Comparative efficacy of five different rep-PCR methods to discriminate Escherichia coli populations in aquatic environments

Development of efficient techniques to discriminate the sources of E. coli in aquatic environments is essential to improve the surveillance of fecal pollution indicators, to develop strategies to identify the sources of fecal contamination, and to implement appropriate management practices to minimize gastrointestinal disease transmission. In this study the robustness of five different rep-PCR methods, such as REP-PCR, ERIC-PCR, ERIC2-PCR, BOX-PCR and (GTG)(5)-PCR were evaluated to discriminate 271 E. coli strains isolated from two watersheds (Lakelse Lake and Okanagan Lake) located in British Columbia, Canada. Cluster analysis of (GTG)(5)-PCR, BOX-PCR, REP-PCR, ERIC-PCR and ERIC2-PCR profiles of 271 E. coli revealed 43 clusters, 35 clusters, 28 clusters, 23 clusters and 14 clusters, respectively. The discriminant analysis of rep-PCR genomic fingerprints of 271 E. coli isolates yielded an average rate of correct classification (watershed-specific) of 86.8%, 82.3%, 78.4%, 72.6% and 55.8% for (GTG)(5)-PCR, BOX-PCR, REP-PCR, ERIC-PCR and ERIC2-PCR, respectively. Based on the results of cluster analysis and discriminant function analysis, (GTG)(5)-PCR was found to be the most robust molecular tool for differentiation of E. coli populations in aquatic environments.

Modeling of trihalomethane (THM) formation via chlorination of the water from Dongjiang River (source water for Hong Kong's drinking water)

The Dongjiang River is the major source of drinking water supply for Hong Kong. The deterioration of the water quality of the Dongjiang River and excessive trihalomethanes (THMs) in the tap water of some districts in Hong Kong have become causes for public concern. The main objective of the present study is to investigate and model THM formation due to the chlorination of the Dongjiang River water under different chlorination conditions. The results showed that the total THM formation ranged between 11.7 and 91.8 mg L(-1) and that control of the levels was primarily due to the reaction time and the Br(-) level in the water. Bromide concentration was a key factor in determining bromine-containing THM formation and consequently the speciation of THMs. Higher concentrations of bromide shifted THM species to more-bromine-containing ones, while the kinetics reflected the competing halogenation reactions. As the two mixed-halogen THMs had high cancer potency, the cancer risk of total THMs appeared to reach a peak at a bromide concentration ranging between 218 and 262 mg L(-1) (with a bromide to dissolved organic carbon molar ratio (Br(-)/DOC) ranging between 15 and 18 mM/mM).

Gene profiling of tumor tissue in the diagnosis of patients with carcinoma of unknown primary site (CUP): Evaluation of the Veridex 10-gene molecular assay

21109

Background: Standard treatment for most patients with CUP involves empiric chemotherapy. Since specific treatment now exists for most types of advanced carcinoma, precise identification of the primary site could lead to improved therapy. Veridex developed an optimized set of 10 gene markers, for a qRTPCR assay to identify tissue of origin of metastatic carcinoma in formalin-fixed, paraffin-embedded (FFPE) tissue samples (J Mol Diagn 8:320, 2006). The assay includes markers for 6 primary sites: lung, pancreas, colon, breast, ovary, and prostate. In this retrospective study, we evaluated the Veridex assay in patients with CUP. Methods: We obtained FFPE tissue from diagnostic biopsies on 69 CUP patients previously enrolled in empiric chemotherapy studies. The Veridex assay was performed as previously described. Assay results were correlated with clinical features, pathologic features, and response to treatment. Results: The Veridex assay yielded provisional diagnoses in 42 of 69 patients (61%): lung (15), pancreas (11), colon (12 ), ovary (4), breast (0), and prostate, (0 ). Most patients with diagnoses of lung and pancreas cancer had clinical and pathologic features compatible with these diagnoses; response rates to empiric chemotherapy (usually taxane/platinum-based) in patients with these diagnoses were 29% and 9%, respectively. The 12 patients with colon cancer diagnoses had predominantly intra-abdominal metastases (liver, peritoneum); response rate to therapy (usually taxane/platinum- based) was low (8%). The 4 patients with ovarian cancer had atypical clinical and pathologic features, and only 1 of 4 had PR to first-line taxane/platinum therapy. Conclusions: In this retrospective study, the Veridex 10-gene molecular assay was feasible and provided provisional diagnoses in a majority of patients with CUP. The diagnoses made using this assay (except ovarian cancer) were compatible with clinicopathologic features. The efficacy of cancer-specific treatment in patients diagnosed by this assay will be evaluated in prospective studies.

