1,721,364 research outputs found
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
The maternally expressed WRKY transcription factor TTG2 controls lethality in interploidy crosses of Arabidopsis.
Full text linkThe molecular mechanisms underlying lethality of F1 hybrids between diverged parents are one target of speciation research. Crosses between diploid and tetraploid individuals of the same genotype can result in F1 lethality, and this dosage-sensitive incompatibility plays a role in polyploid speciation. We have identified variation in F1 lethality in interploidy crosses of Arabidopsis thaliana and determined the genetic architecture of the maternally expressed variation via QTL mapping. A single large-effect QTL, DR. STRANGELOVE 1 (DSL1), was identified as well as two QTL with epistatic relationships to DSL1. DSL1 affects the rate of postzygotic lethality via expression in the maternal sporophyte. Fine mapping placed DSL1 in an interval encoding the maternal effect transcription factor TTG2. Maternal parents carrying loss-of-function mutations in TTG2 suppressed the F1 lethality caused by paternal excess interploidy crosses. The frequency of cellularization in the endosperm was similarly affected by both natural variation and ttg2 loss-of-function mutants. The simple genetic basis of the natural variation and effects of single-gene mutations suggests that F1 lethality in polyploids could evolve rapidly. Furthermore, the role of the sporophytically active TTG2 gene in interploidy crosses indicates that the developmental programming of the mother regulates the viability of interploidy hybrid offspring
A Mutual Support Mechanism through Intercellular Movement of CAPRICE and GLABRA3 Can Pattern the Arabidopsis Root Epidermis
Full text linkThe patterning of the Arabidopsis root epidermis depends on a genetic regulatory network that operates both within and between cells. Genetic studies have identified a number of key components of this network, but a clear picture of the functional logic of the network is lacking. Here, we integrate existing genetic and biochemical data in a mathematical model that allows us to explore both the sufficiency of known network interactions and the extent to which additional assumptions about the model can account for wild-type and mutant data. Our model shows that an existing hypothesis concerning the autoregulation of WEREWOLF does not account fully for the expression patterns of components of the network. We confirm the lack of WEREWOLF autoregulation experimentally in transgenic plants. Rather, our modelling suggests that patterning depends on the movement of the CAPRICE and GLABRA3 transcriptional regulators between epidermal cells. Our combined modelling and experimental studies show that WEREWOLF autoregulation does not contribute to the initial patterning of epidermal cell fates in the Arabidopsis seedling root. In contrast to a patterning mechanism relying on local activation, we propose a mechanism based on lateral inhibition with feedback. The active intercellular movements of proteins that are central to our model underlie a mechanism for pattern formation in planar groups of cells that is centred on the mutual support of two cell fates rather than on local activation and lateral inhibition
Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite
Full text linkHow generalist parasites with wide host ranges can evolve is a central question in parasite evolution. Albugo candida is an obligate biotrophic parasite that consists of many physiological races that each specialize on distinct Brassicaceae host species. By analyzing genome sequence assemblies of five isolates, we show they represent three races that are genetically diverged by ~1%. Despite this divergence, their genomes are mosaic-like, with ~25% being introgressed from other races. Sequential infection experiments show that infection by adapted races enables subsequent infection of hosts by normally non-infecting races. This facilitates introgression and the exchange of effector repertoires, and may enable the evolution of novel races that can undergo clonal population expansion on new hosts. We discuss recent studies on hybridization in other eukaryotes such as yeast, Heliconius butterflies, Darwin's finches, sunflowers and cichlid fishes, and the implications of introgression for pathogen evolution in an agro-ecological environment
microRNAs in Arabidopsis: biologische Funktionen und Selektion von Ziel-Genen
No full textSpatial and temporal control of gene activity is a prerequisite of multicellular development, as the local accumulation of gene products is required to specify different cell fates. The regulation of gene expression involves a large number of different effectors, and also single-stranded RNAs of ~19-25 nucleotides in length. MicroRNAs (miRNAs) constitute a large group of endogenous small RNAs, and they negatively regulate their target genes by base-pairing to complementary nucleic acids. In animals, miRNAs typically trigger translational arrest of their targets, to which they pair with only limited complementarity. Plant miRNAs, on contrary, trigger cleavage of target transcripts, with which they share high sequence complementarity. Predictions of new plant miRNA targets have therefore focused on genes with only a small number of mismatches to miRNAs.
