition, the first annotated checklist and a taxonomic key with illustrations for Leptochelia species are included. The list includes the type locality, type depository, distribution, habitat and, in some cases, remarks. PMID:25781398

  6. The nucleotide exchange factor MGE exerts a key function in the ATP-dependent cycle of mt-Hsp70-Tim44 interaction driving mitochondrial protein import.

    PubMed Central

    Schneider, H C; Westermann, B; Neupert, W; Brunner, M

    1996-01-01

    Import of preproteins into the mitochondrial matrix is driven by the ATP-dependent interaction of mt-Hsp70 with the peripheral inner membrane import protein Tim44 and the preprotein in transit. We show that Mge1p, a co-chaperone of mt-Hsp70, plays a key role in the ATP-dependent import reaction cycle in yeast. Our data suggest a cycle in which the mt-Hsp70-Tim44 complex forms with ATP: Mge1p promotes assembly of the complex in the presence of ATP. Hydrolysis of ATP by mt-Hsp70 occurs in complex with Tim44. Mge1p is then required for the dissociation of the ADP form of mt-Hsp70 from Tim44 after release of inorganic phosphate but before release of ADP. ATP hydrolysis and complex dissociation are accompanied by tight binding of mt-Hsp70 to the preprotein in transit. Subsequently, the release of mt-Hsp70 from the polypeptide chain is triggered by Mge1p which promotes release of ADP from mt-Hsp70. Rebinding of ATP to mt-Hsp70 completes the reaction cycle. Images PMID:8918457

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

    SciTech Connect

    Noisakran, Sansanee; Sengsai, Suchada; Thongboonkerd, Visith; Kanlaya, Rattiyaporn; Sinchaikul, Supachok; Chen, Shui-Tein; Puttikhunt, Chunya

    2008-07-18

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

  8. A report of rifampin-resistant leprosy from northern and eastern India: identification and in silico analysis of molecular interactions.

    PubMed

    Vedithi, Sundeep Chaitanya; Lavania, Mallika; Kumar, Manoj; Kaur, Punit; Turankar, Ravindra P; Singh, Itu; Nigam, Astha; Sengupta, Utpal

    2015-04-01

    Presence of point mutations within the drug resistance determining regions of Mycobacterium leprae (M. leprae) genome confers molecular basis of drug resistance to dapsone, rifampin and ofloxacin in leprosy. This study is focused on the identification of mutations within the rpoB gene region of M. leprae that are specific for rifampin interaction, and further in silico analysis was carried out to determine the variations in the interactions. DNA and RNA were isolated from slit skin scrapings of 60 relapsed leprosy patients. PCR targeting rpoB gene region and amplicon sequencing was performed to determine point mutations. mRNA expression levels of rpoB and high-resolution melt analysis of mutants were performed using Rotor Gene Q Realtime PCR. Molecular docking was performed using LigandFit Software. Ten cases having point mutations within the rpoB gene region were identified and were clinically confirmed to be resistant to rifampin. A new mutation at codon position Gln442His has been identified. There is a 9.44-fold upregulation in the mRNA expression of rpoB gene in mutant/resistant samples when compared with the wild/sensitive samples. In silico docking analysis of rifampin with wild-type and Gln442His mutant RpoB proteins revealed a variation in the hydrogen-bonding pattern leading to a difference in the total interaction energy and conformational change at position Asp441. These preliminary downstream functional observations revealed that the presence of point mutations within the rifampin resistance determining regions of rpoB gene plays a vital role in conferring genetic and molecular basis of resistance to rifampin in leprosy. PMID:25201810

  9. Key Nutrients.

    ERIC Educational Resources Information Center

    Federal Extension Service (USDA), Washington, DC.

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

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

    PubMed

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

    2010-04-11

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-06-01

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

  12. Identification and calibration of the interaction matrix parameters for AO and MCAO systems

    NASA Astrophysics Data System (ADS)

    Neichel, Benoit; Parisot, Amelie; Petit, Cyril; Fusco, Thierry; Rigaut, François

    2012-07-01

    New tomographic Adaptive Optics (AO) concepts require a good knowledge of the system geometry and characteristics. These parameters are used to feed the tomographic reconstructors. In this paper we present a method to precisely identify the parameters required to construct an accurate synthetic set of models such as inuence functions, mis-registrations, directions of analysis or altitude of the DMs. The method is based on a multiparameter t of the interaction matrix. This identication method nds also its application in high contrast AO systems, such as SPHERE : in that case it is used as a diagnostic tool in order to precisely realign the system. The method has been tested and successfully implemented on HOMER, SPHERE and GeMS. Experimental results for these three systems are presented.

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

    PubMed

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

    2013-11-01

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

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

    PubMed Central

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

    1996-01-01

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

  15. Identification of the Mind Bomb1 Interaction Domain in Zebrafish DeltaD.

    PubMed

    Palardy, Gregory; Chitnis, Ajay B

    2015-01-01

    Ubiquitylation promotes endocytosis of the Notch ligands like Delta and Serrate and is essential for them to effectively activate Notch in a neighboring cell. The RING E3 ligase Mind bomb1 (Mib1) ubiquitylates DeltaD to facilitate Notch signaling in zebrafish. We have identified a domain in the intracellular part of the zebrafish Notch ligand DeltaD that is essential for effective interactions with Mib1. We show that elimination of the Mind bomb1 Interaction Domain (MID) or mutation of specific conserved motifs in this domain prevents effective Mib1-mediated ubiquitylation and internalization of DeltaD. Lateral inhibition mediated by Notch signaling regulates early neurogenesis in zebrafish. In this context, Notch activation suppresses neurogenesis, while loss of Notch-mediated lateral inhibition results in a neurogenic phenotype, where too many cells are allowed to become neurons. While Mib1-mediated endocytosis of DeltaD is essential for effective activation of Notch in a neighboring cell (in trans) it is not required for DeltaD to inhibit function of Notch receptors in the same cell (in cis). As a result, forms of DeltaD that have the MID can activate Notch in trans and suppress early neurogenesis when mRNA encoding it is ectopically expressed in zebrafish embryos. On the other hand, when the MID is eliminated/mutated in DeltaD, its ability to activate Notch in trans fails but ability to inhibit in cis is retained. As a result, ectopic expression of DeltaD lacking an effective MID results in a failure of Notch-mediated lateral inhibition and a neurogenic phenotype. PMID:26020642

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

    PubMed Central

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

    2013-01-01

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

  17. Peptide labeling with photoactivatable trifunctional cadaverine derivative and identification of interacting partners by biotin transfer.

    PubMed

    App, Christine; Knop, Jana; Huff, Thomas; Seebahn, Angela; Becker, Cord-Michael; Iavarone, Federica; Castagnola, Massimo; Hannappel, Ewald

    2014-07-01

    A new photoactivatable trifunctional cross-linker, cBED (cadaverine-2-[6-(biotinamido)-2-(p-azidobenzamido) hexanoamido]ethyl-1,3'-dithiopropionate), was synthesized by chemical conversion of sulfo-SBED (sulfosuccinimidyl-2-[6-(biotinamido)-2-(p-azidobenzamido) hexanoamido]ethyl-1,3'-dithiopropionate) with cadaverine. This cross-linker was purified by reversed-phase high-performance liquid chromatography (RP-HPLC) and characterized using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis. cBED is based on sulfo-SBED that has a photoactivatable azido group, a cleavable disulfide bond for label transfer methods, and a biotin moiety for highly sensitive biotin/avidin detection. By ultraviolet (UV) light, the azido group is converted to a reactive nitrene, transforming transient bindings of interacting structures to covalent bonds. In contrast to the sulfo-N-hydroxysuccinimide (sulfo-NHS) moiety of sulfo-SBED, which attaches quite unspecifically to amino groups, cBED includes a cadaverine moiety that can be attached by transglutaminase more specifically to certain glutamine residues. For instance, thymosin β4 can be labeled with cBED using tissue transglutaminase. By high-resolution HPLC/ESI-MS (electrospray ionization-mass spectrometry) and tandem MS (MS/MS) of the trypsin digest, it was established that glutamine residues at positions 23 and 36 were labeled, whereas Q39 showed no reactivity. The covalent binding of cBED to thymosin β4 did not influence its G-actin sequestering activity, and the complex could be used to identify new interaction partners. Therefore, cBED can be used to better understand the multifunctional role of thymosin β4 as well as of other proteins and peptides. PMID:24732115

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

    PubMed

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

    2013-03-01

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

  19. Taxonomy of the hyper-diverse ant genus Tetramorium Mayr in the Malagasy region (Hymenoptera, Formicidae, Myrmicinae) – first record of the T. setigerum species group and additions to the Malagasy species groups with an updated illustrated identification key

    PubMed Central

    Hita Garcia, Francisco; Fisher, Brian L.

    2015-01-01

    Abstract In this study we provide an update to the taxonomy of the ant genus Tetramorium Mayr in Madagascar. We report the first record of the Tetramorium setigerum species group in Madagascar and describe the only Malagasy representative as Tetramorium cavernicola sp. n., which is known only from a cave in Ankarana. In addition, we provide an overview of the 19 proposed Malagasy species groups, and discuss their zoogeography and relationships to other groups and larger lineages within the hyper-diverse genus Tetramorium. At present, we recognise a highly unique Malagasy Tetramorium fauna with 113 species endemic to the island of Madagascar out of a total of 125 translating into an endemism rate of 93%. We hypothesise that this fauna is based on one or a few colonisation events from the Afrotropical region, with subsequent adaptive radiation in Madagascar. Furthermore, we present an updated and illustrated identification key to the Tetramorium species groups in the Malagasy region. PMID:26257564

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

    PubMed Central

    2009-01-01

    Background Archaea share with bacteria the ability to bias their movement towards more favorable locations, a process known as taxis. Two molecular systems drive this process: the motility apparatus and the chemotaxis signal transduction system. The first consists of the flagellum, the flagellar motor, and its switch, which allows cells to reverse the rotation of flagella. The second targets the flagellar motor switch in order to modulate the switching frequency in response to external stimuli. While the signal transduction system is conserved throughout archaea and bacteria, the archaeal flagellar apparatus is different from the bacterial one. The proteins constituting the flagellar motor and its switch in archaea have not yet been identified, and the connection between the bacterial-like chemotaxis signal transduction system and the archaeal motility apparatus is unknown. Results Using protein-protein interaction analysis, we have identified three proteins in Halobacterium salinarum that interact with the chemotaxis (Che) proteins CheY, CheD, and CheC2, as well as the flagella accessory (Fla) proteins FlaCE and FlaD. Two of the proteins belong to the protein family DUF439, the third is a HEAT_PBS family protein. In-frame deletion strains for all three proteins were generated and analyzed as follows: a) photophobic responses were measured by a computer-based cell tracking system b) flagellar rotational bias was determined by dark-field microscopy, and c) chemotactic behavior was analyzed by a swarm plate assay. Strains deleted for the HEAT_PBS protein or one of the DUF439 proteins proved unable to switch the direction of flagellar rotation. In these mutants, flagella rotate only clockwise, resulting in exclusively forward swimming cells that are unable to respond to tactic signals. Deletion of the second DUF439 protein had only minimal effects. HEAT_PBS proteins could be identified in the chemotaxis gene regions of all motile haloarchaea sequenced so far, but not in those of other archaeal species. Genes coding for DUF439 proteins, however, were found to be integral parts of chemotaxis gene regions across the archaeal domain, and they were not detected in other genomic context. Conclusion Altogether, these results demonstrate that, in the archaeal domain, previously unrecognized archaea-specific Che proteins are essential for relaying taxis signaling to the flagellar apparatus. PMID:19291314

  1. The ENA Ribbon and the ISN Flow as Key Tools for the ISM-Heliosphere Interaction - Open Questions, the Need for Future Observations with IBEX and IMAP

    NASA Astrophysics Data System (ADS)

    Moebius, E.; Bzowski, M.; Frisch, P. C.; Funsten, H. O.; Fuselier, S.; Kucharek, H.; McComas, D. J.; Schwadron, N.; Wimmer-Schweingruber, R. F.; Wurz, P.; Zank, G. P.

