Diversity of Bacillus And Actinomycetes in the water and sediment samples from Kumarakom region of Vembanadu lake

Diversity of different groups of Bacillus and Actinomycetes in the water and sediment samples from kumarakom estuary was analysed to find out potential strains for further application. Bacillus genera was identified and grouped into five phenogroups .Phenogroups show differences in the shape of the spore,position of the spore,and swelling of the sporangium.Ability of the isolates to elaborate various hydrolytic enzymes and their ability to reduce nitrate and ferment various carbohydrate sources were also studied.

Human papillomavirus detection from human immunodeficiency virus-infected colombian women's paired urine and cervical samples

Infection, coinfection and type-specific human papillomavirus (HPV) distribution was evaluated in human immunodeficiency virus (HIV)-positive women from paired cervical and urine samples. Paired cervical and urine samples (n = 204) were taken from HIV-positive women for identifying HPV-DNA presence by using polymerase chain reaction (PCR) with three generic primer sets (GP5+/6+, MY09/11 and pU1M/2R). HPV-positive samples were typed for six high-risk HPV (HR-HPV) (HPV-16, -18, -31, -33, -45 and -58) and two low-risk (LR-HPV) (HPV-6/11) types. Agreement between paired sample results and diagnostic performance was evaluated. HPV infection prevalence was 70.6% in cervical and 63.2% in urine samples. HPV-16 was the most prevalent HPV type in both types of sample (66.7% in cervical samples and 62.0% in urine) followed by HPV-31(47.2%) in cervical samples and HPV-58 (35.7%) in urine samples. There was 55.4% coinfection (infection by more than one type of HPV) in cervical samples and 40.2% in urine samples. Abnormal Papanicolau smears were observed in 25.3% of the women, presenting significant association with HPV-DNA being identified in urine samples. There was poor agreement of cervical and urine sample results in generic and type-specific detection of HPV. Urine samples provided the best diagnosis when taking cytological findings as reference. In conclusion including urine samples could be a good strategy for ensuring adherence to screening programs aimed at reducing the impact of cervical cancer, since this sample is easy to obtain and showed good diagnostic performance.

Geometric characterization of red blood cells. Differentiation of normal and pathologic samples

Introduction. Fractal geometry measures the irregularity of abstract and natural objects with the fractal dimension. Fractal calculations have been applied to the structures of the human body and to quantifications in physiology from the theory of dynamic systems.Material and Methods. The fractal dimensions were calculated, the number of occupation spaces in the space border of box counting and the area of two red blood cells groups, 7 normal ones, group A, and 7 abnormal, group B, coming from patient and of bags for transfusion, were calculated using the method of box counting and a software developed for such effect. The obtained measures were compared, looking for differences between normal and abnormal red blood cells, with the purpose of differentiating samples.Results. The abnormality characterizes by a number of squares of occupation of the fractal space greater or equal to 180; values of areas between 25.117 and 33.548 correspond to normality. In case that the evaluation according to the number of pictures is of normality, must be confirmed with the value of the area applied to adjacent red blood cells within the sample, that in case of having values by outside established and/or the greater or equal spaces to 180, they suggest abnormality of the sample.Conclusions. The developed methodology is effective to differentiate the red globules alterations and probably useful in the analysis of bags of transfusion for clinical use 

Pyrohydrolysis-IRMS determination of silicate chlorine stable isotope compositions. Application to oceanic crust and meteorite samples

