Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions

Spatial organisation of proteins according to their function plays an important role in the specificity of their molecular interactions. Emerging proteomics methods seek to assign proteins to sub-cellular locations by partial separation of organelles and computational analysis of protein abundance distributions among partially separated fractions. Such methods permit simultaneous analysis of unpurified organelles and promise proteome-wide localisation in scenarios wherein perturbation may prompt dynamic re-distribution. Resolving organelles that display similar behavior during a protocol designed to provide partial enrichment represents a possible shortcoming. We employ the Localisation of Organelle Proteins by Isotope Tagging (LOPIT) organelle proteomics platform to demonstrate that combining information from distinct separations of the same material can improve organelle resolution and assignment of proteins to sub-cellular locations. Two previously published experiments, whose distinct gradients are alone unable to fully resolve six known protein-organelle groupings, are subjected to a rigorous analysis to assess protein-organelle association via a contemporary pattern recognition algorithm. Upon straightforward combination of single-gradient data, we observe significant improvement in protein-organelle association via both a non-linear support vector machine algorithm and partial least-squares discriminant analysis. The outcome yields suggestions for further improvements to present organelle proteomics platforms, and a robust analytical methodology via which to associate proteins with sub-cellular organelles.

Effects of sand burial on biomass, chlorophyll fluorescence and extracellular polysaccharides of man-made cyanobacterial crusts under experimental conditions

Soil cyanobacterial crusts occur throughout the world, especially in the semiarid and arid regions. It always encounters sand burial, which is an important feature of mobile sand dunes. A greenhouse 41 study was conducted to determine the effects of sand burial on biomass, chlorophyll fluorescence and extracellular polysaccharides of man-made cyanobacterial crusts in six periods of time (0, 5, 10, 15, 20 and 30 d after burying) and at five depths (0, 0.2, 0.5, 1 and 2cm). The results indicated that with the increase of the burial time and burial depth extracellular polysaccharides content and Fv/Fm decreased correspondingly and there were no significant differences between 20 and 30 burial days under different burial depths. The degradation of chlorophyll a content appeared only at 20 and 30 burial days and there was also no significant difference between them under different burial depths. It was also observed a simultaneous decrease of the values of the Fv/Fm and the content of extracellular polysaccharides happened in the crusted cyanobacterium Microcoleus vaginatus Gom. It may suggest that there exists a relationship between extracellular polysaccharides and recovery of the activity of photosystem II (PS II) after rehydration.

Changing planar thin film growth into self-assembled island formation by adjusting experimental conditions

Illustrated in this paper are two examples of altering planar growth into self-assembled island formation by adapting experimental conditions. Partial oxidation, undersaturated solution and high temperature change Frank-Van der Merwe (FM) growth of Al0.3Ga0.7As in liquid phase epitaxy (LPE) into isolated island deposition. Low growth speed, high temperature and in situ annealing in molecular beam epitaxy (MBE) cause the origination of InAs/GaAs quantum dots (QDs) to happen while the film is still below critical thickness in Stranski-Krastanow (SK) mode. Sample morphologies are characterized by scanning electron microscopy (SEM) or atomic force microscopy (AFM). It is suggested that such achievements are of value not only to fundamental researches but also to spheres of device applications as well. (c) 2004 Elsevier B.V. All rights reserved.

Probing The effects of Experimental Conditions on the Character of Drug-Polymer Phase Diagrams Constructed Using Flory-Huggins Theory

