Optimal designs for 2-color microarray experiments.

Statisticians can play a crucial role in the design of gene expression studies to ensure the most effective allocation of available resources. This paper considers Pareto optimal designs for gene expression studies involving 2-color microarrays. Pareto optimality enables the recommendation of designs that are particularly efficient for the effects of most interest to biologists. This is relevant in the microarray context where analysis is typically carried out separately for those effects. Our approach will allow for effects of interest that correspond to contrasts rather than solely considering parameters of the linear model. We further develop the approach to cater for additional experimental considerations such as contrasts that are of equal scientific interest. This amounts to partitioning all relevant contrasts into subsets of effects that are of equal importance. Based on the partitions, a penalty is employed in order to recommend designs for complex and varied microarray experiments. Finally, we address the issue of gene-specific dye bias. We illustrate using studies of leukemia and breast cancer.

Acneiform eruption caused by amineptine. A case report and review of the literature.

Acne caused by amineptine has always been described with typical characteristic clinical features, and the retentional and cutaneous lesions are dose related. We present a case of acne-like eruption due to amineptine in a woman under treatment for chronic depression.

The Salmonella mutagenicity assay in a surface water quality monitoring program based on a 20-year survey.

Since 1979, the Environmental Agency of São Paulo State in Brazil, CETESB, has been using the Salmonella mutagenicity assay to assess the quality of natural waters. This paper is a compilation of data obtained during the last 20 years from more than a thousand samples. Potencies up to 30,000 revertants/l were observed in 137 positive samples. The Salmonella typhimurium strain TA98 was more sensitive than TA100; 79% of the mutagenicity was detected by this strain, regardless of the presence of S9-mix. A classification of the mutagenic response was proposed to facilitate in the dissemination of the information to the public. The classification was low, moderate, high and extreme for samples with mutagenic potency (revertants/l equivalent) of < 500, 500-2500, 2500-5000 and > 5000, respectively. As a result of this effort to standardize methodologies, compile and classify the mutagenic effect of water pollution, in 1998, the Salmonella mutagenicity assay was officially and systematically included in the São Paulo State Water Quality Monitoring Program. This assay has proven to be a useful tool in the identification of important pollution sources. Correction and prevention actions in Water Pollution Control Programs were generated as a result.

Detection of cholera (ctx) and zonula occludens (zot) toxin genes in Vibrio cholerae O1, O139 and non-O1 strains.

Vibrio cholerae O1 and V. cholerae non-O1 strains isolated from environmental samples collected in São Paulo, Brazil, during cholera epidemics and pre-epidemic periods were examined for the presence of toxin genes. V. cholerae O1 strains isolated from clinical samples in Peru and Mexico, and V. cholerae O139 strains from India were also examined for the presence of ctx (cholera toxin gene) and zot (zonula occludens toxin gene) by polymerase chain reaction (PCR). A modified DNA-extraction method applied in this study yielded satisfactory recovery of genomic DNA from vibrios. Results showed that strains of V. cholerae O1 isolated during the preepidemic period were ctx (-)/zot (-) whereas strains isolated during the epidemic were ctx (+)/zot (+). All V. cholerae non-O1 strains tested in the study were ctx (-)/zot (-), whereas all V. cholerae O139 strains were ctx (+)/zot (+). Rapid detection of the virulence genes (ctx and zot) can be achieved by PCR and this can serve as an important tool in the epidemiology and surveillance of V. cholerae.

Potentially pathogenic vibrios associated with mussels from a tropical region on the Atlantic coast of Brazil.

Mussels (Perna perna) harvested on the coast of Ubatuba, in three different stations in the State of São Paulo, Brazil, were examined for Vibrio spp. over a 1 year period. The ranges of most probable number (MPN 100 g-1) were: Vibrio alginolyticus (< 3-24,000), V. parahaemolyticus (< 3-24,000), V. fluvialis (< 3-1100), V. cholerae non-O1 (< 3-23), V. furnissii (< 3-30), V. mimicus (< 3-9) and V. vulnificus (< 3-3). The highest incidence was observed for V. alginolyticus (92-100%), followed by V. parahaemolyticus (67-92%), V. fluvialis (34-67%), V. vulnificus (8-17%), V. furnissii (0-17%), V. mimicus (0-17%) and V. cholerae non-O1 (0-8%). Tests for virulence factors were positive in 34.1% of the vibrios in the rabbit ileal loop and 31.7% in the Dean test. Positive results in the Kanagawa test were obtained with 0.51% of V. parahaemolyticus strains. The mean values (MPN 100 g-1) of faecal coliforms in mussels from the three regions varied from 1100 to 44,000, and seawater collected at the same stations gave average values for faecal coliforms in the range 18-3300 MPN 100 ml-1. These results highlight the potential risks of food poisoning associated with raw or undercooked seafood.

Detection of Vibrio cholerae O1 in the aquatic environment in Brazil employing direct immunofluorescence microscopy.