No significant financial relationships to disclose.

The effect of induction therapy with novel agents on stem cell mobilization in multiple myeloma

8102

Background: Thalidomide or bortezomib combined with dexamethasone (TD or BD respectively) are now being increasingly used as induction regimens for newly diagnosed multiple myeloma. There are conflicting reports on the effects of T on stem cell mobilization. Since we have used both these regimens at our center, we performed a retrospective analysis of stem cell mobilization after induction therapy with either TD (n = 22) or BD (n = 18). Methods: The patients were balanced with respect to initial Durie-Salmon stage, median number of cycles of induction therapy prior to collection, response to induction therapy, bone marrow cellularity and involvement, and time from end of therapy to collection. All patients were mobilized with G-CSF 10mcg/kg and collected in a large volume pheresis, with a goal of at least 6x10(6) CD34+ cells/kg (for tandem transplant). Results: To achieve our stem cell goal, the number of patients who required 3 or more phereses in the TD group was 17/22 whereas it was only 4/18 in the BD group. (p<0.005). 3/3 patients who had received lenalidomide also required 3 or more phereses. Also, the number of CD34+ cells/kg obtained in the TD group was less–mean of 2.8x10(6) per pheresis, as compared to a mean of 5.2x10(6) per pheresis in the BD group (p<0.01). Time to neutrophil engraftment was similar in both groups. However in the TD group there was a 1 day delay in platelets > 20,000/ul (p<0.05). Conclusions: Thus, thalidomide induction led to a lower yield of stem cells when compared to bortezomib. Differences in stem cell markers are being investigated. This may become especially important when limiting numbers of stem cells are available from elderly patients, those with prior radiation or bulk disease and when used for in vitro manipulation. It is possible that agents such as bortezomib may alter the bone marrow microenviroment differently from imids such as thalidomide.

No significant financial relationships to disclose.

antitussive potentiality offlower extract using a cough model induced by sulfur dioxide in mice

The methanol extract of the flowers of Lagerstroemia parviflora Roxb (Family: Lythraceae) was investigated for its effect on a cough model induced by sulphur dioxide gas in mice. It exhibited significant antitussive activity when compared with the control in a dose-dependent manner. The extract (100, 200, 300 mg kg(-1)) showed maximum inhibition of cough reflex at 90 min after drug administration and the antitussive activity was comparable to that of codeine phosphate, a standard antitussive agent.

Studies on Pharmacognostical features of Curcuma domestica Val

The microscopic and macroscopic characters of the rhizome of Curcuma domestica Val. were studied. The behavior of the powdered drug in the presence of various chemicals was also studied. Preliminary phytochemical screening on the various extracts of the rhizome was done in order to ascertain the various chemical constituents present. These studies were carried out to identify this plant for future research work.

Anthelmintic activity of root bark of Carissa carandas

The anthelmintic activity of the Imethanolic extract of the root bark of Carissa carandas was evaluated on adult Indian earthworm (Pheretima posthuma) using albendazole as a reference standard. The extract caused paralysis followed by the death of worm at the tested dose level. The extract at the highest tested concentration has anthelmintic activity comparable with that of standard drug albendazole.

Antidiarrhoeal evaluation of Aegle Marmelos (Correa) Linn. root extract

A study was undertaken to evaluate the in vitro and in vivo antidiarrhoeal potential of chloroform extract of the root of Aegle marmelos (Correa) Linn. The in vitro activity was determined by agar dilution and disc diffusion techniques. The extract was studied in vivo in rats. Of the 35 tested pathogenic diarrhoea causing strains, the extract was found to be mostly active against the strains of Vibrio cholerae, followed by Escherichia coli and Shigella spp. The in vitro activity was found to be comparable to that of ciprofloxacin. Further, Aegle marmelos root extract (AMRE) treated animals showed significant inhibitory activity against castor oil-induced diarrhoea. The results so obtained thus established the efficacy of AMRE as an effective antidiarrhoeal agent.