    2014-12-01

    The unexpected ribbon in the IBEX energetic neutral atom (ENA) maps is still far from understood. According to most models, the interstellar magnetic field (BISM) controls its location and shape, with the direction in agreement with the termination shock (TS) asymmetry found by the Voyagers, the deflection of the interstellar neutral (ISN) flow, and the high energy cosmic ray anisotropy. With direct ISN flow velocity vector VISM and temperature observations, along with secondary neutrals, most likely from the outer heliosheath, IBEX also probes the conditions and interaction outside the heliospheric boundary. Precise knowledge of the ISN flow direction is key, because small differences have substantial leverage on the VISM-BISM plane, which controls the large-scale heliosphere structure. For quantitative tools, the ribbon formation must be understood and the ISN flow parameters must be further refined. IBEX maps show that the latitudinal ribbon structure carries the imprint of fast and slow solar wind (SW). These results support models that involve charge exchange with the SW, currently in two renditions: secondary ENAs from neutral SW reaching into the outer heliosheath and reflection of SW at the TS. In the TS model, the ribbon distance maps the TS, and reactions to changing SW at 1 AU follow within 1 - 2 years. In the secondary ENA model, ribbon ENAs provide an energy-dependent spatio-temporal probe of the outer heliosheath over several years after SW changes at 1 AU. Therefore, observations over a full solar cycle with IBEX, probing the ribbon depth with SW modulation, are key to its understanding. Likewise, expanding the successful variation of the IBEX pointing strategy over times with varying ionization rates will refine the ISN flow vector. The capabilities of the Interstellar Mapping and Acceleration Probe (IMAP), which has highest priority in the recent NRC Heliophysics Decadal Survey, are needed to probe the spatio-temporal fine-structure of the ribbon, extend observations to higher energy with better resolution, and provide precision observations of the ISN flow and secondary neutrals from different vantage points. To that end, IMAP will provide a combination of increased collecting power, angular, and energy resolution, the capability to scan the ISN flow, and a dedicated pickup ion instrument.

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

    SciTech Connect

    Rothe, Francoise; Gueydan, Cyril; Bellefroid, Eric; Huez, Georges; Kruys, Veronique . E-mail: vkruys@ulb.ac.be

    2006-04-28

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

  3. Identification of single-stranded-DNA-binding proteins that interact with muscle gene elements.

    PubMed Central

    Santoro, I M; Yi, T M; Walsh, K

    1991-01-01

    A sequence-specific DNA-binding protein from skeletal-muscle extracts that binds to probes of three muscle gene DNA elements is identified. This protein, referred to as muscle factor 3, forms the predominant nucleoprotein complex with the MCAT gene sequence motif in an electrophoretic mobility shift assay. This protein also binds to the skeletal actin muscle regulatory element, which contains the conserved CArG motif, and to a creatine kinase enhancer probe, which contains the E-box motif, a MyoD-binding site. Muscle factor 3 has a potent sequence-specific, single-stranded-DNA-binding activity. The specificity of this interaction was demonstrated by sequence-specific competition and by mutations that diminished or eliminated detectable complex formation. MyoD, a myogenic determination factor that is distinct from muscle factor 3, also bound to single-stranded-DNA probes in a sequence-specific manner, but other transcription factors did not. Multiple copies of the MCAT motif activated the expression of a heterologous promoter, and a mutation that eliminated expression was correlated with diminished factor binding. Muscle factor 3 and MyoD may be members of a class of DNA-binding proteins that modulate gene expression by their abilities to recognize DNA with unusual secondary structure in addition to specific sequence. Images PMID:2005890

  4. Imbalance in chemical space: How to facilitate the identification of protein-protein interaction inhibitors

    PubMed Central

    Kuenemann, Mélaine A.; Labbé, Céline M.; Cerdan, Adrien H.; Sperandio, Olivier

    2016-01-01

    Protein-protein interactions (PPIs) play vital roles in life and provide new opportunities for therapeutic interventions. In this large data analysis, 3,300 inhibitors of PPIs (iPPIs) were compared to 17 reference datasets of collectively ~566,000 compounds (including natural compounds, existing drugs, active compounds on conventional targets, etc.) using a chemoinformatics approach. Using this procedure, we showed that comparable classes of PPI targets can be formed using either the similarity of their ligands or the shared properties of their binding cavities, constituting a proof-of-concept that not only can binding pockets be used to group PPI targets, but that these pockets certainly condition the properties of their corresponding ligands. These results demonstrate that matching regions in both chemical space and target space can be found. Such identified classes of targets could lead to the design of PPI-class-specific chemical libraries and therefore facilitate the development of iPPIs to the stage of drug candidates. PMID:27034268

  5. Identification of Nuclear Effects in Neutrino-Carbon Interactions at Low Three-Momentum Transfer.

    PubMed

    Rodrigues, P A; Demgen, J; Miltenberger, E; Aliaga, L; Altinok, O; Bellantoni, L; Bercellie, A; Betancourt, M; Bodek, A; Bravar, A; Budd, H; Cai, T; Carneiro, M F; Chvojka, J; Devan, J; Dytman, S A; Díaz, G A; Eberly, B; Elkins, M; Felix, J; Fields, L; Fine, R; Gago, A M; Galindo, R; Gallagher, H; Ghosh, A; Golan, T; Gran, R; Harris, D A; Higuera, A; Hurtado, K; Kiveni, M; Kleykamp, J; Kordosky, M; Le, T; Leistico, J R; Lovlein, A; Maher, E; Manly, S; Mann, W A; Marshall, C M; Martinez Caicedo, D A; McFarland, K S; McGivern, C L; McGowan, A M; Messerly, B; Miller, J; Mislivec, A; Morfín, J G; Mousseau, J; Muhlbeier, T; Naples, D; Nelson, J K; Norrick, A; Nuruzzaman; Osta, J; Paolone, V; Patrick, C E; Perdue, G N; Ramirez, M A; Ransome, R D; Ray, H; Ren, L; Rimal, D; Ruterbories, D; Schellman, H; Schmitz, D W; Solano Salinas, C J; Tagg, N; Tice, B G; Valencia, E; Walton, T; Wolcott, J; Wospakrik, M; Zavala, G; Zhang, D

    2016-02-19

    Two different nuclear-medium effects are isolated using a low three-momentum transfer subsample of neutrino-carbon scattering data from the MINERvA neutrino experiment. The observed hadronic energy in charged-current ν_{μ} interactions is combined with muon kinematics to permit separation of the quasielastic and Δ(1232) resonance processes. First, we observe a small cross section at very low energy transfer that matches the expected screening effect of long-range nucleon correlations. Second, additions to the event rate in the kinematic region between the quasielastic and Δ resonance processes are needed to describe the data. The data in this kinematic region also have an enhanced population of multiproton final states. Contributions predicted for scattering from a nucleon pair have both properties; the model tested in this analysis is a significant improvement but does not fully describe the data. We present the results as a double-differential cross section to enable further investigation of nuclear models. Improved description of the effects of the nuclear environment are required by current and future neutrino oscillation experiments. PMID:26943528

  6. Identification of Interactions in the NMD Complex Using Proximity-Dependent Biotinylation (BioID)

    PubMed Central

    Schweingruber, Christoph; Soffientini, Paolo; Ruepp, Marc-David; Bachi, Angela; Mühlemann, Oliver

    2016-01-01

    Proximity-dependent trans-biotinylation by the Escherichia coli biotin ligase BirA mutant R118G (BirA*) allows stringent streptavidin affinity purification of proximal proteins. This so-called BioID method provides an alternative to the widely used co-immunoprecipitation (co-IP) to identify protein-protein interactions. Here, we used BioID, on its own and combined with co-IP, to identify proteins involved in nonsense-mediated mRNA decay (NMD), a post-transcriptional mRNA turnover pathway that targets mRNAs that fail to terminate translation properly. In particular, we expressed BirA* fused to the well characterized NMD factors UPF1, UPF2 and SMG5 and detected by liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) the streptavidin-purified biotinylated proteins. While the identified already known interactors confirmed the usefulness of BioID, we also found new potentially important interactors that have escaped previous detection by co-IP, presumably because they associate only weakly and/or very transiently with the NMD machinery. Our results suggest that SMG5 only transiently contacts the UPF1-UPF2-UPF3 complex and that it provides a physical link to the decapping complex. In addition, BioID revealed among others CRKL and EIF4A2 as putative novel transient interactors with NMD factors, but whether or not they have a function in NMD remains to be elucidated. PMID:26934103

  7. Identification of Subnanometric Ag Species, Their Interaction with Supports and Role in Catalytic CO Oxidation.

    PubMed

    Kotolevich, Yulia; Kolobova, Ekaterina; Khramov, Evgeniy; Cabrera Ortega, Jesús Efren; Farías, Mario H; Zubavichus, Yan; Zanella, Rodolfo; Mota-Morales, Josué D; Pestryakov, Alexey; Bogdanchikova, Nina; Cortés Corberán, Vicente

    2016-01-01

    The nature and size of the real active species of nanoparticulated metal supported catalysts is still an unresolved question. The technique of choice to measure particle sizes at the nanoscale, HRTEM, has a practical limit of 1 nm. This work is aimed to identify the catalytic role of subnanometer species and methods to detect and characterize them. In this frame, we investigated the sensitivity to redox pretreatments of Ag/Fe/TiO₂, Ag/Mg/TiO₂ and Ag/Ce/TiO₂ catalysts in CO oxidation. The joint application of HRTEM, SR-XRD, DRS, XPS, EXAFS and XANES methods indicated that most of the silver in all samples is in the form of Ag species with size <1 nm. The differences in catalytic properties and sensitivity to pretreatments, observed for the studied Ag catalysts, could not be explained taking into account only the Ag particles whose size distribution is measured by HRTEM, but may be explained by the presence of the subnanometer Ag species, undetectable by HRTEM, and their interaction with supports. This result highlights their role as active species and the need to take them into account to understand integrally the catalysis by supported nanometals. PMID:27110757

  8. Identification and Functional Characterization of Arabidopsis PEROXIN4 and the Interacting Protein PEROXIN22W⃞

    PubMed Central

    Zolman, Bethany K.; Monroe-Augustus, Melanie; Silva, Illeana D.; Bartel, Bonnie

    2005-01-01

    Peroxins are genetically defined as proteins necessary for peroxisome biogenesis. By screening for reduced response to indole-3-butyric acid, which is metabolized to active auxin in peroxisomes, we isolated an Arabidopsis thaliana peroxin4 (pex4) mutant. This mutant displays sucrose-dependent seedling development and reduced lateral root production, characteristics of plant peroxisome malfunction. We used yeast two-hybrid analysis to determine that PEX4, an apparent ubiquitin-conjugating enzyme, interacts with a previously unidentified Arabidopsis protein, PEX22. A pex4 pex22 double mutant enhanced pex4 defects, confirming that PEX22 is a peroxin. Expression of both Arabidopsis genes together complemented yeast pex4 or pex22 mutant defects, whereas expression of either gene individually failed to rescue the corresponding yeast mutant. Therefore, it is likely that the Arabidopsis proteins can function similarly to the yeast PEX4–PEX22 complex, with PEX4 ubiquitinating substrates and PEX22 tethering PEX4 to the peroxisome. However, the severe sucrose dependence of the pex4 pex22 mutant is not accompanied by correspondingly strong defects in peroxisomal matrix protein import, suggesting that this peroxin pair may have novel plant targets in addition to those important in fungi. Isocitrate lyase is stabilized in pex4 pex22, indicating that PEX4 and PEX22 may be important during the remodeling of peroxisome matrix contents as glyoxysomes transition to leaf peroxisomes. PMID:16272432

  9. Identification of a novel interaction between corticotropin releasing hormone (Crh) and macroautophagy

    PubMed Central

    Giannogonas, Panagiotis; Apostolou, Athanasia; Manousopoulou, Antigoni; Theocharis, Stamatis; Macari, Sofia A.; Psarras, Stelios; Garbis, Spiros D.; Pothoulakis, Charalabos; Karalis, Katia P.

    2016-01-01

    In inflammatory bowel disease (IBD), compromised restitution of the epithelial barrier contributes to disease severity. Owing to the complexity in the pathogenesis of IBD, a variety of factors have been implicated in its progress. In this study, we report a functional interaction between macroautophagy and Corticotropin Releasing Hormone (Crh) in the gut. For this purpose we used DSS colitis model on Crh −/− or wild-type (wt) with pharmacological inhibition of autophagy. We uncovered sustained basal autophagy in the gut of Crh −/− mice, which persisted over the course of DSS administration. Autophagy inhibition resulted in partial rescue of Crh −/− mice, while it increased the expression of Crh in the wt gut. Similarly, Crh deficiency was associated with sustained activation of base line autophagy. In vitro models of amino acid deprivation- and LPS-induced autophagy confirmed the in vivo findings. Our results indicate a novel role for Crh in the intestinal epithelium that involves regulation of autophagy, while suggesting the complementary action of the two pathways. These data suggest the intriguing possibility that targeting Crh stimulation in the intestine may provide a novel therapeutic approach to support the integrity of the epithelial barrier and to protect from chronic colitis. PMID:26987580

  10. Investigation of antioxidant interactions between Radix Astragali and Cimicifuga foetida and identification of synergistic antioxidant compounds.