Studying the biological function of three plant miRNAs, I have over- and misexpressed their precursors in Arabidopsis thaliana. The different abnormalities, which could be observed in transgenic plants, strongly suggest a role of these miRNAs as regulators of plant development. Overexpression of miR156 extended the vegetative phase of Arabidopsis seedlings, and also increased the speed and number of organ initiation events. Conversely, miR172 was shown to decrease the time of vegetative development when overexpressed, and also to control floral organ identity. MiRNA164 was shown to control separation of above ground organs throughout the life cycle of Arabidopsis plants. The observed defects can be partially correlated with known loss-of-function mutants in predicted target genes, however they also postulate additional miRNA functions. These might be mediated by other predicted target genes, which had not been functionally characterized before.
I have studied direct effects of miRNA expression on target RNA accumulation and confirmed that many predicted target genes were strongly responsive to miRNA overaccumulation. This finding is consistent with phenotypes of miRNA overexpressers resembling mutants in target genes, and also with cleavage of mRNAs as the mode of plant miRNA function. In order to test for the presence of additional targets with similar or lower sequence complementarity, I monitored genome-wide expression changes caused by overexpression of five different miRNAs. In brief, these analyses suggest that plant miRNAs directly regulate only a very small number of target genes, to which they pair with high sequence complementarity.
Comparing authentic miRNA targets to other, non-responsive genes with similar mismatch numbers, I established positional determinants of plant miRNA target selection. These, unlike previous computational efforts, almost unambiguously discriminate targets from non-targets not only in the small set of miRNAs analyzed, but also when compared to other plant miRNAs.
Feedback regulation can add another level of complexity to miRNA mediated effects, as I have discovered for the case of miR172. It has been previously suggested that miR172 overexpression results in changes of target protein, rather than transcript abundance, and translational inhibition was proposed as a mechanistic basis. However, since cleavage of target transcripts was efficiently increased in miR172 overexpressing tissue, additional regulatory events have to be present. To uncouple miRNA mediated from other effects on target genes, I overexpressed a miRNA resistant version of the target gene AP2, and confirmed the presence of a negative feedback of AP2 on its own expression. This suggests that miR172 functions by simultaneously triggering cleavage and translational inhibition of its target genes.
Since the action spectrum of plant miRNAs is very narrow, it contrasts with the broad selectivity of animal miRNAs. This difference might reflect either only intrinsic properties of the plant miRNA machinery, or selection against miRNAs with broader specificity has reduced the number of plant miRNA targets. In order to distinguish between the two possibilities, I have generated artificial miRNAs (amiRNAs) targeting endogenous genes and found that their specificity was as high as that of natural plant miRNAs. This finding supports the idea that extensive basepairing with target genes is required for plant miRNA function. Since amiRNAs were efficiently produced and could be designed to specifically silence single, or groups of endogenous genes, they can easily be used as a tool for directed gene silencing in plants. In addition to conventional silencing of single genes, which is already possible by RNA interference, amiRNAs can specifically downregulate expression of multiple related genes. As they function with high specificity, they can potentially also function in strand or allele specific gene silencing, which is not possible by other means. Furthermore, introduction of amiRNA-insensitive variants of targets can be generates to compensate for defects in amiRNA expressing plants. A web-based tool has been established to automatically design amiRNAs for genes of interest and is available to the scientific community for further studies.Die Regulierung der zellulären Gen-Aktivität spielt eine entscheidende Rolle in der Entwicklung vielzelliger Organismen, da sie die lokale Spezifizierung verschiedener Zell-Identitäten ermöglicht. Eine Vielzahl molekularer Komponenten beeinflusst die Expression einzelner Gene, unter anderen auch regulatorische RNAs. Diese gehören oft zur Klasse der kleinen RNAs von nur 19 bis 25 Nukleotiden Länge, die durch komplementäre Basenpaarung eine selektive Bindung and Ziel-Gene erreicht, welche sie in der Regel negativ beeinflusst. MicroRNAs sind eine Gruppe kleiner RNAs, die wie Proteine im Genom kodiert werden, und meist an Boten-RNAs binden. In Pflanzen zeigen diese meist hohe Sequenz-Komplementarität zur jeweiligen microRNA und werden in der Regel am Ort der microRNA-Bindung gespalten, wobei die resultierenden Produkte abgebaut werden. In Tieren erfolgt in den meisten Fällen ein Block der Protein-Synthese der jeweiligen Ziel-Gene, welche aufgrund der geringen erforderlichen Sequenz-Komplementarität oft sehr zahlreich sind.
