Identification of Mycobacteria by Thin Layer Chromatographic Analysis of Mycolic Acids and Conventional Biochemical Method: Four Years of Experience

Mycolic acids analysis by thin-layer chromatography (TLC) has been employed by several laboratories worldwide as a method for fast identification of mycobacteria. This method was introduced in Brazil by our laboratory in 1992 as a routine identification technique. Up to the present, 861 strains isolated were identified by mycolic acids TLC and by standard biochemical tests; 61% out of these strains came as clinical samples, 4% isolated from frogs and 35% as environmental samples. Mycobacterium tuberculosis strains identified by classical methods were confirmed by their mycolic acids contents (I, III and IV). The method allowed earlier differentiation of M. avium complex - MAC (mycolic acids I, IV and VI) from M. simiae (acids I, II and IV), both with similar biochemical properties. The method also permitted to distinguish M. fortuitum (acids I and V) from M. chelonae (acids I and II) , and to detect mixed mycobacterial infections cases as M. tuberculosis with MAC and M. fortuitum with MAC. Concluding, four years experience shows that mycolic acids TLC is an easy, reliable, fast and inexpensive method, an important tool to put together conventional mycobacteria identification methods.

Attributes of irrigated rice and soil solution as affected by salinity levels of the water layer

In the State of Rio Grande do Sul, Brazil, flooded rice fields using Patos Lagoon as the source of water for irrigation are subject to be damaged by salinity, since this source is bound to the sea on its southern end. The sensitivity of rice is variable during plant development, being higher in the seedling and reproductive periods. However, there is not enough information about the behavior of plants under salt stress during the course of its development, especially in the vegetative stage. This study evaluated the effect of different levels of salinity of irrigation water on the salinity of soil solution over time and on some plant attributes, during the vegetative stage of rice. The study was conducted in a greenhouse, where seeds of the variety IRGA 424 were sown in pots and irrigated with water with electrical conductivity (ECi) levels of: 0.3, 0.75, 1.5, 3.0 and 4.5 dS m-1; from the tillering initiation (V4) until the panicle initiation (PI). The evaluations made were the electrical conductiviy of soil solution (ECe), the dry biomass of plants and stems, tillering, height and the transpiration of plants. The ECe increased with the ECi over time, and was determined by water transpiration flux in pots. The ECe values at the end of the experiment were high and, in most cases, higher than the critical values for flooded rice. The growth attributes of rice were negatively affected from ECi of 2.0 dS m-1 and ECe of 4.0 dS m-1.

Influence of litter layer removal on the soil thermal regime of a pine forest in a mediterranean climate

The removal of the litter layer in Portuguese pine forests would reduce fire hazard, but on the other hand this practice would influence the thermal regime of the soil, hence affecting soil biological activity, litter decomposition and nutrient dynamics. Temperature profiles of a sandy soil (Haplic Podzol) under a pine forest were measured with thermocouples at depths to 16 cm, with and without litter layer. The litter layer acted as a thermal insulator, reducing the amplitude of the periodic temperature variation in the mineral soil underneath and increasing damping depths, particularly at low soil water contents. At the mineral soil surface the reduction of amplitudes was about 2.5 ºC in the annual cycle and 5 to 6.7 ºC in the daily cycle, depending on the soil water content. When soil was both cold and wet, mean daily soil temperatures were higher (about 1 - 1.5 ºC) under the litter layer. Improved soil thermal conditions under the litter layer recommend its retention as a forest management practice to follow in general.

Evaluation of Sikora instead of SMP buffer to estimate the potential acidity of brazilian soils

Despite the efficiency of the Shoemaker, McLean, Pratt (SMP) buffer method in estimating soil acidity, the presence of p-nitrophenol and potassium chromate in the solution, both hazardous substances, has caused increasing environmental concerns. The purpose of this study was to test Sikora method (Sikora, 2006) as an alternative to the adapted SMP buffer method, generally used to estimate potential acidity of Southern Brazilian soils. For the test, 21 soils in the South and Cerrado regions of Brazil were sampled. (1) The potential acidity values of these soils range from 35.95 to 4.02 cmol c kg-1 of soil, reflecting a wide acidity variation. The Sikora buffer does not mimic the adapted SMP buffer used in Southern Brazil, since the former has a low ability to distinguish soils with different acidity from each other, probably due to the higher buffer capacity than of the adapted SMP solution.

