Necrosis in grapevine buds (Vitis vinifera cv. Queen of Vineyard) II. Effect of gibberellic acid (GA3) application

The effect of gibberellic acid application on the development of necrosis in cv. Queen of Vineyard grapevine buds was studied. GA3 caused the development of a necrotic layer at the base of the central bud and promoted the development of the  axillary buds. GA3 application to leaves caused necrosis in the buds more readily than direct application to the buds. GA3 fed to the petiole was 100 times more active in inducing necrosis than leaf application. Only developing and relatively young buds were sensitive to GA3. A minimum of 6 X 10-6 mg GA3 in the bud was needed to cause bud necrosis. During the period from 1 week before to 3 weeks after bloom, the movement of GA3 in the grape shoot was acropetal. The possible involvement of gibberellins in the natural necrosis of buds on vigorous grapevines is discussed.Knospennekrosen bei der Rebsorte Queen of Vineyard (Vitis vinifera)II. Einfluß der Gibberellinsäure- (GA3)BehandlungBei der Sorte Queen of Vineyard wurde der Einfluß der GA3-Behandlung auf die Entwicklung von Knospennekrosen untersucht. GA3 bewirkte die Ausbildung einer nekrotischen Gewebeschicht an der Basis der Mittelknospe und förderte die Entwicklung der Axillarknospen. Durch GA3-Behandlung der Blätter ließen sich leichter Knospennekrosen auslösen als durch direkte Behandlung der Knospen. Wurde GA3 über den Blattstiel zugeführt, so war seine Nekrosen induzierende Wirkung 100mal stärker als bei Behandlung der Blattspreite. Nur sich entwickelnde und relativ junge Knospen waren gegen GA3 sensibel. Um eine Knospennekrose auszulösen, mußten in den Knospen mindestens 6 X 10-6 mg GA3 vorliegen. Zwischen 1 Woche vor und 3 Wochen nach der Blüte erfolgte die Bewegung des GA3in den Rebentrieben akropetal. Die mögliche Beteiligung von Gibberellinen am natürlichen Auftreten von Knospennekrosen bei wüchsigen Reben wird diskutiert

Necrosis in grapevine buds (Vitis vinifera cv. Queen of Vineyard) I. Relation to vegetative vigor1)

A study on the occurrence, development and nature of necrotic buds on shoots of the Queen of Vineyard grape cultivar was carried out in the continental Jordan Valley in Israel. A vigorous vineyard having an abundance of necrotic buds and a moderately growing one with few necrotic buds were chosen.Necrosis of the central bud in the Queen of Vineyard winter buds occurred only in the vigorous vineyard. The number of necrotic dry buds was particularly high at nodes 2-3 on the shoot and decreased progressively up to the 7th node above which necrotic buds were not observed. Drying of the central bud occurred over a short period, 15-20 d after bloom. It started with the appearance of a necrotic layer at one of the basal nodes of the central bud which caused a rapid degeneration of the tissues above this layer. A negative correlation was found between the fruiting potential of winter buds and the development of a necrotic layer. The possible relation between vigor, gibberellins and bud necrosis is discussed.Knospennekrosen bei der Rebsorte Queen of Vineyard (Vitis vinifera)I. Beziehung zur vegetativen WüchsigkeitIm binnenländischen Jordantal in Israel wurde eine Untersuchung über Auftreten, Entwicklung und Art von Knospennekrosen an den Trieben der Rebsorte Queen of Vineyard durchgeführt. Hierzu wurden ein wüchsiger Weinberg, in dem nekrotische Knospen gehäuft vorkamen, und ein Weinberg von mittlerer Wüchsigkeit mit wenigen nekrotischen Knospen ausgewählt. In den Winterknospen von Queen of Vineyard trat eine Nekrose der Mittelknospe nur in der wüchsigen Rebanlage auf. Die Anzahl vertrockneter nekrotischer Knospen war besonders hoch an den Knoten 2-3 der Triebe; sie ging stetig zurück bis zum 7. Knoten; darüber wurden keine nekrotischen Knospen mehr beobachtet. Die Austrocknung der Mittelknospe erfolgte nur während einer kurzen Phase, 15-20 d nach der Blüte. Sie begann mit dem Auftreten einer nekrotischen Schicht an einem der basalen Knoten der Mittelknospe, wodurch die darüberliegenden Gewebe rasch degenerierten. Zwischen der potentiellen Fruchtbarkeit der Winterknospen und der Entwicklung einer nekrotischen Schicht wurde eine negative Korrelation gefunden. Die mögliche Beziehung zwischen Wüchsigkeit, Gibberellingehalt und Nekrosenhäufigkeit wird diskutiert