Culturing and immunofluorescence (FA) methods for detection of Vibrio cholerae O1 in samples collected from the aquatic environment at selected sites in Brazil were compared. Of the samples examined, 90% were positive for V. cholerae O1 by FA but none was positive by culture, although strains of V. cholerae other than O1 strains were readily isolated. Evidence for V. cholerae O1 being autochthonous to the aquatic environment of Brazil is presented. Furthermore, FA methods are recommended for cholera surveillance programmes directed at the natural environment.

Evaluation of the genotoxic activity and acute toxicity of Euphorbia splendens latex, a molluscicide for the control of schistosomiasis.

1. The latex of Euphorbia splendens var. hislopii has a molluscicidal action at low concentration (LD90 less than 1.5 ppm or 1.5 micrograms/ml) against the vector snails of schistosomiasis. 2. In the present study, the latex in natura or after lyophilization was submitted to the Ames test and the chromotest to evaluate genotoxicity, to the Microtox System to determine acute toxicity, and to the Chinese hamster ovary cell assay (CHO) to measure cytotoxicity. 3. The latex had no mutagenic activity in the presence or absence of S9 toward the TA98 and TA100 strains of Salmonella typhimurium (Ames test) at concentrations up to 200 microliters/plate (in natura) and of 200 micrograms/plate (lyophilized). The lyophilized latex had no genotoxic activity (Chromotest) and no acute toxic effect on Photobacterium phosphoreum at concentrations up to 445 micrograms/ml, whereas the sample in natura had a toxic effect with an EC50 of 148,000 microliters/l (or ppm). In the CHO/cytotoxicity assay, the lyophilized latex had no cytotoxic effect in quantities up to 200 micrograms. 4. The latex was found to have no acute toxicity or mutagenic activity at the concentrations of 10 to 12 micrograms/ml (or ppm) that are being proposed for molluscicidal use in the field.

Evaluation of the genotoxic activity and acute toxicity of Euphorbia splendens latex, a molluscicide for the control of Schistosomiasis

The latex of euphorbia splendens var. hislopii has a molluscicidal action at low concentration (LD90 less than 1.5 ppm or 1.5 */ml) against the vector snails of schistosomiasis. In the present study, the latex in natura or after lyophilization was submitted to the Ames test and the chromotest to evaluate genotoxicity, to the Microtox System to determine acute toxicity, and to the Chinese hamster ovary cell assay (CHO) to measure cytotoxicity. The latex had no mutagenic activity in the presence or absence of S9 toward the TA98 and TA100 strains of Salmonella typhimurium (Ames test) at concentration up to 200 */plate (in natura) and of 200 *g/plate (lyophilized). The lyophilized latex had no genotoxic activity (Chromotest) and acute toxic effect on Photobacterium phosphoreum at concentrations up to 445 *g/ml, whereas the sample in natura had a toxic effect with an EC50 of 148,000 *l/l (or ppm). In the CHO/cytotoxicity assay, the lyophilized latex had no cytotoxicit effect in quantities up to 200 *g. The latex was found to have no acute toxicity or mutagenic at the concentrations of 10 to 12 *g/ml (or ppm) that are being proposed for molluscicidal use in the field

Evaluation of the fecal coliforms/fecal streptococci ration in the characterization of fecal pollution in a subtropical river

Em um estudo para determinacao da qualidade bacteriologica do Rio Atibaia Sao Paulo Brasil, desenvolvido durante o periodo de agosto de 1977 a julho de 1978, foi utilizada a relacao coliformes fecais-estreptococos fecais (CF/EF), para a caracterizacao da origem da poluicao fecal.A determinacao quantitativa de coliformes fecais e estreptococos fecais foi efetuada pela tecnica de tubos multiplos, segundo descricao no Standard Methods for the Examination of Water and Wastewater, 14a. ed. A aplicacao da relacao CF/EF permitiu caracterizar como sendo predominantemente humana a origem da contaminacao fecal ao longo do rio, embora se tenha verificado a possivel influencia de lancamentos de efluentes industriais e da distancia dos lancamentos de esgoto na caracterizacao da origem da populacao fecal em alguns pontos do rio

Isolation of enterotoxigenic Escherichia coli in water and sewage in Sao Paulo, Brazil.

A pesquisa de Escherichia coli enterotoxigenica em esgoto aguas superficiais e agua potavel contaminada revelou a presenca dessa bacteria em sete (1,9%) das 365 amostras de esgoto e em 12 (2,4%) das 495 amostras de agua examinadas. Todas as cepas, com excecao de uma, produziram somente enterotoxina termolabil e nenhuma delas apresentou os fatores de colonizacao CFA/I e CFA/II. A maioria das cepas foi sensivel aos antibioticos testados. Grande diversidade de sorotipos foi encontrada, alguns dos quais associados com diarreia em humanos