1,720,961 research outputs found
Scaffold Protein SLP-76 Primes PLCγ1 for Activation by ITK-Mediated Phosphorylation
Full text linkActivation of the phospholipase, PLCγ1, is critical for proper T cell signaling following antigen receptor engagement. In T cells, the Tec family kinase, ITK, phosphorylates PLCγ1 at tyrosine 783 (Y783) leading to activation of phospholipase function and subsequent production of the second messengers IP3 and DAG. In this work we demonstrate that PLCγ1 can be primed for ITK mediated phosphorylation on Y783 by a specific region of the adaptor protein, SLP-76. The SLP-76 phosphotyrosine containing sequence, pY173IDR, does not conform to the canonical recognition motif for an SH2 domain yet binds with significant affinity to the C-terminal SH2 domain of PLCγ1 (SH2C). The SLP-76 pY173 motif competes with the autoinhibited conformation surrounding the SH2C domain of PLCγ1 leading to exposure of the ITK recognition element on the PLCγ1 SH2 domain and release of the target tyrosine, Y783. These data contribute to the evolving model for the molecular events occurring early in the T cell activation process.This is a manuscript of an article published as Devkota, Sujan, Raji E. Joseph, Lie Min, D. Bruce Fulton, and Amy H. Andreotti. "Scaffold protein SLP-76 primes PLCγ1 for activation by ITK-mediated phosphorylation." Journal of molecular biology 427, no. 17 (2015): 2734-2747. doi: 10.1016/j.jmb.2015.04.012. Posted with permission.</p
Accessible and usable web interface forpPower grid database
Full text linkDifferent stakeholders of the electric power grid sector need data for their research and decision-making tasks. However, the power grid field lacks an accessible and easy-to-use system that contains openly available data sources that is open to use for everyone.
This thesis creates a prototype of an accessible and usable web interface for the power grid database by following the user-centered design (UCD) methodology. The web interface is targeted to be used by different stakeholders of the power grid sector. The principles of universal design and concepts of accessibility and usability were considered throughout different activities in the thesis.
Different qualitative research methods and research methods from human-computer interaction (HCI) have been used in this study. The research methods employed in this thesis are survey, coding, interviews, paper prototyping, personas, automatic testing, heuristic testing, and discounted testing. Further, ethnographic observation and thinking out aloud methods have also been used.
The prototype development process followed an iterative approach for finding user requirements and deliver a prototype of a web-based interface for the power grid database. The prototype was tested for its accessibility and usability. The prototype presented uses modern web technologies and is found to meet the accessibility and usability requirements of its target users. The prototype and the instructions to install it have also been uploaded along with this thesis.
Finally, some topics for future work to further extend this study and to make the software prototype more effective have been presented.publishedVersio
Elucidation of regulatory mechanisms of the ITK and its substrate PLCγ1
Full text linkThis dissertation studies the regulatory mechanism of IL-2 inducible tyrosine kinase (ITK) and its substrate phospholipase C γ1 (PLCγ1). ITK and PLCγ1 are key mediators of the signaling pathway downstream of the T cell receptor that results in the T cell part of the adaptive immune response. In T cells, ITK is phosphorylated and activated by LCK. ITK then phosphorylates PLCγ1 at tyrosine 783 and activates phospholipase activity. This phosphorylation is dependent upon various coordinated intermolecular and intramolecular interactions within and between ITK and PLCγ1. This dissertation identifies and characterizes various regulatory interactions in ITK and its substrate PLCγ1 that regulates ITK mediated phosphorylation of PLCγ1.
For ITK, this thesis explores the function of the N-terminal Pleckstrin homology (PH) domain in regulating the activation of the ITK. The ITK PH domain engages in direct interaction with ITK kinase domain and the region of the kinase domain interaction is mapped in the ITK PH domain. Mutations in ITK PH domain, that disrupts its interaction with kinase domain, lead to the increase in the activity of ITK. The ITK interaction surface mapped on the ITK PH domain lies adjacent to its phosphatidylinositol (3,4,5)-triphosphate (PI (3,4,5) P3) binding pocket. Hence, IP4, the soluble head group of (PI (3,4,5) P3) competes with the ITK kinase domain for ITK PH domain binding. Also, PI (3,4,5) P3 binding of ITK PH domain increases the catalytic activity of the ITK. In addition, PI (3,4,5) P3 binding increases the activation loop Y511 accessibility for LCK phosphorylation. This study expanded our knowledge on regulation of ITK by its N terminal PH domain (Chapter 3).
ITK is a key modulator of immune response and has therefore been very attractive target for small molecule intervention for immunity related diseases such as autoimmune disease and asthma. The key novel regulatory ITK PH/kinase site can be a plausible allosteric target for small molecule discovery efforts. Part of this thesis contributes to assay development to detect the ITK PH/Kinase interaction in cells. Bimolecular Fluorescence complementation (BiFC) assay confirms that the ITK PH/Kinase interaction occurs in cell (Chapter 4). This assay can now be used to screen for small molecules that modulate the ITK PH/Kinase interaction.
For PLCγ1, this thesis studies the mechanism of disruption of its autoinhibitory conformation. The PLCγ1 autoinhibitory conformation is characterized by an intramolecular interaction between the C terminal SRC homology 2 (SH2C) domain and the adjacent linker containing Y783. This conformation makes the crucial phosphorylation target (Y783) inaccessible to ITK. I have described the mechanism on how this autoinhibitory interaction is broken (Chapter 2). Our results suggest that the scaffold protein SLP-76 disrupts the autoinhibitory PLCγ1 conformation. More specifically, SLP-76 phosphotyrosine 173 (Y173) binds the SH2C domain of the PLCγ1, competing with the autoinhibitory conformation of PLCγ1 and releasing the linker, making the Y783 more accessible to ITK. Our results identify the new role of the scaffold protein SLP-76 adding to its previously described role in co-localizing the enzyme and substrate pair. This role is defined as the substrate priming as SLP-76 primes PLCγ1, the substrate for ITK for efficient phosphorylation. Our results provide further understanding of the regulation of ITK mediated phosphorylation of PLCγ1 and create a foundation for small molecule discovery efforts that should yield new ways to either enhance or diminish T cell function.</p
Accessible and usable web interface forpPower grid database
No full textDifferent stakeholders of the electric power grid sector need data for their research and decision-making tasks. However, the power grid field lacks an accessible and easy-to-use system that contains openly available data sources that is open to use for everyone.
This thesis creates a prototype of an accessible and usable web interface for the power grid database by following the user-centered design (UCD) methodology. The web interface is targeted to be used by different stakeholders of the power grid sector. The principles of universal design and concepts of accessibility and usability were considered throughout different activities in the thesis.
Different qualitative research methods and research methods from human-computer interaction (HCI) have been used in this study. The research methods employed in this thesis are survey, coding, interviews, paper prototyping, personas, automatic testing, heuristic testing, and discounted testing. Further, ethnographic observation and thinking out aloud methods have also been used.
The prototype development process followed an iterative approach for finding user requirements and deliver a prototype of a web-based interface for the power grid database. The prototype was tested for its accessibility and usability. The prototype presented uses modern web technologies and is found to meet the accessibility and usability requirements of its target users. The prototype and the instructions to install it have also been uploaded along with this thesis.
Finally, some topics for future work to further extend this study and to make the software prototype more effective have been presented
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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