Evolutionary trends in RuBisCO kinetics and their co‐evolution with CO2 concentrating mechanisms

RuBisCO‐catalyzed CO₂ fixation is the main source of organic carbon in the biosphere. This enzyme is present in all domains of life in different forms (III, II, and I) and its origin goes back to 3500 Mya, when the atmosphere was anoxygenic. However, the RuBisCO active site also catalyzes oxygenation of ribulose 1,5‐bisphosphate, therefore, the development of oxygenic photosynthesis and the subsequent oxygen‐rich atmosphere promoted the appearance of CO₂ concentrating mechanisms (CCMs) and/or the evolution of a more CO₂‐specific RuBisCO enzyme. The wide variability in RuBisCO kinetic traits of extant organisms reveals a history of adaptation to the prevailing CO₂/O₂ concentrations and the thermal environment throughout evolution. Notable differences in the kinetic parameters are found among the different forms of RuBisCO, but the differences are also associated with the presence and type of CCMs within each form, indicative of co‐evolution of RuBisCO and CCMs. Trade‐offs between RuBisCO kinetic traits vary among the RuBisCO forms and also among phylogenetic groups within the same form. These results suggest that different biochemical and structural constraints have operated on each type of RuBisCO during evolution, probably reflecting different environmental selective pressures. In a similar way, variations in carbon isotopic fractionation of the enzyme point to significant differences in its relationship to the CO₂ specificity among different RuBisCO forms. A deeper knowledge of the natural variability of RuBisCO catalytic traits and the chemical mechanism of RuBisCO carboxylation and oxygenation reactions raises the possibility of finding unrevealed landscapes in RuBisCO evolution.     

Angiotensin converting enzyme insertion/deletion polymorphism is associated with increased adiposity and blood pressure in obese children and adolescents

Background

The insertion/deletion polymorphism in the gene encoding the angiotensin-converting enzyme (ACE I/D) was associated with arterial hypertension and obesity in adults, but the data in children are scarce and yielded contrasting results. We assessed the impact of the ACE I/D on blood pressure and obesity related traits in a Brazilian cohort of obese children and adolescents.

Methods and results

ACE I/D was genotyped in 320 obese children and adolescents (64% of girls) aged 7–16 years, referred for a weight-loss program. We observed an association of the D-allele with blood pressure and with pre-hypertension/hypertension in boys (odds ratio 2.44, 95% C.I. 1.34–4.68, p = 0.005 for a codominant model). The D-allele, insulin resistance and body fat mass had independent and additive effects and explained 14% of the variance of pre-hypertension/hypertension. The BMI, waist circumference, and body fat mass were significantly higher in DD/ID boys than in II boys (p < 0.005). Allelic associations with obesity related traits were independent of the association with blood pressure. No genotype associations were observed in girls.

Conclusions

The D-allele of the ACE I/D polymorphism was associated with arterial hypertension and with obesity related traits in boys, but not in girls, in a cohort of obese children and adolescents. These associations were independent of each other, as well as of the effects of other confounding traits such as insulin secretion, insulin sensitivity and glucose tolerance. Our results are in agreement with experimental evidences suggesting that the renin–angiotensin system plays a role in the regulation of visceral adipose tissue accumulation.     

Comparison of Phylogeny,Venom Composition and Neutralization by Antivenom in Diverse Species of Bothrops Complex

In Latin America, Bothrops snakes account for most snake bites in humans, and the recommended treatment is administration of multispecific Bothrops antivenom (SAB – soro antibotrópico). However, Bothrops snakes are very diverse with regard to their venom composition, which raises the issue of which venoms should be used as immunizing antigens for the production of pan-specific Bothrops antivenoms. In this study, we simultaneously compared the composition and reactivity with SAB of venoms collected from six species of snakes, distributed in pairs from three distinct phylogenetic clades: Bothrops, Bothropoides and Rhinocerophis. We also evaluated the neutralization of Bothrops atrox venom, which is the species responsible for most snake bites in the Amazon region, but not included in the immunization antigen mixture used to produce SAB. Using mass spectrometric and chromatographic approaches, we observed a lack of similarity in protein composition between the venoms from closely related snakes and a high similarity between the venoms of phylogenetically more distant snakes, suggesting little connection between taxonomic position and venom composition. P-III snake venom metalloproteinases (SVMPs) are the most antigenic toxins in the venoms of snakes from the Bothrops complex, whereas class P-I SVMPs, snake venom serine proteinases and phospholipases A₂ reacted with antibodies in lower levels. Low molecular size toxins, such as disintegrins and bradykinin-potentiating peptides, were poorly antigenic. Toxins from the same protein family showed antigenic cross-reactivity among venoms from different species; SAB was efficient in neutralizing the B. atrox venom major toxins. Thus, we suggest that it is possible to obtain pan-specific effective antivenoms for Bothrops envenomations through immunization with venoms from only a few species of snakes, if these venoms contain protein classes that are representative of all species to which the antivenom is targeted.     

