1,721,102 research outputs found
Influence of Opa1 mutation on survival and function of retinal ganglion cells
No full textSupported by grants from the Deutsche Forschungsgemeinschaft (DFG; Bonn, Germany) to the Werner Reichardt Centre for Integrative Neuroscience (DFG EXC 307), by the Bundesministerium fūr Bildung and Forschung (‘‘Bernstein Center for Computational Neuroscience,’’ FKZ 01GQ1002 [TAM], and E-Rare "ERMION," FZ 01GM1006 [BW], and a Stipend of the Pro Retina Foundation [KR]; Frankfurt, Germany
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
Untersuchungen zur Regulierung der Transkription in der humanen Retina: Kartierung von Transkriptionsstartpunkten retinal exprimierter Gene und funktionale Charakterisierung des CNGA3-Promotors
No full textBackground
The proper assembly of the transcriptional initiation machinery is a key regulatory step in the execution of the correct program of mRNA synthesis. The use of alternative transcription start sites (TSSs) provides a mechanism for cell and tissue specific gene regulation. Our knowledge of transcriptional initiation sequences in the human genome is limited despite the availability of the complete genome sequence. While genome wide experimental and bioinformatic approaches are improving our knowledge of TSSs, they lack information concerning genes expressed in a restricted manner or at very low levels, such as tissue specific genes, such as retinal genes. The importance of this work is that new TSSs and transcribed sequences are essential for further exploration of the promoter and other cis-regulatory sequences at the 5´end of genes. In this study we further characterize the promoter of the CNGA3 gene.
Chapter I: Identification of the Transcription Start Sites (TSSs) in human retinal expressed genes
The first part of this work was dedicated to the identification of TSSs of human retinal expressed genes and to improve and complete gene annotation concerning the 5’-UTR. This work was based on the following goals:
- In silico analysis of ESTs and known algorithm predictions of genes expressed in human retina to select the best candidate genes for TSS experimental study.
- Comparison of whole available pull of mRNA transcripts in order to understand and predict potential alternative TSSs for human retinal expressed genes.
- Experimental validation via Cap-finder RACE mapping of the TSSs of selected human retinal expressed genes.
- Analysis of the selectivity of genes for TSSs on human retinal tissue.
This work reports the mapping of TSSs of 54 retina expressed genes: This means new sequences for 41 genes of them.
Results analysis and classification put those 41 genes into five categories (i) TSS located in new first exons, (ii) splicing variation of the second exon, (iii) extension of the annotated first exon, (iv) shortening of the annotated first exon, (v) confirmation of previously annotated TSS.
In silico and experimental analysis of the transcripts proved to be essential for the ultimate mapping of TSSs. Our results highlight the necessity of a tissue specific approach to complete the existing gene annotation.
Chapter II: Identification and Characterization of the human CNGA3 gene promoter
Based on the knowledge generated with the first part, the second major task of this work was to identify and characterize the basic promoter of the human CNGA3 gene. This was done by means of:
- In silico analysis of the putative promoter region of CNGA3.
- Interspecies comparison of the TSS and the putative promoter region of CNGA3 by 5’-RACE experiments performed with human, mouse and zebrafish retinal mRNA. In human, data indicate that transcription of the CNGA3 gene can start within two alternative exons: TSS.1 located in exon U1 and TSS.2 located in exon 1.
- Generation of reporter constructs containing the putative promoter regions of CNGA3 transfected into ARPE-19, HEK 293, Y79, WERI-Rb1 and 661W cells for promoter activity measured by luciferase reporter assay. Only the upstream region of exon 1 exhibits promoter activity in reporter gene assays.
- Interspecies sequence comparison and predictions of putative transcription factor binding sites done to identify potential regulatory candidates.
- Generation of individual deletions for putative-transcription factor-binding sites on reporter that contain promoter activity. Data suggests the promoter is negatively regulated by the transcription factor YY1.
- Cotransfection of specific plasmids for transcription factors together with the reporter constructs containing promoter activity. Interestingly, this promoter is negatively regulated by the transcription factor YY1.
- Localization of different CNGA3 transcripts within the human retina.
In Conclusion, we have identified two TSS for the human retinal CNGA3. The transcription of the human CNGA3 gene is controlled by a promoter located immediately upstream of exon 1. Furthermore, we identified the minimal promoter needed for transcription. Finally, we have also defined a region in the CNGA3 promoter regulated by YY1. These findings reveal a previously unknown level of complexity in the regulation of the expression of the CNGA3 gene, and provide the basis for further studies of its transcriptional regulation.Hintergrund
Der korrekte Zusammenbau der Initiationsmaschinerie für die Transkription ist ein regulatorischer Schlüsselschritt für die Ausführung des korrekten Programms der mRNA-Synthese. Einen Mechanismus der zell- und gewebespezifischen Genregulierung bietet die Verwendung alternativer Transkriptionsstartpunkte (TSS = transcription start sites). Unser Wissen über die Initiationssequenzen zur Transkription im menschlichen Genom ist trotz der Verfügbarkeit der vollständigen Gensequenzen begrenzt. Während genomweite experimentelle und bioinformatische Ansätze unser Wissen über die TSS erweitern, fehlen Informationen über Gene, die nur eingeschränkt oder auf sehr geringem Niveau exprimiert werden, so wie gewebespezifische Gene wie retinale Gene. Die Bedeutung dieser Arbeit liegt darin, dass neue TSS und transkribierte Sequenzen essentiell für die weitere Erforschung der Promotoren und anderer cis-regulativer Sequenzen am 5'-Ende von Genen sind. In dieser Studie charakterisieren wir die Promotoren der CNGA3-Gene genauer.
