Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

<p>Abstract</p> <p>Background</p> <p>Sequencing projects have allowed diverse retroviruses and LTR retrotransposons from different eukaryotic organisms to be characterized. It is known that retroviruses and other retro-transcribing viruses evolve from LTR retrotransposons and that this whole system clusters into five families: <it>Ty3/Gypsy, Retroviridae, Ty1/Copia, Bel/Pao </it>and <it>Caulimoviridae</it>. Phylogenetic analyses usually show that these split into multiple distinct lineages but what is yet to be understood is how deep evolution occurred in this system.</p> <p>Results</p> <p>We combined phylogenetic and graph analyses to investigate the history of LTR retroelements both as a tree and as a network. We used 268 non-redundant LTR retroelements, many of them introduced for the first time in this work, to elucidate all possible LTR retroelement phylogenetic patterns. These were superimposed over the tree of eukaryotes to investigate the dynamics of the system, at distinct evolutionary times. Next, we investigated phenotypic features such as duplication and variability of amino acid motifs, and several differences in genomic ORF organization. Using this information we characterized eight reticulate evolution markers to construct phenotypic network models.</p> <p>Conclusion</p> <p>The evolutionary history of LTR retroelements can be traced as a time-evolving network that depends on phylogenetic patterns, epigenetic host-factors and phenotypic plasticity. The <it>Ty1/Copia </it>and the <it>Ty3/Gypsy </it>families represent the oldest patterns in this network that we found mimics eukaryotic macroevolution. The emergence of the <it>Bel/Pao, Retroviridae </it>and <it>Caulimoviridae </it>families in this network can be related with distinct inflations of the <it>Ty3/Gypsy </it>family, at distinct evolutionary times. This suggests that <it>Ty3/Gypsy </it>ancestors diversified much more than their <it>Ty1/Copia </it>counterparts, at distinct geological eras. Consistent with the principle of preferential attachment, the connectivities among phenotypic markers, taken as network-represented combinations, are power-law distributed. This evidences an inflationary mode of evolution where the system diversity; 1) expands continuously alternating vertical and gradual processes of phylogenetic divergence with episodes of modular, saltatory and reticulate evolution; 2) is governed by the intrinsic capability of distinct LTR retroelement host-communities to self-organize their phenotypes according to emergent laws characteristic of complex systems.</p> <p>Reviewers</p> <p>This article was reviewed by Eugene V. Koonin, Eric Bapteste, and Enmanuelle Lerat (nominated by King Jordan)</p

Two nucleotide positions in the Citrus exocortis viroid RNA associated with symptom expression in Etrog citron but not in experimental herbaceous hosts

P&gt;Citrus exocortis viroid (CEVd) is the causal agent of exocortis disease of citrus. CEVd has a wide host range that includes woody and herbaceous species. A new CEVd strain (CEVdCOL), phylogenetically clustering with CEVd variants of Class A inducing severe symptoms in tomato, was identified in Colombia and shown to induce only extremely mild symptoms in Etrog citron indicator plants. Using site-directed mutagenesis, two nucleotide substitutions (314A -&gt; G and 315U -&gt; A) in the lower strand of the P domain of the predicted CEVdCOL secondary structure resulted in a severe artificial CEVdMCOL variant. Conversely, two nucleotide exchanges (314G -&gt; A and 315A -&gt; U) in the same region of the severe variant CEVdE-117 resulted in a symptomless artificial CEVdME-117 variant. Infectivity assays conducted with the natural and mutated variants showed that all induced severe symptoms in Gynura aurantiaca, tomato and chrysanthemum. This is the first report of the identification of pathogenic determinants of CEVd in citrus, and shows that these pathogenicity determinants are host dependent