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  12. Imbalance in chemical space: How to facilitate the identification of protein-protein interaction inhibitors

    NASA Astrophysics Data System (ADS)

    Kuenemann, Mélaine A.; Labbé, Céline M.; Cerdan, Adrien H.; Sperandio, Olivier

    2016-04-01

    Protein-protein interactions (PPIs) play vital roles in life and provide new opportunities for therapeutic interventions. In this large data analysis, 3,300 inhibitors of PPIs (iPPIs) were compared to 17 reference datasets of collectively ~566,000 compounds (including natural compounds, existing drugs, active compounds on conventional targets, etc.) using a chemoinformatics approach. Using this procedure, we showed that comparable classes of PPI targets can be formed using either the similarity of their ligands or the shared properties of their binding cavities, constituting a proof-of-concept that not only can binding pockets be used to group PPI targets, but that these pockets certainly condition the properties of their corresponding ligands. These results demonstrate that matching regions in both chemical space and target space can be found. Such identified classes of targets could lead to the design of PPI-class-specific chemical libraries and therefore facilitate the development of iPPIs to the stage of drug candidates.

  13. Identification of a novel interaction between corticotropin releasing hormone (Crh) and macroautophagy.

    PubMed

    Giannogonas, Panagiotis; Apostolou, Athanasia; Manousopoulou, Antigoni; Theocharis, Stamatis; Macari, Sofia A; Psarras, Stelios; Garbis, Spiros D; Pothoulakis, Charalabos; Karalis, Katia P

    2016-01-01

    In inflammatory bowel disease (IBD), compromised restitution of the epithelial barrier contributes to disease severity. Owing to the complexity in the pathogenesis of IBD, a variety of factors have been implicated in its progress. In this study, we report a functional interaction between macroautophagy and Corticotropin Releasing Hormone (Crh) in the gut. For this purpose we used DSS colitis model on Crh -/- or wild-type (wt) with pharmacological inhibition of autophagy. We uncovered sustained basal autophagy in the gut of Crh -/- mice, which persisted over the course of DSS administration. Autophagy inhibition resulted in partial rescue of Crh -/- mice, while it increased the expression of Crh in the wt gut. Similarly, Crh deficiency was associated with sustained activation of base line autophagy. In vitro models of amino acid deprivation- and LPS-induced autophagy confirmed the in vivo findings. Our results indicate a novel role for Crh in the intestinal epithelium that involves regulation of autophagy, while suggesting the complementary action of the two pathways. These data suggest the intriguing possibility that targeting Crh stimulation in the intestine may provide a novel therapeutic approach to support the integrity of the epithelial barrier and to protect from chronic colitis. PMID:26987580

  14. Identification of Nuclear Effects in Neutrino-Carbon Interactions at Low Three-Momentum Transfer

    NASA Astrophysics Data System (ADS)

    Rodrigues, P. A.; Demgen, J.; Miltenberger, E.; Aliaga, L.; Altinok, O.; Bellantoni, L.; Bercellie, A.; Betancourt, M.; Bodek, A.; Bravar, A.; Budd, H.; Cai, T.; Carneiro, M. F.; Chvojka, J.; Devan, J.; Dytman, S. A.; Díaz, G. A.; Eberly, B.; Elkins, M.; Felix, J.; Fields, L.; Fine, R.; Gago, A. M.; Galindo, R.; Gallagher, H.; Ghosh, A.; Golan, T.; Gran, R.; Harris, D. A.; Higuera, A.; Hurtado, K.; Kiveni, M.; Kleykamp, J.; Kordosky, M.; Le, T.; Leistico, J. R.; Lovlein, A.; Maher, E.; Manly, S.; Mann, W. A.; Marshall, C. M.; Martinez Caicedo, D. A.; McFarland, K. S.; McGivern, C. L.; McGowan, A. M.; Messerly, B.; Miller, J.; Mislivec, A.; Morfín, J. G.; Mousseau, J.; Muhlbeier, T.; Naples, D.; Nelson, J. K.; Norrick, A.; Nuruzzaman; Osta, J.; Paolone, V.; Patrick, C. E.; Perdue, G. N.; Ramirez, M. A.; Ransome, R. D.; Ray, H.; Ren, L.; Rimal, D.; Ruterbories, D.; Schellman, H.; Schmitz, D. W.; Solano Salinas, C. J.; Tagg, N.; Tice, B. G.; Valencia, E.; Walton, T.; Wolcott, J.; Wospakrik, M.; Zavala, G.; Zhang, D.; Minerva Collaboration

    2016-02-01

    Two different nuclear-medium effects are isolated using a low three-momentum transfer subsample of neutrino-carbon scattering data from the MINERvA neutrino experiment. The observed hadronic energy in charged-current νμ interactions is combined with muon kinematics to permit separation of the quasielastic and Δ (1232 ) resonance processes. First, we observe a small cross section at very low energy transfer that matches the expected screening effect of long-range nucleon correlations. Second, additions to the event rate in the kinematic region between the quasielastic and Δ resonance processes are needed to describe the data. The data in this kinematic region also have an enhanced population of multiproton final states. Contributions predicted for scattering from a nucleon pair have both properties; the model tested in this analysis is a significant improvement but does not fully describe the data. We present the results as a double-differential cross section to enable further investigation of nuclear models. Improved description of the effects of the nuclear environment are required by current and future neutrino oscillation experiments.

  15. Identification of Novel Tau Interactions with Endoplasmic Reticulum Proteins in Alzheimer’s Disease Brain

    PubMed Central

    Meier, Shelby; Bell, Michelle; Lyons, Danielle N.; Ingram, Alexandria; Chen, Jing; Gensel, John C.; Zhu, Haining; Nelson, Peter T.; Abisambra, Jose F.

    2016-01-01

    Alzheimer’s disease (AD) is a progressive neurodegenerative disorder that is pathologically characterized by the formation of extracellular amyloid plaques and intraneuronal tau tangles. We recently identified that tau associates with proteins known to participate in endoplasmic reticulum (ER)-associated degradation (ERAD); consequently, ERAD becomes dysfunctional and causes neurotoxicity. We hypothesized that tau associates with other ER proteins, and that this association could also lead to cellular dysfunction in AD. Portions of human AD and non-demented age matched control brains were fractionated to obtain microsomes, from which tau was co-immunoprecipitated. Samples from both conditions containing tau and its associated proteins were analyzed by mass spectrometry. In total, we identified 91 ER proteins that co-immunoprecipitated with tau; 15.4% were common between AD and control brains, and 42.9% only in the AD samples. The remainder, 41.8% of the proteins, was only seen in the control brain samples. We identified a variety of previously unreported interactions between tau and ER proteins. These proteins participate in over sixteen functional categories, the most abundant being involved in RNA translation. We then determined that association of tau with these ER proteins was different between the AD and control samples. We found that tau associated equally with the ribosomal protein L28 but more robustly with the ribosomal protein P0. These data suggest that the differential association between tau and ER proteins in disease could reveal the pathogenic processes by which tau induces cellular dysfunction. PMID:26402096

  16. Identification, localization and interaction of SNARE proteins in atrial cardiac myocytes.

    PubMed

    Peters, Christian G; Miller, Daniel F; Giovannucci, David R

    2006-03-01

    Atrial cardiac myocytes secrete the vasoactive hormone atrial natriuretic peptide (ANP) by both constitutive and regulated exocytotic fusion of ANP-containing large dense core vesicles (LDCV) with the sarcolemma. Detailed information, however, regarding the identity and function of specific membrane fusion proteins (SNARE proteins) involved in exocytosis in the endocrine heart is lacking. In the current study, we identified SNARE proteins and determined their association with ANP-containing secretory granules using primary cultures of neonatal and adult rat atrial cardiac myocytes. Using RT-PCR, cardiac myocytes were screened for SNARE and SNARE-associated transcripts. Identified SNARE proteins that have been implicated in exocytosis in neuroendocrine cells were further characterized by Western blot analysis. Functional interaction between SNARE proteins was demonstrated using immunoprecipitation. Using cell fractionation and immunocytochemical methods, it was revealed that VAMP-1, VAMP-2 and synaptotagmin-1 (the putative Ca(2+) sensor) localized to subpopulations of ANP-containing secretory granules in atrial myocytes. Currently, there is conflicting data regarding the role of Ca(2+) in ANP exocytosis. To judge whether secretory activity could be evoked by intracellular Ca(2+) elevation, time-resolved membrane capacitance measurements were used in combination with the flash photolysis of caged compounds to follow the exocytotic activity of single neonatal atrial myocytes. These studies demonstrated that multiple SNARE proteins are present in neonatal and adult cardiac myocytes and suggest the importance of Ca(2+) in exocytosis of ANP from neonatal atrial cardiac myocytes. PMID:16458920

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

    PubMed

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

    2005-01-01

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

  18. Identification of key residues involved in fibril formation by the conserved N-terminal region of Plasmodium falciparum merozoite surface protein 2 (MSP2)

    PubMed Central

    Yang, Xiaodong; Adda, Christopher G.; MacRaild, Christopher A.; Low, Andrew; Zhang, Xuecheng; Zeng, Weiguang; Jackson, David C.; Anders, Robin F.; Norton, Raymond S.

    2010-01-01

    Merozoite surface protein 2 (MSP2) from the human malaria parasite Plasmodium falciparum is expressed as a GPI-anchored protein on the merozoite surface. MSP2 is assumed to have a role in erythrocyte invasion and is a leading vaccine candidate. Recombinant MSP2 forms amyloid-like fibrils upon storage, as do peptides corresponding to sequences in the conserved N-terminal region, which constitutes the structural core of fibrils formed by full-length MSP2. We have investigated the roles of individual residues in fibril formation and local ordered structure in two peptides, a recombinant 25-residue peptide corresponding to the entire N-terminal domain of mature MSP2 and an 8-residue peptide from the central region of this domain (residues 8–15). Both peptides formed fibrils that were similar to amyloid-like fibrils formed by full-length MSP2. Phe11 and Ile12 have important roles both in stabilising local structure in these peptides and promoting fibril formation; the F11A and I12A mutants of MSP28–15 were essentially unstructured in solution and fibril formation at pH 7.4 and 4.7 was markedly retarded. The T10A mutant showed intermediate behaviour, having a less well-defined structure than wild-type and slower fibril formation at pH 7.4. The mutation of Phe11 and Ile12 in MSP21–25 significantly retarded but did not abolish fibril formation, indicating that these residues also play a key role in fibril formation by the entire N-terminal conserved region. These mutations had little effect on the aggregation of full-length MSP2, however, suggesting that regions outside the conserved N-terminus have unanticipated importance for fibril formation in the full-length protein. PMID:20542076

  19. Gamete Interactions in Xenopus laevis: Identification of Sperm Binding Glycoproteins in the Egg Vitelline Envelope

    PubMed Central

    Tian, Jingdong; Gong, Hui; Thomsen, Gerald H.; Lennarz, William J.

    1997-01-01

    A quantitative assay was developed to study the interaction of Xenopus laevis sperm and eggs. Using this assay it was found that sperm bound in approximately equal numbers to the surface of both hemispheres of the unfertilized egg, but not to the surface of the fertilized egg. To understand the molecular basis of sperm binding to the egg vitelline envelope (VE), a competition assay was used and it was found that solubilized total VE proteins inhibited sperm-egg binding in a concentration-dependent manner. Individual VE proteins were then isolated and tested for their ability to inhibit sperm binding. Of the seven proteins in the VE, two related glycoproteins, gp69 and gp64, inhibited sperm-egg binding. Polyclonal antibody was prepared that specifically recognized gp69 and gp64. This gp69/64 specific antibody bound to the VE surface and blocked sperm binding, as well as fertilization. Moreover, agarose beads coated with gp69/64 showed high sperm binding activity, while beads coated with other VE proteins bound few sperm. Treatment of unfertilized eggs with crude collagenase resulted in proteolytic modification of only the gp69/64 components of the VE, and this modification abolished sperm-egg binding. Small glycopeptides generated by Pronase digestion of gp69/64 also inhibited sperm-egg binding and this inhibition was abolished by treatment of the glycopeptides with periodate. Based on these observations, we conclude that the gp69/64 glycoproteins in the egg vitelline envelope mediate sperm-egg binding, an initial step in Xenopus fertilization, and that the oligosaccharide chains of these glycoproteins may play a critical role in this process. PMID:9060474

  20. Identification of Interactions between Abscisic Acid and Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase

    PubMed Central

    Galka, Marek M.; Rajagopalan, Nandhakishore; Buhrow, Leann M.; Nelson, Ken M.; Switala, Jacek; Cutler, Adrian J.; Palmer, David R. J.; Loewen, Peter C.; Abrams, Suzanne R.; Loewen, Michele C.

