Observation of correlated X-ray scattering at atomic resolution

Tools to study disordered systems with local structural order, such as proteins in solution, remain limited. Such understanding is essential for e.g. rational drug design. Correlated X-ray scattering (CXS) has recently attracted new interest as a way to leverage next-generation light sources to study such disordered matter. The CXS experiment measures angular correlations of the intensity caused by the scattering of X-rays from an ensemble of identical particles, with disordered orientation and position. Averaging over 15 496 snapshot images obtained by exposing a sample of silver nanoparticles in solution to a micro-focused synchrotron radiation beam, we report on experimental efforts to obtain CXS signal from an ensemble in three dimensions. A correlation function was measured at wide angles corresponding to atomic resolution that matches theoretical predictions. These preliminary results suggest that other CXS experiments on disordered ensembles—such as proteins in solution—may be feasible in the future.     

Ebola in great apes – current knowledge,possibilities for vaccination,and implications for conservation and human health

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Adenovirus in Rural Côte D`Ivoire: High Diversity and Cross-Species Detection

The Taï region in Western Côte d`Ivoire is characterized by extensive overlap of human and animal habitats. This could influence patterns of adenovirus transmission between humans and domestic animals. Fecal samples from humans and various domestic animals were tested for the presence of adenoviruses by PCR. Phylogenetic and species delineation analyses were performed to further characterize the adenoviruses circulating in the region and to identify potential cross-species transmission events. Among domestic animals, adenovirus shedding was frequent (21.6% of domestic mammals and 41.5% of chickens) and the detected strains were highly diverse, several of them representing novel types. Although no evidence for zoonotic transmission of animal adenovirus was obtained, the present study provides concordant evidence in favor of common cross-species transmission of adenoviruses between different animal species and first indications for adenovirus transmission from humans to animals. These findings underline the thus far underestimated importance of reverse zoonotic transmission of viruses and of the role of domestic animals as pathogen reservoirs, “bridge species,” or intermediate hosts.     

Genotype versus phenotype in the circumscription of bacterial species: the case of Pseudomonas stutzeri and Pseudomonas chloritidismutans

The phenotypic characteristic of strain AW-1(T) of Pseudomonas chloritidismutans that is most relevant from the taxonomic point of view appears to be the capacity of growth under anaerobic conditions using chlorate as electron acceptor. This property is not restricted to this species only within the genus Pseudomonas, since it is also present in strains of genomovars 1 or 5, and 3 of Pseudomonas stutzeri. P. chloritidismutans has been described as a non-denitrifying species, but the isolation of variants that are able to grow anaerobically in the presence of nitrate is possible after subcultivation under selective conditions. The subdivision of P. stutzeri into a number of species on the basis of these characteristics does not help to clarify the phylogenetic relationships among the members of an otherwise coherent group of strains, and the considerations presented in this communication support the reclassification of the new species name P. chloritidismutans, which in our opinion, should be considered as a Junior name of P. stutzeri. A multilocus sequence analysis, together with a phenotypic analysis of the anaerobic oxidative metabolism, gives new insights into the phylogeny and evolution of the species.     

Putative drug binding conformations of monoamine transporters

Structural information about monoamine transporters and their interactions with psychotropic drugs is important for understanding their molecular mechanisms of action and for drug development. The crystal structure of a Major Facilitator Superfamily (MFS) transporter, the lactose permease symporter (lac permease), has provided insight into the three-dimensional structure and mechanisms of secondary transporters. Based on the hypothesis that the 12 transmembrane alpha-helix (TMH) secondary transporters belong to a common folding class, the lac permease structure was used for molecular modeling of the serotonin transporter (SERT), the dopamine transporter (DAT), and the noradrenaline transporter (NET). The molecular modeling methods used included amino acid sequence alignment, homology modeling, and molecular mechanical energy calculations. The lac permease crystal structure has an inward-facing conformation, and construction of outward-facing SERT, DAT, and NET conformations allowing ligand binding was the most challenging step of the modeling procedure. The psychomotor stimulants cocaine and S-amphetamine, and the selective serotonin reuptake inhibitor (SSRI) S-citalopram, were docked into putative binding sites on the transporters to examine their molecular binding mechanisms. In the inward-facing conformation of SERT the translocation pore was closed towards the extracellular side by hydrophobic interactions between the conserved amino acids Phe105, Pro106, Phe117, and Ala372. An unconserved amino acid, Asp499 in TMH10 in NET, may contribute to the low affinity of S-citalopram to NET.     

