The best of both worlds: Phylogenetic eigenvector regression and mapping

Eigenfunction analyses have been widely used to model patterns of autocorrelation in time, space and phylogeny. In a phylogenetic context, Diniz-Filho et al. (1998) proposed what they called Phylogenetic Eigenvector Regression (PVR), in which pairwise phylogenetic distances among species are submitted to a Principal Coordinate Analysis, and eigenvectors are then used as explanatory variables in regression, correlation or ANOVAs. More recently, a new approach called Phylogenetic Eigenvector Mapping (PEM) was proposed, with the main advantage of explicitly incorporating a model-based warping in phylogenetic distance in which an Ornstein-Uhlenbeck (O-U) process is fitted to data before eigenvector extraction. Here we compared PVR and PEM in respect to estimated phylogenetic signal, correlated evolution under alternative evolutionary models and phylogenetic imputation, using simulated data. Despite similarity between the two approaches, PEM has a slightly higher prediction ability and is more general than the original PVR. Even so, in a conceptual sense, PEM may provide a technique in the best of both worlds, combining the flexibility of data-driven and empirical eigenfunction analyses and the sounding insights provided by evolutionary models well known in comparative analyses.     

Effects of density and predation risk on leaf litter processing by Phylloicus sp.

The allochthonous detritus that accumulates in the substrate of streams is used by aquatic invertebrate shredders for shelter and food. Shredders are considered rare in tropical systems, and little information is available about the role of density effects and predation risk (associated with the perception of predators by prey) in relationship to the resources used by these organisms. The aim of this study was to examine experimentally the effects of increased predation risk and of the density of Phylloicus sp. (i.e. of two types of biological relationships) on the processing of the leaf litter of Nectandra megapotamica (Spreng.) Mez. Phylloicus sp. can use leaf litter for case building and as a food resource. The density effect was measured using four treatments that differed only in the number of individuals (one, two, three or four). A second experiment with five treatments was performed to test the risk of non‐lethal predation on detritus consumption (shelter and food) by Phylloicus sp. (T1: Caddisfly; T2: Mayfly; T3: Astyanax sp./fish; T4: Damselflies; T5: Stonefly). A single Phylloicus and one other organism (a potential predator blocked with 0.5 mm fine mesh) were placed in each tank (0.002 m³ volume). We observed a negative effect of density on per capita litter consumption (experiment 1). The low density of Phylloicus may be a natural factor that decreases intraspecific competition. In the presence of fish, Phylloicus showed the lowest amount of litter processing observed in the experiment, indicating top‐down control (experiment 2). In treatments that involved the presence of invertebrates (non‐predatory and predatory), Phylloicus showed the highest amount and an intermediate amount of leaf litter processing, respectively (experiment 2). This observation also suggests that the predation effect is more probable for specific predator–prey pairs. Population density and predation risk in Phylloicus may be important factors controlling leaf litter processing.     

HMB supplementation: clinical and athletic performance-related effects and mechanisms of action

Amino acids such as leucine and its metabolite α-ketoisocaproate (KIC), are returning to be the focus of studies, mainly because of their anti-catabolic properties, through inhibition of muscle proteolysis and enhancement of protein synthesis. It is clear that these effects may counteract catabolic conditions, as well as enhance skeletal muscle mass and strength in athletes. Moreover, beta-hydroxy-beta-methylbutyrate (HMB) has been shown to produce an important effect in reducing muscle damage induced by mechanical stimuli of skeletal muscle. This review aims to describe the general scientific evidence of KIC and HMB supplementation clinical relevance, as well as their effects (e.g., increases in skeletal muscle mass and/or strength), associated with resistance training or other sports. Moreover, the possible mechanisms of cell signaling regulation leading to increases and/or sparing (during catabolic conditions) of skeletal muscle mass are discussed in detail based on the recent literature.     

Use of experimental design to investigate biodiesel production by multiple-stage Ultra-Shear reactor

This work presents biodiesel production from soybean oil and bioethanol by multiple-stage Ultra-Shear reactor (USR). The experiments were carried out in the following conditions: reaction time from 6 to 12 min; catalyst concentration from 0.5% to 1.5% by weight of soybean oil; ethanol: soybean oil molar ratio from 6:1 to 10:1. The experimental design was used to investigate the influence of process variables on the conversion in biodiesel. The best ethyl ester conversion obtained was 99.26 wt.%, with ethanol:soybean oil molar ratio of 6:1, catalyst concentration of 1.35% and with 12 min of reaction time.     