    2015-01-01

    Abscisic acid ((+)-ABA) is a phytohormone involved in the modulation of developmental processes and stress responses in plants. A chemical proteomics approach using an ABA mimetic probe was combined with in vitro assays, isothermal titration calorimetry (ITC), x-ray crystallography and in silico modelling to identify putative (+)-ABA binding-proteins in crude extracts of Arabidopsis thaliana. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) was identified as a putative ABA-binding protein. Radiolabelled-binding assays yielded a Kd of 47 nM for (+)-ABA binding to spinach Rubisco, which was validated by ITC, and found to be similar to reported and experimentally derived values for the native ribulose-1,5-bisphosphate (RuBP) substrate. Functionally, (+)-ABA caused only weak inhibition of Rubisco catalytic activity (Ki of 2.1 mM), but more potent inhibition of Rubisco activation (Ki of ~ 130 μM). Comparative structural analysis of Rubisco in the presence of (+)-ABA with RuBP in the active site revealed only a putative low occupancy (+)-ABA binding site on the surface of the large subunit at a location distal from the active site. However, subtle distortions in electron density in the binding pocket and in silico docking support the possibility of a higher affinity (+)-ABA binding site in the RuBP binding pocket. Overall we conclude that (+)-ABA interacts with Rubisco. While the low occupancy (+)-ABA binding site and weak non-competitive inhibition of catalysis may not be relevant, the high affinity site may allow ABA to act as a negative effector of Rubisco activation. PMID:26197050

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

    PubMed Central

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

    2012-01-01

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

  2. Magnetic hyperthermia properties of nanoparticles inside lysosomes using kinetic Monte Carlo simulations: Influence of key parameters and dipolar interactions, and evidence for strong spatial variation of heating power

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    Understanding the influence of dipolar interactions in magnetic hyperthermia experiments is of crucial importance for fine optimization of nanoparticle (NP) heating power. In this study we use a kinetic Monte Carlo algorithm to calculate hysteresis loops that correctly account for both time and temperature. This algorithm is shown to correctly reproduce the high-frequency hysteresis loop of both superparamagnetic and ferromagnetic NPs without any ad hoc or artificial parameters. The algorithm is easily parallelizable with a good speed-up behavior, which considerably decreases the calculation time on several processors and enables the study of assemblies of several thousands of NPs. The specific absorption rate (SAR) of magnetic NPs dispersed inside spherical lysosomes is studied as a function of several key parameters: volume concentration, applied magnetic field, lysosome size, NP diameter, and anisotropy. The influence of these parameters is illustrated and comprehensively explained. In summary, magnetic interactions increase the coercive field, saturation field, and hysteresis area of major loops. However, for small amplitude magnetic fields such as those used in magnetic hyperthermia, the heating power as a function of concentration can increase, decrease, or display a bell shape, depending on the relationship between the applied magnetic field and the coercive/saturation fields of the NPs. The hysteresis area is found to be well correlated with the parallel or antiparallel nature of the dipolar field acting on each particle. The heating power of a given NP is strongly influenced by a local concentration involving approximately 20 neighbors. Because this local concentration strongly decreases upon approaching the surface, the heating power increases or decreases in the vicinity of the lysosome membrane. The amplitude of variation reaches more than one order of magnitude in certain conditions. This transition occurs on a thickness corresponding to approximately 1.3 times the mean distance between two neighbors. The amplitude and sign of this variation is explained. Finally, implications of these various findings are discussed in the framework of magnetic hyperthermia optimization. It is concluded that feedback on two specific points from biology experiments is required for further advancement of the optimization of magnetic NPs for magnetic hyperthermia. The present simulations will be an advantageous tool to optimize magnetic NPs heating power and interpret experimental results.

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

    PubMed

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

    2009-01-01

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

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

    SciTech Connect

    Fang, Ti; Li, De-Feng; Zhou, Ning-Yi

    2011-07-08

    Highlights: {yields} Application of site-directed mutagenesis to probe the active site residues of glutathione-dependent maleylpyruvate isomerase. {yields} Two conserved residues, Arg8 and Arg176, in zeta class glutathione S-transferases are critical for maleylpyruvate orientation and enolization. {yields} Arg109, found exclusively in NagL, participates in k{sub cat} regulation. {yields} The T11A mutant exhibited a significantly decreased K{sub m} value for glutathione with little impact on maleylpyruvate kinetics. {yields} The Thr11 residue appears to have significance in the evolution of glutathione S-transferase classes. -- Abstract: The maleylpyruvate isomerase NagL from Ralstonia sp. strain U2, which has been structurally characterized previously, catalyzes the isomerization of maleylpyruvate to fumarylpyruvate. It belongs to the class zeta glutathione S-transferases (GSTZs), part of the cytosolic GST family (cGSTs). In this study, site-directed mutagenesis was conducted to probe the functions of 13 putative active site residues. Steady-state kinetic information for mutants in the reduced glutathione (GSH) binding site, suggested that (a) Gln64 and Asp102 interact directly with the glutamyl moiety of glutathione, (b) Gln49 and Gln64 are involved in a potential electron-sharing network that influences the ionization of the GSH thiol. The information also suggests that (c) His38, Asn108 and Arg109 interact with the GSH glycine moiety, (d) His104 has a role in the ionization of the GSH sulfur and the stabilization of the maleyl terminal carboxyl group in the reaction intermediate and (e) Arg110 influences the electron distribution in the active site and therefore the ionization of the GSH thiolate. Kinetic data for mutants altered in the substrate-binding site imply that (a) Arg8 and Arg176 are critical for maleylpyruvate orientation and enolization, and (b) Arg109 (exclusive to NagL) participates in k{sub cat} regulation. Surprisingly, the T11A mutant had a decreased GSH K{sub m} value, whereas little impact on maleylpyruvate kinetics was observed, suggesting that this residue plays an important role in GSH binding. An evolutionary trend in this residue appears to have developed not only in prokaryotic and eukaryotic GSTZs, but also among the wider class of cGSTs.

  5. Key bioactive reaction products of the NO/H2S interaction are S/N-hybrid species, polysulfides, and nitroxyl

    PubMed Central

    Cortese-Krott, Miriam M.; Kuhnle, Gunter G. C.; Dyson, Alex; Fernandez, Bernadette O.; Grman, Marian; DuMond, Jenna F.; Barrow, Mark P.; McLeod, George; Nakagawa, Hidehiko; Ondrias, Karol; Nagy, Péter; King, S. Bruce; Saavedra, Joseph E.; Keefer, Larry K.; Singer, Mervyn; Kelm, Malte; Butler, Anthony R.; Feelisch, Martin

    2015-01-01

    Experimental evidence suggests that nitric oxide (NO) and hydrogen sulfide (H2S) signaling pathways are intimately intertwined, with mutual attenuation or potentiation of biological responses in the cardiovascular system and elsewhere. The chemical basis of this interaction is elusive. Moreover, polysulfides recently emerged as potential mediators of H2S/sulfide signaling, but their biosynthesis and relationship to NO remain enigmatic. We sought to characterize the nature, chemical biology, and bioactivity of key reaction products formed in the NO/sulfide system. At physiological pH, we find that NO and sulfide form a network of cascading chemical reactions that generate radical intermediates as well as anionic and uncharged solutes, with accumulation of three major products: nitrosopersulfide (SSNO−), polysulfides, and dinitrososulfite [N-nitrosohydroxylamine-N-sulfonate (SULFI/NO)], each with a distinct chemical biology and in vitro and in vivo bioactivity. SSNO− is resistant to thiols and cyanolysis, efficiently donates both sulfane sulfur and NO, and potently lowers blood pressure. Polysulfides are both intermediates and products of SSNO− synthesis/decomposition, and they also decrease blood pressure and enhance arterial compliance. SULFI/NO is a weak combined NO/nitroxyl donor that releases mainly N2O on decomposition; although it affects blood pressure only mildly, it markedly increases cardiac contractility, and formation of its precursor sulfite likely contributes to NO scavenging. Our results unveil an unexpectedly rich network of coupled chemical reactions between NO and H2S/sulfide, suggesting that the bioactivity of either transmitter is governed by concomitant formation of polysulfides and anionic S/N-hybrid species. This conceptual framework would seem to offer ample opportunities for the modulation of fundamental biological processes governed by redox switching and sulfur trafficking. PMID:26224837

  6. Key bioactive reaction products of the NO/H2S interaction are S/N-hybrid species, polysulfides, and nitroxyl.

    PubMed

    Cortese-Krott, Miriam M; Kuhnle, Gunter G C; Dyson, Alex; Fernandez, Bernadette O; Grman, Marian; DuMond, Jenna F; Barrow, Mark P; McLeod, George; Nakagawa, Hidehiko; Ondrias, Karol; Nagy, Péter; King, S Bruce; Saavedra, Joseph E; Keefer, Larry K; Singer, Mervyn; Kelm, Malte; Butler, Anthony R; Feelisch, Martin

    2015-08-25

    Experimental evidence suggests that nitric oxide (NO) and hydrogen sulfide (H2S) signaling pathways are intimately intertwined, with mutual attenuation or potentiation of biological responses in the cardiovascular system and elsewhere. The chemical basis of this interaction is elusive. Moreover, polysulfides recently emerged as potential mediators of H2S/sulfide signaling, but their biosynthesis and relationship to NO remain enigmatic. We sought to characterize the nature, chemical biology, and bioactivity of key reaction products formed in the NO/sulfide system. At physiological pH, we find that NO and sulfide form a network of cascading chemical reactions that generate radical intermediates as well as anionic and uncharged solutes, with accumulation of three major products: nitrosopersulfide (SSNO(-)), polysulfides, and dinitrososulfite [N-nitrosohydroxylamine-N-sulfonate (SULFI/NO)], each with a distinct chemical biology and in vitro and in vivo bioactivity. SSNO(-) is resistant to thiols and cyanolysis, efficiently donates both sulfane sulfur and NO, and potently lowers blood pressure. Polysulfides are both intermediates and products of SSNO(-) synthesis/decomposition, and they also decrease blood pressure and enhance arterial compliance. SULFI/NO is a weak combined NO/nitroxyl donor that releases mainly N2O on decomposition; although it affects blood pressure only mildly, it markedly increases cardiac contractility, and formation of its precursor sulfite likely contributes to NO scavenging. Our results unveil an unexpectedly rich network of coupled chemical reactions between NO and H2S/sulfide, suggesting that the bioactivity of either transmitter is governed by concomitant formation of polysulfides and anionic S/N-hybrid species. This conceptual framework would seem to offer ample opportunities for the modulation of fundamental biological processes governed by redox switching and sulfur trafficking. PMID:26224837

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

    PubMed Central

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

    2013-01-01

    Chemolithoautotrophic nitrifying bacteria release soluble organic compounds, which can be substrates for heterotrophic microorganisms. The identities of these heterotrophs and the specificities of their interactions with nitrifiers are largely unknown. In this study, we incubated nitrifying activated sludge with 13C-labeled bicarbonate and used stable isotope probing of 16S rRNA to monitor the flow of carbon from uncultured nitrifiers to heterotrophs. To facilitate the identification of heterotrophs, the abundant 16S rRNA molecules from nitrifiers were depleted by catalytic oligonucleotides containing locked nucleic acids (LNAzymes), which specifically cut the 16S rRNA of defined target organisms. Among the 13C-labeled heterotrophs were organisms remotely related to Micavibrio, a microbial predator of Gram-negative bacteria. Fluorescence in situ hybridization revealed a close spatial association of these organisms with microcolonies of nitrite-oxidizing sublineage I Nitrospira in sludge flocs. The high specificity of this interaction was confirmed by confocal microscopy and a novel image analysis method to quantify the localization patterns of biofilm microorganisms in three-dimensional (3-D) space. Other isotope-labeled bacteria, which were affiliated with Thermomonas, colocalized less frequently with nitrifiers and thus were commensals or saprophytes rather than specific symbionts or predators. These results suggest that Nitrospira spp. are subject to bacterial predation, which may influence the abundance and diversity of these nitrite oxidizers and the stability of nitrification in engineered and natural ecosystems. In silico screening of published next-generation sequencing data sets revealed a broad environmental distribution of the uncultured Micavibrio-like lineage. PMID:23335755