Relationships between Growth,Growth Response to Nutrient Supply,and Ion Content Using a Recombinant Inbred Line Population in Arabidopsis

Growth is an integrative trait that responds to environmental factors and is crucial for plant fitness. A major environmental factor influencing plant growth is nutrient supply. In order to explore this relationship further, we quantified growth-related traits, ion content, and other biochemical traits (protein, hexose, and chlorophyll contents) of a recombinant inbred line population of Arabidopsis (Arabidopsis thaliana) grown on different levels of potassium and phosphate. Performing an all subsets multiple regression analyses revealed a link between growth-related traits and mineral nutrient content. Based on our results, up to 85% of growth variation can be explained by variation in ion content, highlighting the importance of ionomics for a broader understanding of plant growth. In addition, quantitative trait loci (QTLs) were detected for growth-related traits, ion content, further biochemical traits, and their responses to reduced supplies of potassium or phosphate. Colocalization of these QTLs is explored, and candidate genes are discussed. A QTL for rosette weight response to reduced potassium supply was identified on the bottom of chromosome 5, and its effects were validated using selected near isogenic lines. These lines retained over 20% more rosette weight in reduced potassium supply, accompanied by an increase in potassium content in their leaves.Plants in natural environments face abiotic constraints limiting growth and ultimately affecting their fitness. In response to such constraints, flowering time (Korves et al., 2007) and seed dormancy (Donohue et al., 2005) as well as vegetative growth (Barto and Cipollini, 2005; Milla et al., 2009) are the main traits controlling fitness (for review, see Alonso-Blanco et al., 2009). These traits are under the control of complex networks integrating genetic (G) and environmental (E) factors as well as their interaction (G × E). Due to the implications for food and renewable energy sources, dissecting the genetic architecture that underlies plant growth is becoming a priority for plant science (Rengel and Damon, 2008; Carroll and Somerville, 2009; Gilbert, 2009).Plant growth is highly dependent on mineral nutrient uptake (Clarkson, 1980; Sinclair, 1992). Minerals can be distinguished into two categories based on the amount required by plants: micronutrients, which are found in relatively small amounts in the plant (such as copper and iron), and macronutrients, which constitute between 1,000 and 15,000 μg g⁻¹ plant dry weight (such as potassium and phosphate; Marschner, 1995, Buchanan et al., 2002). Phosphate is an important structural and signaling molecule with an essential role in photosynthesis, energy conservation, and carbon metabolism. Its deficiency leads to a reduction of growth and an increase of pathogen susceptibility (Marschner, 1995; Williamson et al., 2001; Abel et al., 2002; López-Bucio et al., 2005; Poirier and Bucher, 2008; Vijayraghavan and Soole, 2010). Potassium is not incorporated into any organic substances but acts as the major osmoticum of the cell, controlling cell expansion, plasma membrane potential and transport, pH value, and many other catalytic processes (Maathuis and Sanders, 1996; Armengaud et al., 2004; Christian et al., 2006; Di Cera, 2006). Potassium deficiency leads to reduced plant growth, a loss of turgor, increased susceptibility to cold stress and pathogens, and the development of chlorosis and necrosis (Marschner, 1995; Véry and Sentenac, 2003; Ashley et al., 2006; Amtmann et al., 2008). To cope with changes in nutrient availability, plants have evolved different mechanisms of adaptation, such as changes in ion transporter expression and activity (Ashley et al., 2006; Jung et al., 2009), morphological changes, such as an increase in root growth to explore more soil volume (Marschner, 1995; Shirvani et al., 2001; Jiang et al., 2007; Jordan-Meille and Pellerin, 2008), or acidification of the surrounding soil in order to mobilize more mineral nutrients (for review, see Ryan et al., 2001). Although these adaptations are well known, the mechanisms involved in sensing and signaling low mineral nutrient status are less well understood, despite significant progress in this area being made (Doerner, 2008; Jung et al., 2009; Luan et al., 2009; Wang and Wu, 2010).One approach to identify genes that are involved in plant responses to environmental factors is to perform a quantitative trait locus (QTL) analysis on a mapping population grown in contrasting environments, allowing the identification of QTL-environment (QTL × E) interactions. Some QTLs for growth-related traits in response to environmental changes were cloned already. For example, the differential response of root growth of some Arabidopsis (Arabidopsis thaliana) accessions to phosphate starvation led to the identification of allelic differences responsible for this phenotype (Reymond et al., 2006; Svistoonoff et al., 2007). Other studies have identified QTLs for shoot dry matter under changing nitrogen supply (Rauh et al., 2002; Loudet et al., 2003). In parallel to natural variation for growth, natural variation for ion content has also been reported. In Arabidopsis, considerable variation in the content of mineral nutrients exists both in seeds (Vreugdenhil et al., 2004; Waters and Grusak, 2008) and in leaves (Harada and Leigh, 2006; Rus et al., 2006; Baxter et al., 2008a; Morrissey et al., 2009). Furthermore, changes in mineral nutrient homeostasis have also been reported to be associated with characteristic multivariate changes in the leaf ionome, the mineral nutrient and trace element composition of an organism or an organ (Baxter et al., 2008b). Due to higher throughput and lower costs, such “omics” analyses examining alterations of large numbers of certain molecules at once have recently become available for mapping purposes. Some QTL studies have linked the variations of these omics data to variation of growth or other physiological traits. For instance, Meyer et al. (2007) and Schauer et al. (2008) linked plant growth or morphological traits to a synergistic network of metabolomic compounds in Arabidopsis and tomato (Solanum lycopersicum), respectively. In addition, Sulpice et al. (2009) associated differences in growth with starch content using a set of Arabidopsis accessions. Compiling the importance of ions in the process of cell division (Lai et al., 2007; Sano et al., 2007) or cell expansion (Philippar et al., 1999; Elumalai et al., 2002), ionomics appears to be a major unexplored field for understanding growth.In this study, we focus on variation in plant growth, the root and leaf ionomes, and their response to varying supplies of potassium and phosphate. Studying variations for these traits among recombinant inbred lines (RILs) in Arabidopsis enabled us to detect QTL and QTL × E interactions for all of these traits. To understand the observed variation in plant growth, predictors that explained a high percentage of variation of growth-related traits have been selected especially among the root and leaf ionomes. The colocalization between growth-related trait QTLs and QTLs for their predictors allowed us to point out genetic regions of possible causality. In addition, the effect of a growth-response QTL on reduced potassium supply was validated with selected near isogenic lines (NILs) that maintained a higher rosette weight when grown in reduced potassium supply. This growth advantage went along with significant changes in ion contents that further emphasize the impact of the ionome in plant growth variations.     

