GroEL and the maintenance of bacterial endosymbiosis

Many eukaryotic organisms have symbiotic associations with obligate intracellular bacteria. The clonal transmission of endosymbionts between host generations should lead to the irreversible fixation of slightly deleterious mutations in their non-recombinant genome by genetic drift. However, the stability of endosymbiosis indicates that some mechanism is involved in the amelioration of the effects of these mutations. We propose that the chaperone GroEL was involved in the acquisition of an endosymbiotic lifestyle not only by means of its over-production, as proposed by Moran, but also by its adaptive evolution mediated by positive selection to improve the interaction with the unstable endosymbiont proteome

GroEL and the maintenance of bacterial endosymbiosis

Many eukaryotic organisms have symbiotic associations with obligate intracellular bacteria. The clonal transmission of endosymbionts between host generations should lead to the irreversible fixation of slightly deleterious mutations in their non-recombinant genome by genetic drift. However, the stability of endosymbiosis indicates that some mechanism is involved in the amelioration of the effects of these mutations. We propose that the chaperone GroEL was involved in the acquisition of an endosymbiotic lifestyle not only by means of its over-production, as proposed by Moran, but also by its adaptive evolution mediated by positive selection to improve the interaction with the unstable endosymbiont proteome

Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis

<p>Abstract</p> <p>Background</p> <p>The origin of vertebrate retroviruses (<it>Retroviridae</it>) is yet to be thoroughly investigated, but due to their similarity and identical gag-pol (and env) genome structure, it is accepted that they evolve from <it>Ty3/Gypsy </it>LTR retroelements the retrotransposons and retroviruses of plants, fungi and animals. These 2 groups of LTR retroelements code for 3 proteins rarely studied due to the high variability – gag polyprotein, protease and GPY/F module. In relation to 3 previously proposed <it>Retroviridae </it>classes I, II and II, investigation of the above proteins conclusively uncovers important insights regarding the ancient history of <it>Ty3/Gypsy </it>and <it>Retroviridae </it>LTR retroelements.</p> <p>Results</p> <p>We performed a comprehensive study of 120 non-redundant <it>Ty3/Gypsy </it>and <it>Retroviridae </it>LTR retroelements. Phylogenetic reconstruction inferred based on the concatenated analysis of the gag and pol polyproteins shows a robust phylogenetic signal regarding the clustering of OTUs. Evaluation of gag and pol polyproteins separately yields discordant information. While pol signal supports the traditional perspective (2 monophyletic groups), gag polyprotein describes an alternative scenario where each <it>Retroviridae </it>class can be distantly related with one or more <it>Ty3/Gypsy </it>lineages. We investigated more in depth this evidence through comparative analyses performed based on the gag polyprotein, the protease and the GPY/F module. Our results indicate that contrary to the traditional monophyletic view of the origin of vertebrate retroviruses, the <it>Retroviridae </it>class I is a molecular fossil, preserving features that were probably predominant among <it>Ty3/Gypsy </it>ancestors predating the split of plants, fungi and animals. In contrast, classes II and III maintain other phenotypes that emerged more recently during <it>Ty3/Gypsy </it>evolution.</p> <p>Conclusion</p> <p>The 3 <it>Retroviridae </it>classes I, II and III exhibit phenotypic differences that delineate a network never before reported between <it>Ty3/Gypsy </it>and <it>Retroviridae </it>LTR retroelements. This new scenario reveals how the diversity of vertebrate retroviruses is polyphyletically recurrent into the <it>Ty3/Gypsy </it>evolution, i.e. older than previously thought. The simplest hypothesis to explain this finding is that classes I, II and III trace back to at least 3 <it>Ty3/Gypsy </it>ancestors that emerged at different evolutionary times prior to protostomes-deuterostomes divergence. We have called this "the three kings hypothesis" concerning the origin of vertebrate retroviruses.</p

New empirical potential energy functions for the heavier homonuclear rare gas pairs: nN2, Ar2, Kr2, and Xe2

The many decades of work on determining accurate analytic pair potentials for rare gas dimers from experimental data focussed largely on the use of bulk non-ideal gas and collisional properties, with the use of spectroscopic data being somewhat of an afterthought, for testing the resulting functions. This was a natural result of experimental challenges, as the very weak binding of ground-state rare gas pairs made high resolution spectroscopy a relatively late arrival as a practical tool in this area. However, we believe that it is now time for a comprehensive reassessment. Following up on a preliminary report at this meeting five years ago,\footnote{R.J.\ Le~Roy, C.J.W.\ Mackie, P.\ Chandrasekhar and K.M.\ Sentjens, ``{\it Accurate New Potential Energy Functions From Spectroscopic and Virial Coefficient Data for the Ten Rare Gas Pairs formed from Ne, Ar, Kr and Xe}, paper MF03 at the 66$^{th}$ Ohio State University International Symposium on Molecular Spectroscopy, Columbus, Ohio, June 13-17 (2011).} this paper describes work to determine a new generation of empirical potential energy functions for the four heavier (i.e., not involving He) homonuclear rare gas pairs from direct fits to all available spectroscopic, pressure virial, and acoustic virial coefficient data, with the resulting functions being `tuned' by comparisons with available thermal transport property data: viscosity, mass diffusion and thermal diffusion, and thermal conductivity data, and tested against the best available {\it ab initio} potentials. The resulting functions are everywhere smooth and differentiable to all orders, incorporate the correct (damped) theoretical inverse-power long-range behaviour, and have sensible short-range extrapolation behaviour

