Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses

<p>Abstract</p> <p>Background</p> <p>Positive selection is recognized as the prevalence of nonsynonymous over synonymous substitutions in a gene. Models of the functional evolution of duplicated genes consider neofunctionalization as key to the retention of paralogues. For instance, duplicate transcription factors are specifically retained in plant and animal genomes and both positive selection and transcriptional divergence appear to have played a role in their diversification. However, the relative impact of these two factors has not been systematically evaluated. Class B MADS-box genes, comprising <it>DEF</it>-like and <it>GLO</it>-like genes, encode developmental transcription factors essential for establishment of perianth and male organ identity in the flowers of angiosperms. Here, we contrast the role of positive selection and the known divergence in expression patterns of genes encoding class B-like MADS-box transcription factors from monocots, with emphasis on the family Orchidaceae and the order Poales. Although in the monocots these two groups are highly diverse and have a strongly canalized floral morphology, there is no information on the role of positive selection in the evolution of their distinctive flower morphologies. Published research shows that in Poales, class B-like genes are expressed in stamens and in lodicules, the perianth organs whose identity might also be specified by class B-like genes, like the identity of the inner tepals of their lily-like relatives. In orchids, however, the number and pattern of expression of class B-like genes have greatly diverged.</p> <p>Results</p> <p>The <it>DEF</it>-like genes from Orchidaceae form four well-supported, ancient clades of orthologues. In contrast, orchid <it>GLO</it>-like genes form a single clade of ancient orthologues and recent paralogues. <it>DEF</it>-like genes from orchid clade 2 (<it>OMADS3</it>-like genes) are under less stringent purifying selection than the other orchid <it>DEF</it>-like and <it>GLO</it>-like genes. In comparison with orchids, purifying selection was less stringent in <it>DEF</it>-like and <it>GLO</it>-like genes from Poales. Most importantly, positive selection took place before the major organ reduction and losses in the floral axis that eventually yielded the zygomorphic grass floret.</p> <p>Conclusion</p> <p>In <it>DEF</it>-like genes of Poales, positive selection on the region mediating interactions with other proteins or DNA could have triggered the evolution of the regulatory mechanisms behind the development of grass-specific reproductive structures. Orchidaceae show a different trend, where gene duplication and transcriptional divergence appear to have played a major role in the canalization and modularization of perianth development.</p

Diversification of defensins and NLRs in Arabidopsis species by different evolutionary mechanisms

Background: Genes encoding proteins underlying host-pathogen co-evolution and which are selected for new resistance specificities frequently are under positive selection, a process that maintains diversity. Here, we tested the contribution of natural selection, recombination and transcriptional divergence to the evolutionary diversification of the plant defensins superfamily in three Arabidopsis species. The intracellular NOD-like receptor (NLR) family was used for comparison because positive selection has been well documented in its members. Similar to defensins, NLRs are encoded by a large and polymorphic gene family and many of their members are involved in the immune response. Results: Gene trees of Arabidopsis defensins (DEFLs) show a high prevalence of clades containing orthologs. This indicates that their diversity dates back to a common ancestor and species-specific duplications did not significantly contribute to gene family expansion. DEFLs are characterized by a pervasive pattern of neutral evolution with infrequent positive and negative selection as well as recombination. In comparison, most NLR alignment groups are characterized by frequent occurrence of positive selection and recombination in their leucine-rich repeat (LRR) domain as well negative selection in their nucleotide-binding (NB-ARC) domain. While major NLR subgroups are expressed in pistils and leaves both in presence or absence of pathogen infection, the members of DEFL alignment groups are predominantly transcribed in pistils. Furthermore, conserved groups of NLRs and DEFLs are differentially expressed in response to Fusarium graminearum regardless of whether these genes are under positive selection or not. Conclusions: The present analyses of NLRs expands previous studies in Arabidopsis thaliana and highlights contrasting patterns of purifying and diversifying selection affecting different gene regions. DEFL genes show a different evolutionary trend, with fewer recombination events and significantly fewer instances of natural selection. Their heterogeneous expression pattern suggests that transcriptional divergence probably made the major contribution to functional diversification. In comparison to smaller families encoding pathogenesis-related (PR) proteins under positive selection, DEFLs are involved in a wide variety of processes that altogether might pose structural and functional trade-offs to their family-wide pattern of evolution

Improper use of privileged information in public procurement in Colombia

En la contratación estatal en Colombia los desafíos del legislador consisten en evitar y controlar la corrupción en las diferentes entidades de orden nacional, departamental y municipal; por lo anterior, el funcionario público tiene un papel importante en proceder de conformidad a las leyes, decretos y dar cumplimiento a los principios de la contratación. El presente trabajo aborda el estudio del uso indebido de la información privilegiada por parte de los funcionarios públicos con ocasión a su función de contratar con particulares a través de las diferentes modalidades de contratación establecidas por la Ley 80 del 1993, es así que a través de un método inductivo-hermenéutico con enfoque cualitativo se logró determinar la responsabilidad que le asiste a los funcionarios públicos cuando hacen uso indebido de información privilegiada al interior de la contratación pública. Siendo la principal conclusión de este ejercicio académico, que las entidades estatales deben implementar políticas públicas de gobierno corporativo y sensibilizar al funcionario de las consecuencias de las responsabilidades en materia: penal, laboral, disciplinario y civil por sus acciones del uso indebido de información privilegiada en la contratación estatal explicado desde distintas fuentes jurídicas.In state contracting in Colombia, the legislator's challenges consist of avoiding and controlling corruption in the different national, departmental and municipal entities; Therefore, the public official has an important role in proceeding in accordance with the laws, decrees and complying with the principles of contracting. The present work deals with the study of the improper use of privileged information by public officials on the occasion of their function of contracting with individuals through the different contracting modalities established by Law 80 of 1993, so that through an inductive-hermeneutical method with a qualitative approach was able to determine the responsibility that public officials attend when they make improper use of privileged information within public contracting. Being the main conclusion of this academic exercise, that the state entities must implement public policies of corporate governance and sensitize the official of the consequences of the responsibilities in matters: criminal, labor, disciplinary and civil for their actions of improper use of privileged information in State contracting explained from different legal sources