Purpose: Amorphous drug-polymer solid dispersions have been found to result in improved drug dissolution rates when compared to their crystalline counterparts. However, when the drug exists in the amorphous form it will possess a higher Gibb’s free energy than its associated crystalline state and can recrystallize. Drug-polymer phase diagrams constructed through the application of the Flory Huggins (F-H) theory contain a wealth of information regarding thermodynamic and kinetic stability of the amorphous drug-polymer system. This study was aimed to evaluate the effects of various experimental conditions on the solubility and miscibility detections of drug-polymer binary system. Methods: Felodipine (FD)-Polyvinylpyrrolidone (PVP) K15 (PVPK15) and FD-Polyvinylpyrrolidone/vinyl acetate (PVP/VA64) were the selected systems for this research. Physical mixtures with different drug loadings were mixed and ball milled. These samples were then processed using Differential Scanning Calorimetry (DSC) and measurements of melting point (Tend) and glass transition (Tg) were detected using heating rates of 0.5, 1.0 and 5.0°C/min. Results: The melting point depression data was then used to calculate the F-H interaction parameter (χ) and extrapolated to lower temperatures to complete the liquid–solid transition curves. The theoretical binodal and spinodal curves were also constructed which were used to identify regions within the phase diagram. The effects of polymer selection, DSC heating rate, time above parent polymer Tg and polymer molecular weight were investigated by identifying amorphous drug miscibility limits at pharmaceutically relevant temperatures. Conclusion: The potential implications of these findings when applied to a non-ambient processing method such as Hot Melt Extrusion (HME) are also discussed.

Characteristics of the biological cycle of lutzomyia evandroi Costa Lima & Antunes, 1936 (diptera: psychodidae) under experimental conditions

XIMENES, Maria de Fátima Freire de Melo; MACIEL, Janaína Cunha; JERONIMO, Selma Maria Bezerra. Characteristics of the Biological Cycle of Lutzomyia evandroi Costa Lima & Antunes, 1936 (diptera: psychodidae) under experimental conditions. Memorias do Instituto Oswaldo Cruz, Rio de Janeiro, v.96, n.6, p.883-886, ago. 2001. Disponivel em: Acesso em: 4 out. 2010.

Comparison of the univariate and multivariate methods in the optimization of experimental conditions for determining Cu, Pb, Ni and Cd in biodiesel by GFAAS

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions

Background: Quantitative data from gene expression experiments are often normalized by transcription levels of reference or housekeeping genes. An inherent assumption for their use is that the expression of these genes is highly uniform in living organisms during various phases of development, in different cell types and under diverse environmental conditions. To date, the validation of reference genes in plants has received very little attention and suitable reference genes have not been defined for a great number of crop species including Coffea arabica. The aim of the research reported herein was to compare the relative expression of a set of potential reference genes across different types of tissue/organ samples of coffee. We also validated the expression profiles of the selected reference genes at various stages of development and under a specific biotic stress.Results: The expression levels of five frequently used housekeeping genes (reference genes), namely alcohol dehydrogenase (adh), 14-3-3, polyubiquitin (poly), beta-actin (actin) and glyceraldehyde-3-phosphate dehydrogenase (gapdh) was assessed by quantitative real-time RT-PCR over a set of five tissue/organ samples (root, stem, leaf, flower, and fruits) of Coffea arabica plants. In addition to these commonly used internal controls, three other genes encoding a cysteine proteinase (cys), a caffeine synthase (ccs) and the 60S ribosomal protein L7 (rpl7) were also tested. Their stability and suitability as reference genes were validated by geNorm, NormFinder and BestKeeper programs. The obtained results revealed significantly variable expression levels of all reference genes analyzed, with the exception of gapdh, which showed no significant changes in expression among the investigated experimental conditions.Conclusion: Our data suggests that the expression of housekeeping genes is not completely stable in coffee. Based on our results, gapdh, followed by 14-3-3 and rpl7 were found to be homogeneously expressed and are therefore adequate for normalization purposes, showing equivalent transcript levels in different tissue/ organ samples. Gapdh is therefore the recommended reference gene for measuring gene expression in Coffea arabica. Its use will enable more accurate and reliable normalization of tissue/organ-specific gene expression studies in this important cherry crop plant.

Demographic aspects of Chrysomya megracephala (Diptera, Calliphoridae) adults maintained under experimental conditions: Reproductive rate estimates

The objective of this work was to evaluate some aspects of the populational ecology of Chrysomya megacephala, analyzing demographic aspects of adults kept under experimental conditions. Cages of C. megacephala adults were prepared with four different larval densities (100, 200, 400 and 800). For each cage, two tables were made: one with demographic parameters for the life expectancy estimate at the initial age (eo), and another with the reproductive rate and average reproduction age estimates. Populational parameters such as the intrinsic growth rate (i) and thefinite growth rate (lambda) were calculated as well.