Incremento de solubilidad de etoricoxib por codisolvencia

La baja solubilidad de muchos fármacos es una propiedad fisicoquímica limitante del desarrollo de formas farmacéuticas líquidas. Un método para favorecer la solubilidad es el uso de codisolventes. El comportamiento de solubilidad de un fármaco en estos sistemas se describe mediante modelos que estiman la contribución de cada disolvente, siendo el de Yalkowsky-Roseman el más común. En la presente investigación se analizó la solubilidad de etoricoxib en mezclas acuosas binarias a 298.15K y 310.15K con la finalidad de establecer proporciones capaces de contribuir al desarrollo de una forma farmacéutica liquida. Los codisolventes empleados fueron metanol, etanol, propanol, Transcutol®HP, Labrasol® y NMP. Los resultados demostraron que todos proveen un incremento en la solubilidad del etoricoxib siendo metanol y Transcutol®HP aquellos con mejores resultados. Así mismo el comportamiento de solubilidad se ajustó al modelo de Yalkowsky-Roseman para así estimar proporciones de mezcla capaces de solubilizar dosis requeridas para una forma farmacéutica líquida.The low solubility of many drugs is a limiting physicochemical property of the development of liquid pharmaceutical forms. One method to enhance solubility is the cosolvency. The solubility behavior of a drug in these systems is described by models that estimate the contribution of each solvent being the Yalkowsky-Roseman model the most common. In this study the solubility of etoricoxib was determined in aqueous mixtures at 298.15K and 310.15K in order to establish proportions capable of contributing to the development of a liquid pharmaceutical form. The cosolvents used were methanol, ethanol, propanol, Transcutol®HP, Labrasol® and NMP. The results showed that all of them provide enhancement in the solubility of etoricoxib being methanol and Transcutol®HP those that showed the greatest increase. Also, the solubility observed fit to the Yalkowsky-Roseman model and is possible to estimate proportions in mixtures capable of solubilizing doses required for a liquid pharmaceutical form

Desarrollo y evaluación de un sistema autoemulsionable de Etoricoxib

La solubilidad acuosa limitada de algunos fármacos ha llevado a buscar alternativas como lo son los Sistemas autoemulsionables de entrega de Fármacos (SEDDS, por sus siglas en inglés), que aumentan la solubilidad y permeabilidad gastrointestinal de los fármacos. El objetivo de este trabajo fue desarrollar y evaluar un SEDDS para etoricoxib, antiinflamatorio perteneciente al cuadro básico de medicamentos del Sector Salud en México. Los SEDDS cargados con etoricoxib se desarrollaron a partir de diferentes mezclas ternarias de aceite, surfactante y co-surfactante evaluando la eficiencia de autoemulsificación y la capacidad de solubilizar al fármaco. A las mezclas con tales características se les evaluó tamaño de partícula de la emulsión formada obteniendo valores entre 9-230 nm y potencial zeta de -4.07 a -16.43 mV con tiempos de autoemulsificación de hasta 24 segundos. El incremento de la solubilidad del fármaco con esta estrategia fue de hasta 1600 veces con respecto al agua.The limited aqueous solubility of many drugs which has led to develop alternatives, such as the Self-Emulsifying Drug Delivery System (SEDDS) for increasing gastrointestinal solubility and improve its permeability. The objective of this work was to develop and evaluate a SEDDS system for an anti-inflammatory linked to the Health Sector in Mexico: etoricoxib. Ten different ternary mixtures of oil, surfactant and co-surfactant are developed to subsequently characterize the self-emulsification efficiency and select the optimal mixtures to solubilize the drug. From these points, other properties such as particle size were evaluated obtaining values between 9-250 nm and zeta potential of -4.07 to -16.43 mV with self-emulsification times of up to 24 sec. The increase in the solubility of the drug with this type of delivery system was up to 1600 times with respect to water

Viroids in Gummy Bark Sources from the Sultanate of Oman

The gummy bark disease affects sweet oranges and rough lemon in some Mediterranean countries and most countries of the Near and Middle East regions. Diseased trees are usually stunted, and scraping the bark reveals gum deposits. Symptoms of gummy bark in sweet orange resemble those of cachexia on mandarin but the cachexia agent fails to induce symptoms in sweet orange. The causal agent of gummy bark is suspected to be a viroid, but previous studies conducted with sources from Turkey failed to identify a sequence variant of HSVd as the putative disease agent. In the present study, samples collected from Baladi, Valencia, Washington navel and Succari sweet orange trees showing the characteristic gummy bark symptoms were graftinoculated on Etrog citron and analyzed by sPAGE and slot-blot hybridization using viroid-specific probes. In addition to HSVd, all samples also contained CEVd, CVd-III and CVd-IV. Sequence analysis of DNA amplicons generated by RT-PCR using specific primers for these viroids identified novel variants of CEVd (CEVd-gb) and CVd-III (CVd-III-gb) in all the gummy sources, whereas CVd-IV was identical to previously reported sequences. The relationship of these viroids to the putative agent(s) of gummy bark is discussed