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

    PubMed Central

    2011-01-01

    Background "Candidatus Phytoplasma aurantifolia", is the causative agent of witches' broom disease in Mexican lime trees (Citrus aurantifolia L.), and is responsible for major losses of Mexican lime trees in Southern Iran and Oman. The pathogen is strictly biotrophic, and thus is completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. Therefore, we have applied a cDNA- amplified fragment length polymorphism (AFLP) approach to analyze gene expression in Mexican lime trees infected by "Ca. Phytoplasma aurantifolia". Results We carried out cDNA-AFLP analysis on grafted infected Mexican lime trees of the susceptible cultivar at the representative symptoms stage. Selective amplifications with 43 primer combinations allowed the visualisation of 55 transcript-derived fragments that were expressed differentially between infected and non-infected leaves. We sequenced 51 fragments, 36 of which were identified as lime tree transcripts after homology searching. Of the 36 genes, 70.5% were down-regulated during infection and could be classified into various functional groups. We showed that Mexican lime tree genes that were homologous to known resistance genes tended to be repressed in response to infection. These included the genes for modifier of snc1 and autophagy protein 5. Furthermore, down-regulation of genes involved in metabolism, transcription, transport and cytoskeleton was observed, which included the genes for formin, importin β 3, transducin, L-asparaginase, glycerophosphoryl diester phosphodiesterase, and RNA polymerase β. In contrast, genes that encoded a proline-rich protein, ubiquitin-protein ligase, phosphatidyl glycerol specific phospholipase C-like, and serine/threonine-protein kinase were up-regulated during the infection. Conclusion The present study identifies a number of candidate genes that might be involved in the interaction of Mexican lime trees with "Candidatus Phytoplasma aurantifolia". These results should help to elucidate the molecular basis of the infection process and to identify genes that could be targeted to increase plant resistance and inhibit the growth and reproduction of the pathogen. PMID:21194490

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

    PubMed Central

    2010-01-01

    Background It has been understood that biological networks have modular organizations which are the sources of their observed complexity. Analysis of networks and motifs has shown that two types of hubs, party hubs and date hubs, are responsible for this complexity. Party hubs are local coordinators because of their high co-expressions with their partners, whereas date hubs display low co-expressions and are assumed as global connectors. However there is no mutual agreement on these concepts in related literature with different studies reporting their results on different data sets. We investigated whether there is a relation between the biological features of Saccharomyces Cerevisiae's proteins and their roles as non-hubs, intermediately connected, party hubs, and date hubs. We propose a classifier that separates these four classes. Results We extracted different biological characteristics including amino acid sequences, domain contents, repeated domains, functional categories, biological processes, cellular compartments, disordered regions, and position specific scoring matrix from various sources. Several classifiers are examined and the best feature-sets based on average correct classification rate and correlation coefficients of the results are selected. We show that fusion of five feature-sets including domains, Position Specific Scoring Matrix-400, cellular compartments level one, and composition pairs with two and one gaps provide the best discrimination with an average correct classification rate of 77%. Conclusions We study a variety of known biological feature-sets of the proteins and show that there is a relation between domains, Position Specific Scoring Matrix-400, cellular compartments level one, composition pairs with two and one gaps of Saccharomyces Cerevisiae's proteins, and their roles in the protein interaction network as non-hubs, intermediately connected, party hubs and date hubs. This study also confirms the possibility of predicting non-hubs, party hubs and date hubs based on their biological features with acceptable accuracy. If such a hypothesis is correct for other species as well, similar methods can be applied to predict the roles of proteins in those species. PMID:21167069

  10. Identification of the mitogen-activated protein kinase phosphorylation sites on human Sos1 that regulate interaction with Grb2.

    PubMed Central

    Corbalan-Garcia, S; Yang, S S; Degenhardt, K R; Bar-Sagi, D

    1996-01-01

    The Son of sevenless proteins (Sos) are guanine nucleotide exchange factors involved in the activation of Ras by cytoplasmic and receptor tyrosine kinases. Growth factor stimulation rapidly induces the phosphorylation of Sos on multiple serine and threonine sites. Previous studies have demonstrated that growth factor-induced Sos phosphorylation occurs at the C-terminal region of the protein and is mediated, in part, by mitogen-activated protein (MAP) kinase. In this report, we describe the identification of five MAP kinase sites (S-1137, S-1167, S-1178, S-1193, and S-1197) on hSos1. We demonstrate that four of these sites, S-1132, S-1167, S-1178, and S-1193, become phosphorylated following growth factor stimulation. The MAP kinase phosphorylation sites are clustered within a region encompassing three proline-rich SH3-binding sites in the C-terminal domain of hSos1. Replacing the MAP kinase phosphorylation sites with alanine residues results in an increase in the binding affinity of Grb2 to hSos1. Interestingly, hSos2 contains only one MAP kinase phosphorylation site and, as demonstrated previously, has an increased affinity toward Grb2 compared with hSos1. These results suggest a role for MAP kinase in the regulation of Grb2-Sos interactions. Since the binding of Grb2 is important for Sos function, the phosphorylation-dependent modulation of Grb2-Sos association may provide a means of controlling Ras activation. PMID:8816480

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

    PubMed

    Poyer, Salom; Loutelier-Bourhis, Corinne; Coadou, Gal; Mondeguer, Florence; Enche, Julien; Bosse, Anne; Hess, Philipp; Afonso, Carlos

    2015-01-01

    The aim of this work was to develop a reliable and efficient analytical method to characterise and differentiate saxitoxin analogues (STX), including sulphated (gonyautoxins, GTX) and non-sulphated analogues. For this purpose, hydrophilic interaction liquid chromatography (HILIC) was used to separate sulphated analogues. We also resorted to ion mobility spectrometry to differentiate the STX analogues because this technique adds a new dimension of separation based on ion gas phase conformation. Positive and negative ionisation modes were used for gonyautoxins while positive ionisation mode was used for non-sulphated analogues. Subsequently, the coupling of these three complementary techniques, HILIC-IM-MS, permitted the separation and identification of STX analogues; isomer differentiation was achieved in HILIC dimension while non-sulphated analogues were separated in the IM-MS dimension. Additional structural characteristics concerning the conformation of STXs could be obtained using IM-MS measurements. Thus, the collision cross sections (CCS) of STXs are reported for the first time in the positive ionisation mode. These experimental CCSs correlated well with the calculated CCS values using the trajectory method. PMID:25601690

  12. Identification of Genetic Modules Mediating the Jekyll and Hyde Interaction of Dinoroseobacter shibae with the Dinoflagellate Prorocentrum minimum

    PubMed Central

    Wang, Hui; Tomasch, Jürgen; Michael, Victoria; Bhuju, Sabin; Jarek, Michael; Petersen, Jörn; Wagner-Döbler, Irene

    2015-01-01

    The co-cultivation of the alphaproteobacterium Dinoroseobacter shibae with the dinoflagellate Prorocentrum minimum is characterized by a mutualistic phase followed by a pathogenic phase in which the bacterium kills aging algae. Thus it resembles the “Jekyll-and-Hyde” interaction that has been proposed for other algae and Roseobacter. Here, we identified key genetic components of this interaction. Analysis of the transcriptome of D. shibae in co-culture with P. minimum revealed growth phase dependent changes in the expression of quorum sensing, the CtrA phosphorelay, and flagella biosynthesis genes. Deletion of the histidine kinase gene cckA which is part of the CtrA phosphorelay or the flagella genes fliC or flgK resulted in complete lack of growth stimulation of P. minimum in co-culture with the D. shibae mutants. By contrast, pathogenicity was entirely dependent on one of the extrachromosomal elements of D. shibae, the 191 kb plasmid. The data show that flagella and the CtrA phosphorelay are required for establishing mutualism and prove a cell density dependent killing effect of D. shibae on P. minimum which is mediated by an unknown factor encoded on the 191 kb plasmid. PMID:26617596

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2013-08-01

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

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

    PubMed Central

    2010-01-01

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

  17. Identification of Microcystis aeruginosa Peptides Responsible for Allergic Sensitization and Characterization of Functional Interactions between Cyanobacterial Toxins and Immunogenic Peptides

    PubMed Central

    Geh, Esmond N.; Ghosh, Debajyoti; McKell, Melanie; de la Cruz, Armah A.; Stelma, Gerard

    2015-01-01

    Background The cyanobacterium species Microcystis aeruginosa produces microcystin and an array of diverse metabolites believed responsible for their toxicity and/or immunogenicity. Previously, chronic rhinitis patients were demonstrated to elicit a specific IgE response to nontoxic strains of M. aeruginosa by skin-prick testing, indicating that cyanobacteria allergenicity resides in a non-toxin–producing component of the organism. Objectives We sought to identify and characterize M. aeruginosa peptide(s) responsible for allergic sensitization in susceptible individuals, and we investigated the functional interactions between cyanobacterial toxins and their coexpressed immunogenic peptides. Methods Sera from patients and extracts from M. aeruginosa toxic [MC(+)] and nontoxic [MC(–)] strains were used to test IgE-specific reactivity by direct and indirect ELISAs; 2D gel electrophoresis, followed by immunoblots and mass spectrometry (MS), was performed to identify the relevant sensitizing peptides. Cytotoxicity and mediator release assays were performed using the MC(+) and MC(–) lysates. Results We found specific IgE to be increased more in response to the MC(–) strain than the MC(+) strain. This response was inhibited by preincubation of MC(–) lysate with increasing concentrations of microcystin. MS revealed that phycocyanin and the core-membrane linker peptide are the responsible allergens, and MC(–) extracts containing these proteins induced β-hexosaminidase release in rat basophil leukemia cells. Conclusions Phycobiliprotein complexes in M. aeruginosa have been identified as the relevant sensitizing proteins. Our finding that allergenicity is inhibited in a dose-dependent manner by microcystin toxin suggests that further investigation is warranted to understand the interplay between immunogenicity and toxicity of cyanobacteria under diverse environmental conditions. Citation Geh EN, Ghosh D, McKell M, de la Cruz AA, Stelma G, Bernstein JA. 2015. Identification of Microcystis aeruginosa peptides responsible for allergic sensitization and characterization of functional interactions between cyanobacterial toxins and immunogenic peptides. Environ Health Perspect 123:1159–1166; http://dx.doi.org/10.1289/ehp.1409065 PMID:25902363

  18. Identification of More Feasible MicroRNA-mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction.

    PubMed

    Taguchi, Y-H

    2016-01-01

    MicroRNA(miRNA)-mRNA interactions are important for understanding many biological processes, including development, differentiation and disease progression, but their identification is highly context-dependent. When computationally derived from sequence information alone, the identification should be verified by integrated analyses of mRNA and miRNA expression. The drawback of this strategy is the vast number of identified interactions, which prevents an experimental or detailed investigation of each pair. In this paper, we overcome this difficulty by the recently proposed principal component analysis (PCA)-based unsupervised feature extraction (FE), which reduces the number of identified miRNA-mRNA interactions that properly discriminate between patients and healthy controls without losing biological feasibility. The approach is applied to six cancers: hepatocellular carcinoma, non-small cell lung cancer, esophageal squamous cell carcinoma, prostate cancer, colorectal/colon cancer and breast cancer. In PCA-based unsupervised FE, the significance does not depend on the number of samples (as in the standard case) but on the number of features, which approximates the number of miRNAs/mRNAs. To our knowledge, we have newly identified miRNA-mRNA interactions in multiple cancers based on a single common (universal) criterion. Moreover, the number of identified interactions was sufficiently small to be sequentially curated by literature searches. PMID:27171078

  19. Identification of More Feasible MicroRNA–mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction

    PubMed Central

    Taguchi, Y-h.

    2016-01-01

    MicroRNA(miRNA)–mRNA interactions are important for understanding many biological processes, including development, differentiation and disease progression, but their identification is highly context-dependent. When computationally derived from sequence information alone, the identification should be verified by integrated analyses of mRNA and miRNA expression. The drawback of this strategy is the vast number of identified interactions, which prevents an experimental or detailed investigation of each pair. In this paper, we overcome this difficulty by the recently proposed principal component analysis (PCA)-based unsupervised feature extraction (FE), which reduces the number of identified miRNA–mRNA interactions that properly discriminate between patients and healthy controls without losing biological feasibility. The approach is applied to six cancers: hepatocellular carcinoma, non-small cell lung cancer, esophageal squamous cell carcinoma, prostate cancer, colorectal/colon cancer and breast cancer. In PCA-based unsupervised FE, the significance does not depend on the number of samples (as in the standard case) but on the number of features, which approximates the number of miRNAs/mRNAs. To our knowledge, we have newly identified miRNA–mRNA interactions in multiple cancers based on a single common (universal) criterion. Moreover, the number of identified interactions was sufficiently small to be sequentially curated by literature searches. PMID:27171078

  20. [Sporadic upper urinary tract urothelial cell carcinomas: identification of interaction between toxic carcinogens and individuals genetic susceptibility].

