The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti

<p>Abstract</p> <p>Background</p> <p><it>Rhizobium</it>-Legume symbiosis is an attractive biological process that has been studied for decades because of its importance in agriculture. However, this system has undergone extensive study and although many of the major factors underpinning the process have been discovered using traditional methods, much remains to be discovered.</p> <p>Results</p> <p>Here we present an analysis of the 'Symbiosis Interactome' using novel computational methods in order to address the complex dynamic interactions between proteins involved in the symbiosis of the model bacteria <it>Sinorhizobium meliloti </it>with its plant hosts. Our study constitutes the first large-scale analysis attempting to reconstruct this complex biological process, and to identify novel proteins involved in establishing symbiosis. We identified 263 novel proteins potentially associated with the Symbiosis Interactome. The topology of the Symbiosis Interactome was used to guide experimental techniques attempting to validate novel proteins involved in different stages of symbiosis. The contribution of a set of novel proteins was tested analyzing the symbiotic properties of several <it>S. meliloti </it>mutants. We found mutants with altered symbiotic phenotypes suggesting novel proteins that provide key complementary roles for symbiosis.</p> <p>Conclusion</p> <p>Our 'systems-based model' represents a novel framework for studying host-microbe interactions, provides a theoretical basis for further experimental validations, and can also be applied to the study of other complex processes such as diseases.</p

Integrating local environmental data and information from non-driven citizen science to estimate jellyfish abundance in Costa del Sol (southern Spain)

Tourism, fishing and aquaculture are key economic sectors of Costa del Sol (southern Iberian Peninsula). The management of these activities is sometimes disturbed by the onshore arrival and stranding of jellyfish swarms. In the absence data on the occurrence of these organisms, it may be interesting to explore data from non-driven systems, such as social networks. The present study show how data in text format from a mobile app called Infomedusa can be processed and used to model the relationship between estimated abundance of jellyfish on the beaches and local environmental conditions. The data retrieved from this app using artificial intelligence procedures (transition network or TN algorithm), were used as input for GAM models to estimate the abundance of jellyfish based on wind speed and direction. The analysis of data provided by Infomedusa indicated that only 30.39% of messages provided by the users had information about absence/presence of jellyfishes in the beaches. On the other hand, the TN processing capacity showed an accuracy level to discriminate messages with information on absence/presence of jellyfish slightly higher than 80%. GAM models considering the wind direction and speed of previous day explained between 37% and 77% of the variance of jellyfish abundance estimate from Infomedusa data. In conclusion, this approach may contribute to the development of a system for predicting the onshore arrival of jellyfish in the Costa del Sol.Versión del edito

Bloqueo IPACK asociado a bloqueo del canal de los aductores frente a bloqueo femoral, calidad analgésica y uso de rescate tras artroplastia total de rodilla.

Total knee arthroplasty and its postoperative period can be very painful. Usually patients undergoing locoregional or general anesthetic techniques to which peripheral nerve blocks are associated for postoperative analgesia, within which femoral nerve block is the most widespread an adequate analgesic quality of the anterior compartment of the knee. It is widely described in the literature that blockage of the adductor canal or Hunter confers an analgesic quality similar to that achieved with the femoral block without objectifying that motor block that can limit its use for rapid rehabilitation. Recently also described in the literature, the blockade that is defined as IPACK (Infiltration between Popliteal Artery and Capsule Knee) or SPANK (Posterior Articular Sensory Nerves of the Knee) achieves an adequate analgesia of the posterior compartment of the knee. We believe that the combination of these two peripheral nerve blocks associated with the usual anesthetic technique may result in better analgesic quality in our patients and a lower consumption of opioids in the form of rescue

