1,721,055 research outputs found
Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes
No full textSingle-molecule real-time (SMRT) sequencing developed by PacBio, also called third-generation sequencing (TGS), offers longer reads than the second-generation sequencing (SGS). Given its ability to obtain full-length transcripts without assembly, isoform sequencing (Iso-Seq) of transcriptomes by PacBio is advantageous for genome annotation, identification of novel genes and isoforms, as well as the discovery of long non-coding RNA (lncRNA). In addition, Iso-Seq gives access to the direct detection of alternative splicing, alternative polyadenylation (APA), gene fusion, and DNA modifications. Such applications of Iso-Seq facilitate the understanding of gene structure, post-transcriptional regulatory networks, and subsequently proteomic diversity. In this review, we summarize its applications in plant transcriptome study, specifically pointing out challenges associated with each step in the experimental design and highlight the development of bioinformatic pipelines. We aim to provide the community with an integrative overview and a comprehensive guidance to Iso-Seq, and thus to promote its applications in plant research
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
The WHIRLY proteins from Arabidopsis thaliana
Get PDFIm Mittelpunkt der Arbeit stehen die Lokalisation und die Funktionen der Proteine WHIRLY1 und WHIRLY3 von Arabidopsis thaliana. Es konnte gezeigt werden, dass das dual lokalisierte Protein WHIRLY1 aus den Plastiden in den Zellkern umverteilt wird. Neben WHIRLY1 besitzt A. thaliana mit WHIRLY3 ein zweites plastidäres WHIRLY-Protein. Ergebnisse aus der vorliegenden Arbeit deuten auf eine zusätzliche Lokalisation von WHIRLY3 in den Mitochondrien hin. Eine Doppelmutante, die gleichzeitig Mutationen in den Genen WHIRLY1 und WHIRLY3 besitzt, zeigte bei Anzucht unter höheren Lichtintensitäten eine gestörte Entwicklung der Chloroplasten. Untersuchungen zur Keimung ergaben, dass Samen von why1-Mutanten sowohl unempfindlich gegenüber Salicylsäure als auch gegenüber Abscisinsäure sind. Mit einem Hemmstoff konnte gezeigt werden, dass Salicylsäure die Keimung inhibiert, indem sie die Synthese von Abscisinsäure fördert. WHIRLY1 ist also wichtig für die Wahrnehmung von Salicylsäure und Abscisinsäure während der Keimung. Untersuchungen mit transgenen Linien, in denen das WHIRLY1-Protein entweder in Plastiden und dem Zellkern oder nur im Zellkern akkumuliert, zeigten, dass spezifisch die plastidäre Form von WHIRLY1 die Empfindlichkeit von Samen gegenüber Abscisinsäure erhöht. WHIRLY1 ist daher an der Wahrnehmung von Abscisinsäure in Plastiden beteiligt. Das WHIRLY1-Protein wird als Kandidat für die Übertragung von Plastidensignalen zum Zellkern diskutiert.Es wurde gezeigt, dass WHIRLY1 an der Übertragung retrograder Signale beteiligt ist.This study focuses on the localization and functions of the WHIRLY1 and WHIRLY3 proteins from Arabidopsis thaliana. It was shown that the dually located WHIRLY1 protein is redistributed from plastids to the nucleus. In addition to WHIRLY1, A. thaliana has a second plastid WHIRLY protein named WHIRLY3. WHIRLY3 was shown to be dually localized to plastids and mitochondria. Plants having mutations in the genes WHIRLY1 and WHIRLY3 show disturbed chloroplast development when grown under elevated light intensities.
Germination assays showed that why1 mutants are less sensitive towards salicylic acid as well as abscisic acid. It was shown that salicylic acid inhibits germination by promoting the synthesis of abscisic acid. Accordingly, WHIRLY1 is crucial for salicylic acid and abscisic acid perception during germination. Experiments with transgenic lines, that accumulate WHIRLY1 in plastids and the nucleus or in the nucleus alone, indicate that it is the plastid located isoform of WHIRLY1 which enhances the responsiveness of seeds towards abscisic acid. Hence, WHIRLY1 is important for perception of abscisic acid inside plastids. It was shown that WHIRLY1 can transmit plastid retrograde signals
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
Untersuchungen zur transkriptionellen Kontrolle der Genexpression während der Blattseneszenz der Gerste (Hordeum vulgare L.)