Kapitel I: Identifizierung der Transkriptionsstartpunkte (TSS) in retinal-exprimierten Genen des Menschen.
Der erste Teil dieser Arbeit wurde der Identifizierung von TSS in menschlichen, retinal exprimierten Genen gewidmet und der Verbesserung und Vervollständigung der Gen-Besschriftung bezüglich des 5'UTR (untranslatierter Bereich = untranslated region). Diese Arbeit hatte die folgende Zielstellung:
- In-silico-Analyse von ESTs und bekannten Algorithmus-Prognosen von in der humanen Retina exprimierten Genen, um die besten Kandidatengene für experimentelle Studien der TSS auszuwählen.
- Vergleich des gesamten verfügbaren Pools des mRNA-Transkripts, um mögliche alternative TSS von humanen retinal-exprimierten Genen zu verstehen und vorauszusagen.
- Experimentelle Validierung der TSS ausgewählter humaner retinal-exprimierter Gene per Capfinder-RACE-mapping.
- Analyse der Selektivität von Genen für TSS in menschlichem Retinagewebe.
Diese Arbeit stellt die Kartierung von TSS von 54 in der Retina exprimierten Genen dar: Das bedeutet neue Sequenzen für 41 dieser Gene.
Die Ergebnisanalyse und -klassifizierung teilt diese 41 Gene in fünf Kategorien ein: (i) in neuen ersten Exons lokalisierte TSS, (ii) Splicingvariationen des zweiten Exons, (iii) Erweiterungen des annotierten ersten Exons, (iv) Verkürzungen des annotierten ersten Exons, (v) Bestätigung früher annotierter TSS.
In-silico und experimentelle Analysen des Transkripts erwiesen sich als essentiell für die endgültige Kartierung der TSS. Unsere Ergebnisse zeigen die Notwendigkeit einer gewebespezifischen Vorgehensweise auf, um die existierende Gen-Annotation zu vervollständigen.
Kapitel II: Identifizierung und Charakterisierung des humanen CNGA3-Genpromotors
Auf dem im ersten Teil generierten Wissen basierend, ist es die zweite Hauptaufgabe dieser Arbeit, die elementaren Promotoren des humanen CNGA3-Gens zu identifizieren und zu charakterisieren. Dies wurde mit folgenden Mitteln durchgeführt:
- In-silico-Analyse der mutmaßlichen Promotorregion von CNGA3.
- Inter-Spezies-Vergleich der TSS und der wahrscheinlichen Promotorregion von CNGA3 durch 5'RACE-Experimente mit retinaler mRNA von Mensch, Maus und Zebrafisch. Die Daten weisen darauf hin, dass die Transkription des CNA3-Gens beim Menschen in zwei alternativen Exonen beginnen kann: in TSS.1, das in Exon U1 lokalisiert ist, und in TSS.2, das in Exon 1 lokalisiert ist.
- Generierung von Raporter-Konstrukten, die wahrscheinliche Promoterregion von CNGA3 enthalten un in ARPE-19-, HEK 293-, Y79-, WERI-Rb1- und 661W-Zellen transfiziert werden, um mittels eines Luziferase-Reporter Assays die Promoteraktivität zu messen. Lediglich die vorgelagerte Region von Exon 1 zeigt Promotoraktivität im Reportergen-Assay.
- Zwischenartliche Sequenzvergleiche und Prognosen der wahrscheinlichen Transkriptionsfaktor-Bindungsstellen, durchgeführt um potentielle Regulierungskandidaten zu identifizieren.
- Generierung von individuellen Deletionen vermutlicher Transkriptionsfaktor-Bindungsstellen in Reportern, die Promotoraktivität besitzen. Die Daten deuten darauf hin, dass der Promotor vom Transkriptionsfaktor YY1 negativ reguliert wird.
- Lokalisierung verschiedener CNGA3-Transkripte innerhalb der humanen Retina.
Zusammengefasst haben wir zwei TSS des humanen Retina-CNGA3 identifiziert. Die Transkription des humanen CNGA3-Gens wird von einem Promotor kontrolliert, der dem Exon 1 unmittelbar vorgelagert ist. Des Weiteren haben wir den Promotor identifiziert, der zur Transkription minimal nötig ist. Schlussendlich haben wir eine Region im CNGA3-Promotor definiert, die von YY1 reguliert wird. Diese Resultate offenbaren einen zuvor unbekannten Grad der Komplexität bei der Regulierung der Expression von CNGA3-Genen und liefern die Grundlage für weitere Untersuchungen ihrer Transkriptionsregulation
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
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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