A Thermochemical Investigation of Gas Phase Anionic Nucleobase Complexes by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations

In this thesis, a computational and experimental investigation of gas phase cation-molecule complexes has been undertaken to analyse the gas phase clustering behaviour of biologically relevant cyclic anionic species. Evaluation of computationally determined thermochemical properties to predict the energetic favourability for the formation the cation-molecule clusters as well as the vibrational frequencies unique to each cluster has been carried out. The computational analyses performed in this thesis used the Becke 3-Parameter, Lee, Yang, and Parr (B3LYP) level of theory for geometric optimization and frequency calculations and second order Møller-Plesset perturbation theory (MP2) for single-point energy calculations. In both cases, a split basis set was used to evaluate the non-metallic atoms at 6-311++g(d,p) and the metallic sodium cation at aug-cc-pCVTZ to more accurately evaluate each of the electrons in the system. Complete characterization of each cluster includes comparison to experimentally determined vibrational spectra, which in turn allows for further geometric, electronic, and structural analysis. High-powered lasers, such as a free-electron laser (FEL), produce experimental vibrational spectra through a process known as infrared multiple photon dissociation (IRMPD). IRMPD induces fragmentation of ions produced by electrospray ionization (ESI) through a phenomenon known as internal vibrational redistribution (IVR) where energy absorbed by the analyte ion is redistributed to other vibrational modes. The process of IRMPD can be coupled with electronic structure calculations to gain significant insight into the characterization of ions in the gas phase. The energetic favourability for deprotonating nucleobase monomers is investigated in Chapter 3 to determine the isomer most likely to exist for each nucleobase. Once the most energetically favourable nucleobase isomer was validated experimentally, the clustering behaviour of the monomers with sodium cations was further explored. The clustering of a single deprotonated isomer with one cationic sodium yielded one minimum energy structure for each of the nucleobases, however, as the complexity of the clusters increased the number of possible clustering geometries increased as well. The pyrimidines exhibited unusually favourable complexation of three deprotonated nucleobase monomers in a near C3 symmetry, as well as an extremely favourable linear arrangement. These two favourable geometrical structures were further explored in thymine and uracil complexes as they were the only high-complexity experimental data collected for the nucleobases. Unfortunately, for the purines and cytosine, there was no experimental vibrational spectra to draw conclusions from, however, general trends from computational analysis, as well as similarities between the pyrimidines, were possible to evaluate. This examination found that the clustering behaviour for all the deprotonated nucleobases (at each level of complexity) demonstrated extremely energetically favourable clustering behaviour the gas phase. In addition, the gas phase acidities (GPAs) of each nucleobase were determined to be of comparable strength to other well-documented gas phase acid strengths and found to have acid strengths non-linearly correlated to their respective solution phase pKas. Moreover, novel clustering geometries for multiple deprotonated nucleobase monomers with cationic sodium were revealed. Thus, the importance of evaluating deprotonated nucleobases, in the gas phase, was demonstrated by this study. This investigation revealed strong evidence to support the favourable clustering behaviour of the deprotonated nucleobases with cationic sodium, as well as novel geometries that describe these interesting new complexes in the gas phase. In each case, novel theoretical clustering geometries and thermodynamic properties for each of the biological species evaluated were determined. The hope is to be able to experimentally corroborate these findings in the future