Antimicrobial potentiality of Phyllanthus amarus against drug resistant pathogens

The antimicrobial potentiality of the methanolic extract of Phyllanthus amarus (Family: Euphorbiaceae) was studied against some drug resistant pathogenic bacterial strains by disc diffusion and agar dilution method. The extract showed significant concentration-dependent antibacterial activity particularly against gram-negative microbes. The study illustrated the claim of the usefulness of the plant in dysenteric and diarrheal infections and also suggested its use in fever. The antibacterial action was mainly due to the isolated phyllanthin.

The use and performance of BioSand filters in the Artibonite Valley of Haiti: a field study of 107 households

INTRODUCTION

Approximately one billion people world-wide lack access to adequate amounts of safe water. Most are in developing countries, especially in rapidly expanding urban fringes, poor rural areas, and indigenous communities.

METHODS

In February and March 2005, a field study of 107 households was conducted to evaluate the use and performance of the Manz BioSand filter in the Artibonite Valley of Haiti. Approximately 2000 filters had been installed in this area over the preceding 5 years by the staff in Community Development at Hospital Albert Schweitzer, Deschappelle, Haiti. Interviews, observations, and water samplings were carried-out by two teams of Haitian enumerators, each consisting of a nurse and a filter technician. Water analyses were performed by Haitian lab technicians using the membrane filtration method to determine Escherichia coli counts. The enumerators and the lab technicians completed a 2 week training program before beginning the study; they worked under the direct supervision of the primary investigator. Laboratory quality was monitored by running 10% blank and 10% duplicate samples.

RESULTS

The households contained an average of 5.4 persons. Filters had been in use for an average of 2.5 years, and participants were generally satisfied with their filter's performance. Shallow, hand-dug wells provided the only source of water for 61% of the households, with 26% using water piped from springs or deep wells, and 13% having access to both. Only 3% had plumbing in their homes. Source water from shallow wells contained an average of 234 E. coli cfu/100 mL. Piped sources averaged 195 E. coli cfu/100 mL. Of the source water samples 26% contained 0-10 E. coli cfu/100 mL. Of the filtered water samples 97% contained 0-10 E. coli cfu/100 mL (80% with 0 cfu/100 mL, and 17% with 1-10 cfu/100 mL). Overall bacterial removal efficiency for the filters was calculated to be 98.5%. Turbidity decreased from an average of 6.2 NTU in source water samples to 0.9 NTU in the filtered water. None of the households treated the water after filtering; 91% used the filtered water only for drinking. No problems related to filter construction were observed; 13% were found to have significantly decreased flow rates (all restored by cleaning the filter). Recontamination was found to occur, with only 3% of the samples from the filters' spouts containing >10 E. coli cfu/100 mL and 22% of the stored filtered water samples at point-of-use containing >10 cfu/100 mL.

CONCLUSION

The Manz BioSand filters are an attractive option for supplying water treatment to family units in rural areas of poorly developed countries.

Antibacterial and antifungal activities of extracts of combretum molle

OBJECTIVE

In traditional medical practices of Ethiopia the aqueous extracts obtained from the stem bark of Combretum molle (R. Br. Ex. G. Don.) Engl & Diels (Combretaceae) have a longstanding reputation for the treatment of liver diseases malaria and tuberculosis. Owing to the widespread traditional uses of this plant, the studyinvestigated the antimicrobial activity the bark extract of this plant against Gram positive and and Gram negative bacteria.

METHODS

Petroleum ether, dichloromethane and acetone fractions of the bark of the plant were prepared by soxhlet extraction and screened for their antimicrobial activity. The acetone fraction exhibited a powerful activity and was therefore further tested against twenty-one bacterial and six fungal strains. The minimum inhibitory concentration (MIC) of this extract was determined by checker board technique using nutrient agar medium. The zones of inhibition produced by the extract against bacteria and fungi were determined and compared by disc diffusion technique with those of pure ciprofloxacin and griseofulvin, respectively.