Get PDFIn der vorliegenden Arbeit wurden Veränderungen in der Transkriptionsrate und im Transkriptgehalt von 37 Genen während der dunkelinduzierten Seneszenz von Primärblättern und der Seneszenz von Fahnenblättern der Gerste unter Freilandbedingungen analysiert. Nach Isolierung transkriptionsaktiver Kerne aus Gerstenblättern wurden "Run-on"-Transkriptionsexperimente durchgeführt und mit den markierten Transkripten DNA-"Dot Blot"-Membranen hybridisiert. Für die vergleichende Analyse des Transkriptgehalts wurde Gesamt-RNA in cDNA umgeschrieben ("multiplex messenger assay") und für die Hybridisierung derselben DNA-"Dot Blot"-Membranen verwendet. Während der dunkelinduzierten Seneszenz besitzen nur sechs der 37 untersuchten Gene eine signifikant veränderte Transkription. Zusätzlich konnte gezeigt werden, dass bei 32 % bzw. 39 % der untersuchten seneszenzassoziierten und der Photosynthesegene während der dunkelinduzierten Seneszenz der Primärblätter und der Seneszenz der Fahnenblätter die Regulation der Genexpression vorwiegend auf posttranskriptioneller Ebene erfolgt. Ein Vergleich der Ergebnisse zur Transkription und zum Transkriptgehalt zwischen der artifiziell durch Dunkelinkubation induzierten Seneszenz einerseits und der natürlichen Seneszenz der Fahnenblätter andererseits zeigt deutlich, daß die Dunkelinkubation von Pflanzen kein geeignetes Modell für die Untersuchung der Genexpression während Seneszenz von Gerstenblättern
Drought-stress-related reprogramming of gene expression in barley involves differential histone modifications at ABA-related genes
No full textPlants respond to drought by the major reprogramming of gene expression, enabling the plant to survive this threatening environmental condition. The phytohormone abscisic acid (ABA) serves as a crucial upstream signal, inducing this multifaceted process. This report investigated the drought response in barley plants (Hordeum vulgare, cv. Morex) at both the epigenome and transcriptome levels. After a ten-day drought period, during which the soil water content was reduced by about 35%, the relative chlorophyll content, as well as the photosystem II efficiency of the barley leaves, decreased by about 10%. Furthermore, drought-related genes such as HvS40 and HvA1 were already induced compared to the well-watered controls. Global ChIP-Seq analysis was performed to identify genes in which histones H3 were modified with euchromatic K4 trimethylation or K9 acetylation during drought. By applying stringent exclusion criteria, 129 genes loaded with H3K4me3 and 2008 genes loaded with H3K9ac in response to drought were identified, indicating that H3K9 acetylation reacts to drought more sensitively than H3K4 trimethylation. A comparison with differentially expressed genes enabled the identification of specific genes loaded with the euchromatic marks and induced in response to drought treatment. The results revealed that a major proportion of these genes are involved in ABA signaling and related pathways. Intriguingly, two members of the protein phosphatase 2C family (PP2Cs), which play a crucial role in the central regulatory machinery of ABA signaling, were also identified through this approach
The senescence associated gene HvS40 of barley
Get PDFIn der vorliegenden Arbeit wurde das seneszenzassoziierte Gen HvS40 der Gerste als dual kodierendes Gen charakterisiert. Damit wurde ein solches Gen erstmals in Pflanzen beschrieben. Der alternative S40+1-Leserahmen, der den kanonischen Leserahmen im 5'-Bereich überragt, konnte auch in anderen monokotylen, jedoch nicht in dikotylen Arten gefunden werden.
Das S40-Protein, das durch den kanonischen Leserahmen S40+3 kodiert wird, kann der pflanzenspezifischen Proteinfamilie DUF584 zugeordnet werden. Diese kommt sowohl in monokotylen als auch in dikotylen Pflanzen vor. Der in dieser Arbeit generierte Stammbaum zeigt, dass die DUF584-Proteine monokotyler Arten in sieben Gruppen eingeteilt werden können. Dabei bilden die Proteine, die einen alternativen Leserahmen in ihrer kodierenden Sequenz aufweisen, eine eigene phylogenetische Untergruppe.
Versuche zur subzellulären Lokalisation mit PEND- und GFP-Fusionsproteinen zeigten, dass die Alt-S40-Proteine von Gerste und Weizen mit dem PEND-Protein von Arabidopsis in Plastiden und Zellkern derselben Zelle ko-loklisiert waren. Die S40-Proteine zeigten in transient transformierten Zwiebelepidermiszellen hingegen eine ausschließliche Lokalisation im Zellkern. Es konnte gezeigt werden, dass der Transport von Alt-HvS40:GFP in die Plastiden abhängig vom Entwicklungszustand der Zelle ist: In Gerstenprotoplasten aus jungem Gewebe war Alt-HvS40:GFP im Cytoplasma und im Zellkern detektierbar, in Protoplasten aus seneszierendem Gewebe hingegen in den Plastiden und im Zellkern derselben Zelle lokalisiert.
Untersuchungen an Gerstentransformanten mit verändertem S40-Transkriptgehalt zeigten, dass beide Proteine eine regulatorische Funktion während des Seneszenzprozesses ausüben. Dabei agiert das HvS40-Protein als negativer Regulator der Seneszenz, während das alternative S40-Protein den Seneszenzprozess fördert. Es ist wahrscheinlich, dass beide Proteine eine regulatorische Funktion als DNA-Bindeproteine ausüben.In this study the senescence associated gene HvS40 of barley was identified as dual coding gene thereby being the first dual coding gene described in plants. The alternative reading frame S40+1 which overlaps the canonical reading frame S40+3 in 5' direction can also be found in other monocotyledonous but not in dicotyledonous plants like Arabidopsis.
The S40 protein of barley encoded by the canonical reading frame S40+3 belongs to the plant specific DUF584-protein family which is present in monocotyledons as well as in dicotyledons. A phylogenetic tree was created using the protein sequences of the monocotyledonous DUF584-proteins. Within this phylogenetic tree the DUF584-protein showing an alternative reading frame in the coding sequence constitute an own subgroup.
Co-localization experiments with transiently transformed onion epidermis cells confirmed the subcellular localization of Alt-HvS40:GFP and Alt-TdS40:GFP in plastids and the nucleus of the same cell, whereas the S40-proteins of barley and wheat show an exclusive subcellular localization in the nucleus of transiently transformed onion epidermis cells. It was further demonstrated that the subcellular localization of Alt-HvS40:GFP in the chloroplasts is age dependent: In barley protoplasts isolated from young, non-senescent leaves, Alt-HvS40:GFP showed a subcellular localization in the cytoplasma and the nucleus, whereas a subcellular localization in the chloroplasts could only be observed in protoplasts derived from senescent tissue.
To gain more insight into the function of the S40 proteins as potential senescence regulators, transgenic barley lines with altered S40 transcript levels were characterized. The S40 protein from barley was shown to be a negative regulator of senescence whereas the Alt-S40 protein might act as a positive regulator of the senescence process. It is likely that both proteins function as DNA binding proteins
- …