Rill erosion on an oxisol influenced by a thin compacted layer

The presence of compacted layers in soils can induce subprocesses (e.g., discontinuity of water flow) and induces soil erosion and rill development. This study assesses how rill erosion in Oxisols is affected by a plow pan. The study shows that changes in hydraulic properties occur when the topsoil is eroded because the compacted layer lies close below the surface. The hydraulic properties that induce sediment transport and rill formation (i.e., hydraulic thresholds at which these processes occur) are not the same. Because of the resistance of the compacted layer, the hydraulic conditions leading to rill incision on the soil surface differed from the conditions inducing rill deepening. The Reynolds number was the best hydraulic predictor for both processes. The formed rills were shallow and could easily be removed by tillage between crops. However, during rill development, large amounts of soil and contaminants could also be transferred.

Organic Matter Fractions and Quality of the Surface Layer of a Constructed and Vegetated Soil After Coal Mining. I - Humic Substances and Chemical Characterization

After open coal mining, soils are “constructed”, which usually contain low levels and quality of organic matter (OM). Therefore, the use of plant species for revegetation and reclamation of degraded areas is essential. This study evaluated the distribution of carbon (C) in the chemical fractions as well as the chemical characteristics and humification degree of OM in a soil constructed after coal mining under cultivation of perennial grasses. The experiment was established in 2003 with the following treatments: Hemarthria altissima (T1), Paspalum notatum (T2), Cynodon dactilon (T3), Urochloa brizantha (T4), bare constructed soil (T5), and natural soil (T6). In 2009, soil samples were collected from the 0.00-0.03 m layer and the total organic carbon stock (TOC) and C stock in the chemical fractions: acid extract (CHCl), fulvic acid (CFA), humic acid (CHA), and humin (CHU) were determined. The humic acid (HA) fraction was characterized by infrared spectroscopy and the laser-induced fluorescence index (ILIF) of OM was also calculated. After six years, differences were only observed in the CHA stocks, which were highest in T1 (0.89 Mg ha-1) and T4 (1.06 Mg ha-1). The infrared spectra of HA in T1, T2 and T4 were similar to T6, with greater contribution of aliphatic organic compounds than in the other treatments. In this way, ILIF decreased in the sequence T5>T3>T4>T1>T2>T6, indicating higher OM humification in T3 and T5 and more labile OM in the other treatments. Consequently, the potential of OM quality recovery in the constructed soil was greatest in treatments T1 and T4.

Organic Matter Fractions and Quality of the Surface Layer of a Constructed and Vegetated Soil After Coal Mining. II - Physical Compartments and Carbon Management Index

Soils constructed after mining often have low carbon (C) stocks and low quality of organic matter (OM). Cover crops are decisive for the recovery process of these stocks, improving the quality of constructed soils. Therefore, the goal of this study was to evaluate the effect of cover crops on total organic C (TOC) stocks, C distribution in physical fractions of OM and the C management index (CMI) of a soil constructed after coal mining. The experiment was initiated in 2003 with six treatments: Hemarthria altissima (T1), Paspalum notatum (T2), Cynodon dactylon (T3), Urochloa brizantha (T4), bare constructed soil (T5), and natural soil (T6). Soil samples were collected in 2009 from the 0.00-0.03 m layer, and the TOC and C stocks in the physical particle size fractions (carbon in the coarse fraction - CCF, and mineral-associated carbon - MAC) and density fractions (free light fraction - FLF; occluded light fraction - OLF, and heavy fraction - HF) of OM were determined. The CMI components: carbon pool index (CPI), lability (L) and lability index (LI) were estimated by both fractionation methods. No differences were observed between TOC, CCF and MAC stocks. The lowest C stocks in FLF and OLF fractions were presented by T2, 0.86 and 0.61 Mg ha-1, respectively. The values of TOC stock, C stock in physical fractions and CMI were intermediate, greater than T5 and lower than T6 in all treatments, indicating the partial recovery of soil quality. As a result of the better adaptation of the species Hemarthria and Brizantha, resulting in greater accumulation of labile organic material, the CPI, L, LI and CMI values were higher in these treatments, suggesting a greater potential of these species for recovery of constructed soils.

Photometric procedure for quantitative analysis of Aflatoxin B1 in peanuts by thin-layer chromatography using charge coupled device detector

A photometric procedure was developed for determination of aflatoxin B1 in peanuts by TLC-CCD technique. The quantification and detection limit were 1.2 μg kg-1 and 0.4 ng per spot, respectively, with mean recovery of 98%. The CCD camera is sufficiently sensitive to detect small changes in spots fluorescence intensity and the results for performance confirmed the efficiency of the method. Another important property of CCD detector is its linearity for a wide range of luminous stimulus determined by analysis of five-point calibration curves using the intensity of AFB1 fluorescence versus AFB1 concentration (0.8 to 4.8 ng per spot). The method was applied to the analysis of thirty nine peanut samples and aflatoxin B1 levels ranged from 16 to 115 μg kg-1. The TLC-CCD and the photometric procedure developed in this study demonstrated to be a simple and efficient tool for quantitative analyses of AFB1 in peanut samples.

