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

Genome engineering and plant breeding : impact on trait discovery and development

Key message: New tools for the precise modification of crops genes are now available for the engineering of new ideotypes. A future challenge in this emerging field of genome engineering is to develop efficient methods for allele mining. Abstract: Genome engineering tools are now available in plants, including major crops, to modify in a predictable manner a given gene. These new techniques have a tremendous potential for a spectacular acceleration of the plant breeding process. Here, we discuss how genetic diversity has always been the raw material for breeders and how they have always taken advantage of the best available science to use, and when possible, increase, this genetic diversity. We will present why the advent of these new techniques gives to the breeders extremely powerful tools for crop breeding, but also why this will require the breeders and researchers to characterize the genes underlying this genetic diversity more precisely. Tackling these challenges should permit the engineering of optimized alleles assortments in an unprecedented and controlled way

Evolution of plant phenotypes, from genomes to traits

Connecting genotype to phenotype is a grand challenge of biology. Over the past 50 years, there have been numerous and powerful advances to meet this challenge, including next-generation sequencing approaches (Jackson et al. 2011), molecular genetic mapping techniques, computational modeling, and the integration of evolutionary theory and tools. In plants, the long history of domestication and breeding has provided multiple insights into the genotype–phenotype equation (Meyer and Purugganan 2013; Olsen and Wendel 2013). Domestication and breeding provide unique systems with which to study the evolution of traits and adaptation to new environments. At present, agriculture faces unprecedented challenges, with the need to continue to increase food quality and food production for a population that will likely exceed 9 billion by 2050, combined with the urgent need to make agriculture more sustainable in an environment that will be altered by climate change (Diouf 2009). Crop wild relatives, however, have evolved under ecological settings that often are more extreme than those under cultivation and thus represent a reservoir of useful adaptive traits. This genetic diversity has mostly been untapped because of a lack of appropriate tools, both at the genetic level and in describing plant phenotypes and adaptation (Mace et al. 2013). In this context, crop improvement needs to undergo a qualitative leap forward by exploiting the knowledge from the interface of the fields of molecular evolution, bioinformatics, plant physiology, and genetics. With the objective of reviewing the most recent advances and identifying unanswered questions at this interface, a group of scientists met in Barcelona in March 2015 for a workshop organized by B-Debate (www.bdebate.org) and the Center for Research in Agricultural Genomics (CRAG, www.cragenomica.es), with the support of the US National Science Foundation. The meeting was divided into three scientific sessions. The first concentrated on the mechanisms that generate genomic diversity in plants, with a particular emphasis on transposable elements and polyploidy, while the second and third sessions were devoted to the evolution of plant phenotypes in wild and domesticated species, and to domestication and plant improvement processes, respectively

Prevalence of integrons and insertion sequences in ESBL-producing E-coli isolated from different sources in Navarra, Spain

Mobile genetic elements play an important role in the dissemination of antibiotic resistant bacteria among human and environmental sources. Therefore, the aim of this study was to determine the occurrence and patterns of integrons and insertion sequences of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from different sources in Navarra, northern Spain. A total of 150 isolates coming from food products, farms and feeds, aquatic environments, and humans (healthy people and hospital inpatients), were analyzed. PCRs were applied for the study of class 1, 2, and 3 integrons (intI1, intI2, and intI3), as well as for the determination of insertion sequences (IS26, ISEcp1, ISCR1, and IS903). Results show the wide presence and dissemination of intI1 (92%), while intI3 was not detected. It is remarkable, the prevalence of intI2 among food isolates, as well as the co-existence of class 1 and class 2 (8% of isolates). The majority of isolates have two or three IS elements, with the most common being IS26 (99.4%). The genetic pattern IS26–ISEcp1 (related with the pathogen clone ST131) was present in the 22% of isolates (including human isolates). In addition, the combination ISEcp1–IS26–IS903–ISCR1 was detected in 11 isolates being, to our knowledge, the first study that describes this genetic complex. Due to the wide variability observed, no relationship was determined among these mobile genetic elements and β-lactam resistance. More investigations regarding the genetic composition of these elements are needed to understand the role of multiple types of integrons and insertion sequences on the dissemination of antimicrobial resistance genes among different environments

Gums induced microstructure stability in Ca(II)-alginate beads containing lactase analyzed by SAXS

[EN] Previous works show that the addition of trehalose and gums in ß-galactosidase (lactase) Ca(II)-alginate encapsulation systems improved its intrinsic stability against freezing and dehydration processes in the pristine state. However, there is no available information on the evolution in microstructure due to the constraints imposed by the operational conditions. The aim of this research is to study the time course of microstructural changes of Ca(II)-alginate matrices driven by the presence of trehalose, arabic and guar gums as excipients and to discuss how these changes in¿uence the di¿usional transport (assessed by LF-NMR) and the enzymatic activity of the encapsulated lactase. The structural modi¿cations at di¿erent scales were assessed by SAXS. The incorporation of gums as second excipients induces a signi¿cant stabilization in the microstructure not only at the rod scale, but also in the characteristic size and density of alginate dimers (basic units of construction of rods) and the degree of interconnection of rods at a larger scale, improving the performance in terms of lactase activity.This work was supported by the Brazilian Synchrotron Light Laboratory (LNLS, Brazil, proposal SAXS1-20160278), Universidad de Buenos Aires (UBACyT 20020130100610BA), Agencia Nacional de Promocion Cientifica y Tecnologica (ANPCyT PICT 2013 0434 and 2013 1331), CIN-CONICET (PDTS 2015 no 196), and Consejo Nacional de Investigaciones Cientificas y Tecnicas. The author Maria Victoria Traffano-Schiffo wants to thank "Programa para la Formacion de Personal Investigador (FPI)" Pre-doctoral Program of the Universitat Politecnica de Valencia (UPV) for support her PhD studies and also her mobility to Argentina.Traffano-Schiffo, MV.; Castro Giraldez, M.; Fito Suñer, PJ.; Perullini, M.; Santagapita, PR. (2018). Gums induced microstructure stability in Ca(II)-alginate beads containing lactase analyzed by SAXS. Carbohydrate Polymers. 179:402-407. https://doi.org/10.1016/j.carbpol.2017.09.096S40240717