RESULTS

The highest antibacterial action of the acetone extract was against the Gram negative organisms EscherIchia coli and Shigella spp with an MIC value of 50 mg/ml. The activity of the extract against these bacteria was comparable to that of ciprofloxacin when assessed by the disc diffusion technique. Among the fungal strains tested Candida albicans showed high susceptibility to the extract and growth was completely inhibited at a concentration of 400 microg/ml. At the same concentration, the acetone extract and the standard antifungal drug griseofulvin produced comparable zones of inhibition on C. albicans. Studies on the mode of action of the extract indicated that it was bactericidal and fungicidal. The antimicrobial activity of the extract was attributed to the high amount of hydrolysable tannins present in the bark of the plant.

CONCLUSION

The acetone extract of the stem bark of C. molle has the potential for use as a natural antimicrobial agent. Further in vivo antimicrobial, phytochemical and toxicological studies are requireed to evaluate the chemotherapeutic effect of the plant.

Development of a clinically feasible molecular assay to predict recurrence of Dukes’ B colon cancer

20110

Background: The 5-year survival rate of Dukes’ B colon cancer patients is approximately 75%. In our earlier genome-wide measurements of gene expression we have identified a 23-gene signature that sub-classifies Dukes’ B tumors and may provide better means of risk assessment on an individual basis for these colon cancer patients. The aim of this study is to validate this gene signature in an independent and more diverse group of patients, and further develop this prognostic signature into a clinical feasible test using formalin-fixed paraffin-embedded (FFPE) tissue samples. Methods: Using Affymetrix U133a GeneChip we analyzed the expression of the 23 genes in total RNA of frozen tumor samples from 123 Dukes’ B patients who did not receive adjuvant systemic treatment. Furthermore, we developed a quantitative RT-PCR assay for this gene signature in order to perform the test with standard clinical FFPE samples. Results: In the independent validation set of 123 patients, the gene signature proved to be informative in identifying patients who would develop distant metastasis (hazard ratio, HR 2.56; 95% confidence interval CI, 1.01–6.48), even when corrected for the traditional prognostic factors in multivariate analysis (HR, 2.73; 95% CI, 0.97–7.73). The RT-PCR assay developed for this gene signature was also validated in an independent set of 114 patients as a strong prognostic factor for the development of distant recurrence (HR, 6.38; 95% CI, 2.88–14.2) in univariate analysis and in multivariate analysis (HR, 13.3; 95% CI, 5.13–34.4). Conclusions: Our data provide not only a validation of the pre-defined prognostic gene signature for Dukes’ B colon cancer patients but also a clear feasibility of testing the gene signature using RT-PCR with standard FFPE specimens. The ability of such a test to identify patients that have an unfavorable outcome demonstrates potential clinical importance that could lead clinicians to choose a more aggressive therapeutic option for the high-risk patients.

[Table: see text]

A quantitative reverse transcriptase polymerase chain reaction assay to identify metastatic carcinoma tissue of origin

20024

Background: Carcinoma of unknown primary (CUP) wherein metastatic disease presents without an identifiable primary tumor site represents approximately 3–5% of all cancers. Identifying the origin of the primary tumor in patients with CUP can enable rational choice of therapeutic regimens. We developed an optimized set of ten gene markers for a quantitative reverse transcriptase polymerase chain reaction (qRTPCR) assay, and demonstrated high accuracy in predicting the tissue of origin when used on with formalin-fixed, paraffin-embedded (FFPE) metastatic carcinoma samples. Methods: Twenty-three putative tissue-specific markers for lung, colon, pancreas, breast, prostate and ovarian carcinomas were nominated by querying a gene expression profile database and by performing a literature search. Ten of these marker candidates were then selected based on validation by qRTPCR on 205 FFPE metastatic carcinomas of known tissue origin. Next, we optimized the RNA isolation and qRTPCR methods for these ten markers, and tested the qRTPCR assay on two sets of FFPE metastatic tumors. Results: We applied the 10-gene qRTPCR assay to a set of 260 metastatic tumors of known origin, generating an overall accuracy of 78%. Furthermore we tested an independent set of 48 metastatic samples, including thirty-seven samples where either the tissue of origin was known or which initially presented as CUP but were subsequently resolved. In these 48 samples, our assay demonstrated an accuracy of 76%. Conclusions: Our results suggested that optimized ten-gene markers qRTPCR assay reliably predicts tissue of origin of metastatic carcinomas in FFPE tissues. Such assay can significantly improve the rate of tissue of origin identification for carcinoma of unknown primary.