MicroRNAs wurden erst vor wenigen Jahren als zentraler Bestandteil der Genregulation beschrieben, sodass viele Eigenschaften ihrer biochemischen Funktionalität als auch ihrer biologischen Relevanz noch nicht beschrieben worden sind.
Im Rahmen dieser Dissertation wurden verschiedene funktionale Aspekte von microRNAs in der Modell-Pflanze Arabidopsis thaliana (Ackerschmalwand) untersucht.
1. Biologische Relevanz einzelner microRNAs
Die gezielte Über- und Misexpression einzelner microRNAs führte zu verschiedenen phänotypischen Abnormalitäten, welche sich zum Teil durch bekannte Rollen einzelner Ziel-Gene erklären ließen, aber auch weitreichendere Funktionen der microRNAs in der Regulation von Entwicklungsprozessen absehen ließen. Sie erlaubten ferner den Schluss, dass eine koordinierte räumliche und zeitliche Akkumulation von microRNAs von entscheidender Bedeutung für die Entwicklung der Pflanze ist.
2. Ziel-Gene von microRNAs
Die meisten bisher bekannten microRNA Ziel-Gene in Pflanzen wurden aufgrund ihrer sehr hohen Sequenz-Komplementarität vorhergesagt, und in vielen Fällen auch bestätigt. Nicht bekannt hingegen war, ob es weitere Ziel-Gene mit geringerer Sequenz-Komplementarität geben würde.
Da pflanzliche microRNAs in der Regel die Spaltung ihrer Ziel-RNAs bewirken, sollte deren Expressionsniveau in Gegenwart erhöhter microRNA Mengen verringert sein. Dies wurde mit Hilfe von Microarrays in vielen Fällen bestätigt. Microarrays erlaubten außerdem genomweite Studien zur veränderten Genexpression in microRNA überproduzierenden Pflanzen, und damit eine Beschreibung der vollständigen Zahl von microRNA Ziel-Genen. Diese war in allen fünf analysierten Fällen sehr gering, im Gegensatz zu den meisten bekannten tierischen microRNAs. In der Folge wurden die ermittelten Ziel-Gene zum Vergleich mit anderen Genen herangezogen, was zur Formulierung von Sequenz-Determinanten zur Selektion von microRNA Ziel-Genen führte.
3. Künstliche microRNAs
Unter Beachtung der ermittelten Sequenz-Determinanten von microRNA Ziel-Genen wurden künstliche microRNAs generiert, welche der negativen Regulierung endogener, normalerweise nicht von microRNAs regulierten Genen dienen sollten. Diese künstlichen microRNAs zeigten ein ebenso enges Wirkspektrum wie endogene microRNAs, was den Schluss erlaubte, dass einzig die involvierten enzymatischen Komponenten für diese Spezifität verantwortlich sind. Somit können microRNAs zur gezielten Regulierung einzelner oder mehrerer Gene herangezogen werden. In weiteren Experimenten wurde gezeigt, dass die Genregulation durch künstliche microRNAs auch unter gewebespezifischen und induzierbaren Promotoren erfolgreich ist, und weitgehend zellautonome Effekte induziert
Two-step recruitment of RNA-directed DNA methylation to tandem repeats.
