The effect of frequency-specific sound signals on the germination of maize seeds

Objective: the effects of sound treatments on the germination of maize seeds were determined. - Results: white noise and bass sounds (300 Hz) had a positive effect on the germination rate. Only 3 h treatment produced an increase of about 8%, and 5 h increased germination in about 10%. Fast-green staining shows that at least part of the effects of sound are due to a physical alteration in the integrity of the pericarp, increasing the porosity of the pericarp and facilitating oxygen availability and water and oxygen uptake. Accordingly, by removing the pericarp from the seeds the positive effect of the sound on the germination disappeared

Genome-wide identification of Reverse Transcriptase domains of recently inserted endogenous plant pararetrovirus (Caulimoviridae)

Altres ajuts: CERCA Programme/Generalitat de CatalunyaEndogenous viral elements (EVEs) are viral sequences that have been integrated into the nuclear chromosomes. Endogenous pararetrovirus (EPRV) are a class of EVEs derived from DNA viruses of the family Caulimoviridae. Previous works based on a limited number of genome assemblies demonstrated that EPRVs are abundant in plants and are present in several species. The availability of genome sequences has been immensely increased in the recent years and we took advantage of these resources to have a more extensive view of the presence of EPRVs in plant genomes. We analyzed 278 genome assemblies corresponding to 267 species (254 from Viridiplantae) using tBLASTn against a collection of conserved domains of the Reverse Transcriptases (RT) of Caulimoviridae. We concentrated our search on complete and well-conserved RT domains with an uninterrupted ORF comprising the genetic information for at least 300 amino acids. We obtained 11.527 sequences from the genomes of 202 species spanning the whole Tracheophyta clade. These elements were grouped in 57 clusters and classified in 13 genera, including a newly proposed genus we called Wendovirus. Wendoviruses are characterized by the presence of four open reading frames and two of them encode for aspartic proteinases. Comparing plant genomes, we observed important differences between the plant families and genera in the number and type of EPRVs found. In general, florendoviruses are the most abundant and widely distributed EPRVs. The presence of multiple identical RT domain sequences in some of the genomes suggests their recent amplification

Integrative meta-analysis of protein interaction data identified multiple GID/MRCTLH protein complexes in plants

GID/MRCTLH is a protein complex involved in the regulation of several cellular processes through the polyubiquitination and proteosome degradation. It has been described in yeast and mammals. Genes coding for homologous proteins are also present in plant genomes but have been little studied. BLAST analyses revealed that genes coding for members of the GID/MRCTLH complex are found in multiple copies in plants, compared to mammals and yeast. The potential structure of the Arabidopsis GID/MRCTLH complex was estimated based on the Arabidopsis protein interaction database Interactome 2.0. According to these data, Arabidopsis may contain two GID/MRCTLH complexes instead of the one described in yeast and mammals. The structure of the two Arabidopsis complexes seem to be similar to the yeast GID complex, and seem to interact with several other proteins out of the complex. These data suggest that, similarly to yeast and mammals, the plant GID/MRCTLH complexes are involved in the regulation of several cellular processes through proteosome protein degradation

Use of ultrasonication to increase germination rates of Arabidopsis seeds

Background: Arabidopsis thaliana is widely used as model organism in plant biology. Although not of agronomic significance, it offers important advantages for basic research in genetics and molecular biology including the availability of a large number of mutants and genetically modified lines. However, Arabidopsis seed longevity is limited and seeds stored for more than 10 years usually show a very low capacity for germination. - Results: the influence of ultrasonic stimulation was investigated on the germination of A. thaliana L. seeds. All experiments have been performed using a frequency of 45 kHz at constant temperature (24 °C). No germination rate differences were observed when using freshly collected seeds. However, using artificially deteriorated seeds, our results show that short ultrasonic stimulation (<1 min) significantly increased germination. Ultrasonic stimulation application of 30 s is the optimal treatment. A significant increase in the germination rate was also verified in naturally aged seeds after ultrasonic stimulation. Scanning electron microscopy observations showed an increase in the presence of pores in the seed coat after sonication that may be the cause, at least in part, of the increase in germination. The ultrasound treated seeds developed normally to mature fertile plants. - Conclusions: ultrasound technology can be used to enhance the germination process of old Arabidopsis seeds without negatively affecting seedling development. This effect seems to be, at least in part, due to the opening of pores in the seed coat. The use of ultrasonic stimulation in Arabidopsis seeds may contribute to the recovering of long time stored lines

