Human disease and drug pharmacology, complex as real life

In the past decades drug discovery practice has escaped from the complexity of the formerly used phenotypic screening in animals to focus on assessing drug effects on isolated protein targets in the search for drugs that exclusively and potently hit one selected target, thought to be critical for a given disease, while not affecting at all any other target to avoid the occurrence of side-effects. However, reality does not conform to these expectations, and, conversely, this approach has been concurrent with increased attrition figures in late-stage clinical trials, precisely due to lack of efficacy and safety. In this context, a network biology perspective of human disease and treatment has burst into the drug discovery scenario to bring it back to the consideration of the complexity of living organisms and particularly of the (patho)physiological environment where protein targets are (mal)functioning and where drugs have to exert their restoring action. Under this perspective, it has been found that usually there is not one but several disease-causing genes and, therefore, not one but several relevant protein targets to be hit, which do not work on isolation but in a highly interconnected manner, and that most known drugs are inherently promiscuous. In this light, the rationale behind the currently prevailing single-target-based drug discovery approach might even seem a Utopia, while, conversely, the notion that the complexity of human disease must be tackled with complex polypharmacological therapeutic interventions constitutes a difficult-torefuse argument that is spurring the development of multitarget therapies.

Efficiency of informational transfer in regular and complex networks

We analyze the process of informational exchange through complex networks by measuring network efficiencies. Aiming to study nonclustered systems, we propose a modification of this measure on the local level. We apply this method to an extension of the class of small worlds that includes declustered networks and show that they are locally quite efficient, although their clustering coefficient is practically zero. Unweighted systems with small-world and scale-free topologies are shown to be both globally and locally efficient. Our method is also applied to characterize weighted networks. In particular we examine the properties of underground transportation systems of Madrid and Barcelona and reinterpret the results obtained for the Boston subway network.

Supergenes and complex phenotypes.

Understanding the molecular underpinnings of evolutionary adaptations is a central focus of modern evolutionary biology. Recent studies have uncovered a panoply of complex phenotypes, including locally adapted ecotypes and cryptic morphs, divergent social behaviours in birds and insects, as well as alternative metabolic pathways in plants and fungi, that are regulated by clusters of tightly linked loci. These 'supergenes' segregate as stable polymorphisms within or between natural populations and influence ecologically relevant traits. Some supergenes may span entire chromosomes, because selection for reduced recombination between a supergene and a nearby locus providing additional benefits can lead to locus expansions with dynamics similar to those known for sex chromosomes. In addition to allowing for the co-segregation of adaptive variation within species, supergenes may facilitate the spread of complex phenotypes across species boundaries. Application of new genomic methods is likely to lead to the discovery of many additional supergenes in a broad range of organisms and reveal similar genetic architectures for convergently evolved phenotypes.

Phorbol 12-myristate 13-acetate induces surface expression of T3 on human immature T cell lines with and without concomitant expression of the T cell antigen receptor complex.

The T3 complex is known to be expressed on the cell surface of mature T cells together with either the alpha-beta heterodimeric T cell receptor (TCR) or the TCR gamma protein. In a number of immature T cell malignancies, however, T3 has been described exclusively in the cytoplasm. We have investigated five such T cell lines with cytoplasmic T3 and could demonstrate by biosynthetic labeling the presence of the alpha and beta chains of the TCR in the cytoplasm of two of them, CEM and Ichikawa. No surface TCR alpha-beta protein could be detected by staining with the WT31 antibody. These observations, therefore, argue against the concept that expression of the TCR alpha chain controls the surface expression of the T3/TCR complex. Interestingly, phorbol 12-myristate 13-acetate (PMA) induced cell surface expression of T3 protein in these two cell lines only. Moreover, on surface-iodinated CEM cells no association of T3 and TCR molecules could be demonstrated after treatment with PMA, and expression of TCR alpha and beta chains was limited to the cytoplasm. In Ichikawa cells, however, PMA induced surface expression of a mature T3/TCR complex. Our findings indicate that separate regulatory mechanisms may exist for the surface expression of the T3 proteins and for the assembly of the T3/TCR complex.

Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis.

Recognition by the T-cell receptor (TCR) of immunogenic peptides presented by class I major histocompatibility complexes (MHCs) is the determining event in the specific cellular immune response against virus-infected cells or tumor cells. It is of great interest, therefore, to elucidate the molecular principles upon which the selectivity of a TCR is based. These principles can in turn be used to design therapeutic approaches, such as peptide-based immunotherapies of cancer. In this study, free energy simulation methods are used to analyze the binding free energy difference of a particular TCR (A6) for a wild-type peptide (Tax) and a mutant peptide (Tax P6A), both presented in HLA A2. The computed free energy difference is 2.9 kcal/mol, in good agreement with the experimental value. This makes possible the use of the simulation results for obtaining an understanding of the origin of the free energy difference which was not available from the experimental results. A free energy component analysis makes possible the decomposition of the free energy difference between the binding of the wild-type and mutant peptide into its components. Of particular interest is the fact that better solvation of the mutant peptide when bound to the MHC molecule is an important contribution to the greater affinity of the TCR for the latter. The results make possible identification of the residues of the TCR which are important for the selectivity. This provides an understanding of the molecular principles that govern the recognition. The possibility of using free energy simulations in designing peptide derivatives for cancer immunotherapy is briefly discussed.

Investigation of the hepatitis C virus replication complex.

The NS5A protein of HCV is an essential component of the viral RNA replication machinery and may also function in modulation of the host cell environment. The exact function of NS5A in these processes remains unknown. NS5A is a large hydrophilic phosphoprotein protein consisting of three domains. The amino-terminal domain, designated domain I, coordinates a single zinc atom that is required for virus replication. We have determined the X-ray crystallographic structure of the domain I region of NS5A, and the structure sheds some light on the previously reported RNA binding activity observed for NS5A and suggests that the protein functions as a dimer. Here we describe the bacterial expression, purification, crystallization, and structural determination of the amino-terminal domain I of NS5A. The methods described herein should be of use for the generation of domain I for biochemical studies as well as future crystallization studies as antiviral compounds directed against this region of NS5A become available.

Improvement of productivity and polysaccharide-protein complex in Agaricus blazei

The objective of this work was to assess the productivity and polysaccharide-protein complex content of Agaricus blazei on rice straw medium, in comparison to conventional sawdust, using four casing soils. The A. blazei strain used was BCRC36814T, purchased from the Food Industry Research and Development Institute, Hsin-Chu, Taiwan. The two media were evaluated as to A. blazei productivity, harvesting time, and production costs. The experimental design used was a randomized complete block, with four replicates. Three local casing soils - Typic Paleudult (CCe), Typic Udorthent (Tq) and Oxyaquic Paleudult (TSp) - were compared to imported peat soil (PS, Saprists, Histosols), used as the control. The productivity of A. blazei using Tq and TSp soil was significantly higher. The TSp casing treatment resulted in earlier harvest by at least 14 to 27 days, when compared to the other treatments. The polysaccharide content in CCe (13.2%) and Tq soils (13.2%) did not differ significantly from the PS (13.4%) and TSp (10.6%) treatments. Local casing soils decreased the production costs of A. blazei cultivation. Composted rice straw can substitute sawdust as the culture medium for A. blazei production with increased yield.

Early Jurassic to Early late Cretaceous radiolarians from the Santa Rosa accretionary complex (Northwestern Costa Rica)