The fitness cost of mis-splicing is the main determinant of alternative splicing patterns

Background Most eukaryotic genes are subject to alternative splicing (AS), which may contribute to the production of protein variants or to the regulation of gene expression via nonsense-mediated messenger RNA (mRNA) decay (NMD). However, a fraction of splice variants might correspond to spurious transcripts and the question of the relative proportion of splicing errors to functional splice variants remains highly debated. Results We propose a test to quantify the fraction of AS events corresponding to errors. This test is based on the fact that the fitness cost of splicing errors increases with the number of introns in a gene and with expression level. We analyzed the transcriptome of the intron-rich eukaryote Paramecium tetraurelia. We show that in both normal and in NMD-deficient cells, AS rates strongly decrease with increasing expression level and with increasing number of introns. This relationship is observed for AS events that are detectable by NMD as well as for those that are not, which invalidates the hypothesis of a link with the regulation of gene expression. Our results show that in genes with a median expression level, 92–98% of observed splice variants correspond to errors. We observed the same patterns in human transcriptomes and we further show that AS rates correlate with the fitness cost of splicing errors. Conclusions These observations indicate that genes under weaker selective pressure accumulate more maladaptive substitutions and are more prone to splicing errors. Thus, to a large extent, patterns of gene expression variants simply reflect the balance between selection, mutation, and drift

Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

Drivers of genetic diversity in secondary metabolic gene clusters within a fungal speciesFilamentous fungi produce a diverse array of secondary metabolites (SMs) critical for defense, virulence, and communication. The metabolic pathways that produce SMs are found in contiguous gene clusters in fungal genomes, an atypical arrangement for metabolic pathways in other eukaryotes. Comparative studies of filamentous fungal species have shown that SM gene clusters are often either highly divergent or uniquely present in one or a handful of species, hampering efforts to determine the genetic basis and evolutionary drivers of SM gene cluster divergence. Here, we examined SM variation in 66 cosmopolitan strains of a single species, the opportunistic human pathogen Aspergillus fumigatus. Investigation of genome-wide within-species variation revealed 5 general types of variation in SM gene clusters: nonfunctional gene polymorphisms; gene gain and loss polymorphisms; whole cluster gain and loss polymorphisms; allelic polymorphisms, in which different alleles corresponded to distinct, nonhomologous clusters; and location polymorphisms, in which a cluster was found to differ in its genomic location across strains. These polymorphisms affect the function of representative A. fumigatus SM gene clusters, such as those involved in the production of gliotoxin, fumigaclavine, and helvolic acid as well as the function of clusters with undefined products. In addition to enabling the identification of polymorphisms, the detection of which requires extensive genome-wide synteny conservation (e.g., mobile gene clusters and nonhomologous cluster alleles), our approach also implicated multiple underlying genetic drivers, including point mutations, recombination, and genomic deletion and insertion events as well as horizontal gene transfer from distant fungi. Finally, most of the variants that we uncover within A. fumigatus have been previously hypothesized to contribute to SM gene cluster diversity across entire fungal classes and phyla. We suggest that the drivers of genetic diversity operating within a fungal species shown here are sufficient to explain SM cluster macroevolutionary patterns.National Science Foundation (grant number DEB-1442113). Received by AR. U.S. National Library of Medicine training grant (grant number 2T15LM007450). Received by ALL. Conselho Nacional de Desenvolvimento Cientı´fico e 573 Tecnológico. Northern Portugal Regional Operational Programme (grant number NORTE-01- 0145-FEDER-000013). Received by FR. Fundação de Amparo à Pesquisa do 572 Estado de São Paulo. Received by GHG. National Institutes of Health (grant number R01 AI065728-01). Received by NPK. National Science Foundation (grant number IOS-1401682). Received by JHW. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Global regulation of alternative splicing during myogenic differentiation

Recent genome-wide analyses have elucidated the extent of alternative splicing (AS) in mammals, often focusing on comparisons of splice isoforms between differentiated tissues. However, regulated splicing changes are likely to be important in biological transitions such as cellular differentiation, or response to environmental stimuli. To assess the extent and significance of AS in myogenesis, we used splicing-sensitive microarray analysis of differentiating C2C12 myoblasts. We identified 95 AS events that undergo robust splicing transitions during C2C12 differentiation. More than half of the splicing transitions are conserved during differentiation of avian myoblasts, suggesting the products and timing of transitions are functionally significant. The majority of splicing transitions during C2C12 differentiation fall into four temporal patterns and were dependent on the myogenic program, suggesting that they are integral components of myogenic differentiation. Computational analyses revealed enrichment of many sequence motifs within the upstream and downstream intronic regions near the alternatively spliced regions corresponding to binding sites of splicing regulators. Western analyses demonstrated that several splicing regulators undergo dynamic changes in nuclear abundance during differentiation. These findings show that within a developmental context, AS is a highly regulated and conserved process, suggesting a major role for AS regulation in myogenic differentiation.National Institutes of Health (U.S.) (grant number R01GM076493)Ford Foundation (Predoctoral Diversity Fellowship)Baylor College of Medicine. Graduate School of Biomedical Sciences (Baylor Research Advocates for Student Scientists