Additional ORFs in plant LTR-retrotransposons

Altres ajuts: CERCA Programme/Generalitat de CatalunyaLTR-retrotransposons share a common genomic organization in which the 5' long terminal repeat (LTR) is followed by the gag and pol genes and terminates with the 3' LTR. Although GAG-POL-encoded proteins are considered sufficient to accomplish the LTR-retrotransposon transposition, a number of elements carrying additional open reading frames (aORF) have been described. In some cases, the presence of an aORF can be explained by a phenomenon similar to retrovirus gene transduction, but in these cases the aORFs are present in only one or a few copies. On the contrary, many elements contain aORFs, or derivatives, in all or most of their copies. These aORFs are more frequently located between pol and 3' LTR, and they could be in sense or antisense orientation with respect to gag-pol. Sense aORFs include those encoding for ENV-like proteins, so called because they have some structural and functional similarities with retroviral ENV proteins. Antisense aORFs between pol and 3' LTR are also relatively frequent and, for example, are present in some characterized LTR-retrotransposon families like maize Grande, rice RIRE2, or Silene Retand, although their possible roles have been not yet determined. Here, we discuss the current knowledge about these sense and antisense aORFs in plant LTR-retrotransposons, suggesting their possible origins, evolutionary relevance, and function

Global-local word embedding for text classification

Only humans can understand and comprehend the actual meaning that underlies natural written language, whereas machines can form semantic relationships only after humans have provided the parameters that are necessary to model the meaning. To enable computer models to access the underlying meaning in written language, accurate and sufficient document representation is crucial. Recent word embedding approaches have drawn much attention to text mining research. One of the main benefits of such approaches is the use of global corpuses with the generation of pre-trained word vectors. Although very effective, these approaches have their disadvantages, namely sole reliance on pre-trained word vectors that may neglect the local context and increase word ambiguity. In this thesis, four new document representation approaches are introduced to mitigate the risk of word ambiguity and inject a local context into globally pre-trained word vectors. The proposed approaches, which are frameworks for document representation while using word embedding learning features for the task of text classification, are: Content Tree Word Embedding; Composed Maximum Spanning Content Tree; Embedding-based Word Clustering; and Autoencoder-based Word Embedding. The results show improvement in the F_score accuracy measure for a document classification task applied to IMDB Movie Reviews, Hate Speech Identification, 20 Newsgroups, Reuters-21578, and AG News as benchmark datasets in comparison to using three deep learning-based word embedding approaches, namely GloVe, Word2Vec, and fastText, as well as two other document representations: LSA and Random word embedding

Drought tolerance induced by sound in Arabidopsis plants

We examined the responses of sound-treated arabidopsis adult plants to water deprivation and the associated changes on gene expression. The survival of drought-induced plants was significantly higher in the sound treated plants (24,8%) compared with plants kept in silence (13,3%). RNA-seq revealed significant upregulation of 87 genes including 32 genes involved in abiotic stress responses, 31 involved in pathogen responses, 11 involved in oxidation-reduction processes, 5 involved in the regulation of transcription, 2 genes involved in protein phosphorylation/dephosphorylation and 13 involved in jasmonic acid or ethylene synthesis or responses. In addition, 2 genes involved in the responses to mechanical stimulus were also induced by sound, suggesting that touch and sound have at least partially common perception and signaling events

