Single-cell sequencing and mini-sequencing for preimplantation genetic diagnosis

There is increasing interest in the use of preimplantation genetic diagnosis (PGD) as an alternative to routine prenatal diagnosis. However, the costs associated with development and testing of new PGD protocols have forced some PGD centres to limit the number of diseases for which PGD is offered. One of the main factors in the design of new protocols, which affects cost and accuracy, is the choice of the mutation-detection technique. We have assessed the reliability of DNA sequencing and mini-sequencing for clinical diagnosis at the single-cell level and have found them to be rapid and accurate. Extensive optimisation for individual mutations is not usually necessary when employing these versatile techniques and consequently a smaller investment of time and resources should be required during development of new protocols. Additionally, we report single-cell protocols for the diagnoses of cystic fibrosis, sickle cell anaemia and β-thalassaemia, which utilise mini-sequencing. Unlike most mutation-detection techniques, mini-sequencing permits analysis of very small DNA fragments. Small amplicons experience low allele dropout (ADO) rates, and consequently this approach could potentially improve the reliability of PGD. Copyright © 2003 John Wiley & Sons, Ltd.     

How to evaluate models: Observed vs. predicted or predicted vs. observed?

A common and simple approach to evaluate models is to regress predicted vs. observed values (or vice versa) and compare slope and intercept parameters against the 1:1 line. However, based on a review of the literature it seems to be no consensus on which variable (predicted or observed) should be placed in each axis. Although some researchers think that it is identical, probably because r² is the same for both regressions, the intercept and the slope of each regression differ and, in turn, may change the result of the model evaluation. We present mathematical evidence showing that the regression of predicted (in the y-axis) vs. observed data (in the x-axis) (PO) to evaluate models is incorrect and should lead to an erroneous estimate of the slope and intercept. In other words, a spurious effect is added to the regression parameters when regressing PO values and comparing them against the 1:1 line. Observed (in the y-axis) vs. predicted (in the x-axis) (OP) regressions should be used instead. We also show in an example from the literature that both approaches produce significantly different results that may change the conclusions of the model evaluation.     

Design and first experimental results of a bubbling fluidized bed for air gasification of plastic waste

Plastic wastes have an especially high potential for use as alternative fuels, considering their high heating value and their large and stable availability. They could be used in electricity production based on gasification technologies, wherein electricity is produced in engines by means of the conversion of plastic wastes into a valuable gas. However, there are still some technical barriers to overcome before this technology can access the commercial stage, and further scientific research is needed to gain deeper understanding of the process and to be able to control and optimize it. This research presents the design and first experimental results of a bubbling fluidized bed gasifier conceived for the gasification of actual plastic residues. The experimental tests revealed that the selection and design of the reactor were adequate and proved some of the advantages of using plastic as a fuel, related in part to the absence of ashes and char. A valuable syngas over 5 MJ/m³ was generated, which contained a considerable fraction of methane as well as hydrogen and carbon monoxide as main combustible gases. The highest efficiency was achieved when the equivalence ratio was increased to 0.35, reaching 61 % in terms of cold gas efficiency and 66 % carbon conversion.     

Laboratory study on the leaching potential of spent alkaline batteries using a MSW landfill leachate

Two leaching tests were carried out, one with whole batteries and another with cross-cut batteries. In both cases, NEN 7343 (a Nederland’s Standard) procedure was followed using a municipal solid waste (MSW) landfill leachate as extraction solution. Seven fractions were collected corresponding to cumulative liquid/solid (L/S) ratio from 0.1 to 10.0. Those fractions were separately characterized in terms of pH, conductivity, redox potential, density, sulphate, chloride, As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Sb, Tl and Zn. Results showed that the influence of the alkaline batteries in the landfill leachate composition varies with their physical integrity and with the L/S ratio, and several variations were observed throughout the tests. The leachate pH and redox potential increased as result of the contact with batteries, particularly pH in the test with the cross-cut batteries. The leachate density and conductivity did not change significantly with the whole batteries, in contrast with the test with cross-cut batteries.     

Laboratory study on the behaviour of spent AA household alkaline batteries in incineration

The quantitative evaluation of emissions from incineration is essential when Life Cycle Assessment (LCA) studies consider this process as an end-of-life solution for some wastes. Thus, the objective of this work is to quantify the main gaseous emissions produced when spent AA alkaline batteries are incinerated. With this aim, batteries were kept for 1h at 1273K in a refractory steel tube hold in a horizontal electric furnace with temperature control. At one end of the refractory steel tube, a constant air flow input assures the presence of oxygen in the atmosphere and guides the gaseous emissions to a filter system followed by a set of two bubbler flasks having an aqueous solution of 10% (v/v) nitric acid. After each set of experiments, sulphur, chlorides and metals (As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Sb, Tl and Zn) were analyzed in both the solutions obtained from the steel tube washing and from the bubblers. Sulphur, chlorides and metals were quantified, respectively, using barium sulfate gravimetry, the Volhard method and atomic absorption spectrometry (AAS). The emissions of zinc, the most emitted metal, represent about 6.5% of the zinc content in the batteries. Emissions of manganese (whose oxide is the main component of the cathode) and iron (from the cathode collector) are negligible when compared with their amount in AA alkaline batteries. Mercury is the metal with higher volatility in the composition of the batteries and was collected even in the second bubbler flask. The amount of chlorides collected corresponds to about 36% of the chlorine in the battery sleeve that is made from PVC. A considerable part of the HCl formed in PVC plastic sleeve incineration is neutralized with KOH, zinc and manganese oxides and, thus, it is not totally released in the gas. Some of the emissions are predictable through a thermodynamic data analysis at temperatures in the range of 1200-1300K taking into account the composition of the batteries. This analysis was done for most of potential reactions between components in the batteries as well as between them and the surrounding atmosphere and it reasonably agrees the experimental results. The results obtained show the role of alkaline batteries at the acid gases cleaning process, through the neutralization reactions of some of their components. Therefore, LCA of spent AA alkaline batteries at the municipal solid waste (MSW) incineration process must consider this contribution.     

