Leaching of Atrazine in Commercial and Xerogel Formulations in Oxisol Using Bioassay and Chromatographic Methods

Mobility of atrazine in soil has contributed to the detection of levels above the legal limit in surface water and groundwater in Europe and the United States. The use of new formulations can reduce or minimize the impacts caused by the intensive use of this herbicide in Brazil, mainly in regions with higher agricultural intensification. The objective of this study was to compare the leaching of a commercial formulation of atrazine (WG) with a controlled release formulation (xerogel) using bioassay and chromatographic methods of analysis. The experiment was a split plot randomized block design with four replications, in a (2 x 6) + 1 arrangement. The main formulations of atrazine (WG and xerogel) were allocated in the plots, and the herbicide concentrations (0, 3200, 3600, 4200, 5400 and 8000 g ha-1), in the subplots. Leaching was determined comparatively by using bioassays with oat and chromatographic analysis. The results showed a greater concentration of the herbicide in the topsoil (0-4 cm) in the treatment with the xerogel formulation in comparison with the commercial formulation, which contradicts the results obtained with bioassays, probably because the amount of herbicide available for uptake by plants in the xerogel formulation is less than that available in the WG formulation.

Phytotoxic Activity of Parthenium Against Wheat and Canola Differ With Plant Parts and Bioassays Techniques

Phytotoxic effects of invasive weed Parthenium hysterophorus were studied by using whole plant, leaf and root aqueous extracts at 0, 2.5, 5.0, 7.5 and 10% (w/v) concentrations against germination and early seedling growth of wheat and canola. Studies were carried out both in Petri plates with filter paper as substratum placed in controlled conditions and soil-filled plastic pots placed in open environments. Pronounced variation was noted for phytotoxic activity of different plant parts of parthenium, aqueous extract concentrations, test species, and bioassay techniques. Aqueous parthenium extracts either inhibited or delayed the germination and suppressed seedling growth of test species over control. For both test species, all the germination attributes were suppressed to a greater extent in Petri plates than in plastic pots. Leaf extracts were more suppressive to germination of test species than whole plant and root extracts. Increasing extract concentration beyond 2.5% caused significant reduction in seedling dry biomass of both test species. Aqueous parthenium extract diminished chlorophyll contents of wheat and canola by 32-63% and 29 69%, respectively. Nevertheless, an increase of 9-172% and 22-60% in phenolic contents of wheat and canola was recorded. Canola appeared to be more susceptible than wheat at all extract concentrations. Present study concluded that bioassays conducted under controlled condition using filter paper as substratum may be misleading due to over estimation of allelopathic response and variation in potential of receiver and donor species. Furthermore, it implies that threshold concentrations of allelochemicals for test species in Petri plates are rarely reached under field conditions.

Geo-enabling repositories - techniques, tools, and challenges

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Chromosome damage in underground coal miners: detection by conventional cytogenetic techniques and by submitting lymphocytes of unexposed individuals to plasma from at-risk groups

Chromosome abnormalities and the mitotic index in lymphocyte cultures and micronuclei in buccal mucosa cells were investigated in a sample of underground mineral coal miners from Southern Brazil. A decreased mitotic index, an excess of micronuclei and a higher frequency of chromosome abnormalities (fragments, polyploidy and overall chromosome alterations) were observed in the miners when compared to age-paired normal controls from the same area. An alternative assay for clastogenesis in occupational exposition was tested by submitting lymphocytes from non-exposed individuals to a pool of plasmas from the exposed population. This assay proved to be very convenient, as the lymphocytes obtained from the same individuals can be used as target as well as control cells. Also, it yielded a larger number of metaphases and of successful cultures than with common lymphocyte cultures from miners. A significantly higher frequency of chromatid gaps, fragments and overall alterations were observed when lymphocytes from control subjects were exposed to miner plasma pools. Control plasma pools did not significantly induce any type of chromosome alterations in the cultures of normal subjects, thus indicating that the results are not due to the effect of the addition of plasma pools per se.