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

Adición al suelo de residuos de la industria olivícola

El presente estudio se llevó a cabo en laboratorio, con tubos de acrílico donde se colocaron en forma sucesiva los horizontes de suelo, tal como se encuentran en el perfil de suelo. Se aplicaron dosis equivalentes a 0, 20, 40 y 80 Mg ha-1 de alperujo en el horizonte Ap. Todos los tratamientos se sometieron a 4 lavados con agua destilada de 167mm cada uno y se recogieron los extractos de lixiviación de los mismos. Se ha demostrado que la composición catiónica y aniónica de los extractos lixiviados revela la dominancia del Ca2++Mg2+, Na+ y HCO3 -, el pH aumenta a valores cercanos a ocho en todos los tratamientos y la conductividad eléctrica al final del proceso llega a valores de 0,42 dSm-1 para 0 Mg ha-1 y 0,63 dS m-1 para 80 Mg ha-1. Estos resultados no suponen un riesgo de contaminación de las aguas percoladas del perfil. El complejo de intercambio del horizonte Ap sufre por efecto del lavado un proceso de disminución de cationes, en todos los tratamientos, siguiendo la siguientes secuencia Na+ > K+ > Ca2++Mg2+. Los horizontes subyacentes, a medida que aumenta la dosis de alperujo, se enriquece en K+. En las dosis evaluadas la aplicación de alperujo al suelo no produjo efectos adversos. El estudio de la dinámica de cationes tantos como solubles e intercambiables en el perfil del suelo motivada por la incorporación de alperujo ha puesto de manifiesto la eficacia del suelo como depurador de sustancias orgánicas.Publicado en las Actas de las III Jornadas Nacionales de Suelos de Ambientes Semiáridos

Amplification dynamics of miniature inverted-repeat transposable elements and their impact on rice trait variability

Ministerio de Ciencia y Innovación (PID2019-106374RB-I00) - DOI 10.13039/501100011033Transposable elements (TEs) are a rich source of genetic variability. Among TEs, miniature inverted-repeat TEs (MITEs) are of particular interest as they are present in high copy numbers in plant genomes and are closely associated with genes. MITEs are deletion derivatives of class II transposons, and can be mobilized by the transposases encoded by the latter through a typical cut-and-paste mechanism. However, MITEs are typically present at much higher copy numbers than class II transposons. We present here an analysis of 103 109 transposon insertion polymorphisms (TIPs) in 738 Oryza sativa genomes representing the main rice population groups. We show that an important fraction of MITE insertions has been fixed in rice concomitantly with its domestication. However, another fraction of MITE insertions is present at low frequencies. We performed MITE TIP-genome-wide association studies (TIP-GWAS) to study the impact of these elements on agronomically important traits and found that these elements uncover more trait associations than single nucleotide polymorphisms (SNPs) on important phenotypes such as grain width. Finally, using SNP-GWAS and TIP-GWAS we provide evidence of the replicative amplification of MITEs

Valoración de 25 años de autonomía.

Suele afirmarse, con razón, que la historia del proceso de construcción del Estado español y, muy especialmente, la de su organización territorial, es la historia de un largo fracaso colectivo, jalonado de conflictos. La Constitución de 1978, al consagrar el principio de autonomía política, pretendió dar respuesta, desde la modesta posición que al Derecho compete, a la tradicional ineficacia del Estado centralista español y la plural conformación de la comunidad política que está en su base y que, con diversa intensidad, ha manifestado su voluntad de autogobierno [...]

Comparison of antibacterial activity and cytotoxicity of silver nanoparticles and silver-loaded montmorillonite and saponite

Although silver nanoparticles are known for their antibacterial activity, little research has been carried out on what synthesis method provides the most effective particles. In this study, silver nanoparticles were synthesised via chemical reduction by using silver nitrate as the silver precursor, ascorbic acid as the reducing agent and sodium citrate as the stabilising agent. The solutions were adjusted to several pH values employing sodium hydroxide, citric acid or nitric acid. Dynamic light scattering and absorption spectra in the ultraviolet/visible region characterisation revealed that employing nitric acid to adjust the pH produced more varied and larger silver particle sizes. Then, silver nanoparticles were supported on montmorillonite and saponite through wet impregnation or ion exchange methods. Scanning electron microscopy, energy-dispersive X-ray spectroscopy and transmission electron microscopy characterisation confirmed that silver nanoparticles were successfully loaded onto the clay minerals. Next, the antibacterial activity of the samples was evaluated against Escherichia coli and Staphylococcus aureus by determining their minimum inhibitory concentrations and minimum bactericidal concentrations. The free silver nanoparticles did not show any antibacterial activity at 125 mg/L. In contrast, the silver-loaded samples obtained by wet impregnation and with a higher silver content displayed the strongest antibacterial effect. Finally, the cytotoxicity of the samples was determined in GM07492-A cell line by using an XTT colorimetric assay. The calculated IC50 values revealed that the supported silver nanoparticles were barely toxic. Thus, the silver-loaded clay minerals obtained here are promising antibacterial materials with a high-grade safety profile