This contribution describes the optimization of chlorine extraction from silicate samples by pyrohydrolysis prior to the precise determination of Cl stable-isotope compositions (637 Cl) by gas source, dual inlet Isotope Ratio Mass Spectrometry (IRMS) on CH(3)Clg. The complete method was checked on three international reference materials for Cl-content and two laboratory glass standards. Whole procedure blanks are lower than 0. 5 mu mol, corresponding to less than 10 wt.% of most of the sample chloride analysed. In the absence of international chlorine isotope rock, we report here Cl extracted compared to accepted Cl contents and reproducibilities on Cl and delta Cl-37 measurements for the standard rocks. After extraction, the Cl contents of the three international references compared within error with the accepted values (mean yield = 94 +/-10%) with reproducibilities better than 12% (10). The laboratory glass standards - andesite SO100DS92 and phonolite S9(2) - were used specifically to test the effect of chloride amount on the measurements. They gave Cl extraction yields of 100 +/-6% (1 sigma-; n = 15) and 105 +/- 8% (1 sigma-; n = 7), respectively, with delta Cl-37 values of -0.51 0.14%o and -0.39 0.17%o (1g). In summary, for silicate samples with Cl contents between 39 and 9042 ppm, the Pyrohydrolysis/HPLC method leads to overall CI extraction yields of 100 8%, reproducibilities on Cl contents of 7% and on delta Cl-37 measurements of 0.12%o (all 1 sigma). The method was further applied to ten silicate rocks of various mineralogy and chemistry (meteorite, fresh MORB glasses, altered basalts and setpentinized peridotites) chosen for their large range of Cl contents (70-2156 ppm) and their geological significance. delta Cl-37 values range between -2.33 and -0.50%o. These strictly negative values contrast with the large range and mainly positive values previously reported for comparable silicate samples and shown here to be affected by analytical problems. Thus we propose a preliminary, revised terrestrial CI cycle, mainly dominated by negative and zero delta Cl-37 values. (C) 2007 Elsevier B.V. All rights reserved.

Evaluation of PCR to detect Theileria parva in field-collected tick and bovine samples in Tanzania

The ability of PCR to detect infections of Theileria parva, the cause of East Coast Fever, in field-collected tick and bovine samples from Tanzania was evaluated. PCR-detected infection prevalence was high (15/20, 75%) in unfed adult Rhipicephalus appendiculatus ticks that fed as nymphs on an acutely-infected calf, but low (22/836, 2.6%) in unfed adult R. appendiculatus collected from field sites in Tanzania. Tick infection prevalence was comparable to that in previous studies that used salivary gland staining to detect T parva infection in field-collected host-seeking ticks. Of 282 naturally-exposed zebu calves, seven had PCR-positive buffy coat samples prior to detection of Theileria spp. parasites in stained huffy coat cells or lymph node biopsies. Evidence of Theileria spp. infections was detected in stained smears of lymph node biopsies from 109 calves (38.6%) and huffy coat samples from 81 (28.7%), while huffy coat samples from 66 (23.4%) were PCR-positive for T parva. Implications of these findings for the sensitivity and specificity of the PCR are discussed. (C) 2003 Elsevier Science B.V. All rights reserved.

Developing a fluorimetric sequential injection methodology to study adsorption/desorption of glyphosate on soil and sediment samples

This paper describes the development of a sequential injection method to automate the fluorimetric determination of glyphosate based on a first step of oxidation to glycine by hypochlorite at 48 degrees C, followed by reaction with the fluorogenic reagent o-phthaldialdehyde in presence of 2-mercaptoethanol in borate buffer (pH > 9) to produce a fluorescent 1-(2`-hydroxyethylthio)-2-N-alkylisoindole. The proposed method has a linear response for glyphosate concentrations between 0.25 and 25.0 mu mol L(-1), with limits of detection and quantification of 0.08 and 0.25 mu mol L(-1), respectively. The sampling rate of the method is 18 samples per hour, consuming only a fraction of reagents consumed by the chromatographic method based on the same chemistry. The method was applied to study adsorption/desorption properties in a soil and in a sediment sample. Adsorption and desorption isotherms were properly fitted by Freundlich and Langmuir equations, leading to adsorption capacities of 1384 +/- 26 and 295 +/- 30 mg kg(-1) for the soil and sediment samples, respectively. These values are consistent with the literature, with the larger adsorption capacity of the soil being explained by its larger content of clay minerals, while the sediment was predominantly sandy. (C) 2011 Elsevier B.V. All rights reserved.