    PubMed

    Colin, P; Koenig, P; Ballereau, C; Ph, V; Berthon, N; Villers, A; Biserte, J; Rouprt, M

    2010-01-01

    Upper urinary tract urothelial cell carcinomas (UUT UCC) are rare sporadic tumors. Recent epidemiologic and molecular data have shown a singular susceptibility of UUT UCCs for specific risk factors. The main exogenic factors involved in UUT UCCs carcinogenesis remain tobacco and occupational exposure (aromatic amines, polycyclic hydrocarbures and chlored solvents). Enzymatic variants of detoxification system may be responsible of carcinogenesis with these toxics. Tumors induced by phenacetine consumption are decreasing since it was banned in the 1970s. Also, acid aristolochic exposure (Balkan nephropathy, Chinese Herb nephropathy) has been demonstrated to specifically induce UUT UCCs. Familial genic polymorphism of detoxification system would explain geographic distribution in endemic areas. In Taiwan, chronic arsenic exposition would constitute the main risk factor of UUT UCC. However, theses mechanisms of carcinogenesis remain unclear. The knowledge of UUT UCC development mechanisms implying toxic detoxification systems is still incomplete. To date, there is a growing body of evidence supporting that the interaction between individual genetic susceptibilities and environmental toxic exposure is a key to explain carcinogenesis in the majority of sporadic UUT UCC occurrence. PMID:20123521

  1. Identification of Two bZIP Transcription Factors Interacting with the Promoter of Soybean Rubisco Activase Gene (GmRCAα)

    PubMed Central

    Zhang, Jinyu; Du, Hongyang; Chao, Maoni; Yin, Zhitong; Yang, Hui; Li, Yakai; Huang, Fang; Yu, Deyue

    2016-01-01

    Rubisco activase (RCA), a key photosynthetic protein, catalyses the activation of Rubisco and thus plays an important role in photosynthesis. Although the RCA gene has been characterized in a variety of species, the molecular mechanism regulating its transcription remains unclear. Our previous studies on RCA gene expression in soybean suggested that expression of this gene is regulated by trans-acting factors. In the present study, we verified activity of the GmRCAα promoter in both soybean and Arabidopsis and used a yeast one-hybrid (Y1H) system for screening a leaf cDNA expression library to identify transcription factors (TFs) interacting with the GmRCAα promoter. Four basic leucine zipper (bZIP) TFs, GmbZIP04g, GmbZIP07g, GmbZIP1, and GmbZIP71, were isolated, and GmbZIP04g and GmbZIP07g were confirmed as able to bind to a 21-nt G-box-containing sequence. Additionally, the expression patterns of GmbZIP04g, GmbZIp07g, and GmRCAα were analyzed in response to abiotic stresses and during a 24-h period. Our study will help to advance elucidation of the network regulating GmRCAα transcription.

  2. Revision of the African pollen beetle genera Tarchonanthogethes and Xenostrongylogethes, with insect-host plant relationships, identification key, and cladistic analysis of the Anthystrix genus-complex (Coleoptera: Nitidulidae: Meligethinae).

    PubMed

    Audisio, Paolo; Cline, Andrew R; Trizzino, Marco; Mancini, Emiliano; Antonini, Gloria; Sabatelli, Simone; Cerretti, Pierfilippo

    2015-01-01

    The Afrotropical endemic pollen beetle genera Tarchonanthogethes Audisio & Cline and Xenostrongylogethes Audisio & Cline, of the Anthystrix genus-complex, are revised. Eleven new species of Tarchonanthogethes (T. autumnalis, sp. nov., T. bisignatus, sp. nov., T. fasciatus, sp. nov., T. gratiellae, sp. nov., T. hermani, sp. nov., T. hystrix, sp. nov., T. lilliputianus, sp. nov., T. maasai, sp. nov., T. manconiae, sp. nov., T. pectinipes, sp. nov., T. thalycriformis, sp. nov.) and one new Xenostrongylogethes (X. cychramoides, sp. nov.) are described, illustrated and compared with related taxa. Tarchonanthogethes hirtus Kirejtshuk & Easton, 1988 is synonymized with T. martini (syn. nov.). Meligethes assutus Easton, 1960 from Kenya is transferred from Afrogethes Audisio & Cline to Tarchonanthogethes (comb. nov.). Meligethes singularis Grouvelle, 1919 from southern Africa is transferred from Tarchonanthogethes to Meligethinus Grouvelle, 1906 (comb. nov.). Larval host-plants for Tarchonanthogethes and Xenostrongylogethes include dioecious bushes and trees of Tarchonantheae Asteraceae (genera Brachylaena R.Br. and Tarchonanthus L.). All species currently attributed to the genera Anthystrix Kirejtshuk, Sebastiangethes Audisio, Kirk-Spriggs & Cline, Tarchonanthogethes and Xenostrongylogethes (Anthystrix genus-complex) are included in a morphology-based cladistic analysis to provide a rigorous hypothesis of phylogenetic relationships. An identification key to all 25 known species in the Anthystrix genus-complex, including all available data on insect host plant relationships, is presented. PMID:25781242

  3. Identification of microRNA-mRNA functional interactions in UVB-induced senescence of human diploid fibroblasts

    PubMed Central

    2013-01-01

    Background Cellular senescence can be induced by a variety of extrinsic stimuli, and sustained exposure to sunlight is a key factor in photoaging of the skin. Accordingly, irradiation of skin fibroblasts by UVB light triggers cellular senescence, which is thought to contribute to extrinsic skin aging, although molecular mechanisms are incompletely understood. Here, we addressed molecular mechanisms underlying UVB induced senescence of human diploid fibroblasts. Results We observed a parallel activation of the p53/p21WAF1 and p16INK4a/pRb pathways. Using genome-wide transcriptome analysis, we identified a transcriptional signature of UVB-induced senescence that was conserved in three independent strains of human diploid fibroblasts (HDF) from skin. In parallel, a comprehensive screen for microRNAs regulated during UVB-induced senescence was performed which identified five microRNAs that are significantly regulated during the process. Bioinformatic analysis of miRNA-mRNA networks was performed to identify new functional mRNA targets with high confidence for miR-15a, miR-20a, miR-20b, miR-93, and miR-101. Already known targets of these miRNAs were identified in each case, validating the approach. Several new targets were identified for all of these miRNAs, with the potential to provide new insight in the process of UVB-induced senescence at a genome-wide level. Subsequent analysis was focused on miR-101 and its putative target gene Ezh2. We confirmed that Ezh2 is regulated by miR-101 in human fibroblasts, and found that both overexpression of miR-101 and downregulation of Ezh2 independently induce senescence in the absence of UVB irradiation. However, the downregulation of miR-101 was not sufficient to block the phenotype of UVB-induced senescence, suggesting that other UVB-induced processes induce the senescence response in a pathway redundant with upregulation of miR-101. Conclusion We performed a comprehensive screen for UVB-regulated microRNAs in human diploid fibroblasts, and identified a network of miRNA-mRNA interactions mediating UVB-induced senescence. In addition, miR-101 and Ezh2 were identified as key players in UVB-induced senescence of HDF. PMID:23557329

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

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    Within the context of crowd-induced lateral bridge vibration, human-structure interaction (HSI) is a widely studied phenomenon. Central to this study is the self-excited component of the ground reaction force (GRF). This force harmonic, induced by a walking pedestrian, resonates with lateral deck motion, irrespective of the pedestrian's pacing frequency. Its presence can lead to positive feedback between pedestrian GRFs and structural motion. Characterisation of the self-excited force as equivalent structural mass and damping has greatly improved the understanding of HSI and its role in developing lateral dynamic instability. However, despite this evolving understanding, a key question has remained unanswered; what are the features of a pedestrian's balance response to base motion that gives rise to the self-excited force? The majority of the literature has focussed on the effects of HSI with the underlying mechanism receiving comparatively little attention. This paper presents data from experimental testing in which 10 subjects walked individually on a laterally oscillating treadmill. Lateral deck motion as well as the GRFs imposed by the subject was recorded. Three-dimensional motion capture equipment was used to track the position of visual markers mounted on the subject. Thus whole body response to base motion was captured in addition to the GRFs generated. The data presented herein supports the authors' previous findings that the self-excited force is a frequency sideband harmonic resulting from amplitude modulation of the lateral GRF. The gait behaviour responsible for this amplitude modulation is a periodic modulation of stride width in response to a sinusoidally varying inertia force induced by deck motion. In a separate analysis the validity of the passive inverted pendulum model, stabilised by active control of support placement was confirmed. This was established through comparison of simulated and observed frontal plane CoM motion. Despite the relative simplicity of this biomechanical model, remarkable agreement was observed.

  7. The SMN Tudor SIM-like domain is key to SmD1 and coilin interactions and to Cajal body biogenesis.

    PubMed

    Tapia, Olga; Lafarga, Vanesa; Bengoechea, Rocio; Palanca, Ana; Lafarga, Miguel; Berciano, María T

    2014-03-01

    Cajal bodies (CBs) are nuclear organelles involved in the maturation of spliceosomal small nuclear ribonucleoproteins (snRNPs). They concentrate coilin, snRNPs and the survival motor neuron protein (SMN). Dysfunction of CB assembly occurs in spinal muscular atrophy (SMA). Here, we demonstrate that SMN is a SUMO1 target that has a small ubiquitin-related modifier (SUMO)-interacting motif (SIM)-like motif in the Tudor domain. The expression of SIM-like mutant constructs abolishes the interaction of SMN with the spliceosomal SmD1 (also known as SNRPD1), severely decreases SMN-coilin interaction and prevents CB assembly. Accordingly, the SMN SIM-like-mediated interactions are important for CB biogenesis and their dysfunction can be involved in SMA pathophysiology. PMID:24413165

  8. Cocrystal structures of NC6.8 Fab identify key interactions for high potency sweetener recognition: implications for the design of synthetic sweeteners.

    PubMed

    Gokulan, Kuppan; Khare, Sangeeta; Ronning, Donald R; Linthicum, Scott D; Sacchettini, James C; Rupp, Bernhard

    2005-07-26

    The crystal structures of the murine monoclonal IgG2b(kappa) antibody NC6.8 Fab fragment complexed with high-potency sweetener compound SC45647 and nontasting high-affinity antagonist TES have been determined. The crystal structures show how sweetener potency is fine-tuned by multiple interactions between specific receptor residues and the functionally different groups of the sweeteners. Comparative analysis with the structure of NC6.8 complexed with the super-potency sweetener NC174 reveals that although the same residues in the antigen binding pocket of NC6.8 interact with the zwitterionic, trisubstituted guanidinium sweeteners as well as TES, specific differences exist and provide guidance for the design of new artificial sweeteners. In case of the nonsweetener TES, the interactions with the receptor are indirectly mediated through a hydrogen bonded water network, while the sweeteners bind with high affinity directly to the receptor. The presence of a hydrophobic group interacting with multiple receptor residues as a major determinant for sweet taste has been confirmed. The nature of the hydrophobic group is likely a discriminator for super- versus high-potency sweeteners, which can be exploited in the design of new, highly potent sweetener compounds. Overall similarities and partial conservation of interactions indicate that the NC6.8 Fab surrogate is representing crucial features of the T1R2 taste receptor VFTM binding site. PMID:16026161

  9. Talent identification in youth soccer.

    PubMed

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

    2012-01-01

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

  10. Scale Insects, edition 2, a tool for the identification of potential pest scales at U.S.A. ports-of-entry (Hemiptera, Sternorrhyncha, Coccoidea)

    PubMed Central

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

    2014-01-01

    Abstract We provide a general overview of features and technical specifications of an online, interactive tool for the identification of scale insects of concern to the U.S.A. ports-of-entry. Full lists of terminal taxa included in the keys (of which there are four), a list of features used in them, and a discussion of the structure of the tool are provided. We also briefly discuss the advantages of interactive keys for the identification of potential scale insect pests. The interactive key is freely accessible on http://idtools.org/id/scales/index.php PMID:25152668

  11. Identification of sRNA interacting with a transcript of interest using MS2-affinity purification coupled with RNA sequencing (MAPS) technology.