FIRST INSIGHTS INTO THE MIGRATION PATTERN OF AN UPLAND GOOSE (CHLOEPHAGA PICTA) BASED ON SATELLITE TRACKING

Detailed knowledge of the migratory strategies is important to understand the ecology and evolution of migration and the conservation of migratory birds The Argentinean federal government declared sheldgeese (Chloephaga spp.) pests in 1930, claiming that they reduce crop yield. Currently sheldgeese have suffered severe reductions in their populations and are the focus of serious conservation concern. From September to April they breed in southern Patagonia (Argentina and Chile) while from May to September they winter mainly in the southern Pampas (central east Argentina). The precise knowledge of their migratory routes is essential to ensure protection of necessary resources and sites needed on their annual journeys. Here, by using a satellite transmitter for the first time we unravel the migration route of an Upland Goose (Chloephaga picta), a species endemic to southern South America with an unknown migration strategy. We received data for 121 days (from September 2014 to January 2015). During this time, the bird migrated 1485 km from the wintering grounds in Buenos Aires Province to the breeding area in Santa Cruz province, Patagonia. Part of the migration route was over the sea. The largest displacement was 817 km in 19 hours, representing a minimum mean speed of 43 km h-1

Naming and outline of Dothideomycetes-2014 including proposals for the protection or suppression of generic names

Article 59.1, of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN; Melbourne Code), which addresses the nomenclature of pleomorphic fungi, became effective from 30 July 2011. Since that date, each fungal species can have one nomenclaturally correct name in a particular classification. All other previously used names for this species will be considered as synonyms. The older generic epithet takes priority over the younger name. Any widely used younger names proposed for use, must comply with Art. 57.2 and their usage should be approved by the Nomenclature Committee for Fungi (NCF). In this paper, we list all genera currently accepted by us in Dothideomycetes (belonging to 23 orders and 110 families), including pleomorphic and nonpleomorphic genera. In the case of pleomorphic genera, we follow the rulings of the current ICN and propose single generic names for future usage. The taxonomic placements of 1261 genera are listed as an outline. Protected names and suppressed names for 34 pleomorphic genera are listed separately. Notes and justifications are provided for possible proposed names after the list of genera. Notes are also provided on recent advances in our understanding of asexual and sexual morph linkages in Dothideomycetes. A phylogenetic tree based on four gene analyses supported 23 orders and 75 families, while 35 families still lack molecular data

Ευρετικές προσεγγίσεις του μοναδιάστατου προβλήματος πακετοποίησης

Article 59.1, of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN; Melbourne Code), which addresses the nomenclature of pleomorphic fungi, became effective from 30 July 2011. Since that date, each fungal species can have one nomenclaturally correct name in a particular classification. All other previously used names for this species will be considered as synonyms. The older generic epithet takes priority over the younger name. Any widely used younger names proposed for use, must comply with Art. 57.2 and their usage should be approved by the Nomenclature Committee for Fungi (NCF). In this paper, we list all genera currently accepted by us in Dothideomycetes (belonging to 23 orders and 110 families), including pleomorphic and non-pleomorphic genera. In the case of pleomorphic genera, we follow the rulings of the current ICN and propose single generic names for future usage. The taxonomic placements of 1261 genera are listed as an outline. Protected names and suppressed names for 34 pleomorphic genera are listed separately. Notes and justifications are provided for possible proposed names after the list of genera. Notes are also provided on recent advances in our understanding of asexual and sexual morph linkages in Dothideomycetes. A phylogenetic tree based on four gene analyses supported 23 orders and 75 families, while 35 families still lack molecular data

Cauquenes

Conocer sus rutas migratorias es esencial para asegurar que los cauquenes encuentren los recursos y sitios necesarios durante sus desplazamientos entre las áreas de cría hasta las de invernada, incluyendo las áreas intermedias de descanso y alimentación.Fil: Bernad, Lucia. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce; ArgentinaFil: Pedrana, Julieta. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce; Argentin