Spectrophotometric determination of zinc in pharmaceutical and biological samples with di-2-pyridyl ketone benzoylhydrazone: A simple, fast, accurate and sensitive method

A simple, fast, accurate, and sensitive spectrophotometric method was developed to determine zinc(II). This method is based on the reaction of Zn(II) with di-2-pyridyl ketone benzoylhydrazone (DPKBH), at pH=5.5 and 50% (v/v) ethanol. Beers law was obeyed in the range 0.020-1.82 mu g mL(-1) with a molar apsorptivity of 3.64 x 10(4) L mol(-1) cm(-1), and a detection limit (3) of 2.29 mu g L-1. The action of some interfering ions was verified and the developed method applied to pharmaceutical and biological samples. The results were then compared with those obtained by using a flame atomic absorption technique.

Simultaneous analysis of free amino acids and biogenic amines in honey and wine samples using in loop orthophthalaldeyde derivatization procedure

This work presents a RP-HPLC method for the simultaneous quantification of free amino acids and biogenic amines in liquid food matrices and the results of the application to honey and wine samples obtained from different production processes and geographic origins. The developed methodology is based on a pre-column derivatization with o-phthaldialdehyde carried out in the sample injection loop. The compounds were separated in a Nova-Pack RP-C18 column (150 mm × 3.9 mm, 4 μm) at 35 °C. The mobile phase used was a mixture of phase A: 10 mM sodium phosphate buffer (pH 7.3), methanol and tetrahydrofuran (91:8:1); and phase B: methanol and phosphate buffer (80:20), with a flow rate of 1.0 ml/min. Fluorescence detection was used at an excitation wavelength of 335 nm and an emission wavelength of 440 nm. The separation and quantification of 19 amino acids and 6 amines was carried out in a single run as their OPA/MCE derivatives elute within 80 min, ensuring a reproducible quantification. The method showed to be adequate for the purpose, with an average RSD of 2% for the different amino acids; detection limits varying between 0.71 mg/l (Asn) and 8.26 mg/l (Lys) and recovery rates between 63.0% (Cad) and 98.0% (Asp). The amino acids present at the highest concentration in honey and wine samples were phenylalanine and arginine, respectively. Only residual levels of biogenic amines were detected in the analysed samples.

Antimicrobial resistance of Salmonella serotypes isolated from slaughter-age pigs and environmental samples

The aim of this study was to determine the antimicrobial resistance patterns of Salmonella strains isolated from slaughter-age pigs and environmental samples collected at modern swine raising facilities in Brazil. Seventeen isolates of six serotypes of Salmonella enterica subsp. enterica were isolated out of 1,026 collected samples: Salmonella Typhimurium (1), Salmonella Agona (5), Salmonella Sandiego (5), Salmonella Rissen (1), Salmonella Senftenberg (4), and Salmonella Javiana (1). Resistance patterns were determined to extended-spectrum penicillin (ampicillin), broad-spectrum cephalosporins (cefotaxime and ceftriaxone), aminoglycosides (streptomycin, neomycin, gentamicin, amikacin, and tobramycin), narrow-spectrum quinolone (nalidixic acid), broad-spectrum quinolone (ciprofloxacin and norfloxacin), tetracycline, trimethoprim, and chloramphenicol. Antimicrobial resistance patterns varied among serotypes, but isolates from a single serotype consistently showed the same resistance profile. All isolates were resistant to tetracycline, streptomycin, and nalidixic acid. One isolate, Salmonella Rissen, was also resistant to cefotaxime and tobramycin. All serotypes were susceptible to ceftriaxone, norfloxacin, ciprofloxacin, ampicillin, gentamicin, and chloramphenicol. The high resistance to tetracycline and streptomycin may be linked to their common use as therapeutic drugs on the tested farms. No relation was seen between nalidixic acid and fluoroquinolone resistance.