Habitar 2.0 : Más allá del lugar en la arquitectura

¿Qué problemática se va a investigar? ¿Cómo se habita el límite difuso entre lo físico y lo virtual en el entorno urbano contemporáneo? ¿Cómo se va a investigar dicha problemática? Esta problemática se abordará desde el análisis de situaciones en las cuales el acto habitar se encuentre en relación con el límite entre lo físico y lo virtual. A partir de este análisis se generará una conceptualización de las situaciones y la dinámica que se da en el habitar en las ciudades contemporáneas en relación con la tecnología. ¿Por qué se va a investigar dicha problemática? La creciente ola de tecnología que se ha generado desde finales de década de los 70’s y las nuevas concepciones de la arquitectura en esa misma década, han generado un gran cambio en nuestros hábitos, formas de interacción y en la forma de pensar y crear la arquitectura. Debido a esto, la arquitectura se ha visto directamente influenciada por esta virtualidad que ha generado la tecnología y por ende ha cambiado nuestro entorno y así mismo, la forma en la cual habitamos, pensamos y creamos la arquitectura. ¿Qué productos se esperan generar al final del proyecto? -Texto teórico explorando los conceptos del habitar, la virtualidad y la inmersión en espacios virtuales. - Instalación audiovisual ( https://www.youtube.com/watch?v=ZpKuzDF96gI&t=1912s )What problems are going to be investigated? how to dwell the diffuse boundary between the physical and the virtuality at the contemporary urban environment How is the problem going to be investigated? This problem is going to be investigated from the analysis of several situations in which the act of dwelling can be found in the diffuse boundary between the physical and the virtuality. With this analysis, a new conceptualization will be generated to understand the new dynamics that can be found in the contemporary city in relation with the dwelling and the growing technology. Why is this problem going to be investigated? The growing wave of technology that has been generated since the late 70's and the new way to see architecture in the same decade, have generated a huge change in our dynamics, in the ways we interact and the way we think and create architecture. Because of this, the architecture has been directly influenced by this growing virtuality created by technology and have changed our habitat and, the way we dwell, think and create architecture. What products are expected to be generated at the end of the project? -Theoretical text exploring the concepts of dwelling, virtuality and immersive virtual spaces. - Audiovisual installation: https://www.youtube.com/watch?v=ZpKuzDF96gI&t=1912sArquitecto (a)Pregrad

Analysis and hydraulic model (2d) hyper concentrated sediment flows in west of the saws Ambato, Catamarca, Argentina

Los flujos de sedimentos hiper concentrados se pueden clasificar en inundaciones de barro, flujos de barro y flujo de escombros. Estos flujos se diferencian por la reología de la mezcla agua-sedimento. En los flujos de barro los esfuerzos que domina el fenómeno son el límite elástico y el esfuerzo viscoso. Un modelo reológico cuadrático permite simular adecuadamente condiciones de flujos que van desde aguas claras hasta flujos hiper concentrados de sedimentos. En este trabajo se analiza un evento hidrológico severo con flujo de barro ocurrido recientemente en Siján, Catamarca, Argentina aplicando el modelo de simulación (FLO-2D) de diferencias finitas.Hyper concentrated sediment flows have been classifield as mudfloods, mudflows and debris flows. Distinct physical processes differentiate these types of hyper concentrations based on the rheology of thewater-sediment mixture. Mudflows are flows with predominant yield and viscous stresses. A quadratic rheological model enables appropiate simulation offlooding conditions ranging from clear water to hyper concentrated sedimentflows.This paper presents a severe hydrological event recently occurred in Siján, Catamarca, Argentina. In this event mud flow was generated. This paper present a simulation model of finite differences (FLO-2D) to simulate the event.Fil: Eder, Matías. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Estudios Avanzados en Ingeniería y Tecnología. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Estudios Avanzados en Ingeniería y Tecnología; ArgentinaFil: Barbeito, Osvaldo Luis. Secretaria de Ambiente y Desarrollo Sustentable de la Nación. Instituto Nacional del Agua y del Ambiente (Córdoba); Argentina. Universidad Nacional de Córdoba; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Ambrosino, Silvio Norberto. Secretaria de Ambiente y Desarrollo Sustentable de la Nación. Instituto Nacional del Agua y del Ambiente (Córdoba); Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Hillman, Gerardo Daniel. Universidad Nacional de Córdoba; ArgentinaFil: Moya, Gonzalo. Universidad Nacional de Córdoba; ArgentinaFil: Rodriguez, Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Estudios Avanzados en Ingeniería y Tecnología. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Estudios Avanzados en Ingeniería y Tecnología; Argentin

Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus

BACKGROUND: There is an increasing interest to better understand endosymbiont capabilities in insects both from an ecological point of view and for pest control. Blochmannia floridanus provides important nutrients for its host, the ant Camponotus, while the bacterium in return is provided with a niche to proliferate. Blochmannia floridanus proteins and metabolites are difficult to study due to its endosymbiontic life style; however, its complete genome sequence became recently available. RESULTS: Improved sequence analysis algorithms, databanks and gene and pathway context methods allowed us to reveal new information on various enzyme and pathways from the Blochmannia floridanus genome sequence [EMBL-ID BX248583]. Furthermore, these predictions are supported and linked to experimental data for instance from structural genomics projects (e.g. Bfl341, Bfl 499) or available biochemical data on proteins from other species which we show here to be related. We were able to assign a confirmed or at least a putative molecular function for 21 from 27 previously conserved hypothetical proteins. For 48 proteins of 66 with a previous putative assignment the function was further clarified. Several of these proteins occur in many proteobacteria and are found to be conserved even in the compact genome of this endosymbiont. To extend and re-test predictions and links to experimentally verified protein functions, functional clusters and interactions were assembled. These included septum initiation and cell division (Bfl165, Bfl303, Bfl248 et al.); translation; transport; the ubiquinone (Bfl547 et al.), the inositol and nitrogen pathways. CONCLUSION: Taken together, our data allow a better and more complete description of the pathway capabilities and life style of this typical endosymbiont