High performance thin layer chromatographic determination of nifedipine in human serum after liquid-liquid extraction

A method using HPTLC for quantitation of nifedipine in serum was developed and validated. It includes a liquid-liquid extraction, and carbamazepine as internal standard. Chloroform: ethyl acetate: cyclohexane (19:2:2, v/v/v) was the mobile phase. The method showed good relationship (r = 0.996) (2.00 to 25.00 ng/band, corresponding to 0.02 and 0.25 ng/µL in serum). The % RSD of intra-assay and inter-assay, were between 0.57 and 3.56 and 1.16 to 3.60, respectively. LOD and LOQ were 0.72 and 0.86 ng/band, respectively. The recovery values were between 93 and 102%. Rf for nifedipine and carbamazepine were 0.31 and 0.10, respectively.

Distribution of tree species in a geomorphological and pedological gradient of submontane semidecidual seasonal forest in the vicinity of Rio Doce state park, Minas Gerais

The objective of this study was to test the hypothesis that the distribution of tree species in a fragment of submontane seasonal semideciduous forest, a buffer zone in the Parque Estadual do Rio Doce, Minas Gerais, is influenced by geomorphological and weather and soil variables, therefore it can represent a source of information for the restoration of degraded areas where environmental conditions are similar to those of the study area. A detailed soil survey was conducted in the area by sampling three soil profiles per slope segment, totaling 12 profiles. To sample the topsoil, four composite samples were collected from the 10-20 cm layers in each topographic range totaling 16 composite samples. In the low ramp and the lower and upper concave slopes, the texture ranged from clay to sandy-clay. The soil and topographic gradient was characterized by changes in the soil physical-chemical properties. The soil in the 10-20 cm sampled layer was sandier, slightly more fertile and less acid in the low ramp than the clayer soil, nutrient-poor and highly acid soil at the top. The soil conditions in the lower and upper slope of the sampled layers, in turn, were intermediate. The P levels were limiting in all soils. The species distribution along the topographic gradient was associated with variations in chemical fertility, acidity and soil texture. The distribution of Pera leandri, Astronium fraxinifolium, Pouteria torta, Machaerium brasiliense and Myrcia rufipes was correlated with high aluminum levels and to low soil fertility and these species may be indicated for restoration of degraded areas on hillsides and hilltops in regions where environmental conditions are similar. The distribution of Pouteria venosa, Apuleia leiocarpa and Acacia polyphylla was correlated with the less acid and more fertile soil in the environment of the low ramps, indicating the potential for the restoration of similar areas.

The influence of selected pathological states on the somatostatin-like immunoreactive (SOM-LI) endocrine cells in the mucosal layer of the porcine descending colon

This study reports on changes in the number of somatostatin-like immunoreactive (SOM-LI) endocrine cells in the porcine descending colon, caused by chemically driven inflammation, axotomy and proliferative enteropathy (PE). The distribution pattern of SOM-LI endocrine cells has been studied using the routine single-labelling immunofluorescence technique. Semi-quantitative evaluation of the number of the SOM-immunostained endocrine cells within the mucosal layer of the porcine descending colon has been based on counting of all endocrine cells immunoreactive to SOM per unit area (0,1 mm²). Under physiological conditions the number of SOM-LI endocrine cells has been shown to constitute 3,30±0,22. All applied pathological processes resulted in changes in the SOM-like immunoreactivity, which varied in particular processes studied. The number of SOM-LI endocrine cells increased to 6,28±0,31 and 4,43±0,35 during chemically driven inflammation and proliferative enteropathy, respectively, and decreased to 1,17%±0,16 after axotomy. The obtained results suggest that SOM-LI endocrine cells may participate in various pathological states within porcine descending colon and their functions probably depend on the type of pathological factor.

Outbreak of infectious laryngotracheitis in large multi-age egg layer chicken flocks in Minas Gerais, Brazil