Trophic level modulates carabid beetle responses to habitat and landscape structure: a pan‐European study

1. Anthropogenic pressures have produced heterogeneous landscapes expected to influence diversity differently across trophic levels and spatial scales. 2. We tested how activity density and species richness of carabid trophic groups responded to local habitat and landscape structure (forest percentage cover and habitat richness) in 48 landscape parcels (1 km²) across eight European countries. 3. Local habitat affected activity density, but not species richness, of both trophic groups. Activity densities were greater in rotational cropping compared with other habitats; phytophage densities were also greater in grassland than forest habitats. 4. Controlling for country and habitat effects, we found general trophic group responses to landscape structure. Activity densities of phytophages were positively correlated, and zoophages uncorrelated, with increasing habitat richness. This differential functional group response to landscape structure was consistent across Europe, indicated by a lack of a country × habitat richness interaction. Species richness was unaffected by landscape structure. 5. Phytophage sensitivity to landscape structure may arise from relative dependency on seed from ruderal plants. This trophic adaptation, rare in Carabidae, leads to lower phytophage numbers, increasing vulnerability to demographic and stochastic processes that the greater abundance, species richness, and broader diet of the zoophage group may insure against.     

Ecological and environmental footprint of 50 years of agricultural expansion in Argentina

Agriculture expanded during the last 50 years from the Pampas to NW Argentina at the expense of natural forests and rangelands. In parallel, productivity was boosted through the increasing application of external inputs, modern technology and management practices. This study evaluated the impact of agricultural expansion between 1960 and 2005 by assessing the implications of land use, technology and management changes on (i) carbon (C), nitrogen (N) and phosphorous (P) stocks in soil and biomass, (ii) energy, C, N, P and water fluxes and (iii) water pollution, soil erosion, habitat intervention and greenhouse gas (GHG) emissions (impacts). Based on different data sources, these issues were assessed over～1.5 million km² (63% of Argentina), involving 399 political districts during three representative periods: 1956–1960, 1986–1990 and 2001–2005. The ecological and environmental performance of 1197 farming system types was evaluated through the AgroEcoIndex model, which quantified the stocks, fluxes and impacts mentioned above. Cultivation of natural ecosystems and farming intensification caused a noticeable increase of productivity, a strengthening of energy flux, an opening of matter cycles (C, N, P) and a negative impact on habitats and GHGs emission. However, due to the improved tillage practices and the application of less aggressive pesticides, erosion and pollution risk are today lower than those of the mid‐20th century. The consistency of some assumptions and results were checked through uncertainty analysis. Comparing our results with international figures, some impacts (e.g. soil erosion, nutrient balance, energy use) were less significant than those recorded in intensive‐farming countries like China, Japan, New Zealand, USA, or those of Western Europe, showing that farmers in Argentina developed the capacity to produce under relatively low‐input/low‐impact schemes during the last decades. [Correction added after online publication 4 October 2010: In the first sentence of the Abstract, NE was corrected to NW.]     