Natural variation of photosynthetic efficiency in Arabidopsis thaliana accessions under low temperature conditions

Low, but non-freezing, temperatures have negative effects on plant growth and development. Despite some molecular signalling pathways being known, the mechanisms causing different responses among genotypes are still poorly understood. Photosynthesis is one of the processes that are affected by low temperatures. Using an automated phenotyping platform for chlorophyll fluorescence imaging the steady state quantum yield of photosystem II (PSII) electron transport (Φ_PSII) was measured and used to quantify the effect of moderately low temperature on a population of Arabidopsis thaliana natural accessions. Observations were made over the course of several weeks in standard and low temperature conditions and a strong decrease in Φ_PSII upon the cold treatment was found. A genome wide association study identified several quantitative trait loci (QTLs) that are associated with changes in Φ_PSII in low temperature. One candidate for a cold specific QTL was validated with a mutant analysis to be one of the genes that is likely involved in the PSII response to the cold treatment. The gene encodes the PSII associated protein PSB27 which has already been implicated in the adaptation to fluctuating light.     

Differential effects of propofol and ketamine on critical brain dynamics

Whether the brain operates at a critical “tipping” point is a long standing scientific question, with evidence from both cellular and systems-scale studies suggesting that the brain does sit in, or near, a critical regime. Neuroimaging studies of humans in altered states of consciousness have prompted the suggestion that maintenance of critical dynamics is necessary for the emergence of consciousness and complex cognition, and that reduced or disorganized consciousness may be associated with deviations from criticality. Unfortunately, many of the cellular-level studies reporting signs of criticality were performed in non-conscious systems (in vitro neuronal cultures) or unconscious animals (e.g. anaesthetized rats). Here we attempted to address this knowledge gap by exploring critical brain dynamics in invasive ECoG recordings from multiple sessions with a single macaque as the animal transitioned from consciousness to unconsciousness under different anaesthetics (ketamine and propofol). We use a previously-validated test of criticality: avalanche dynamics to assess the differences in brain dynamics between normal consciousness and both drug-states. Propofol and ketamine were selected due to their differential effects on consciousness (ketamine, but not propofol, is known to induce an unusual state known as “dissociative anaesthesia”). Our analyses indicate that propofol dramatically restricted the size and duration of avalanches, while ketamine allowed for more awake-like dynamics to persist. In addition, propofol, but not ketamine, triggered a large reduction in the complexity of brain dynamics. All states, however, showed some signs of persistent criticality when testing for exponent relations and universal shape-collapse. Further, maintenance of critical brain dynamics may be important for regulation and control of conscious awareness.     

Comparative genetic diversity of Pseudomonas stutzeri genomovars, clonal structure, and phylogeny of the species

A combined phylogenetic and multilocus DNA sequence analysis of 26 Pseudomonas stutzeri strains distributed within the 9 genomovars of the species has been performed. Type strains of the two most closely related species (P. balearica, former genomovar 6, and P. mendocina), together with P. aeruginosa, as the type species of the genus, have been included in the study. The extremely high genetic diversity and the clonal structure of the species were confirmed by the sequence analysis. Clustering of strains in the consensus phylogeny inferred from the analysis of seven nucleotide sequences (16S ribosomal DNA, internally transcribed spacer region 1, gyrB, rpoD, nosZ, catA, and nahH) confirmed the monophyletic origin of the genomovars within the Pseudomonas branch and is in good agreement with earlier DNA-DNA similarity analysis, indicating that the selected genes are representative of the whole genome in members of the species.