A recent (November 2010) outbreak of infectious laryngotracheitis (ILT) in a multi-age laying hen facility in Minas Gerais state, Brazil, is described. Previous ILT outbreak in laying hens was only notified in São Paulo state, Brazil, in 2002. In the outbreak described here, the affected population was approximately eight million hens, with flock sizes ranging from 100,000 to 2,900,000 chickens. The average mortality ranged from 1 to 6%, and morbidity was around 90% (most of the twenty seven farms of the area were positive for ILT virus). Three multi-age laying farms from one company were selected for this report. Clinical signs included prostration, dyspnea, conjunctivitis, occasional swelling of the paranasal sinuses and bloody mucous nasal discharge. Severely affected chickens presented with dyspnea, gasping and became cyanotic before death. At necropsy, these chickens had fibrinous exudate blocking the larynx and the lumen of cranial part of the trachea. In addition, conjunctivitis with intense hyperemia, edema and sinuses with caseous exudate were present. On histopathology, there were marked necrosis and desquamation of respiratory ephitelium and conjunctiva with numerous syncytial cells formation and fibrinous exudate. Moderate to marked non suppurative (especially lymphocytes and plasma cells) infiltration in the lamina propria also was observed. Sixteen out of 20 examined chickens, eosinophilic intranuclear inclusion bodies were observed in the syncytial cells. The DNA extracted from larynx and trachea produced positive PCR results for ILT virus (ILTV) DNA using formalin-fixed, paraffin embedded (FFPE) samples. Amplicons from a small region of ICP4 gene were submitted to sequencing and showed 100% identity with ILTV EU104910.1 (USA strain), 99% with ILTV JN596963.1 (Australian strain) and 91% with ILTV JN580316.1 (Gallid herpesvirus 1 CEO vaccine strain) and JN580315.1 (Gallid herpesvirus 1 TCO vaccine strain).

Effect of different surface roughnesses on a turbulent boundary layer

The classical treatment of rough wall turbulent boundary layers consists in determining the effect the roughness has on the mean velocity profile. This effect is usually described in terms of the roughness function delta U+. The general implication is that different roughness geometries with the same delta U+ will have similar turbulence characteristics, at least at a sufficient distance from the roughness elements. Measurements over two different surface geometries (a mesh roughness and spanwise circular rods regularly spaced in the streamwise direction) with nominally the same delta U+ indicate significant differences in the Reynolds stresses, especially those involving the wall-normal velocity fluctuation, over the outer region. The differences are such that the Reynolds stress anisotropy is smaller over the mesh roughness than the rod roughness. The Reynolds stress anisotropy is largest for a smooth wall. The small-scale anisotropy and interniittency exhibit much smaller differences when the Taylor microscale Reynolds number and the Kolmogorov-normalized mean shear are nominally the same. There is nonetheless evidence that the small-scale structure over the three-dimensional mesh roughness conforms more closely with isotropy than that over the rod-roughened and smooth walls.

An experimental/numerical study of the turbulent boundary layer development along a surface with a sudden change in roughness

A theory for the description of turbulent boundary layer flows over surfaces with a sudden change in roughness is considered. The theory resorts to the concept of displacement in origin to specify a wall function boundary condition for a kappa-epsilon model. An approximate algebraic expression for the displacement in origin is obtained from the experimental data by using the chart method of Perry and Joubert(J.F.M., vol. 17, pp. 193-122, 1963). This expression is subsequently included in the near wall logarithmic velocity profile, which is then adopted as a boundary condition for a kappa-epsilon modelling of the external flow. The results are compared with the lower atmospheric observations made by Bradley(Q. J. Roy. Meteo. Soc., vol. 94, pp. 361-379, 1968) as well as with velocity profiles extracted from a set of wind tunnel experiments carried out by Avelino et al.( 7th ENCIT, 1998). The measurements are found to be in good agreement with the theoretical computations. The skin-friction coefficient was calculated according to the chart method of Perry and Joubert(J.F.M., vol. 17, pp. 193-122, 1963) and to a balance of the integral momentum equation. In particular, the growth of the internal boundary layer thickness obtained from the numerical simulation is compared with predictions of the experimental data calculated by two methods, the "knee" point method and the "merge" point method.

Non-Linear Unsteady Aerodynamic Response Approximation Using Multi-Layer Functionals

Non-linear functional representation of the aerodynamic response provides a convenient mathematical model for motion-induced unsteady transonic aerodynamic loads response, that accounts for both complex non-linearities and time-history effects. A recent development, based on functional approximation theory, has established a novel functional form; namely, the multi-layer functional. For a large class of non-linear dynamic systems, such multi-layer functional representations can be realised via finite impulse response (FIR) neural networks. Identification of an appropriate FIR neural network model is facilitated by means of a supervised training process in which a limited sample of system input-output data sets is presented to the temporal neural network. The present work describes a procedure for the systematic identification of parameterised neural network models of motion-induced unsteady transonic aerodynamic loads response. The training process is based on a conventional genetic algorithm to optimise the network architecture, combined with a simplified random search algorithm to update weight and bias values. Application of the scheme to representative transonic aerodynamic loads response data for a bidimensional airfoil executing finite-amplitude motion in transonic flow is used to demonstrate the feasibility of the approach. The approach is shown to furnish a satisfactory generalisation property to different motion histories over a range of Mach numbers in the transonic regime.