1,720,980 research outputs found
Direct Observation of the Activation of MscL in Tethered Lipid Bilayers by an Antimicrobial Peptide
No full textData and Python code to support the manuscript "Direct Observation the Activation of MscL in Tethered Lipid Bilayers by an Antimicrobial Peptide". Abstract: Hypothesis Membrane proteins serve a wide range of vital roles in the functioning of living organisms. They account for approximately 20% to 30% of the genomes across bacterial, archaeal, and eukaryotic organisms. They are responsible for many cellular functions, such as signaling, ion and molecule transport, binding and catalytic reactions. Compared to other classes of proteins, determining membrane protein structures remains a challenge, in large part due to the difficulty in establishing experimental conditions that can preserve the correct conformation and function of the protein in isolation from its native environment. Many therapeutics target membrane proteins which are accessible on the surface of cells. Here we hypothesize that the observed efficacy of antimicrobial peptides (AMPs) that interact with bacterial membranes may in part be associated with their triggering of MscL (Mechansensitive Ion Channel of Large Conductance) gating. We further conjecture that the insertion of peptides into the membrane induces significant changes in membrane tension and/or curvature, leading to prolonged gating of the MscL channels.
Experiments We present realistic model membrane systems containing MscL. We investigated the ion channel in lipid vesicles and in a planar lipid bilayer. We developed a novel method for protein-lipid planar bilayer formation, avoiding the use of detergents. By using a polymeric tether our planar membrane mimetic was not constrained by the underlying solid substrate, making it sufficiently flexible to allow for increases in bilayer curvature and changes in membrane tension. We used quartz crystal microbalance with dissipation (QCM-D), and polarised neutron reflectivity (PNR) to show the formation of MscL containing phospholipid bilayers, tethered with a high density PEG layer onto gold substrates from vesicle rupture. The MscL containing vesicles were separately characterised with small angle neutron scattering (SANS).
Findings MscL was expressed into vesicles using cell free protein expression. Analysing these vesicles with small angle neutron scattering, the radius of gyration of the protein was determined to be between 26-29~\AA{}, consistent with the crystal structure of individual MscL channels. The MscL composition of the formed bilayer was 14\%v/v, close to the initial volume composition of the vesicles at ~13.6% and a protein protrusion extending ca. 46~\AA{} into the solvent was determined by PNR. Addition of 1.6 and 3.2 uM pexiganan resulted in a decrease in the protrusion of MscL (from ~46 to ~38~\AA{}). To our knowledge, these findings represent the first direct experimental evidence of a structural change in the C-terminus containing protrusion of MscL, triggered by an antimicrobial peptide. This adds to our understanding of antimicrobial peptide action in therapeutic treatments.Jupyter notebooks containing code to fit polarized neutron reflectivity data
Tether_bilayer_only_model-RefNX_volumes_final-Copy3.ipynb
MscL_1p6_PXG_model-RefNX_volumes_final.ipynb
MscL_3p2_PXG_model-RefNX_volumes_final.ipynb
SANS model fits and data
LysoPC
LysoPCmodel_1level_GP.csv
SANS_LysoPC_D2O.txt
MscLVesicle
MscLVesicle_2levelGPmodelfit.csv
SANS_MscLVesicle_D2O.txt
MscLVesicle post Lyso-PC
MscLVesicle_model_2level_GP.csv
SANS_MscLVesicle_LysoPC_D2O.txt
MscLVesicle post PXG
MscLvesicleafterPXG_model_2levelGP.csv
SANS_MscLVesicleafterPXG_D2O.txt
MscLVesicle(pre-PXG)
MscLVesicle_model_2level_GP.csv
SANS_MscLVesicle_D2O.txt
Neutron reflectivity datafiles used in the Jupyter notebooks
IvsQ_26838_26839_26840_IvsQ_26838_1_IvsQ_26839_1_IvsQ_26840_1.dat.txt
IvsQ_26841_26842_26843_IvsQ_26841_1_IvsQ_26842_1_IvsQ_26843_1.dat.txt
IvsQ_26841_26842_26843_IvsQ_26841_2_IvsQ_26842_2_IvsQ_26843_2.dat.txt
IvsQ_26844_26845_26846_IvsQ_26844_1_IvsQ_26845_1_IvsQ_26846_1.dat.txt
IvsQ_26844_26845_26846_IvsQ_26844_2_IvsQ_26845_2_IvsQ_26846_2.dat.txt
POLLREFfinalIvsQ_26838_26839_26840_IvsQ_26838_1_IvsQ_26839_1_IvsQ_26840_1.dat
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POLLREFfinalIvsQ_26854_26855_26856_IvsQ_26854_1_IvsQ_26855_1_IvsQ_26856_1.dat.txt
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POLLREFfinalIvsQ_26860_26861_26862_IvsQ_26860_1_IvsQ_26861_1_IvsQ_26862_1.dat.txt
POLLREFfinalIvsQ_26860_26861_26862_IvsQ_26860_2_IvsQ_26861_2_IvsQ_26862_2.dat.txt
POLLREFfinalIvsQ_26863_26864_26865_IvsQ_26863_1_IvsQ_26864_1_IvsQ_26865_1.dat.txt
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POLLREFfinalIvsQ_26875_26876_26877_IvsQ_26875_1_IvsQ_26876_1_IvsQ_26877_1.dat.txt
POLLREFfinalIvsQ_26875_26876_26877_IvsQ_26875_2_IvsQ_26876_2_IvsQ_26877_2.dat.txt
POLLREFfinalIvsQ_26878_26879_26880_IvsQ_26878_1_IvsQ_26879_1_IvsQ_26880_1.dat.txt
POLLREFfinalIvsQ_26878_26879_26880_IvsQ_26878_2_IvsQ_26879_2_IvsQ_26880_2.dat.txt
POLLREFfinalIvsQ_26881_26882_26883_IvsQ_26881_1_IvsQ_26882_1_IvsQ_26883_1.dat.txt
POLLREFfinalIvsQ_26881_26882_26883_IvsQ_26881_2_IvsQ_26882_2_IvsQ_26883_2.dat.tx
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
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
Author Under Sail The Imagination of Jack London, 1893-1902
No full textIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Intro -- Title Page -- Copyright Page -- Dedication -- Contents -- Acknowledgments -- Introduction -- 1. Spirit Truth -- 2. From Absorption to Theatricality and Back Again -- 3. "I Will Build a New Present" -- 4. Sons as Authors -- 5. Fathers as Publishers -- 6. The Daughter as Author -- 7. Lovers as Authors -- 8. At Sea with the Family -- 9. Yellow News, Yellow Stories -- 10. The Return Home -- Notes -- Bibliography -- Index -- About Jay WilliamsIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Description based on publisher supplied metadata and other sources.Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, YYYY. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries
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