Transcriptomic and proteomic profiling of maize embryos exposed to camptothecin

<p>Abstract</p> <p>Background</p> <p>Camptothecin is a plant alkaloid that specifically binds topoisomerase I, inhibiting its activity and inducing double stranded breaks in DNA, activating the cell responses to DNA damage and, in response to severe treatments, triggering cell death.</p> <p>Results</p> <p>Comparative transcriptomic and proteomic analyses of maize embryos that had been exposed to camptothecin were conducted. Under the conditions used in this study, camptothecin did not induce extensive degradation in the genomic DNA but induced the transcription of genes involved in DNA repair and repressed genes involved in cell division. Camptothecin also affected the accumulation of several proteins involved in the stress response and induced the activity of certain calcium-dependent nucleases. We also detected changes in the expression and accumulation of different genes and proteins involved in post-translational regulatory processes.</p> <p>Conclusions</p> <p>This study identified several genes and proteins that participate in DNA damage responses in plants. Some of them may be involved in general responses to stress, but others are candidate genes for specific involvement in DNA repair. Our results open a number of new avenues for researching and improving plant resistance to DNA injury.</p

Impact of transposable elements on polyploid plant genomes

Background: the growing wealth of knowledge on whole-plant genome sequences is highlighting the key role of transposable elements (TEs) in plant evolution, as a driver of drastic changes in genome size and as a source of an important number of new coding and regulatory sequences. Together with polyploidization events, TEs should thus be considered the major players in evolution of plants. -- Scope: this review outlines the major mechanisms by which TEs impact plant genome evolution and how polyploidy events can affect these impacts, and vice versa. These include direct effects on genes, by providing them with new coding or regulatory sequences, an effect on the epigenetic status of the chromatin close to genes, and more subtle effects by imposing diverse evolutionary constraints to different chromosomal regions. These effects are particularly relevant after polyploidization events. Polyploidization often induces bursts of transposition probably due to a relaxation in their epigenetic control, and, in the short term, this can increase the rate of gene mutations and changes in gene regulation due to the insertion of TEs next to or into genes. Over longer times, TE bursts may induce global changes in genome structure due to inter-element recombination including losses of large genome regions and chromosomal rearrangements that reduce the genome size and the chromosome number as part of a process called diploidization. - Conclusions: TEs play an essential role in genome and gene evolution, in particular after polyploidization events. Polyploidization can induce TE activity that may explain part of the new phenotypes observed. TEs may also play a role in the diploidization that follows polyploidization events. However, the extent to which TEs contribute to diploidization and fractionation bias remains unclear. Investigating the multiple factors controlling TE dynamics and the nature of ancient and recent polyploid genomes may shed light on these processes

Development of retrotransposon-based markers IRAP and REMAP for cassava (Manihot esculenta)

Retrotransposons are abundant in the genomes of plants. In the present study, inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers were developed for the cassava genome (Manihot esculenta Crantz). Four cassava cultivars (Fécula Branca, IPR-União, Olho Junto, and Tamboara, two samples per cultivar) were used to obtain IRAP and REMAP fingerprints. Twelve designed primers were amplified alone and in combinations. The 42 IRAP/REMAP primer combinations amplified 431 DNA segments (bands; markers) of which 36 (8.36%) were polymorphic. The largest number of informative markers (16) was detected using the primers AYF2 and AYF2xAYF4. The number of bands for each primer varied from 3 to 16, with an average of 10.26 amplified segments per primer. The size of the amplified products ranged between 100 and 7000 bp. The AYF2 primer generated the highest number of amplified segments and showed the highest number of polymorphic bands (68.75%). Two samples of each cassava cultivar were used to illustrate the usefulness and the polymorphism of IRAP/REMAP markers. IRAP and REMAP markers produced a high number of reproducible bands, and might be informative and reliable for investigation of genetic diversity and relationships among cassava cultivars