Is post-polyploidization diploidization the key to the evolutionary success of angiosperms?

Advances in recent years have revolutionized our understanding of both the context and occurrence of polyploidy in plants. Molecular phylogenetics has vastly improved our understanding of plant relationships, enabling us to better understand trait and character evolution, including chromosome number changes. This, in turn, has allowed us to appreciate better the frequent occurrence and extent of polyploidy throughout the history of angiosperms, despite the occurrence of low chromosome numbers in some groups, such as in Arabidopsis (A. thaliana was the first plant genome to be sequenced and assembled). In tandem with an enhanced appreciation of phylogenetic relationships, the accumulation of genomic data has led to the conclusion that all angiosperms are palaeopolyploids, together with better estimates of the frequency and type of polyploidy in different angiosperm lineages. The focus therefore becomes when a lineage last underwent polyploidization, rather than simply whether a plant is ‘diploid’ or ‘polyploid’. This legacy of past polyploidization in plants is masked by large-scale genome reorganization involving repetitive DNA loss, chromosome rearrangements (including fusions and fissions) and complex patterns of gene loss, a set of processes that are collectively termed ‘diploidization’. We argue here that it is the diploidization process that is responsible for the ‘lag phase’ between polyploidization events and lineage diversification. If so, diploidization is important in determining chromosome structure and gene content, and has therefore made a significant contribution to the evolutionary success of flowering plants

Terapia de reemplazo renal continua en niños: de los conceptos a la prescripción

Acute kidney injury is considered as an abrupt decrease in kidney function that generates an accumulation of waste products, loss of fluid and electrolyte balance, and alteration of acid-base homeostasis. It is an entity with a high incidence that affects pediatric patients in critical condition. One in 10 patients affected by this pathology will require renal replacement therapy for its management. Currently, there is a set of therapeutic modalities that allow continuous circulation of blood through extracorporeal circuits to support and/or replace the normal function of the kidneys continuously 24 hours a day. Such modalities are grouped under the term: “Continuous renal replacement therapy” (CRRT) and have several advantages over traditional methods; however, there is some fear among health professionals when prescribing these therapies due to their complexity. In this literature review, the basic concepts, modalities, and indications of CRRT in children are presented in a practical way to facilitate its prescription.La lesión renal aguda es considerada como una disminución abrupta de la función renal que genera acumulación de productos de desecho, pérdida de balance de líquidos y electrolitos, y alteración de la homeostasis ácido-base. Es una entidad con alta incidencia que afecta a pacientes pediátricos en estado crítico. Uno de cada 10 pacientes afectados por esta patología requerirá terapia de reemplazo renal para su manejo. En la actualidad existe un conjunto de modalidades terapéuticas que permiten la circulación continua de sangre a través de circuitos extracorpóreos con el fin de soportar y/o reemplazar la función normal de los riñones en forma continua durante las 24 horas del día. Tales modalidades se agrupan dentro del término: “Terapia de reemplazo renal continua” (TRRC) y tienen varias ventajas sobre los métodos tradicionales; no obstante, existe entre los profesionales de la salud cierto temor a la hora de prescribir estas terapias debido a su complejidad. En esta revisión de la literatura se presentan los conceptos básicos, modalidades e indicaciones de la TRRC en niños de forma práctica para facilitar su prescripción

Role of transcriptional regulation in the evolution of plant phenotype: A dynamic systems approach

© 2015 Wiley Periodicals, Inc. A growing body of evidence suggests that alterations in transcriptional regulation of genes involved in modulating development are an important part of phenotypic evolution, and this can be documented among species and within populations. While the effects of differential transcriptional regulation in organismal development have been preferentially studied in animal systems, this phenomenon has also been addressed in plants. In this review, we summarize evidence for cis-regulatory mutations, trans-regulatory changes and epigenetic modifications as molecular events underlying important phenotypic alterations, and thus shaping the evolution of plant development. We postulate that a mechanistic understanding of why such molecular alterations have a key role in development, morphology and evolution will have to rely on dynamic models of complex regulatory networks that consider the concerted action of genetic and nongenetic components, and that also incorporate the restrictions underlying the genotype to phenotype mapping process.CONACyT 180098, 180380, 167705, 152649 and PAPIIT UNAM IN203214-3, IN203113-3, IN203814-3. BFU2012–34821 (MINECO) to C.G. and an institutional grant from Fundación Ramón Aceres to CBMSOPeer Reviewe

Recent advances in understanding the roles of whole genome duplications in evolution

Ancient whole-genome duplications (WGDs)—paleopolyploidy events—are key to solving Darwin’s ‘abominable mystery’ of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life