Evaluation of techniques for C and ASG banding of the mitotic chromosomes of Anastrepha species (Diptera, Tephritidae)

Methods previously described by Canovai et al. (Caryologia 47: 241-247, 1994) which produced C and ASG bands in mitotic chromosomes of Ceratitis capitata were applied to the chromosomes of several Anastrepha species. Metaphase plate yield was substantially increased by use of imaginal disks together with cerebral ganglia. The C-bands were quite prominent allowing the resolution of tiny blocks of heterochromatin. The ASG method produced G-like banded chromosomes, which permitted recognition of each individual chromosome. These simple techniques do not require special equipment and may be valuable for karyotype variability studies in fruit flies and other Diptera

Techniques of radioautography for medical and biological research

Standard techniques for radioautography used in biological and medical research can be classified into three categories, i.e., macroscopic radioautography, light microscopic radioautography and electron microscopic radioautography. The routine techniques used in these three procedures are described. With regard to macroscopic radioautography, whole body radioautography is a standard technique which employs freezing and cryosectioning and can demonstrate organ distributions of both soluble and insoluble compounds. In contrast, in light and electron microscopic radioautography, soluble and insoluble techniques are separated. In order to demonstrate insoluble labeled compounds, conventional chemical fixations such as formalin for light microscopy or buffered glutaraldehyde and osmium tetroxide for both light and electron microscopy followed by dehydration, embedding and wet-mounting applications of radioautographic emulsions can be used. For the demonstration of soluble labeled compounds, however, cryotechniques such as cryofixation, cryosectioning, freeze-drying, freeze-substitution followed by dry-sectioning and dry-mounting radioautography should be employed both for light and electron microscopy. The outlines of these techniques, which should be utilized in various fields of biological and medical research, are described in detail

Complementarity of radioautographic and immunohistochemical techniques for localizing neuroreceptors at the light and electron microscopy level

To assess relationships between neuropeptide-binding sites and receptor proteins in rat brain, the distribution of radioautographically labeled somatostatin and neurotensin-binding sites was compared to that of immunolabeled sst2A and NTRH receptor subtypes, respectively. By light microscopy, immunoreactive sst2A receptors were either confined to neuronal perikarya and dendrites or diffusely distributed in tissue. By electron microscopy, areas expressing somatodendritic sst2A receptors displayed only low proportions of membrane-associated, as compared to intracellular, receptors. Conversely, regions displaying diffuse sst2A labeling exhibited higher proportions of membrane-associated than intracellular receptors. Furthermore, the former showed only low levels of radioautographically labeled somatostatin-binding sites whereas the latter contained high densities of somatostatin-binding suggesting that membrane-associated receptors are preferentially recognized by the radioligand. In the case of NTRH receptors, there was a close correspondence between the light microscopic distribution of NTRH immunoreactivity and that of labeled neurotensin-binding sites. Within the substantia nigra, the bulk of immuno- and autoradiographically labeled receptors were associated with the cell bodies and dendrites of presumptive DA neurons. By electron microscopy, both markers were detected inside as well as on the surface of labeled neurons. At the level of the plasma membrane, their distribution was highly correlated and characterized by a lack of enrichment at the level of synaptic junctions and by a homogeneous distribution along the remaining neuronal surface, in conformity with the hypothesis of an extra-synaptic action of this neuropeptide. Inside labeled dendrites, there was a proportionally higher content of immunoreactive than radiolabeled receptors. Some of the immunolabeled receptors not recognized by the radioligand were found in endosome-like organelles suggesting that, as in the case of sst2A receptors, they may have undergone endocytosis subsequent to binding to the endogenous peptide

A comparative analysis of preprocessing techniques of cardiac event series for the study of heart rhythm variability using simulated signals

