A high-density immunoblotting methodology for quantification of total protein levels and phosphorylation modifications

The components of many signaling pathways have been identified and there is now a need to conduct quantitative data-rich temporal experiments for systems biology and modeling approaches to better understand pathway dynamics and regulation. Here we present a modified Western blotting method that allows the rapid and reproducible quantification and analysis of hundreds of data points per day on proteins and their phosphorylation state at individual sites. The approach is of particular use where samples show a high degree of sample-to-sample variability such as primary cells from multiple donors. We present a case study on the analysis of >800 phosphorylation data points from three phosphorylation sites in three signaling proteins over multiple time points from platelets isolated from ten donors, demonstrating the technique's potential to determine kinetic and regulatory information from limited cell numbers and to investigate signaling variation within a population. We envisage the approach being of use in the analysis of many cellular processes such as signaling pathway dynamics to identify regulatory feedback loops and the investigation of potential drug/inhibitor responses, using primary cells and tissues, to generate information about how a cell's physiological state changes over time.

Intake of total and subgroups of fat minimally affect the associations between selected single nucleotide polymorphisms in the PPARγ pathway and changes in anthropometry among European adults from cohorts of the DiOGenes study

BACKGROUND: Although the peroxisome proliferator-activated receptor γ (PPARγ) pathway is central in adipogenesis, it remains unknown whether it influences change in body weight (BW) and whether dietary fat has a modifying effect on the association. OBJECTIVES: We examined whether 27 single nucleotide polymorphisms (SNPs) within 4 genes in the PPARγ pathway are associated with the OR of being a BW gainer or with annual changes in anthropometry and whether intake of total fat, monounsaturated fat, polyunsaturated fat, or saturated fat has a modifying effect on these associations. METHODS: A case-noncase study included 11,048 men and women from cohorts in the European Diet, Obesity and Genes study; 5552 were cases, defined as individuals with the greatest BW gain during follow-up, and 6548 were randomly selected, including 5496 noncases. We selected 4 genes [CCAAT/enhancer binding protein β (CEBPB), phosphoenolpyruvate carboxykinase 2, PPARγ gene (PPARG), and sterol regulatory element binding transcription factor 1] according to evidence about biologic plausibility for interactions with dietary fat in weight regulation. Diet was assessed at baseline, and anthropometry was followed for 7 y. RESULTS: The ORs for being a BW gainer for the 27 genetic variants ranged from 0.87 (95% CI: 0.79, 1.03) to 1.12 (95% CI: 0.96, 1.22) per additional minor allele. Uncorrected, CEBPB rs4253449 had a significant interaction with the intake of total fat and subgroups of fat. The OR for being a BW gainer for each additional rs4253449 minor allele per 100 kcal higher total fat intake was 1.07 (95% CI: 1.02, 1.12; P = 0.008), and similar associations were found for subgroups of fat. CONCLUSIONS: Among European men and women, the influence of dietary fat on associations between SNPs in the PPARγ pathway and anthropometry is likely to be absent or marginal. The observed interaction between rs4253449 and dietary fat needs confirmation.

Dietary predictors of serum total carotene in low-income women living in Sao Paulo, south-east Brazil

Objective Dietary intake and nutritional status of antioxidant vitamins have been reported to protect against some cancers The objective of the present study was to assess the correlations between serum levels of carotenoids (including beta-, alpha- and gamma-carotene), lycopene, retinol, alpha- and gamma-tocopherols, and dietary intakes estimated by an FFQ, among low-income women in the Brazilian Investigation into Nutrition and Cervical Cancer Prevention (BRINCA) study. Design Cross-sectional study of data for 918 women aged 21-65 years participating in the BRINCA study in Sao Paulo city. Multiple linear regression models were used with serum nutrient levels as the dependent variable and dietary intake levels as the independent variable, adjusted for confounding factors. Results In energy-adjusted analyses, the intakes of dark green and deep yellow vegetables and fruits (partial R(2) = 4.8%), total fruits and juices (partial R(2) = 1.8%), vegetables and fruits (partial R(2) = 1.8%), carrots (partial R(2) = 1.4%) and citrus fruits and juices only (partial R(2) = 0.8%) were positively correlated only with serum total carotene levels, after adjusting for serum total cholesterol concentration, age, hospital attended, smoking status. BMI and presence of cervical lesions Multiple-adjusted serum levels of carotenoids were positively correlated with intake quartiles of dark green and deep yellow vegetables and fruits and total fruits and juices independent of smoking status. Conclusions The intake of specific fruits and vegetables was an independent predictor of serum total carotene levels in low-income women living in Sao Paulo

Effects of Mate Tea (Ilex paraguariensis) Ingestion on mRNA Expression of Antioxidant Enzymes, Lipid Peroxidation, and Total Antioxidant Status in Healthy Young Women

