Evolution of rhodopsin ion pumps in haloarchaea

<p>Abstract</p> <p>Background</p> <p>The type 1 (microbial) rhodopsins are a diverse group of photochemically reactive proteins that display a broad yet patchy distribution among the three domains of life. Recent work indicates that this pattern is likely the result of lateral gene transfer (LGT) of rhodopsin genes between major lineages, and even across domain boundaries. Within the lineage in which the microbial rhodopsins were initially discovered, the haloarchaea, a similar patchy distribution is observed. In this initial study, we assess the roles of LGT and gene loss in the evolution of haloarchaeal rhodopsin ion pump genes, using phylogenetics and comparative genomics approaches.</p> <p>Results</p> <p>Mapping presence/absence of rhodopsins onto the phylogeny of the RNA polymerase B' subunit (RpoB') of the haloarchaea supports previous notions that rhodopsins are patchily distributed. The phylogeny for the bacteriorhodopsin (BR) protein revealed two discrepancies in comparison to the RpoB' marker, while the halorhodopsin (HR) tree showed incongruence to both markers. Comparative analyses of bacteriorhodopsin-linked regions of five haloarchaeal genomes supported relationships observed in the BR tree, and also identified two open reading frames (ORFs) that were more frequently linked to the bacteriorhodopsin gene than those genes previously shown to be important to the function and expression of BR.</p> <p>Conclusion</p> <p>The evidence presented here reveals a complex evolutionary history for the haloarchaeal rhodopsins, with both LGT and gene loss contributing to the patchy distribution of rhodopsins within this group. Similarities between the BR and RpoB' phylogenies provide supportive evidence for the presence of bacteriorhodopsin in the last common ancestor of haloarchaea. Furthermore, two loci that we have designated bacterio-opsin associated chaperone (<it>bac</it>) and bacterio-opsin associated protein (<it>bap</it>) are inferred to have important roles in BR biogenesis based on frequent linkage and co-transfer with bacteriorhodopsin genes.</p

Direct observation of delithiation as the origin of analog memristance in LixNbO2

The discovery of analog LixNbO2 memristors revealed a promising new memristive mechanism wherein the diffusion of Li+ rather than O2- ions enables precise control of the resistive states. However, directly correlating lithium concentration with changes to the electronic structure in active layers remains a challenge and is required to truly understand the underlying physics. Chemically delithiated single crystals of LiNbO2 present a model system for correlating lithium variation with spectroscopic signatures from operando soft x-ray spectroscopy studies of device active layers. Using electronic structure modeling of the x-ray spectroscopy of LixNbO2 single crystals, we demonstrate that the intrinsic memristive behavior in LixNbO2 active layers results from field-induced degenerate p-type doping. We show that electrical operation of LixNbO2-based memristors is viable even at marginal Li deficiency and that the analog memristive switching occurs well before the system is fully metallic. This study serves as a benchmark for material synthesis and characterization of future LixNbO2-based memristor devices and suggests that valence change switching is a scalable alternative that circumvents the electroforming typically required for filamentary-based memristors

Eukaryotic influence on the oceanic biological carbon pump in the Scotia Sea as revealed by 18S rRNA gene sequencing of suspended and sinking particles

Suspended marine particles constitute most of the particulate organic matter pool in the oceans, thereby providing substantial substrates for heterotrophs, especially in the mesopelagic. Conversely, sinking particles are major contributors to carbon fluxes defining the strength of the biological carbon pump (BCP). This study is the first to investigate the differential influence of eukaryotic communities to suspended and sinking particles, using 18S rRNA gene sequencing on particles collected with a marine snow catcher in the mixed layer and upper mesopelagic of the Scotia Sea, Southern Ocean. In the upper mesopelagic, most eukaryotic phytoplankton sequences belonged to chain‐forming diatoms in sinking particles and to prymnesiophytes in suspended particles. This suggests that diatom‐enriched particles are more efficient in carbon transfer to the upper mesopelagic than those enriched in prymnesiophytes in the Scotia Sea, the latter more easily disintegrating into suspended particles. In the upper mesopelagic, copepods appeared most influential on sinking particles whereas soft‐tissue metazoan sequences contributed more to suspended particles. Heterotrophic protists and fungi communities were distinct between mixed layer and upper mesopelagic, implying that few protists ride along sinking particles. Furthermore, differences between predatory flagellates and radiolarians between suspended and sinking particles implied different ecological conditions between the two particles pools, and roles in the BCP. Molecular analyses of sinking and suspended particles constitute powerful diagnostic tools to study the eukaryotic influence on the BCP in a more holistic manner compared to classic carbon export studies focusing on sinking particles