In the present study, using noise-free simulated signals, we performed a comparative examination of several preprocessing techniques that are used to transform the cardiac event series in a regularly sampled time series, appropriate for spectral analysis of heart rhythm variability (HRV). First, a group of noise-free simulated point event series, which represents a time series of heartbeats, was generated by an integral pulse frequency modulation model. In order to evaluate the performance of the preprocessing methods, the differences between the spectra of the preprocessed simulated signals and the true spectrum (spectrum of the model input modulating signals) were surveyed by visual analysis and by contrasting merit indices. It is desired that estimated spectra match the true spectrum as close as possible, showing a minimum of harmonic components and other artifacts. The merit indices proposed to quantify these mismatches were the leakage rate, defined as a measure of leakage components (located outside some narrow windows centered at frequencies of model input modulating signals) with respect to the whole spectral components, and the numbers of leakage components with amplitudes greater than 1%, 5% and 10% of the total spectral components. Our data, obtained from a noise-free simulation, indicate that the utilization of heart rate values instead of heart period values in the derivation of signals representative of heart rhythm results in more accurate spectra. Furthermore, our data support the efficiency of the widely used preprocessing technique based on the convolution of inverse interval function values with a rectangular window, and suggest the preprocessing technique based on a cubic polynomial interpolation of inverse interval function values and succeeding spectral analysis as another efficient and fast method for the analysis of HRV signals

Algorithmic Techniques in Gene Expression Processing. From Imputation to Visualization

The amount of biological data has grown exponentially in recent decades. Modern biotechnologies, such as microarrays and next-generation sequencing, are capable to produce massive amounts of biomedical data in a single experiment. As the amount of the data is rapidly growing there is an urgent need for reliable computational methods for analyzing and visualizing it. This thesis addresses this need by studying how to efficiently and reliably analyze and visualize high-dimensional data, especially that obtained from gene expression microarray experiments. First, we will study the ways to improve the quality of microarray data by replacing (imputing) the missing data entries with the estimated values for these entries. Missing value imputation is a method which is commonly used to make the original incomplete data complete, thus making it easier to be analyzed with statistical and computational methods. Our novel approach was to use curated external biological information as a guide for the missing value imputation. Secondly, we studied the effect of missing value imputation on the downstream data analysis methods like clustering. We compared multiple recent imputation algorithms against 8 publicly available microarray data sets. It was observed that the missing value imputation indeed is a rational way to improve the quality of biological data. The research revealed differences between the clustering results obtained with different imputation methods. On most data sets, the simple and fast k-NN imputation was good enough, but there were also needs for more advanced imputation methods, such as Bayesian Principal Component Algorithm (BPCA). Finally, we studied the visualization of biological network data. Biological interaction networks are examples of the outcome of multiple biological experiments such as using the gene microarray techniques. Such networks are typically very large and highly connected, thus there is a need for fast algorithms for producing visually pleasant layouts. A computationally efficient way to produce layouts of large biological interaction networks was developed. The algorithm uses multilevel optimization within the regular force directed graph layout algorithm.

Minimizing Conducted RF-Emissions in Switch Mode Power Supplies Using Spread-Spectrum Techniques

Switching power supplies are usually implemented with a control circuitry that uses constant clock frequency turning the power semiconductor switches on and off. A drawback of this customary operating principle is that the switching frequency and harmonic frequencies are present in both the conducted and radiated EMI spectrum of the power converter. Various variable-frequency techniques have been introduced during the last decade to overcome the EMC problem. The main objective of this study was to compare the EMI and steady-state performance of a switch mode power supply with different spread-spectrum/variable-frequency methods. Another goal was to find out suitable tools for the variable-frequency EMI analysis. This thesis can be divided into three main parts: Firstly, some aspects of spectral estimation and measurement are presented. Secondly, selected spread spectrum generation techniques are presented with simulations and background information. Finally, simulations and prototype measurements from the EMC and the steady-state performance are carried out in the last part of this work. Combination of the autocorrelation function, the Welch spectrum estimate and the spectrogram were used as a substitute for ordinary Fourier methods in the EMC analysis. It was also shown that the switching function can be used in preliminary EMC analysis of a SMPS and the spectrum and autocorrelation sequence of a switching function correlates with the final EMI spectrum. This work is based on numerous simulations and measurements made with the prototype. All these simulations and measurements are made with the boost DC/DC converter. Four different variable-frequency modulation techniques in six different configurations were analyzed and the EMI performance was compared to the constant frequency operation. Output voltage and input current waveforms were also analyzed in time domain to see the effect of the spread spectrum operation on these quantities. According to the results presented in this work, spread spectrum modulation can be utilized in power converter for EMI mitigation. The results from steady-state voltage measurements show, that the variable-frequency operation of the SMPS has effect on the voltage ripple, but the ripple measured from the prototype is still acceptable in some applications. Both current and voltage ripple can be controlled with proper main circuit and controller design.