Surface fitting of 2D diffusion-edited 1H NMR spectroscopy data for the characterisation of human plasma lipoproteins

Determining the concentration and size of lipoprotein complexes is very important due to their role in cardiovascular diseases and metabolic disorders. However, standard methods for lipoprotein fractionation are manual and time consuming and cannot be used as standard diagnostic tools. Because different subclasses of lipoproteins have different radii and, hence, different diffusion velocities, we propose a fast and reliable method that uses 2D diffusion-edited ¹H NMR spectroscopy to acquire a set of 2D spectra of plasma samples, followed by a surface fitting algorithm based on Lorentzian functions to estimate the sizes and the relative proportions of different lipoprotein subclasses. We were able to demonstrate that the derived sizes and positions related to the Lorentzian functions follow an exponential relationship for normolipidaemic and dislipaemic samples with coefficients of determination (r ²) of 0.85 and 0.81, respectively. Moreover, we found a linear relationship between the width and size of the Lorentzian functions for normolipidaemic samples (r ² = 0.88) while for dislipaemic samples this relation was nonlinear (r ² = 0.62). Dividing our samples set into four different lipoprotein profiles (normal lipid values, low HDL/LDL ratio, high triglycerides values and both risk factors) and using principal component analysis (PCA) followed by multivariate analysis of variance (MANOVA), our method was able to statistically discriminate between those groups, with p-values of 0.0016, 0.0006, <1e⁻⁴ and 0.0035, respectively. These parameters are characteristic and indicative of different lipoprotein profiles and can be used to distinguish between normolipidaemic, hypercholesterolaemic, hypertriglyceridaemic and chylomicronaemic profiles.     

Probing the growth dynamics of Neurospora crassa with microfluidic structures

Despite occupying physically and chemically heterogeneous natural environments, the growth dynamics of filamentous fungi is typically studied on the surface of homogeneous laboratory media. Fungal exploration and exploitation of complex natural environments requires optimal survival and growth strategies at the colony, hyphal, and intra hyphal level, with hyphal space-searching strategies playing a central role. We describe a new methodology for the characterisation and analysis of hyphal space-searching strategies, which uses purposefully designed three-dimensional microfluidics structures mimicking some of the characteristics of natural environments of the fungi. We also demonstrate this new methodology by running a comparative examination of two Neurospora crassa strains, i.e., the wild type of N. crassa -- a commonly used model organism for the study of filamentous fungi -- and the N. crassa ro-1 mutant strain -- which is deficient in hyphal and mycelial growth. Continuous live imaging showed that both strains responded actively to the geometrically confined microstructured environments without any detectable temporal delay or spatial adjustment. While both strains navigated the test structures exhibiting similar geometry-induced space-searching mechanisms, they presented fundamentally different growth patterns that could not be observed on geometrically unconfined, flat agar surfaces.     

Conformational spread in the flagellar motor switch: a model study

The reliable response to weak biological signals requires that they be amplified with fidelity. In E. coli, the flagellar motors that control swimming can switch direction in response to very small changes in the concentration of the signaling protein CheY-P, but how this works is not well understood. A recently proposed allosteric model based on cooperative conformational spread in a ring of identical protomers seems promising as it is able to qualitatively reproduce switching, locked state behavior and Hill coefficient values measured for the rotary motor. In this paper we undertook a comprehensive simulation study to analyze the behavior of this model in detail and made predictions on three experimentally observable quantities: switch time distribution, locked state interval distribution, Hill coefficient of the switch response. We parameterized the model using experimental measurements, finding excellent agreement with published data on motor behavior. Analysis of the simulated switching dynamics revealed a mechanism for chemotactic ultrasensitivity, in which cooperativity is indispensable for realizing both coherent switching and effective amplification. These results showed how cells can combine elements of analog and digital control to produce switches that are simultaneously sensitive and reliable.     

CD4+ lipid bilayers. A model for human immunodeficiency virus type 1 coat protein binding.

gp120, the coat glycoprotein of the human immunodeficiency virus type 1 (HIV1) binds to a molecule on the surface of a class of T-lymphocytes, CD4, which is also the receptor for major histocompatibility complex class II (MHCII). To study the events that follow the interaction of gp120 with CD4, we have incorporated CD4 into lipid bilayers and recorded the electrical changes which occur after the addition of gp120. Interaction of gp120 to CD4-containing bilayers induces multistate ion-permeable channels with a maximum conductance of 380-400 picosiemens. When CD4+ bilayers were preexposed to either MHCII or to OKT4A antibody, no channels were formed after the addition of gp120. These results indicate that CD(4+)-containing bilayers bind gp120, MHCII, and OKT4A, that binding of gp120 produces ion-permeable channels, and that CD4+ bilayers can be used to assay for gp120 in the solution bathing the bilayer.