Statistical Mechanics of Glass Formation in Molecular Liquids with OTP as an Example

We extend our statistical mechanical theory of the glass transition from examples consisting of point particles to molecular liquids with internal degrees of freedom. As before, the fundamental assertion is that super-cooled liquids are ergodic, although becoming very viscous at lower temperatures, and are therefore describable in principle by statistical mechanics. The theory is based on analyzing the local neighborhoods of each molecule, and a statistical mechanical weight is assigned to every possible local organization. This results in an approximate theory that is in very good agreement with simulations regarding both thermodynamical and dynamical properties

Considering Intra-individual Genetic Heterogeneity to Understand Biodiversity

In this chapter, I am concerned with the concept of Intra-individual Genetic Hetereogeneity (IGH) and its potential influence on biodiversity estimates. Definitions of biological individuality are often indirectly dependent on genetic sampling -and vice versa. Genetic sampling typically focuses on a particular locus or set of loci, found in the the mitochondrial, chloroplast or nuclear genome. If ecological function or evolutionary individuality can be defined on the level of multiple divergent genomes, as I shall argue is the case in IGH, our current genetic sampling strategies and analytic approaches may miss out on relevant biodiversity. Now that more and more examples of IGH are available, it is becoming possible to investigate the positive and negative effects of IGH on the functioning and evolution of multicellular individuals more systematically. I consider some examples and argue that studying diversity through the lens of IGH facilitates thinking not in terms of units, but in terms of interactions between biological entities. This, in turn, enables a fresh take on the ecological and evolutionary significance of biological diversity

Relaxational study of poly(vinylpyrrolidone-co-butyl acrylate) membrane by dielectric and dynamic mechanical spectroscopy

[EN] A poly(vinylpyrrolidone-co-butyl acrylate) (60VP-40BA) membrane is synthesized as a tractable and hydrophilic material, obtaining a water-swelling percentage around 60%. An investigation of molecular mobility by means of differential scanning calorimetry, dynamic mechanical analysis and broadband dielectric relaxation spectroscopy (DRS) is fulfilled in the dry membrane. Dielectric and viscoelastic relaxation measurements are carried out on the 60VP-40BA sample at several frequencies between -150 and 150 degrees C. The dielectric spectrum shows several relaxation processes labelled gamma, beta and alpha in increasing order of temperature, whereas in the mechanical spectrum only the beta and alpha relaxation processes are completely defined. In the dielectric measurements, conductive contributions overlap the alpha-relaxation. The apparent activation energies have similar values for the beta-relaxation in both, the mechanical and the dielectric measurements. The beta process is a Johari-Golstein secondary relaxation and it is related to the local motions of the pyrrolidone group accompanied by the motion of the segments of the polymer backbone. The gamma process is connected with the butyl unit's motions, both located in the side chains of the polymer.BRF, MC, PO and MJS are grateful to CICYT for grant MAT2012-33483. FG and JMG thank the Spanish Ministerio de Economia y Competitividad-FEDER (MAT2011-22544) and the Consejeria de Educacion-Junta de Castilla y Leon (BU001A10-2).Redondo Foj, MB.; Carsí Rosique, M.; Ortiz Serna, MP.; Sanchis Sánchez, MJ.; García, FC.; García. José Miguel (2013). Relaxational study of poly(vinylpyrrolidone-co-butyl acrylate) membrane by dielectric and dynamic mechanical spectroscopy. JOURNAL OF PHYSICS D-APPLIED PHYSICS. 46(29):295304-1-295304-12. https://doi.org/10.1088/0022-3727/46/29/295304S295304-1295304-12462

Simultaneous free-volume modeling of the self-diffusion coefficient and dynamic viscosity at high pressure

International audienceA free-volume model of the dynamic viscosity and the self-diffusion coefficients was discussed. The temperature-pressure variations of the dynamic viscosity and the self-diffusion coefficients of small molecules were predicted. The compounds, carbon tetrachloride, cyclohexane, benzene, chlorotrifluoromethane, tetramethylsilane and methylcyclohexane were used for the investigation. The relation between microstructure, free volume and different complex thermophysical properties were emphasized by the model

