1,721,006 research outputs found
Adjusted Confidence Intervals for the Expression Change of Proteins observed in 2-Dimensional Difference Gel Electrophoresis
No full textDifferential proteome analyses focus on the detection and quantification of expression changes between samples from different biological groups. While the significance of an expression change is detected by some statistical test, the strength of an expression change is usually quantified by some ratio estimate, e.g. the ‘fold change’. Due to its quantitative character, the fold change is more intuitively for biologists than the decision of a statistical test. However, strong expression changes are often misleading if this change is not significant. For this reason, we propose the employment of confidence intervals, adjusted for multiple hypotheses testing, which naturally comprise both, test decision and quantification. The adjusted confidence intervals can be used for making test decisions under the control of error rates typically considered in multiple hypotheses testing (e.g. the familywise error rate or the false discovery rate). For biologists, test decisions based on adjusted confidence intervals offer a more intuitive method for selecting proteins with a significant expression change between two groups. The length of the intervals can be used for sample size planning of upcoming experiments. Our approach is primarily addressed to protein expression data recorded by two-dimensional Difference Gel Electrophoresis
Molecular basis for the enzymatic inactivity of class III glutaredoxin ROXY9 on standard glutathionylated substrates
Full text linkAbstract Class I glutaredoxins (GRXs) are nearly ubiquitous proteins that catalyse the glutathione (GSH)-dependent reduction of mainly glutathionylated substrates. In land plants, a third class of GRXs has evolved (class III). Class III GRXs regulate the activity of TGA transcription factors through yet unexplored mechanisms. Here we show that Arabidopsis thaliana class III GRX ROXY9 is inactive as an oxidoreductase on widely used model substrates. Glutathionylation of the active site cysteine, a prerequisite for enzymatic activity, occurs only under highly oxidizing conditions established by the GSH/glutathione disulfide (GSSG) redox couple, while class I GRXs are readily glutathionylated even at very negative GSH/GSSG redox potentials. Thus, structural alterations in the GSH binding site leading to an altered GSH binding mode likely explain the enzymatic inactivity of ROXY9. This might have evolved to avoid overlapping functions with class I GRXs and raises questions of whether ROXY9 regulates TGA substrates through redox regulation
Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design
No full textAbstract
Besides vaccines, the development of antiviral drugs targeting SARS-CoV-2 is critical for preventing future COVID outbreaks. The SARS-CoV-2 main protease (M
pro
), a cysteine protease with essential functions in viral replication, has been validated as an effective drug target. Here, we show that M
pro
is subject to redox regulation in vitro and reversibly switches between the enzymatically active dimer and the functionally dormant monomer through redox modifications of cysteine residues. These include a disulfide-dithiol switch between the catalytic cysteine C145 and cysteine C117, and generation of an allosteric cysteine-lysine-cysteine SONOS bridge that is required for structural stability under oxidative stress conditions, such as those exerted by the innate immune system. We identify homo- and heterobifunctional reagents that mimic the redox switching and inhibit M
pro
activity. The discovered redox switches are conserved in main proteases from other coronaviruses, e.g. MERS-CoV and SARS-CoV, indicating their potential as common druggable sites.Open-Access-Publikationsfonds 202
A fluorescent sensor for real-time monitoring of DPP8/9 reveals crucial roles in immunity and cancer
No full textDipeptidyl peptidases 8 and 9 (DPP8/9) are critical for the quality control of mitochondrial and endoplasmic reticulum protein import, immune regulation, cell adhesion, and cell migration. Dysregulation of DPP8/9 is associated with pathologies including tumorigenesis and inflammation. Commonly, DPP8/9 activity is analysed by in vitro assays using artificial substrates, which allow neither continuously monitoring DPP8/9 activity in individual, living cells nor detecting effects from endogenous interactors and posttranslational modifications. Here, we developed DiPAK (for DPP8/9 activity sensor based on AK2), a ratiometric genetically encoded fluorescent sensor, which enables studying DPP8/9 activity in living cells. Using DiPAK, we determined the dynamic range of DPP8/9 activity in cells overexpressing or lacking DPP9. We identified distinct activity levels among melanoma cell lines and found that LPS-induced primary B-cell activation depends on DPP8/9 as the absence of DPP8/9 activity results in apoptotic but not pyroptotic cell death. Consistently, we observed increasing DPP8/9 activity during B-cell maturation. Overall, DiPAK is a versatile tool for real-time single-cell monitoring of DPP8/9 activity in a broad range of cells and organisms.Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/50110000165
Assessing the risk to develop a growing teratoma syndrome based on molecular and epigenetic subtyping as well as novel secreted biomarkers
No full texthttp://dx.doi.org/10.13039/100008672 Wilhelm Sander Foundationhttp://dx.doi.org/10.13039/501100001659 German Research Foundatio
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
Einfluss von MUPP1 auf die Funktion des 5- Rezeptors der Maus
No full textDas multi-PDZ Protein 1 MUPP1 besitzt 13 PDZ Domänen und hat so das Potential mit diversen Partnerproteinen zu interagieren. In der Arbeit wurde das Expressionsmuster von MUPP1 in verschiedenen Mausgeweben und insbesondere im Maushirn ermittelt. Es konnte die Bindung von MUPP1 an den 5- Rezeptor, TAPP2 und den demonstriert werden.
Nach der Stimulation von Zellen mit zeigte sich eine durch TAPP2 vermittelte Translokation von MUPP1 zur Plasmamembran. Dieser Prozess führte nach Agonistapplikation zu einer erhöhten Signalantwort von 5- Rezeptoren. Ausserdem konnte nach Überexpression der 10. PDZ Domäne von MUPP1 eine verzögerte Resensitisierung des 5- Rezeptors nach Agoniststimulation beobachtet werden. Dies deutet darauf hin, dass MUPP1 eine modulatorische Wirkung auf die 5- Rezeptorfunktion ausübt. Des Weiteren wurden für Mausmodelle, mit denen die Interaktion zwischen MUPP1 und dem 5- Rezeptor in vivo untersucht werden kann, die Grundlagen gelegt
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