In the circum-Pacific ophiolitic belts, when no other biogenic constituents are found, radiolarians have the potential to provide significant biostratigraph- ic information. The Santa Rosa Accretionary Complex, which crops out in several half-windows (Carrizal, Sitio Santa Rosa, Bahia Nancite, Playa Naranjo) along the south shores of the Santa Elena Peninsula in northwestern Costa Rica, is one of these little-known ophiolitic mélanges. It contains various oceanic assemblages of alkaline basalt, radiolarite and polymictic breccias. The radiolarian biochronology presented in this work is mainly based by correlation on the biozonations of Carter et al. (2010), Baumgartner et al. (1995b), and O'Dogherty (1994) and indicate an Early Jurassic to early Late Cretaceous (early Pliensbachian to earliest Turonian) age for the sediments associated with oceanic basalts or recovered from blocks in breccias or megabreccias. The 19 illus- trated assemblages from the Carrizal tectonic window and Sitio Santa Rosa contain in total 162 species belonging to 65 genera. The nomenclature of tecton- ic units is the one presented by (Baumgartner and Denyer, 2006). This study brings to light the Early Jurassic age of a succession of radiolarite, which was previously thought to be of Cretaceous age, intruded by alkaline basalts sills (Unit 3). The presence of Early Jurassic large reworked blocks in a polymictic megabreccia, firstly reported by De Wever et al. (1985) is confirmed (Unit 4). Therefore, the alkaline basalt associated with the radiolarites of these two units (and maybe also Units 5 and 8) could be of Jurassic age. In the Carrizal tectonic window, Middle to early Late Jurassic radiolarian chert blocks associ- ated with massive tholeitic basalts and Early Cretaceous brick-red ribbon cherts overlying pillow basalts are interpreted as fragments of a Middle Jurassic oceanic basement accreted to an Early Cretaceous oceanic Plate, in an intra-oceanic subduction context. Whereas, the knobby radiolarites and black shales of Playa Carrizal are indicative of a shallower middle Cretaceous paleoenvironment. Other remnants of this oceanic basin are found in Units 2, 6, and 7, which documented the rapid approach of the depocentre to a subduction trench during the late Early Cretaceous (Albian-Cenomanian), to possibly early Late Cretaceous (Turonian).

High precision U/Pb zircon dating of the Chalten Plutonic Complex (Cerro Fitz Roy, Patagonia) and its relationship to arc migration in the southernmost Andes

We report new high-precision U/Pb ages and geochemical data from the Chalten Plutonic Complex to better understand the link between magmatism and tectonics in Southern Patagonia. This small intrusion located in the back-arc region east of the Patagonian Batholith provides important insights on the role of arc migration and subduction erosion. The Chalten Plutonic Complex consists of a suite of calc-alkaline gabbroic to granitic rocks, which were emplaced over 530 kyr between 16.90 +/- 0.05 Ma and 16.37 +/- 0.02 Ma. A synthesis of age and geochemical data from other intrusions in Patagonia reveals (a) striking similarities between the Chalten Plutonic Complex and the Neogene intrusions of the batholith and differences to other back-arc intrusions such as Torres del Paine (b) a distinct E-W trend of calc-alkaline magmatic activity between 20 and 17 Ma. We propose that this trend reflects the eastward migration of the magmatic arc, and the consistent age pattern between the subduction segments north and south of the Chile triple junction suggests a causal relation with a period of fast subduction of the Farallon-Nazca plate during the Early Miocene. Previously proposed flat slab models are not consistent with the present location and morphology of the Southern Patagonian Batholith. We advocate, alternatively, that migration of the magmatic arc is caused by subduction erosion due to the increasing subduction velocities during the Early Miocene.

CR1Dmod: A Matlab program to model 1D complex resistivity effects in electrical and electromagnetic surveys

We have constructed a forward modelling code in Matlab, capable of handling several commonly used electrical and electromagnetic methods in a 1D environment. We review the implemented electromagnetic field equations for grounded wires, frequency and transient soundings and present new solutions in the case of a non-magnetic first layer. The CR1Dmod code evaluates the Hankel transforms occurring in the field equations using either the Fast Hankel Transform based on digital filter theory, or a numerical integration scheme applied between the zeros of the Bessel function. A graphical user interface allows easy construction of 1D models and control of the parameters. Modelling results are in agreement with other authors, but the time of computation is less efficient than other available codes. Nevertheless, the CR1Dmod routine handles complex resistivities and offers solutions based on the full EM-equations as well as the quasi-static approximation. Thus, modelling of effects based on changes in the magnetic permeability and the permittivity is also possible.