Evaluation of GC-ion trap-MS/MS methodology for monitoring PCDD/Fs in infant formulas

The application of high resolution gas chromatography in combination with low resolution mass spectrometry with electron ionization and MS/MS detection (HRGC-MS/MS) is tested for its use in the analysis of PCDD/Fs in infant formulas. Development of the analytical method was based upon EPA directrices and international recommendations. Calibration linearity was tested and average relative response for any native and labelled compound over the five-point calibration range below 14% was found. The precision and accuracy of the proposed analytical procedure are also presented. Results obtained are in agreement with EPA criteria. The method is applied to the analysis of a number of initial and follow-on milk based infant formulas. In general, HRGC-MS/MS constitutes an interesting method for the analysis of dioxins in such matrices.     

Simulation of stomatal conductance for Aleppo pine to estimate its ozone uptake

The data from a previous experiment carried out in open-top chambers to assess the effects of ozone (O3) exposure on growth and physiology of Aleppo pine (Pinus halepensis Mill.) were re-assessed to test the performance of the EMEP O3 stomatal conductance model used to estimate tree O3 uptake at a European scale. Aleppo pine seedlings were exposed during three consecutive years to three different O3 treatments: charcoal filtered air, non-filtered air and non-filtered air supplemented with 40 nl l(-1). The results of the model using the default parameterisation already published for Mediterranean conifers showed a poor performance when compared to measured data. Therefore, modifications of g(max), f(min), and new f(VPD), f(temp) and f(phen) functions were developed according to the observed data. This re-parameterisation resulted in a significant improvement of the performance of the model when compared to its original version.     

Effect of herbicide and soil amendment on growth and photosynthetic responses in olive crops

Diuron [3-(3,4-dichlorophenyl)- = 1,1-dimethylurea] and simazine (6-chloro-N(2), N(4)-diethyl-1,3,5-triazine-2,4-diamine) are soil-applied herbicides used in olive crops. The objective of this study is to investigate the combined effect of these herbicides and the amendment of soil with an organic waste (OW) from the olive oil production industry on the growth and photosynthetic apparatus of adult olive trees and to compare the results with those obtained by Redondo-Gómez et al. for two-year-old trees. For this purpose, growth rate, gas exchange and chlorophyll fluorescence parameters were measured in 38-year-old olive trees, after one and two months of soil herbicide treatment and/or OW amendment. Soil co-application of OW and herbicide increases the quantum efficiency of Photosystem II (PSII) and the assimilation of CO(2) in olive trees, which led to a higher relative growth rate of the branches and leaves in length. Herbicide treatment reduced the photosynthetic efficiency in olive trees after two months of soil application, while this reduction is evident from week one in younger trees.     

Water quality of the Ribeirão Preto Stream, a watercourse under anthropogenic influence in the southeast of Brazil

It is known that Brazil still has a privileged position of water quantity and quality, but water use has not proceeded in a responsible manner and often results in impairment of quality. This study aims to evaluate limnological parameters, parasites and bacteria, and concentrations of heavy metals (Cd, Pb, Cu, Cr, Mn, Hg, and Zn) in surface water of Ribeirão Preto Stream. The Ribeirão Preto Stream is located in urban areas under anthropogenic influence. The results showed that the levels of dissolved oxygen values were lower than those established by the National Environmental Council (CONAMA Resolution No 357/2005). The reading of electrical conductivity showed values typical of impacted environments. The parasitological analysis revealed the presence of nematode larvae. The bacteriological analysis showed higher values for total coliform and Escherichia coli than those set by the Brazilian National Environment Council (CONAMA). The heavy metals Cd, Pb, Cu, Cr, Mn, Hg, and Zn showed concentrations in accordance with the guidelines established by CONAMA. The results provide data on the quality of these waters and showed the necessity to protect the watercourse from point sources of contamination, recommending their continued monitoring.     

Analysis of the usefulness of biological parameters for the control of activated sludge wastewater treatment plants in an interlaboratory study context

The quality of the sludge in Wastewater Treatment Plants (WWTPs) depends on the suitable colonization of the flocs by microorganisms. Due to the functional importance of these biological constituents, several biological or biological-related parameters have been commonly used for the control of depuration efficiency. According to national and international water regulation recommendations, interlaboratory studies have a great relevance to determine which parameters are more reliable for their extensive application in routine control. However, these studies are also very useful to demonstrate consistency in results from multiple laboratories and to develop reliable and reproducible methodologies which might be necessary for protocol validation and also for accreditation issues to meet regulatory environmental requirements. The main purpose of this work was to assess the results obtained in consecutive interlaboratory assays in order to determine the concordance degree in the application of biological parameters by participating laboratories. Following the international recommendations about these studies, a common working protocol was proposed. Statistical tests indicated that Sludge Index and several routine physical-chemical analyses [V30, Mixed Liquor Suspended Solids (MLSS), Mixed Liquor Volatile Solids (MLVS) and Sludge Volumetric Index (SVI)] show low variability and therefore are suitable tools for laboratory control. Shannon Index and Sludge Biotic Index also presented low variability although a more precise protocol would be necessary, in particular the methodology to count small flagellates. The abundance and identification of protist species showed low concordance among laboratories and three factors were responsible for the low reliability of data: population density, size and morphological distinguishable characters of the specimens.