Impact of local recharge on arsenic concentrations in shallow aquifers inferred from the electromagnetic conductivity of soils in Araihazar, Bangladesh

The high-degree of spatial variability of dissolved As levels in shallow aquifers of the Bengal Basin has been well documented but the underlying mechanisms remain poorly understood. We compare here As concentrations measured in groundwater pumped from 4700 wells <22 m (75 ft) deep across a 25 km2 area of Bangladesh with variations in the nature of surface soils inferred from 18,500 measurements of frequency domain electromagnetic induction. A set of 14 hand auger cores recovered from the same area indicate that a combination of grain size and the conductivity of soil water dominate the electromagnetic signal. The relationship between pairs of individual EM conductivity and dissolved As measurements within a distance of 50 m is significant but highly scattered (r2 = 0.12; n = 614). Concentrations of As tend to be lower in shallow aquifers underlying sandy soils and higher below finer-grained and high conductivity soils. Variations in EM conductivity account for nearly half the variance of the rate of increase of As concentration with depth, however, when the data are averaged over a distance of 50 m (r2 = 0.50; n = 145). The association is interpreted as an indication that groundwater recharge through permeable sandy soils prevents As concentrations from rising in shallow reducing groundwater

CoRoT high-precision photometry of the B0.5 IV star HD 51756

OB stars are important constituents for the ecology of the Universe, and there are only a few studies on their pulsational properties detailed enough to provide important feedback on current evolutionary models. Our goal is to analyse and interpret the behaviour present in the CoRoT light curve of the B0.5 IV star HD 51756 observed during the second long run of the space mission, and to determine the fundamental stellar parameters from ground-based spectroscopy gathered with the CORALIE and HARPS instruments after checking for signs of variability and binarity, thus making a step further in mapping the top of the Beta Cep instability strip. We compare the newly obtained high-resolution spectra with synthetic spectra of late O-type and early B-type stars computed on a grid of stellar parameters. We match the results with evolutionary tracks to estimate stellar parameters. We use various time series analysis tools to explore the nature of the variations present in the light curve. Additional calculations are carried out based on distance and historical position measurements of the components to impose constraints on the binary orbit. We find that HD 51756 is a wide binary with both a slow (v sin i \approx 28 km s^-1) and a fast (v sin i \approx 170 km s^-1) early-B rotator whose atmospheric parameters are similar (T_eff \approx 30000 K and log g \approx 3.75). We are unable to detect pulsation in any of the components, and we interpret the harmonic structure in the frequency spectrum as sign of rotational modulation, which is compatible with the observed and deduced stellar parameters of both components. The non-detection of pulsation modes provides a feedback on the theoretical treatment, given that non-adiabatic computations applied to appropriate stellar models predict the excitation of both pressure and gravity modes for the fundamental parameters of this star.Comment: Accepted for publication in Astronomy and Astrophysics on 14/01/2011, 11 pages, 9 figures, 4 table

Just how versatile are domains?

<p>Abstract</p> <p>Background</p> <p>Creating new protein domain arrangements is a frequent mechanism of evolutionary innovation. While some domains always form the same combinations, others form many different arrangements. This ability, which is often referred to as versatility or promiscuity of domains, its a random evolutionary model in which a domain's promiscuity is based on its relative frequency of domains.</p> <p>Results</p> <p>We show that there is a clear relationship across genomes between the promiscuity of a given domain and its frequency. However, the strength of this relationship differs for different domains. We thus redefine domain promiscuity by defining a new index, <it>DV I </it>("domain versatility index"), which eliminates the effect of domain frequency. We explore links between a domain's versatility, when unlinked from abundance, and its biological properties.</p> <p>Conclusion</p> <p>Our results indicate that domains occurring as single domain proteins and domains appearing frequently at protein termini have a higher <it>DV I</it>. This is consistent with previous observations that the evolution of domain re-arrangements is primarily driven by fusion of pre-existing arrangements and single domains as well as loss of domains at protein termini. Furthermore, we studied the link between domain age, defined as the first appearance of a domain in the species tree, and the <it>DV I</it>. Contrary to previous studies based on domain promiscuity, it seems as if the <it>DV I </it>is age independent. Finally, we find that contrary to previously reported findings, versatility is lower in Eukaryotes. In summary, our measure of domain versatility indicates that a random attachment process is sufficient to explain the observed distribution of domain arrangements and that several views on domain promiscuity need to be revised.</p