Demographic aspects of Chrysomya megacephala (Diptera, Calliphoridae) adults maintained under experimental conditions: reproductive rate estimates

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Fish exposure to nano-TiO2 under different experimental conditions: Methodological aspects for nanoecotoxicology investigations

The ecotoxicology of nano-TiO2 has been extensively studied in recent years; however, few toxicological investigations have considered the photocatalytic properties of the substance, which can increase its toxicity to aquatic biota. The aim of this work was to evaluate the effects on fish exposed to different nano-TiO2 concentrations and illumination conditions. The interaction of these variables was investigated by observing the survival of the organisms, together with biomarkers of biochemical and genetic alterations. Fish (Piaractus mesopotamicus) were exposed for 96h to 0, 1, 10, and 100mg/L of nano-TiO2, under visible light, and visible light with ultraviolet (UV) light (22.47J/cm2/h). The following biomarkers of oxidative stress were monitored in the liver: concentrations of lipid hydroperoxide and carbonylated protein, and specific activities of superoxide dismutase, catalase, and glutathione S-transferase. Other biomarkers of physiological function were also studied: the specific activities of acid phosphatase and Na,K-ATPase were analyzed in the liver and brain, respectively, and the concentration of metallothionein was measured in the gills. In addition, micronucleus and comet assays were performed with blood as genotoxic biomarkers. Nano-TiO2 caused no mortality under any of the conditions tested, but induced sublethal effects that were influenced by illumination condition. Under both illumination conditions tested, exposure to 100mg/L showed an inhibition of acid phosphatase activity. Under visible light, there was an increase in metallothionein level in fish exposed to 1mg/L of nano-TiO2. Under UV light, protein carbonylation was reduced in groups exposed to 1 and 10mg/L, while nucleus alterations in erythrocytes were higher in fish exposed to 10mg/L. As well as improving the understanding of nano-TiO2 toxicity, the findings demonstrated the importance of considering the experimental conditions in nanoecotoxicological tests. This work provides information for the development of protocols to study substances whose toxicity is affected by illumination conditions. © 2013 Elsevier B.V..

Nicotinamide nucleotide and adenylate concentrations in mante, siphon and gill tissue of old and young Laternula elliptica individuals under control and experimental conditions

Future oceans are predicted to contain less oxygen than at present. This is because oxygen is less soluble in warmer water and predicted stratification will reduce mixing. Hypoxia in marine environments is thus likely to become more widespread in marine environments and understanding species-responses is important to predicting future impacts on biodiversity. This study used a tractable model, the Antarctic clam, Laternula elliptica, which can live for 36 years, and has a well-characterized ecology and physiology to understand responses to hypoxia and how the effect varied with age. Younger animals had a higher condition index, higher adenylate energy charge and transcriptional profiling indicated that they were physically active in their response to hypoxia, whereas older animals were more sedentary, with higher levels of oxidative damage and apoptosis in the gills. These effects could be attributed, in part, to age-related tissue scaling; older animals had proportionally less contractile muscle mass and smaller gills and foot compared with younger animals, with consequential effects on the whole-animal physiological response. The data here emphasize the importance of including age effects, as large mature individuals appear to be less able to resist hypoxic conditions and this is the size range that is the major contributor to future generations. Thus, the increased prevalence of hypoxia in future oceans may have marked effects on benthic organisms' abilities to persist and this is especially so for long-lived species when predicting responses to environmental perturbation.

Characteristics of the biological cycle of lutzomyia evandroi Costa Lima & Antunes, 1936 (diptera: psychodidae) under experimental conditions

XIMENES, Maria de Fátima Freire de Melo; MACIEL, Janaína Cunha; JERONIMO, Selma Maria Bezerra. Characteristics of the Biological Cycle of Lutzomyia evandroi Costa Lima & Antunes, 1936 (diptera: psychodidae) under experimental conditions. Memorias do Instituto Oswaldo Cruz, Rio de Janeiro, v.96, n.6, p.883-886, ago. 2001. Disponivel em: Acesso em: 4 out. 2010.