Il·lusionisme. Nova Construcció i Rehabilitació Integral de la Vil·la Urània com a complex d'equipaments

Award-winning

Gene transfer of the Ly-3 chain gene of the mouse CD8 molecular complex: co-transfer with the Ly-2 polypeptide gene results in detectable cell surface expression of the Ly-3 antigenic determinants.

The CD8 molecule is a glycoprotein expressed on a subset of mature T lymphocytes. It has been postulated to be a receptor for class I major histocompatibility complex molecules. In the mouse, CD8 is a heterodimer composed of Ly-2 and Ly-3 chains. We have isolated and analyzed cDNA and cosmid clones corresponding to the Ly-3 subunit. One of the isolated, cosmid clones was subsequently transfected, alone or in combination with the Ly-2 gene, into mouse Ltk- cells. Analysis of the Ly-2,3 molecules expressed at the surface of the double transfectants indicated that they are serologically and biochemically indistinguishable from their normal counterparts expressed on lymphoid cells. Ltk- cells transfected with the Ly-2 gene alone were shown to react with a subset of anti-CD8 monoclonal antibodies whereas Ly-3 transfectants did not stain with any of the anti-Ly-3 antibodies employed in this study. Since at least one of these antibodies (53-5.8) has been previously shown to recognize an epitope which is retained on the Ly-3 subunit after dissociation of the heterodimeric Ly-2,3 complex, these observations suggest that the expression of the Ly-2 polypeptide is required to permit the detectable cell surface expression of the antigenic determinants carried by the Ly-3 subunit.

Spatial prediction of monthly wind speeds in complex terrain with adaptive general regression neural networks

This paper presents the general regression neural networks (GRNN) as a nonlinear regression method for the interpolation of monthly wind speeds in complex Alpine orography. GRNN is trained using data coming from Swiss meteorological networks to learn the statistical relationship between topographic features and wind speed. The terrain convexity, slope and exposure are considered by extracting features from the digital elevation model at different spatial scales using specialised convolution filters. A database of gridded monthly wind speeds is then constructed by applying GRNN in prediction mode during the period 1968-2008. This study demonstrates that using topographic features as inputs in GRNN significantly reduces cross-validation errors with respect to low-dimensional models integrating only geographical coordinates and terrain height for the interpolation of wind speed. The spatial predictability of wind speed is found to be lower in summer than in winter due to more complex and weaker wind-topography relationships. The relevance of these relationships is studied using an adaptive version of the GRNN algorithm which allows to select the useful terrain features by eliminating the noisy ones. This research provides a framework for extending the low-dimensional interpolation models to high-dimensional spaces by integrating additional features accounting for the topographic conditions at multiple spatial scales. Copyright (c) 2012 Royal Meteorological Society.

The adaptor complex 2 directly interacts with the alpha 1b-adrenergic receptor and plays a role in receptor endocytosis.

Using the yeast two-hybrid system, we identified the mu 2 subunit of the clathrin adaptor complex 2 as a protein interacting with the C-tail of the alpha 1b-adrenergic receptor (AR). Direct association between the alpha 1b-AR and mu 2 was demonstrated using a solid phase overlay assay. The alpha 1b-AR/mu 2 interaction occurred inside the cells, as shown by the finding that the transfected alpha 1b-AR and the endogenous mu 2 could be coimmunoprecipitated from HEK-293 cell extracts. Mutational analysis of the alpha 1b-AR revealed that the binding site for mu 2 does not involve canonical YXX Phi or dileucine motifs but a stretch of eight arginines on the receptor C-tail. The binding domain of mu 2 for the receptor C-tail involves both its N terminus and the subdomain B of its C-terminal portion. The alpha 1b-AR specifically interacted with mu 2, but not with the mu 1, mu 3, or mu 4 subunits belonging to other AP complexes. The deletion of the mu 2 binding site in the C-tail markedly decreased agonist-induced receptor internalization as demonstrated by confocal microscopy as well as by the results of a surface receptor biotinylation assay. The direct association of the adaptor complex 2 with a G protein-coupled receptor has not been reported so far and might represent a common mechanism underlying clathrin-mediated receptor endocytosis.