Shigatoxigenic Escherichia coli serogroups O157, O111 and O113 in feces, water and milk samples from dairy farms

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

Cheap assays of malate, glycerol and ethanol in fermenting must and food samples

A preparation, enriched with malate dehydrogenase (MDH), alcohol dehydrogenase (ADH), glycerol -3- P dehydrogenase (GPDH) and glycerol kinase (GK), was obtained from dry baker's yeast. This preparation was used to assay glycerol, ethanol and malate measuring the variations in absorbance (NADH formation) at 340 nm. Good degrees of recoveries were obtained when glycerol was added to red wine and fermenting sugar-cane juice and when L-malate was added to commercial apple juice samples. Good results were also obtained when ethanol was assayed in fermented sugar-cane juice and wine samples, using both the partially purified preparation obtained from dry yeast and a purified commercial alcohol dehydrogenase.

Heteroplasmy in Hair: Study of Mitochondrial DNA Third Hypervariable Region in Hair and Blood Samples

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

Organochlorine pesticides and polychlorinated biphenyls in soil and water samples in the northeastern part of São Paulo State, Brazil

Detailed analyses of persistent organic pollutants (POPs) such as organochlorine pesticides (OCPs), hexachlorocyclohexane (HCH) isomers (HCHs), dichlorodiphenyltrichloro ethane (DDT) and its metabolites (DDTs) and congeners of polychlorinated biphenyls (PCBs) in soil and surface water from the northeastern São Paulo, Brazil allowed the evaluation of the contamination status, distribution and possible pollution sources. The pesticides and PCBs demonstrated markedly different distributions, reflecting different agricultural, domestic and industrial usage in each region studied. The ranges of HCH, DDT, and PCBs concentrations in the soil samples were 0.05-0.92, 0.12-11.01, 0.02-0.25 ng g(-1) dry wt, respectively, and in the surface water samples were 0.02-0.6, 0.02-0.58 and 0.02-0.5 ng l(-1), respectively. Overall elevated levels of DDT and PCB were recorded in region 2, a site very close to melting, automotive batteries industries, and agricultural practice regions. High ratios of metabolites of DDT to DDT isomers revealed the recent use of DDT in this environment. The sources of contamination are closely related to human activities, such as domestic and industrial discharge, street runoff, agricultural pesticides and soil erosion, due to deforestation as well as atmospheric transport. (c) 2006 Elsevier Ltd. All rights reserved.

Comparison of conventional PCR, quantitative PCR, bacteriological culture and the Warthin Starry technique to detect Leptospira spp. in kidney and liver samples from naturally infected sheep from Brazil

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

Distribution of Cr, Ni, Cu, Cd and Pb in different molecular size of humic fractions extracted from water and sediment samples collected at Anhumas reservoir - Araraquara/SP

In this work was studied the distribution of Cr, Ni, Cu, Cd and Pb in humic fractions with different molecular size. The HS were extracted from waters (AHS), surface sediments (HESS), interface water sediment (HSIS) and bottom sediment (HSBS) collected in the Anhumas surface water collection reservoir, located in the district of Araraquara - São Paulo State Brazil. The humic substances were extracted by procedures recommended by International Humic Substances Society (IHSS). After purification by dialysis, the humic substances were fractionated using a multistage tangential flow ultrafiltration system. The fractionation patterns of HS characterized a mass distribution relatively uniform among the fractions with different molecular sizes, with larger values in the fractions F-2 (20.8%) and F-4 (23.8%), Except for the ions Pb(II) and Cu(II), which presented relatively higher concentrations in the fractions F-2 and F-4, respectively. In general, chromium, nickel, cadmium and lead have similar distributions in the five fractions with larger and medium molecular sizes (F-1 to F-5). With relation to the mass distributions in the different humic substances fractions extracted from sediment samples collected at three depth, they presented 42-48% of HS in the fractions with larger molecular sizes (F-1 and F-2), 29-31% in the middle fractions (F-3 and F-4) and 13-20% in the fractions with smaller molecular sizes (F-5 and F-6). In general, the metallic ions presented distributions similar among the respective fractions F-1 to F-6, Exceptions for Pb(II) and M(II) in surface sediment with concentrations relatively smaller in the fractions F-2 and F-4, respectively,