Characterization of Plasmodium falciparum glutamate dehydrogenase-soluble antigen

The major aim of this study was to characterize a soluble Plasmodium falciparum antigen from the plasma of malaria-infected humans and Plasmodium falciparum culture supernatants, using immunoabsorbent techniques and Western blotting. An Mr 60-kDa protein was isolated from the plasma of patients with Plasmodium falciparum malaria by affinity chromatography using rabbit anti-Proteus spp GDH(NADP+) serum as ligand. This protein, present in plasma of patients with acute Plasmodium falciparum infection, in Plasmodium falciparum culture supernatants, and in immune complexes, was tested with Plasmodium falciparum malaria hyperimmune serum from patients living in hyperendemic areas and rabbit anti-Proteus spp GDH(NADP+) serum prepared in the laboratory. In this report, we describe the results of a study showing that parasite GDH(NADP+) can be used to detect the presence of Plasmodium falciparum. It appears that this technique permits the chromatographic detection of a Plasmodium falciparum excretion antigen that may be used in the production of monoclonal antibodies to improve immunodiagnostic assays for the detection of antigenemia, and opens the possibility of its use as a non-microscopic screening method.

A chromatographic method for the production of a human immunoglobulin G solution for intravenous use

Immunoglobulin G (IgG) of excellent quality for intravenous use was obtained from the cryosupernatant of human plasma by a chromatographic method based on a mixture of ion-exchange, DEAE-Sepharose FF and arginine Sepharose 4B affinity chromatography and a final purification step by Sephacryl S-300 HR gel filtration. The yield of 10 experimental batches produced was 3.5 g IgG per liter of plasma. A solvent/detergent combination of 1% Tri (n-butyl) phosphate and 1% Triton X-100 was used to inactivate lipid-coated viruses. Analysis of the final product (5% liquid IgG) based on the mean for 10 batches showed 94% monomers, 5.5% dimers and 0.5% polymers and aggregates. Anticomplementary activity was 0.3 CH50/mg IgG and prekallikrein activator levels were less than 5 IU/ml. Stability at 37ºC for 30 days in the liquid state was satisfactory. IgG was stored in flasks (2.5 g/flask) at 4 to 8ºC. All the characteristics of the product were consistent with the requirements of the 1997 Pharmacopée Européenne.

Graphene from Graphite by Chemical and Physical Techniques.

Graphene is a material with extraordinary properties. Its mechanical and electrical properties are unparalleled but the difficulties in its production are hindering its breakthrough in on applications. Graphene is a two-dimensional material made entirely of carbon atoms and it is only a single atom thick. In this work, properties of graphene and graphene based materials are described, together with their common preparation techniques and related challenges. This Thesis concentrates on the topdown techniques, in which natural graphite is used as a precursor for the graphene production. Graphite consists of graphene sheets, which are stacked together tightly. In the top-down techniques various physical or chemical routes are used to overcome the forces keeping the graphene sheets together, and many of them are described in the Thesis. The most common chemical method is the oxidisation of graphite with strong oxidants, which creates a water-soluble graphene oxide. The properties of graphene oxide differ significantly from pristine graphene and, therefore, graphene oxide is often reduced to form materials collectively known as reduced graphene oxide. In the experimental part, the main focus is on the chemical and electrochemical reduction of graphene oxide. A novel chemical route using vanadium is introduced and compared to other common chemical graphene oxide reduction methods. A strong emphasis is placed on electrochemical reduction of graphene oxide in various solvents. Raman and infrared spectroscopy are both used in in situ spectroelectrochemistry to closely monitor the spectral changes during the reduction process. These in situ techniques allow the precise control over the reduction process and even small changes in the material can be detected. Graphene and few layer graphene were also prepared using a physical force to separate these materials from graphite. Special adsorbate molecules in aqueous solutions, together with sonic treatment, produce stable dispersions of graphene and few layer graphene sheets in water. This mechanical exfoliation method damages the graphene sheets considerable less than the chemical methods, although it suffers from a lower yield.

