1,720,972 research outputs found
Single-molecule FRET measures bends and kinks in DNA.
Get PDFWe present advances in the use of single-molecule FRET measurements with flexibly linked dyes to derive full 3D structures of DNA constructs based on absolute distances. The resolution obtained by this single-molecule approach harbours the potential to study in detail also protein- or damage-induced DNA bending. If one is to generate a geometric structural model, distances between fixed positions are needed. These are usually not experimentally accessible because of unknown fluorophore-linker mobility effects that lead to a distribution of FRET efficiencies and distances. To solve this problem, we performed studies on DNA double-helices by systematically varying donor acceptor distances from 2 to 10 nm. Analysis of dye-dye quenching and fluorescence anisotropy measurements reveal slow positional and fast orientational fluorophore dynamics, that results in an isotropic average of the FRET efficiency. We use a nonlinear conversion function based on MD simulations that allows us to include this effect in the calculation of absolute FRET distances. To obtain unique structures, we performed a quantitative statistical analysis for the conformational search in full space based on triangulation, which uses the known helical nucleic acid features. Our higher accuracy allowed the detection of sequence-dependent DNA bending by 16 degrees . For DNA with bulged adenosines, we also quantified the kink angles introduced by the insertion of 1, 3 and 5 bases to be 32 degrees +/- 6 degrees , 56 degrees +/- 4 degrees and 73 +/- 2 degrees , respectively. Moreover, the rotation angles and shifts of the helices were calculated to describe the relative orientation of the two arms in detail
Direct and Model Free Calculation of Force Dependent Dissociation Rates and Free Energy Barriers from Force Spectroscopic Data
No full textKraftinduzierte Sekundärstrukturänderungen in einzelnen Molekülen
Get PDFIn dieser Arbeit wurde die in den letzten Jahren entwickelte Technik der auf
dem Kraftmikroskop basierenden Einzelmolekül-Kraftspektroskopie auf zwei
spezielle Systeme angewendet: Poly(ethylen Glycol) (PEG) und das Membranprotein
Bakteriorhodopsin. Im Vordergrund stand dabei die Analyse der mechanischen
Stabilität von Sekundärstrukturen.
PEG ist aufgrund seiner ungewöhnlich hohen Wasserlöslichkeit eines der
wichtigsten Polymere mit einer Vielzahl von technischen Anwendungen. Es wurden
Messungen zur Elastizität einzelner PEG in Abhängigkeit des Lösungsmittels
durchgeführt. Mit diesen Messungen konnte der genaue molekulare Mechanismus
nachvollzogen werden, der zu der hohen Wasserlöslichkeit führt. Zudem konnte
gezeigt werden, wie mit einem einfachen Modell neben Konformationsänderungen
auch Konformationsenergien des Polymers quantitativ bestimmt werden können.
Die Kraftspektroskopie als Instrument zur Untersuchung von mechanisch
induzierten Strukturänderungen, z.B. der Proteinentfaltung, wurde bisher immer
nur auf polymere Strukturen angewendet. Ziel der Messungen an Bakteriorhodopsin
war es zu zeigen, dass sich diese Technik auch auf Moleküle anwenden lässt, die
nicht aus sich wiederholenden Einheiten aufgebaut sind. Es konnte der genaue
Entfaltungsweg von Bakteriorhodopsin mit all seinen stabilen Zwischenstrukturen
bestimmt werden. Mechanismen der Stabilisierung wie die Nachbarschaft von
Helices, hydrophobe Wechselwirkung und der Einfluss räumlicher Einschränkung
konnten dabei in ihren Auswirkungen auf die Stabilität der Proteinstruktur
beobachtet werden
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Get PDF“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
Get PDFWe 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
Get PDFWe 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
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