Full text linkTandem repeat sequences are frequently associated with gene silencing phenomena. The Arabidopsis thaliana FWA gene contains two tandem repeats and is an efficient target for RNA-directed de novo DNA methylation when it is transformed into plants. We showed that the FWA tandem repeats are necessary and sufficient for de novo DNA methylation and that repeated character rather than intrinsic sequence is likely important. Endogenous FWA can adopt either of two stable epigenetic states: methylated and silenced or unmethylated and active. Surprisingly, we found small interfering RNAs (siRNAs) associated with FWA in both states. Despite this, only the methylated form of endogenous FWA could recruit further RNA-directed DNA methylation or cause efficient de novo methylation of transgenic FWA. This suggests that RNA-directed DNA methylation occurs in two steps: first, the initial recruitment of the siRNA-producing machinery, and second, siRNA-directed DNA methylation either in cis or in trans. The efficiency of this second step varies depending on the nature of the siRNA-producing locus, and at some loci, it may require pre-existing chromatin modifications such as DNA methylation itself. Enhancement of RNA-directed DNA methylation by pre-existing DNA methylation could create a self-reinforcing system to enhance the stability of silencing. Tandem repeats throughout the Arabidopsis genome produce siRNAs, suggesting that repeat acquisition may be a general mechanism for the evolution of gene silencing
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
Generation of New Mutations at Different Time Scales in Plants
Full text linkRapid climate change threatens both food security and biodiversity. The latter is ultimately a reflection of genetic change. Studying genetic variation in wild populations thus provides insight into how genomes change during evolution and may help explain how species adapt to different environments. While most population genetic studies have focused on the nuclear genome, organellar genomes, particularly those of mitochondria, have received much less attention, partly due to difficulties in assembly. Importantly, organellar genomes in land plants evolve more slowly than nuclear genomes and therefore tend to preserve signals of divergence and evolutionary history over deeper time scales. At the same time, there would be no complex life without mutations, which are the ultimate source of genetic diversity, but how they arise and accumulate remains poorly understood.
The development of long-read sequencing, such as PacBio high-fidelity (HiFi) reads and the most recent versions of Oxford Nanopore Technology (ONT) reads, has made it possible to assemble complete organellar genomes, but the use of these data requires a dedicated bioinformatics tool. The complete and accurate assemblies allow for more comprehensive investigation of organellar genome variation and its evolutionary significance. In parallel, long-read data also improve the quality of nuclear genome assemblies, which in turn enhances the detection of somatic mutations and then deepens our understanding of their mutation patterns and biological context.
This thesis addresses these gaps by developing a tool for assembling plant organellar genomes, applying it to more than one hundred accessions of Arabidopsis thaliana to investigate organellar genetic variation, and by refining mutation detection approach in a highly heterozygous oak genome to detect somatic mutations with higher accuracy in challenging genomes.
In the first chapter, I introduce TIPPo, a reference-free tool I developed for assembling plant organellar genomes using HiFi data. TIPPo addresses challenges specific to organelle genomes, including high copy number, repetitive content, and the presence of organelle-derived sequences in the nuclear genome. Through a combination of read classification and filtering strategies, TIPPo produces high-quality assemblies that outperform existing methods. Because both the nuclear and organellar genomes were assembled from the same sample, the identification of NUPTs and NUMTs and their substitution patterns becomes more reliable.
Building on this, the second chapter presents a population-scale analysis of organellar genomes from 143 A. thaliana accessions. While chloroplast genomes have conserved structure and size, mitochondrial genomes are more variable and they could be grouped into two major classes based on repeat content. I found that the number of large repeats in the mitochondrial genome correlated with sampling latitude, suggesting that geographic or historical factors may have influenced mitochondrial genome structure. In addition, I identified unannotated open reading frames (ORFs) with supporting expression evidence. I found two putative horizontally transferred ORFs, one of which is associated with cytoplasmic male sterility (CMS). These findings suggest that mitochondrial genomes can acquire novel functional elements from related species, enriching their evolutionary plasticity.
The third chapter shifts focus to the origin of new genetic variation, using a long-lived oak tree to study somatic mutations. By reassembling the oak genome with HiFi data and applying a hybrid alignment strategy tailored to high heterozygosity, I recovered substantially more high confidence somatic mutations than previous study. Most of the mutations were C:G > T:A transitions, consistent with the result in mutation accumulation studies. These results provide a clearer view of how mutations accumulate over time and show that high quality assembly and careful alignment strategies are key to detecting somatic mutation in complex plant genomes.
Together, these chapters explore how genetic variation arises, accumulates, and is maintained in plant genomes. By combining tool/approach development with population-scale and individual-level analyses, this work provides new insight into both the structure of organellar genomes and the processes shaping somatic mutation patterns. The methods developed here may be broadly useful for studying genome dynamics in diverse species and offer a foundation for future investigations into the evolutionary and functional consequences of genetic variation
- …