Acute promyelocytic leukemia: the study of t(15;17) translocation by fluorescent in situ hybridization, reverse transcriptase-polymerase chain reaction and cytogenetic techniques

Acute promyelocytic leukemia (AML M3) is a well-defined subtype of leukemia with specific and peculiar characteristics. Immediate identification of t(15;17) or the PML/RARA gene rearrangement is fundamental for treatment. The objective of the present study was to compare fluorescent in situ hybridization (FISH), reverse transcriptase-polymerase chain reaction (RT-PCR) and karyotyping in 18 samples (12 at diagnosis and 6 after treatment) from 13 AML M3 patients. Bone marrow samples were submitted to karyotype G-banding, FISH and RT-PCR. At diagnosis, cytogenetics was successful in 10 of 12 samples, 8 with t(15;17) and 2 without. FISH was positive in 11/12 cases (one had no cells for analysis) and positivity varied from 25 to 93% (mean: 56%). RT-PCR was done in 6/12 cases and all were positive. Four of 8 patients with t(15;17) presented positive RT-PCR as well as 2 without metaphases. The lack of RT-PCR results in the other samples was due to poor quality RNA. When the three tests were compared at diagnosis, karyotyping presented the translocation in 80% of the tested samples while FISH and RT-PCR showed the PML/RARA rearrangement in 100% of them. Of 6 samples evaluated after treatment, 3 showed a normal karyotype, 1 persistence of an abnormal clone and 2 no metaphases. FISH was negative in 4 samples studied and 2 had no material for analysis. RT-PCR was positive in 4 (2 of which showed negative FISH, indicating residual disease) and negative in 2. When the three tests were compared after treatment, they showed concordance in 2 of 6 samples or, when there were not enough cells for all tests, concordance between karyotype and RT-PCR in one. At remission, RT-PCR was the most sensitive test in detecting residual disease, as expected (positive in 4/6 samples). An incidence of about 40% of 5' breaks and 60% of 3' breaks, i.e., bcr3 and bcr1/bcr2, respectively, was observed.

Measuring higher order optical aberrations of the human eye: techniques and applications

In the present paper we discuss the development of "wave-front", an instrument for determining the lower and higher optical aberrations of the human eye. We also discuss the advantages that such instrumentation and techniques might bring to the ophthalmology professional of the 21st century. By shining a small light spot on the retina of subjects and observing the light that is reflected back from within the eye, we are able to quantitatively determine the amount of lower order aberrations (astigmatism, myopia, hyperopia) and higher order aberrations (coma, spherical aberration, etc.). We have measured artificial eyes with calibrated ametropia ranging from +5 to -5 D, with and without 2 D astigmatism with axis at 45º and 90º. We used a device known as the Hartmann-Shack (HS) sensor, originally developed for measuring the optical aberrations of optical instruments and general refracting surfaces in astronomical telescopes. The HS sensor sends information to a computer software for decomposition of wave-front aberrations into a set of Zernike polynomials. These polynomials have special mathematical properties and are more suitable in this case than the traditional Seidel polynomials. We have demonstrated that this technique is more precise than conventional autorefraction, with a root mean square error (RMSE) of less than 0.1 µm for a 4-mm diameter pupil. In terms of dioptric power this represents an RMSE error of less than 0.04 D and 5º for the axis. This precision is sufficient for customized corneal ablations, among other applications.