The antioxidant activity of mate tea, the roasted product derived from yerba mate (Ilex paraguarienis), was observed in vitro and in animal models, but studies in humans are lacking. The aim of this study was to investigate the effects of mate tea supplementation on plasma susceptibility to oxidation and on antioxidant enzyme gene expression in healthy nonsmoking women, after acute or prolonged ingestion. We evaluated plasma total antioxidant status (TAS), the kinetics of diene conjugate generation, and thiobarbituric acid reactive substance (TBARS) contents in plasma, as well as mRNA levels of antioxidant gluthatione peroxidase (GPx), superoxide dismutase (SOD), and catalase (CAT). After the supplementation period with mate tea, lipid peroxidation was acutely lowered, an effect that was maintained after prolonged administration. Total antioxidant status and the level of antioxidant enzyme gene expression were also demonstrated after prolonged consumption. These results suggest that regular consumption of mate tea may increase antioxidant defense of the body by multiple mechanisms.

Downwelling solar irradiance in the biomass burning region of the southern Amazon: Dependence on aerosol intensive optical properties and role of water vapor

The sensitivity of solar irradiance at the surface to the variability of aerosol intensive optical properties is investigated for a site (Alta Floresta) in the southern portion of the Amazon basin using detailed comparisons between measured and modeled irradiances. Apart from aerosol intensive optical properties, specifically single scattering albedo (omega(o lambda)) and asymmetry parameter (g(lambda)), which were assumed constant, all other relevant input to the model were prescribed based on observation. For clean conditions, the differences between observed and modeled irradiances were consistent with instrumental uncertainty. For polluted conditions, the agreement was significantly worse, with a root mean square difference three times larger (23.5 Wm(-2)). Analysis revealed a noteworthy correlation between the irradiance differences (observed minus modeled) and the column water vapor (CWV) for polluted conditions. Positive differences occurred mostly in wet conditions, while the differences became more negative as the atmosphere dried. To explore the hypothesis that the irradiance differences might be linked to the modulation of omega(o lambda) and g(lambda) by humidity, AERONET retrievals of aerosol properties and CWV over the same site were analyzed. The results highlight the potential role of humidity in modifying omega(o lambda) and g(lambda) and suggest that to explain the relationship seen between irradiances differences via aerosols properties the focus has to be on humidity-dependent processes that affect particles chemical composition. Undoubtedly, there is a need to better understand the role of humidity in modifying the properties of smoke aerosols in the southern portion of the Amazon basin.

Analysis of total visual and CCD V-broadband observations of Comet C/1995 O1 (Hale-Bopp): 1995-2001

We developed a general method for determination of water production rates from groundbased visual observations and applied it to Comet Hale-Bopp. Our main objective is to extend the method to include total visual magnitude observations obtained with CCD detector and V filter in the analysis of total visual magnitudes. We compare the CCD V-broadband careful observations of Liller [Liller, W. Pre-perihelion CCD photometry of Comet 1995 01 (Hale-Bopp). Planet. Space Sci. 45, 1505-1513, 1997; Liller, W. CCD photometry of Comet C/1995 O1 (Hale-Bopp): 1995-2000. Int. Comet Quart. 23(3), 93-97, 2001] with the total visual magnitude observations from experienced international observers found in the International Comet Quarterly (ICQ) archive. A data set of similar to 400 CCD observations covering about the same 6 years time span of the similar to 12,000 ICQ selected total visual magnitude observations were used in the analysis. A least-square method applied to the water production rates, yields power laws as a function of the heliocentric distances for the pre- and post-perihelion phases. The average dimension of the nucleus as well as its effective active area is determined and compared with values published in the literature. (C) 2009 COSPAR. Published by Elsevier Ltd. All rights reserved.

Life-history, thallus ontogeny, and the effects of temperature, irradiance and salinity on growth of the edible green seaweed Gayralia spp. (Chlorophyta) from Southern Brazil

Gayralia K.L. Vinogr. is a monostromatic green alga of commercial importance in the southern Brazil, and its cultivation is being considered. This paper reports some basic aspects of the biology of this poorly known genus. Two populations of Gayralia spp., from outer and inner sectors of Paranagua Bay, showed an asexual life history with a distinct pattern of thallus ontogeny. In one population (Gayralia sp. 1), zooids developed an expanded monostromatic blade directly, while in the other (Gayralia sp. 2) zooids produced an intermediate saccate stage, before giving rise to a monostromatic blade. Thalli of the two species differ in size and in cell diameter. The effects of temperature (16-30 degrees C), irradiance (50-100 mu mol photons m(-2) s(-1)), and salinity (5-40 psu) on the growth of both populations were assessed. Plantlets of Gayralia sp. 1 from in vitro cultures showed a broader tolerance to all salinity and irradiance levels tested, with the highest growth rate (GR; mean 17% day-1) at 21.5 degrees C and 100 mu mol photons m(-2) s(-1). Plantlets of Gayralia sp. 1 collected during the winter in the field showed higher GR, ranging from 5% day(-1) to 7.5% day(-1) in salinities from 20 to 40 psu, and 2.0% day(-1) and 4.3% day(-1) for plantlets collected during the summer. Gayralia sp. 2 from the field showed highest GR at salinity of 15 psu. These results suggest distinct physiological responses of the two species, in accordance with their distribution: Gayralia sp. 2 is limited to the inner areas of the estuary, while Gayralia sp. 1 grows in outer areas, where salinity values are higher than 20 psu. These data indicate that Gayralia sp. 1 has a higher potential for aquaculture than Gayralia sp. 2 due to its larger thalli, higher GR, and wider tolerance to environmental variations.