The Effect of Chaperonin Buffering on Protein Evolution

Molecular chaperones are highly conserved and ubiquitous proteins that help other proteins in the cell to fold. Pioneering work by Rutherford and Lindquist suggested that the chaperone Hsp90 could buffer (i.e., suppress) phenotypic variation in its client proteins and that alternate periods of buffering and expression of these variants might be important in adaptive evolution. More recently, Tokuriki and Tawfik presented an explicit mechanism for chaperone-dependent evolution, in which the Escherichia coli chaperonin GroEL facilitated the folding of clients that had accumulated structurally destabilizing but neofunctionalizing mutations in the protein core. But how important an evolutionary force is chaperonin-mediated buffering in nature? Here, we address this question by modeling the per-residue evolutionary rate of the crystallized E. coli proteome, evaluating the relative contributions of chaperonin buffering, functional importance, and structural features such as residue contact density. Previous findings suggest an interaction between codon bias and GroEL in limiting the effects of misfolding errors. Our results suggest that the buffering of deleterious mutations by GroEL increases the evolutionary rate of client proteins. We then examine the evolutionary fate of GroEL clients in the Mycoplasmas, a group of bacteria containing the only known organisms that lack chaperonins. We show that GroEL was lost once in the common ancestor of a monophyletic subgroup of Mycoplasmas, and we evaluate the effect of this loss on the subsequent evolution of client proteins, providing evidence that client homologs in 11 Mycoplasma species have lost their obligate dependency on GroEL for folding. Our analyses indicate that individual molecules such as chaperonins can have significant effects on proteome evolution through their modulation of protein folding

ECOS-LINCE : a high-intensity heavy-ion facility for nuclear structure and reactions

Presented at the XXXIV Mazurian Lakes Conference on Physics, Piaski, Poland, September 6–13, 2015During the last years, the ECOS working group has been considering the construction of a new high-intensity accelerator of stable ion beams for the next Long-Range Plan of the nuclear physics community in Europe. The new facility (LINCE) will be a multi-user facility dedicated to ECOS science: fundamental physics, astrophysics, nuclear structure and reaction dynamics. In this paper, we summarize preliminary design studies of the low-energy part of this facility based on the use of a multi-ion supercon- ducting linac.Work partially supported by the Spanish Government under the grant Feder-Interconnecta “Aceltec” ITC-20111070. The authors are also grateful to the companies Alter Technology-Tüv, Avs, Cibernos, Elitt Energy, Faysol, Idom, and Tti Norte for partial funding of this work and active participation in the design and prototyping carried-out in this study

Evolutionary Diversification of Plant Shikimate Kinase Gene Duplicates

Shikimate kinase (SK; EC 2.7.1.71) catalyzes the fifth reaction of the shikimate pathway, which directs carbon from the central metabolism pool to a broad range of secondary metabolites involved in plant development, growth, and stress responses. In this study, we demonstrate the role of plant SK gene duplicate evolution in the diversification of metabolic regulation and the acquisition of novel and physiologically essential function. Phylogenetic analysis of plant SK homologs resolves an orthologous cluster of plant SKs and two functionally distinct orthologous clusters. These previously undescribed genes, shikimate kinase-like 1 (SKL1) and -2 (SKL2), do not encode SK activity, are present in all major plant lineages, and apparently evolved under positive selection following SK gene duplication over 400 MYA. This is supported by functional assays using recombinant SK, SKL1, and SKL2 from Arabidopsis thaliana (At) and evolutionary analyses of the diversification of SK-catalytic and -substrate binding sites based on theoretical structure models. AtSKL1 mutants yield albino and novel variegated phenotypes, which indicate SKL1 is required for chloroplast biogenesis. Extant SKL2 sequences show a strong genetic signature of positive selection, which is enriched in a protein–protein interaction module not found in other SK homologs. We also report the first kinetic characterization of plant SKs and show that gene expression diversification among the AtSK inparalogs is correlated with developmental processes and stress responses. This study examines the functional diversification of ancient and recent plant SK gene duplicates and highlights the utility of SKs as scaffolds for functional innovation