    PubMed

    Lalaouna, David; Massé, Eric

    2015-09-01

    RNA sequencing (RNAseq) technology recently allowed the identification of thousands of small RNAs (sRNAs) within the prokaryotic kingdom. However, drawing the comprehensive interaction map of a sRNA remains a challenging task. To address this problem, we recently developed a method called MAPS (MS2 affinity purification coupled with RNA sequencing) to characterize the full targetome of specific sRNAs. This method enabled the identification of target RNAs interacting with sRNAs, regardless of the type of regulation (positive or negative), type of targets (mRNA, tRNA, sRNA) or their abundance. We also demonstrated that we can use this technology to perform a reverse MAPS experiment, where an RNA fragment of interest is used as bait to identify interacting sRNAs. Here, we demonstrated that RybB and MicF sRNAs co-purified with internal transcribed spacers (ITS) of metZ-metW-metV tRNA transcript, confirming results obtained with MS2-RybB MAPS. Both raw and analyzed RNAseq data are available in GEO database (GSE66517). PMID:26484242

  12. Identification of sRNA interacting with a transcript of interest using MS2-affinity purification coupled with RNA sequencing (MAPS) technology

    PubMed Central

    Lalaouna, David; Massé, Eric

    2015-01-01

    RNA sequencing (RNAseq) technology recently allowed the identification of thousands of small RNAs (sRNAs) within the prokaryotic kingdom. However, drawing the comprehensive interaction map of a sRNA remains a challenging task. To address this problem, we recently developed a method called MAPS (MS2 affinity purification coupled with RNA sequencing) to characterize the full targetome of specific sRNAs. This method enabled the identification of target RNAs interacting with sRNAs, regardless of the type of regulation (positive or negative), type of targets (mRNA, tRNA, sRNA) or their abundance. We also demonstrated that we can use this technology to perform a reverse MAPS experiment, where an RNA fragment of interest is used as bait to identify interacting sRNAs. Here, we demonstrated that RybB and MicF sRNAs co-purified with internal transcribed spacers (ITS) of metZ–metW–metV tRNA transcript, confirming results obtained with MS2-RybB MAPS. Both raw and analyzed RNAseq data are available in GEO database (GSE66517). PMID:26484242

  13. Identification of NS1 domains of avian H5N1 influenza virus which influence the interaction with the NOLC1 protein.

    PubMed

    Zhu, Chun-Yu; Zheng, Fang-Liang; She, Xiao-Shuang; Zhao, Dan; Gu, Ying; Duan, Yan-Ting; Chang, Alan K; Liu, Hong-Sheng

    2015-04-01

    Non-structural protein 1 (NS1) is an important virulence factor encoded by influenza A virus. NS1 can interact with a variety of host cell proteins to interfere with the host innate immune response and to promote effective viral replication. Our previous work has shown that only the effector domain of NS1 (amino acid residues 74-230/237) is sufficient to interact with nucleolar and coiled-body phosphoprotein 1 (NOLC1). To investigate the exact region of NS1 that interacts with NOLC1, we used only the effector domain of NS1 and constructed various mutants having different deletions, and then tested their ability to interact with NOLC1 via pull-down assay. Only the mutant containing amino acid residues 104-200 showed positive interaction with NOLC1. To further determine the key amino acids of the NS1 effector domain which are crucial for interaction with NOLC1, several mutants containing a single amino acid substitution were made and their interaction with NOLC1 was tested. Only the mutant D120A or R195A showed reduced binding with NOLC1, suggesting that D120 and R195 were crucial to the binding of NS1 to NOLC1. This study lays the foundation for further research aiming at furthering our understanding of the interaction between NS1 and host cells. PMID:25645906

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

    PubMed

    Howell, Elizabeth F

    2014-03-01

    No one has described more passionately than Ferenczi the traumatic induction of dissociative trance with its resulting fragmentation of the personality. Ferenczi introduced the concept and term, identification with the aggressor in his seminal "Confusion of Tongues" paper, in which he described how the abused child becomes transfixed and robbed of his senses. Having been traumatically overwhelmed, the child becomes hypnotically transfixed by the aggressor's wishes and behavior, automatically identifying by mimicry rather than by a purposeful identification with the aggressor's role. To expand upon Ferenczi's observations, identification with the aggressor can be understood as a two-stage process. The first stage is automatic and initiated by trauma, but the second stage is defensive and purposeful. While identification with the aggressor begins as an automatic organismic process, with repeated activation and use, gradually it becomes a defensive process. Broadly, as a dissociative defense, it has two enacted relational parts, the part of the victim and the part of the aggressor. This paper describes the intrapersonal aspects (how aggressor and victim self-states interrelate in the internal world), as well as the interpersonal aspects (how these become enacted in the external). This formulation has relevance to understanding the broad spectrum of the dissociative structure of mind, borderline personality disorder, and dissociative identity disorder. PMID:24603172

  15. Key role of electron-phonon interactions in the electronic conductivity of T i3Si C2 : Experiment and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Nassour, A.; Mauchamp, V.; Yu, W.; Cabioch, T.; Piraux, L.; Gauthier-Brunet, V.; Dubois, S.

    2016-02-01

    The electronic conductivity anisotropy of T i3Si C2 is directly evidenced from data collected on (i) a thin film epitaxially grown on a (11 2 ¯0 )-oriented SiC single crystal and (ii) a single crystal. Density functional theory calculations, including the linear-response approach and coupled to a Bloch-Grüneisen model, show that the electron-phonon interactions are mainly responsible for the observed anisotropy. Detailed analysis of the electron-phonon coupling constants allows for the rationalization of these scattering processes in terms of the T i3Si C2 nanostructure, giving insights into the possibility of modifying the electron-phonon interaction in this system by substitution effects.

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

    PubMed Central

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

    2013-01-01

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

  17. Unlocking the Keys to Vortex/Flame Interactions in Turbulent Gas-Jet Diffusion Flames--Dynamic Behavior Explored on the Space Shuttle

    NASA Technical Reports Server (NTRS)

    Stocker, Dennis P.

    1999-01-01

    Most combustion processes in industrial applications (e.g., furnaces and engines) and in nature (e.g., forest fires) are turbulent. A better understanding of turbulent combustion could lead to improved combustor design, with enhanced efficiency and reduced emissions. Despite its importance, turbulent combustion is poorly understood because of its complexity. The rapidly changing and random behavior of such flames currently prevents detailed analysis, whether experimentally or computationally. However, it is possible to learn about the fundamental behavior of turbulent flames by exploring the controlled interaction of steady laminar flames and artificially induced flow vortices. These interactions are an inherent part of turbulent flames, and understanding them is essential to the characterization of turbulent combustion. Well-controlled and defined experiments of vortex interaction with laminar flames are not possible in normal gravity because of the interference of buoyancy- (i.e., gravity) induced vortices. Therefore, a joint microgravity study was established by researchers from the Science and Technology Development Corp. and the NASA Lewis Research Center. The experimental study culminated in the conduct of the Turbulent Gas-Jet Diffusion Flames (TGDF) Experiment on the STS-87 space shuttle mission in November 1997. The fully automated hardware, shown in photo, was designed and built at Lewis. During the mission, the experiment was housed in a Get Away Special (GAS) canister in the cargo bay.

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

    PubMed Central

    Honke, Koichi; Kotani, Norihiro

    2012-01-01

    Important biological events associated with plasma membranes, such as signal transduction, cell adhesion, and protein trafficking, are mediated through the membrane microdomains. We have developed a novel method termed enzyme-mediated activation of radical sources (EMARS) to identify coclustering molecules on the cell surface under living conditions, which features a radical formation from an aryl azide reagent by horseradish peroxidase (HRP). For identification of molecules labeled by the EMARS reaction, antibody array system and mass spectrometry-based proteomics approaches are available. Spatio- temporally-regulated interaction between β1 integrin and ErbB4 involved in fibronectin-dependent cell migration and therapeutic antibody-stimulated interaction between FGFR3 and CD20 were discovered using the EMARS method. PMID:23443365

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

    PubMed Central

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

    2012-01-01

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

  20. Identification of Molecular Fingerprints in Human Heat Pain Thresholds by Use of an Interactive Mixture Model R Toolbox (AdaptGauss).

    PubMed

    Ultsch, Alfred; Thrun, Michael C; Hansen-Goos, Onno; Lötsch, Jörn

    2015-01-01

    Biomedical data obtained during cell experiments, laboratory animal research, or human studies often display a complex distribution. Statistical identification of subgroups in research data poses an analytical challenge. Here were introduce an interactive R-based bioinformatics tool, called "AdaptGauss". It enables a valid identification of a biologically-meaningful multimodal structure in the data by fitting a Gaussian mixture model (GMM) to the data. The interface allows a supervised selection of the number of subgroups. This enables the expectation maximization (EM) algorithm to adapt more complex GMM than usually observed with a noninteractive approach. Interactively fitting a GMM to heat pain threshold data acquired from human volunteers revealed a distribution pattern with four Gaussian modes located at temperatures of 32.3, 37.2, 41.4, and 45.4 °C. Noninteractive fitting was unable to identify a meaningful data structure. Obtained results are compatible with known activity temperatures of different TRP ion channels suggesting the mechanistic contribution of different heat sensors to the perception of thermal pain. Thus, sophisticated analysis of the modal structure of biomedical data provides a basis for the mechanistic interpretation of the observations. As it may reflect the involvement of different TRP thermosensory ion channels, the analysis provides a starting point for hypothesis-driven laboratory experiments. PMID:26516852

  1. Identification of Molecular Fingerprints in Human Heat Pain Thresholds by Use of an Interactive Mixture Model R Toolbox (AdaptGauss)

    PubMed Central

    Ultsch, Alfred; Thrun, Michael C.; Hansen-Goos, Onno; Lötsch, Jörn

    2015-01-01

    Biomedical data obtained during cell experiments, laboratory animal research, or human studies often display a complex distribution. Statistical identification of subgroups in research data poses an analytical challenge. Here were introduce an interactive R-based bioinformatics tool, called “AdaptGauss”. It enables a valid identification of a biologically-meaningful multimodal structure in the data by fitting a Gaussian mixture model (GMM) to the data. The interface allows a supervised selection of the number of subgroups. This enables the expectation maximization (EM) algorithm to adapt more complex GMM than usually observed with a noninteractive approach. Interactively fitting a GMM to heat pain threshold data acquired from human volunteers revealed a distribution pattern with four Gaussian modes located at temperatures of 32.3, 37.2, 41.4, and 45.4 °C. Noninteractive fitting was unable to identify a meaningful data structure. Obtained results are compatible with known activity temperatures of different TRP ion channels suggesting the mechanistic contribution of different heat sensors to the perception of thermal pain. Thus, sophisticated analysis of the modal structure of biomedical data provides a basis for the mechanistic interpretation of the observations. As it may reflect the involvement of different TRP thermosensory ion channels, the analysis provides a starting point for hypothesis-driven laboratory experiments. PMID:26516852

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    AvrRxv is a member of a family of pathogen effectors from both plant and mammalian pathogens. Using a yeast two hybrid screen, we identified a 14-3-3 protein from tomato that interacts with AvrRxv called AvrRxv Interactor 1 (ARI1). The interaction was confirmed in vitro with affinity chromatograph...

  3. Identification of phytochrome-interacting protein candidates in Arabidopsis thaliana by co-immunoprecipitation coupled with MALDI-TOF MS.

    PubMed

    Phee, Bong-Kwan; Shin, Dong Ho; Cho, Jin-Hwan; Kim, Seong-Hee; Kim, Jeong-Il; Lee, Youn-Hyung; Jeon, Jong-Seong; Bhoo, Seong Hee; Hahn, Tae-Ryong

    2006-06-01

    Phytochrome-interacting proteins have been extensively studied to elucidate light-signaling pathway in plants. However, most of these proteins have been identified by yeast two-hybrid screening using the C-terminal domain of phytochromes. We used co-immunoprecipitation followed by proteomic analysis in plant cell extracts in an attempt to screen for proteins interacting either directly or indirectly with native holophytochromes including the N-terminal domain as well as C-terminal domain. A total of 16 protein candidates were identified, and were selected from 2-DE experiments. Using MALDI-TOF MS analysis, 7 of these candidates were predicted to be putative phytochrome A-interacting proteins and the remaining ones to be phytochrome B-interacting proteins. Among these putative interacting proteins, protein phosphatase type 2C (PP2C) and a 66-kDa protein were strong candidates as novel phytochrome-interacting proteins, as knockout mutants for the genes encoding these two proteins had impaired light-signaling functions. A transgenic knockout Arabidopsis study showed that a 66-kDa protein candidate regulates hypocotyl elongation in a light-specific manner, and altered cotyledon development under white light during early developmental stages. The PP2C knockout plants also displayed light-specific changes in hypocotyl elongation. These results suggest that co-immunoprecipitation, followed by proteomic analysis, is a useful method for identifying novel interacting proteins and determining real protein-protein interactions in the cell. PMID:16705748

  4. Identification of entomopathogenic fungi

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  5. RUNX1 is a key target in t(4;11) leukemias that contributes to gene activation through an AF4-MLL complex interaction.

    PubMed

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

    2013-01-31

    The Mixed Lineage Leukemia (MLL) protein is an important epigenetic regulator required for the maintenance of gene activation during development. MLL chromosomal translocations produce novel fusion proteins that cause aggressive leukemias in humans. Individual MLL fusion proteins have distinct leukemic phenotypes even when expressed in the same cell type, but how this distinction is delineated on a molecular level is poorly understood. Here, we highlight a unique molecular mechanism whereby the RUNX1 gene is directly activated by MLL-AF4 and the RUNX1 protein interacts with the product of the reciprocal AF4-MLL translocation. These results support a mechanism of transformation whereby two oncogenic fusion proteins cooperate by activating a target gene and then modulating the function of its downstream product. PMID:23352661

  6. Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations

    PubMed Central

    Verma, Sharad; Grover, Sonam; Tyagi, Chetna; Goyal, Sukriti; Jamal, Salma; Singh, Aditi; Grover, Abhinav

    2016-01-01

    p53, a tumor suppressor protein, has been proven to regulate the cell cycle, apoptosis, and DNA repair to prevent malignant transformation. MDM2 regulates activity of p53 and inhibits its binding to DNA. In the present study, we elucidated the MDM2 inhibition potential of polyphenols (Apigenin, Fisetin, Galangin and Luteolin) by MD simulation and MM/PBSA free energy calculations. All polyphenols bind to hydrophobic groove of MDM2 and the binding was found to be stable throughout MD simulation. Luteolin showed the highest negative binding free energy value of -173.80 kJ/mol followed by Fisetin with value of -172.25 kJ/mol. It was found by free energy calculations, that hydrophobic interactions (vdW energy) have major contribution in binding free energy. PMID:26863418

  7. Mechanism of C-Terminal Fragments of Amyloid ?-Protein as A? Inhibitors: Do C-Terminal Interactions Play a Key Role in Their Inhibitory Activity?