Assessment of orthologous splicing isoforms in human and mouse orthologous genes

<p>Abstract</p> <p>Background</p> <p>Recent discoveries have highlighted the fact that alternative splicing and alternative transcripts are the rule, rather than the exception, in metazoan genes. Since multiple transcript and protein variants expressed by the same gene are, by definition, structurally distinct and need not to be functionally equivalent, the concept of gene orthology should be extended to the transcript level in order to describe evolutionary relationships between structurally similar transcript variants. In other words, the identification of true orthology relationships between gene products now should progress beyond primary sequence and "splicing orthology", consisting in ancestrally shared exon-intron structures, is required to define orthologous isoforms at transcript level.</p> <p>Results</p> <p>As a starting step in this direction, in this work we performed a large scale human- mouse gene comparison with a twofold goal: first, to assess if and to which extent traditional gene annotations such as RefSeq capture genuine splicing orthology; second, to provide a more detailed annotation and quantification of true human-mouse orthologous transcripts defined as transcripts of orthologous genes exhibiting the same splicing patterns.</p> <p>Conclusions</p> <p>We observed an identical exon/intron structure for 32% of human and mouse orthologous genes. This figure increases to 87% using less stringent criteria for gene structure similarity, thus implying that for about 13% of the human RefSeq annotated genes (and about 25% of the corresponding transcripts) we could not identify any mouse transcript showing sufficient similarity to be confidently assigned as a splicing ortholog. Our data suggest that current gene and transcript data may still be rather incomplete - with several splicing variants still unknown. The observation that alternative splicing produces large numbers of alternative transcripts and proteins, some of them conserved across species and others truly species-specific, suggests that, still maintaining the conventional definition of gene orthology, a new concept of "splicing orthology" can be defined at transcript level.</p

Coding potential of the products of alternative splicing in human

Background: Analysis of the human genome has revealed that as much as an order of magnitude more of the genomic sequence is transcribed than accounted for by the predicted and characterized genes. A number of these transcripts are alternatively spliced forms of known protein coding genes; however, it is becoming clear that many of them do not necessarily correspond to a functional protein. Results: In this study we analyze alternative splicing isoforms of human gene products that are unambiguously identified by mass spectrometry and compare their properties with those of isoforms of the same genes for which no peptide was found in publicly available mass spectrometry datasets. We analyze them in detail for the presence of uninterrupted functional domains, active sites as well as the plausibility of their predicted structure. We report how well each of these strategies and their combination can correctly identify translated isoforms and derive a lower limit for their specificity, that is, their ability to correctly identify non-translated products. Conclusions: The most effective strategy for correctly identifying translated products relies on the conservation of active sites, but it can only be applied to a small fraction of isoforms, while a reasonably high coverage, sensitivity and specificity can be achieved by analyzing the presence of non-truncated functional domains. Combining the latter with an assessment of the plausibility of the modeled structure of the isoform increases both coverage and specificity with a moderate cost in terms of sensitivity

CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs

CSpritz is a web server for the prediction of intrinsic protein disorder. It is a combination of previous Spritz with two novel orthogonal systems developed by our group (Punch and ESpritz). Punch is based on sequence and structural templates trained with support vector machines. ESpritz is an efficient single sequence method based on bidirectional recursive neural networks. Spritz was extended to filter predictions based on structural homologues. After extensive testing, predictions are combined by averaging their probabilities. The CSpritz website can elaborate single or multiple predictions for either short or long disorder. The server provides a global output page, for download and simultaneous statistics of all predictions. Links are provided to each individual protein where the amino acid sequence and disorder prediction are displayed along with statistics for the individual protein. As a novel feature, CSpritz provides information about structural homologues as well as secondary structure and short functional linear motifs in each disordered segment. Benchmarking was performed on the very recent CASP9 data, where CSpritz would have ranked consistently well with a Sw measure of 49.27 and AUC of 0.828. The server, together with help and methods pages including examples, are freely available at URL: http://protein.bio.unipd.it/cspritz/