Phylogeny of the Neotropical genus Acestrorhynchus (Ostariophysi: Characiformes) based on nuclear and mitochondrial gene sequences and morphology: A total evidence approach

Acestrorhynchus is the sole genus of the family Acestrorhynchidae which includes 14 species currently recognized as valid. Species of Acestrorhynchus comprise small-to-medium sized piscivorous fishes and have been traditionally grouped on the basis of well-defined color patterns. A recent phylogeny, based on morphological characters, could not resolve the phylogenetic affinities of A. heterolepis and the relationships among the species of the clade formed by A. abbreviatus, A. altus, A. falcatus, A. lacustris, and A. pantaneiro. The simultaneous analysis of two mitochondrial genes (16S and ATP synthase subunits 6 and 8) and one nuclear intron (S7) was able to resolve the latter clade, but the position of A. heterolepis remained unresolved. The combination of the molecular and morphological data sets in a total evidence analysis resulted in a well-resolved hypothesis regarding the phylogenetic relationships of Acestrorhynchus species. (C) 2009 Elsevier Inc. All rights reserved.

Taxon surrogates among Amazonian mammals: Can total species richness be predicted by single orders?

Limited financial sources and the difficulty in performing complete surveys, allied to the speed of habitat fragmentation and the urgent necessity in select conservation areas, create the necessity of using some methodologies which bypass these problems. One possibility is the use of surrogate taxa that might be used as indicator of others groups richness and even total richness of an area. We investigated if the use of surrogate taxon is useful among seven mammal orders in Amazon. We tested through Pearson`s correlation (Bonferroni`s adjusted) if (1) there was a correlation between richness of total species and some order; (2) there was a significant pair wise correlation between species richness of each order; and (3) the combination of two orders would give better results as a surrogate for the total richness. The correlations found, in general, were positive. It means that the increase in the richness of an order was followed by its increase in another order, as well as in the total species richness. Only Didelphimorphia was significantly correlated with the total species richness. In the pair wise analyses only one assembly, Primates and Artiodactyla, was significantly correlated with total richness. Since indicator species are more effective within taxonomic groups (life-history characteristics are likely to be more different among than within major taxonomic groups), we suggest that an indicator group might be chosen for each one. In this case, for mammals from Amazon, it would be Didelphimorphia. (C) 2008 Elsevier Ltd. All rights reserved.

Total absolute horospherical curvature of submanifolds in hyperbolic space

We study the horospherical geometry of submanifolds in hyperbolic space. The main result is a formula for the total absolute horospherical curvature of M, which implies, for the horospherical geometry, the analogues of classical inequalities of the Euclidean Geometry. We prove the horospherical Chern-Lashof inequality for surfaces in 3-space and the horospherical Fenchel and Fary-Milnor`s theorems.

GLUON SATURATION AND THE TOTAL PROTON-AIR CROSS SECTION

In this work we propose a simple model for the total proton-air cross section, which is an improvement of the minijet model with the inclusion of a window in the p(T)-spectrum associated to the saturation physics. Our approach introduces a natural cutoff for the perturbative calculations which modifies the energy behavior of this component. The saturated component is calculated with a dipole model. The results are compared with experimental cross sections measured in cosmic ray experiments.

Breakup effects in fusion and total reaction cross sections of weakly bound systems

We use a new technique to investigate the systematic behavior of near barrier complete fusion, total fusion and total reaction cross sections of weakly bound systems. A dimensionless fusion excitation function is used as a benchmark to which renormalized fusion data are compared and dynamic breakup effects can be disentangled from static effects. The same reduction procedure is used to study the effect of the direct reaction mechanisms on the total reaction cross section.

Universal trend for heavy-ion total reaction cross-sections at energies above the Coulomb barrier

Heavy-ion total reaction cross-section measurements for more than 1100 reaction cases covering 61 target nuclei in the range (6)Li-(238)U and 158 projectile nuclei from (2)H to (84)Kr (mostly exotic ones) have been analyzed in a systematic way by using an empirical, three-parameter formula that is applicable to the cases of projectile kinetic energies above the Coulomb barrier. The analysis has shown that the average total nuclear binding energy per nucleon of the interacting nuclei and their radii are the chief quantities that describe the cross-section patterns. A great amount of cross-section data (87%) has been quite satisfactorily reproduced by the proposed formula; therefore, the total reaction cross-section predictions for new, not yet experimentally investigated reaction cases can be obtained within 25% (or much less) uncertainty.