    PubMed

    Zheng, Xueyun; Wu, Chun; Liu, Deyu; Li, Huiyuan; Bitan, Gal; Shea, Joan-Emma; Bowers, Michael T

    2016-03-01

    Targeting the early oligomerization of amyloid ? protein (A?) is a promising therapeutic strategy for Alzheimer's disease (AD). Recently, certain C-terminal fragments (CTFs) derived from A?42 were shown to be potent inhibitors of A?-induced toxicity. The shortest peptide studied, A?(39-42), has been shown to modulate A? oligomerization and inhibit A? toxicity. Understanding the mechanism of these CTFs, especially A?(39-42), is of significance for future therapeutic development of AD and peptidomimetic-based drug development. Here we used ion mobility spectrometry-mass spectrometry to investigate the interactions between two modified A?(39-42) derivatives, VVIA-NH2 and Ac-VVIA, and full-length A?42. VVIA-NH2 was previously shown to inhibit A? toxicity, whereas Ac-VVIA did not. Our mass spectrometry analysis revealed that VVIA-NH2 binds directly to A?42 monomer and small oligomers while Ac-VVIA binds only to A?42 monomer. Ion mobility studies showed that VVIA-NH2 modulates A?42 oligomerization by not only inhibiting the dodecamer formation but also disaggregating preformed A?42 dodecamer. Ac-VVIA also inhibits and removes preformed A?42 dodecamer. However, the A?42 sample with the addition of Ac-VVIA clogged the nanospray tip easily, indicating that larger aggregates are formed in the solution in the presence of Ac-VVIA. Molecular dynamics simulations suggested that VVIA-NH2 binds specifically to the C-terminal region of A?42 while Ac-VVIA binds dispersedly to multiple regions of A?42. This work implies that C-terminal interactions and binding to A? oligomers are important for C-terminal fragment inhibitors. PMID:26439281

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

    SciTech Connect

    Tannukit, Sissada; Crabb, Tara L.; Hertel, Klemens J.; Wen, Xin; Jans, David A.; Paine, Michael L.

    2009-12-18

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

  9. PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data.

    PubMed

    Kalkhof, Stefan; Schildbach, Stefan; Blumert, Conny; Horn, Friedemann; von Bergen, Martin; Labudde, Dirk

    2016-01-01

    The functionality of most proteins is regulated by protein-protein interactions. Hence, the comprehensive characterization of the interactome is the next milestone on the path to understand the biochemistry of the cell. A powerful method to detect protein-protein interactions is a combination of coimmunoprecipitation or affinity purification with quantitative mass spectrometry. Nevertheless, both methods tend to precipitate a high number of background proteins due to nonspecific interactions. To address this challenge the software Protein-Protein-Interaction-Optimizer (PIPINO) was developed to perform an automated data analysis, to facilitate the selection of bona fide binding partners, and to compare the dynamic of interaction networks. In this study we investigated the STAT1 interaction network and its activation dependent dynamics. Stable isotope labeling by amino acids in cell culture (SILAC) was applied to analyze the STAT1 interactome after streptavidin pull-down of biotagged STAT1 from human embryonic kidney 293T cells with and without activation. Starting from more than 2,000 captured proteins 30 potential STAT1 interaction partners were extracted. Interestingly, more than 50% of these were already reported or predicted to bind STAT1. Furthermore, 16 proteins were found to affect the binding behavior depending on STAT1 phosphorylation such as STAT3 or the importin subunits alpha 1 and alpha 6. PMID:26966684

  10. PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data

    PubMed Central

    Schildbach, Stefan; Blumert, Conny; Horn, Friedemann; von Bergen, Martin; Labudde, Dirk

    2016-01-01

    The functionality of most proteins is regulated by protein-protein interactions. Hence, the comprehensive characterization of the interactome is the next milestone on the path to understand the biochemistry of the cell. A powerful method to detect protein-protein interactions is a combination of coimmunoprecipitation or affinity purification with quantitative mass spectrometry. Nevertheless, both methods tend to precipitate a high number of background proteins due to nonspecific interactions. To address this challenge the software Protein-Protein-Interaction-Optimizer (PIPINO) was developed to perform an automated data analysis, to facilitate the selection of bona fide binding partners, and to compare the dynamic of interaction networks. In this study we investigated the STAT1 interaction network and its activation dependent dynamics. Stable isotope labeling by amino acids in cell culture (SILAC) was applied to analyze the STAT1 interactome after streptavidin pull-down of biotagged STAT1 from human embryonic kidney 293T cells with and without activation. Starting from more than 2,000 captured proteins 30 potential STAT1 interaction partners were extracted. Interestingly, more than 50% of these were already reported or predicted to bind STAT1. Furthermore, 16 proteins were found to affect the binding behavior depending on STAT1 phosphorylation such as STAT3 or the importin subunits alpha 1 and alpha 6. PMID:26966684

  11. Silicon-Induced Changes in Antifungal Phenolic Acids, Flavonoids, and Key Phenylpropanoid Pathway Genes during the Interaction between Miniature Roses and the Biotrophic Pathogen Podosphaera pannosa1[W

    PubMed Central

    Shetty, Radhakrishna; Fretté, Xavier; Jensen, Birgit; Shetty, Nandini Prasad; Jensen, Jens Due; Jørgensen, Hans Jørgen Lyngs; Newman, Mari-Anne; Christensen, Lars Porskjær

    2011-01-01

    Application of 3.6 mm silicon (Si+) to the rose (Rosa hybrida) cultivar Smart increased the concentration of antimicrobial phenolic acids and flavonoids in response to infection by rose powdery mildew (Podosphaera pannosa). Simultaneously, the expression of genes coding for key enzymes in the phenylpropanoid pathway (phenylalanine ammonia lyase, cinnamyl alcohol dehydrogenase, and chalcone synthase) was up-regulated. The increase in phenolic compounds correlated with a 46% reduction in disease severity compared with inoculated leaves without Si application (Si−). Furthermore, Si application without pathogen inoculation induced gene expression and primed the accumulation of several phenolics compared with the uninoculated Si− control. Chlorogenic acid was the phenolic acid detected in the highest concentration, with an increase of more than 80% in Si+ inoculated compared with Si− uninoculated plants. Among the quantified flavonoids, rutin and quercitrin were detected in the highest concentrations, and the rutin concentration increased more than 20-fold in Si+ inoculated compared with Si− uninoculated plants. Both rutin and chlorogenic acid had antimicrobial effects on P. pannosa, evidenced by reduced conidial germination and appressorium formation of the pathogen, both after spray application and infiltration into leaves. The application of rutin and chlorogenic acid reduced powdery mildew severity by 40% to 50%, and observation of an effect after leaf infiltration indicated that these two phenolics can be transported to the epidermal surface. In conclusion, we provide evidence that Si plays an active role in disease reduction in rose by inducing the production of antifungal phenolic metabolites as a response to powdery mildew infection. PMID:22021421

  12. Interactive effects of climate change with nutrients, mercury, and freshwater acidification on key taxa in the North Atlantic Landscape Conservation Cooperative region.

    PubMed

    Pinkney, Alfred E; Driscoll, Charles T; Evers, David C; Hooper, Michael J; Horan, Jeffrey; Jones, Jess W; Lazarus, Rebecca S; Marshall, Harold G; Milliken, Andrew; Rattner, Barnett A; Schmerfeld, John; Sparling, Donald W

    2015-07-01

    The North Atlantic Landscape Conservation Cooperative LCC (NA LCC) is a public-private partnership that provides information to support conservation decisions that may be affected by global climate change (GCC) and other threats. The NA LCC region extends from southeast Virginia to the Canadian Maritime Provinces. Within this region, the US National Climate Assessment documented increases in air temperature, total precipitation, frequency of heavy precipitation events, and rising sea level, and predicted more drastic changes. Here, we synthesize literature on the effects of GCC interacting with selected contaminant, nutrient, and environmental processes to adversely affect natural resources within this region. Using a case study approach, we focused on 3 stressors with sufficient NA LCC region-specific information for an informed discussion. We describe GCC interactions with a contaminant (Hg) and 2 complex environmental phenomena-freshwater acidification and eutrophication. We also prepared taxa case studies on GCC- and GCC-contaminant/nutrient/process effects on amphibians and freshwater mussels. Several avian species of high conservation concern have blood Hg concentrations that have been associated with reduced nesting success. Freshwater acidification has adversely affected terrestrial and aquatic ecosystems in the Adirondacks and other areas of the region that are slowly recovering due to decreased emissions of N and sulfur oxides. Eutrophication in many estuaries within the region is projected to increase from greater storm runoff and less denitrification in riparian wetlands. Estuarine hypoxia may be exacerbated by increased stratification. Elevated water temperature favors algal species that produce harmful algal blooms (HABs). In several of the region's estuaries, HABs have been associated with bird die-offs. In the NA LCC region, amphibian populations appear to be declining. Some species may be adversely affected by GCC through higher temperatures and more frequent droughts. GCC may affect freshwater mussel populations via altered stream temperatures and increased sediment loading during heavy storms. Freshwater mussels are sensitive to un-ionized ammonia that more toxic at higher temperatures. We recommend studying the interactive effects of GCC on generation and bioavailability of methylmercury and how GCC-driven shifts in bird species distributions will affect avian exposure to methylmercury. Research is needed on how decreases in acid deposition concurrent with GCC will alter the structure and function of sensitive watersheds and surface waters. Studies are needed to determine how GCC will affect HABs and avian disease, and how more severe and extensive hypoxia will affect fish and shellfish populations. Regarding amphibians, we suggest research on 1) thermal tolerance and moisture requirements of species of concern, 2) effects of multiple stressors (temperature, desiccation, contaminants, nutrients), and 3) approaches to mitigate impacts of increased temperature and seasonal drought. We recommend studies to assess which mussel species and populations are vulnerable and which are resilient to rising stream temperatures, hydrological shifts, and ionic pollutants, all of which are influenced by GCC. PMID:25556986

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-10-01

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

  15. Identification of Hsp90 as a species independent H5N1 avian influenza A virus PB2 interacting protein.

    PubMed

    Jirakanwisal, Krit; Srisutthisamphan, Kanjana; Thepparit, Chutima; Suptawiwat, Ornpreya; Auewarakul, Prasert; Paemanee, Atchara; Roytrakul, Sittiruk; Smith, Duncan R

    2015-12-01

    The avian influenza polymerase protein PB2 subunit is an important mediator of cross species adaptation and adaptation to mammalian cells is strongly but not exclusively associated with an adaptive mutation of the codon at position 627 of the PB2 protein which alters the glutamate normally found at this position to a lysine. This study sought to identify host cell factors in both mammalian and avian cells that interacted in a species specific or species independent manner. Two PB2 fusion proteins differing only in codon 627 were generated and transfected into mammalian and avian cells and interacting proteins identified through co-immunoprecipitation. A number of proteins including Hsp90 were identified and further investigation showed that Hsp90 interacted with both isoforms of PB2 in both mammalian and avian cells. Hsp90 is thus identified as a species independent interacting protein, further confirming that this protein may be a suitable target for anti-influenza drug development. PMID:26616658

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

    PubMed Central

    Teh, Min Yan; Morona, Renato

    2013-01-01

    The Shigella flexneri IcsA (VirG) protein is a polarly distributed outer membrane protein that is a fundamental virulence factor which interacts with neural Wiskott-Aldrich syndrome protein (N-WASP). The activated N-WASP then activates the Arp2/3 complex which initiates de novo actin nucleation and polymerisation to form F-actin comet tails and allows bacterial cell-to-cell spreading. In a previous study, IcsA was found to have three N-WASP interacting regions (IRs): IR I (aa 185–312), IR II (aa 330–382) and IR III (aa 508–730). The aim of this study was to more clearly define N-WASP interacting regions II and III by site-directed mutagenesis of specific amino acids. Mutant IcsA proteins were expressed in both smooth lipopolysaccharide (S-LPS) and rough LPS (R-LPS) S. flexneri strains and characterised for IcsA production level, N-WASP recruitment and F-actin comet tail formation. We have successfully identified new amino acids involved in N-WASP recruitment within diff