Production and characterization of a collagenolytic serine proteinase by <Emphasis Type="Italic">Penicillium aurantiogriseum</Emphasis> URM 4622: A factorial study

A 2⁴ full factorial design was used to identify the main effects and interactions of the initial medium pH, soybean flour concentration, temperature and orbital agitation speed on extracellular collagenase production by Penicillium aurantiogriseum URM4622. The most significant variables for collagenase production were soybean flour concentration and initial medium pH that had positive main effects, and temperature that had a negative one. Protein concentration in soybean flour revealed to be a significant factor for the production of a collagenase serine proteinase. The most favorable production conditions were found to be 0.75% soybean flour, pH 8.0, 200 rpm, and 28°C, which led to a collagenase activity of 164 U. The enzyme showed an optimum activity at 37°C and pH 9.0, was stable over wide ranges of pH and temperature (6.0 ∼ 10.0 and 25 ∼ 45°C, respectively) and was strongly inhibited by 10 mM phenylmethylsulphonylfluoride. The firstorder rate constants for collagenase inactivation in the crude extract, calculated from semi-log plots of the residual activity versus time, were used in Arrhenius and Eyring plots to estimate the main thermodynamic parameters of thermoinactivation (E* _d = 107.4 kJ/mol and ΔH* _d = 104.7 kJ/mol). The enzyme is probably an extracellular neutral serine collagenase effective on azocoll, gelatin and collagen decomposition.     

Assessment of the genetic risks of a metallic alloy used in medical implants

The use of artificial implants provides a palliative or permanent solution for individuals who have lost some bodily function through disease, an accident or natural wear. This functional loss can be compensated for by the use of medical devices produced from special biomaterials. Titanium alloy (Ti-6Al-4V) is a well-established primary metallic biomaterial for orthopedic implants, but the toxicity of the chemical components of this alloy has become an issue of concern. In this work, we used the MTT assay and micronucleus assay to examine the cytotoxicity and genotoxicity, respectively, of an extract obtained from this alloy. The MTT assay indicated that the mitochondrial activity and cell viability of CHO-K1 cells were unaffected by exposure to the extract. However, the micronucleus assay revealed DNA damage and an increase in micronucleus frequency at all of the concentrations tested. These results show that ions released from Ti-6Al-4V alloy can cause DNA and nuclear damage and reinforce the importance of assessing the safety of metallic medical devices constructed from biomaterials.     

Simulation of integrated first and second generation bioethanol production from sugarcane: comparison between different biomass pretreatment methods

Sugarcane bagasse is used as a fuel in conventional bioethanol production, providing heat and power for the plant; therefore, the amount of surplus bagasse available for use as raw material for second generation bioethanol production is related to the energy consumption of the bioethanol production process. Pentoses and lignin, byproducts of the second generation bioethanol production process, may be used as fuels, increasing the amount of surplus bagasse. In this work, simulations of the integrated bioethanol production process from sugarcane, surplus bagasse and trash were carried out. Selected pre-treatment methods followed, or not, by a delignification step were evaluated. The amount of lignocellulosic materials available for hydrolysis in each configuration was calculated assuming that 50% of sugarcane trash is recovered from the field. An economic risk analysis was carried out; the best results for the integrated first and second generation ethanol production process were obtained for steam explosion pretreatment, high solids loading for hydrolysis and 24–48 h hydrolysis. The second generation ethanol production process must be improved (e.g., decreasing required investment, improving yields and developing pentose fermentation to ethanol) in order for the integrated process to be more economically competitive.     

Sugarcane (Saccharum X officinarum): A Reference Study for the Regulation of Genetically Modified Cultivars in Brazil

Global interest in sugarcane has increased significantly in recent years due to its economic impact on sustainable energy production. Sugarcane breeding and better agronomic practices have contributed to a huge increase in sugarcane yield in the last 30?years. Additional increases in sugarcane yield are expected to result from the use of biotechnology tools in the near future. Genetically modified (GM) sugarcane that incorporates genes to increase resistance to biotic and abiotic stresses could play a major role in achieving this goal. However, to bring GM sugarcane to the market, it is necessary to follow a regulatory process that will evaluate the environmental and health impacts of this crop. The regulatory review process is usually accomplished through a comparison of the biology and composition of the GM cultivar and a non-GM counterpart. This review intends to provide information on non-GM sugarcane biology, genetics, breeding, agronomic management, processing, products and byproducts, as well as the current technologies used to develop GM sugarcane, with the aim of assisting regulators in the decision-making process regarding the commercial release of GM sugarcane cultivars.