[Table: see text]

Comparative anti - microbial evaluation studies of the extracts and isolates of leaves & bark of wrightia tomentosa

The Butanol and Ethanol extract of the leaves and bark of Wrightia tomentosa along with its seven pure component isolates (BLF(28), BLF(29*), BBF(29), ELF(3), ELF7, ELF(17*), EBF(7) ) after fractionation by column chromatography were evaluated for antimicrobial activity against Gram positive (S. aureus, S. fecalis, S.albus and B.subtilis) and Gram negative (Escherichia coli, Pseudomonas aeruginosa, Proteus vulgaris & Klebsiella aerogenes) bacteria and the fungi Candida albicans by disc diffusion method. The extracts and isolates showed different degree of activity against pathogenic microbes. The results obtained were compared with standard drugs Ciprofloxacin (10μg) and Clotrimazole (10μg). The isolates of butanol bark extract (BBF(29)) followed by leaf extract(BLF(29*)) were considerably more effective than the ethanol leaf and bark extract in inhibiting all the microbial strains.

Effect of Mesua ferrea Linn. flower extract on Salmonella

Based on its traditional uses in folk medicine, the whole flower extract of Mesua ferrea Linn. was tested for its in vitro antimicrobial efficacy against five different strains of Salmonella spp. All the strains were found to be highly sensitive to the extract, MIC of the extract against each organism being 50 microg/ml. The extract was tested in vitro for its mode of antibacterial activity against S. Typhimurium NCTC 74 and it was found to be bactericidal in action. In vivo studies of this extract offered significant protection to Swiss albino mice at doses approximately 2 and 4 mg/mouse when challenged with 50 median lethal dose of S. Typhimurium NCTC 74. Further, the extract caused statistically significant reduction in viable count of the strain in liver, spleen and heart blood of challenged mice.

PHARMACOGNOSTICAL STUDIES ON THE LEAVES OF Cassia tora Linn. (FAM. CAESALPINIACEAE)

The leaves and seeds of Cassia tora (Family Caesalpinaceae) are used in the treatment of leprosy, ring worm, flatulence, colic, dyspepsia, constipation, cough, bronchitis and cardiac disorders in the Ayurvedic systems of medicine. The present study deals with the study of macroscopic characters of the leaves, ash values, extractive values, behavior on treatment with different chemical reagents and fluorescence characters under ultraviolet light. Preliminary phytochemical studies on different extractives of the leaves were also performed. These studies will help in the identification of the plant for further research.

Evaluation of antitussive activity of Lagerstroemia parviflora leaf extract

The methanol extract of the leaves of Lagerstroemia parviflora Roxb was investigated for its effect on a cough model induced by sulfur dioxide gas in mice. It exhibited significant antitussive activity when compared with the control in a dose-dependent manner. The L. parviflora extract (100, 200, 300 mg/kg) showed maximum inhibition of cough reflex at 90 min after drug administration and the antitussive activity was comparable to that of codeine phosphate, a standard antitussive agent.

Origins and implications of drinking water odours in lakes and reservoirs of British Columbia, Canada

The relationship between commonly measured limnological parameters and odours was examined in 16 reservoirs and lakes used as sources for drinking water and three reference lakes. Odour analysis was conducted using flavour profile analysis (FPA) and, on select lakes, gas chromatography ion-trap mass spectrometry (GC-ITMS) for target compounds. Total phosphorus (TP) was the best single predictor of FPA intensity and multiple regression models accounted for 37-39% of intensity variance in the epilimnion and metalimnion, respectively. Earthy odours were more prevalent in reservoirs and lakes with higher TP, whereas decomposing vegetation and green vegetation+grassy odours almost exclusively occurred when TP was lower (<13 microg P/L). Only geosmin was identified with GC-ITMS, and it was found to occur in lakes and reservoirs of higher trophic status (e.g. more algal biomass). Infrequent episodic events in the Greater Victoria's principal reservoir (e.g. algal blooms) have previously been linked with taste and odour problems in their tap water. However, analysis of odours under the conditions of this study (i.e. no strong odour episodes in the source reservoir) suggest that typical odours prevalent in tap water originating from Sooke Lake Reservoir are derived from treatment processes or the distribution system, not directly from the reservoir. This study demonstrates the utility of employing relatively simple and established methods to better understand management issues of a drinking water system.

Foraminifers as indicators of marine pollution: a culture experiment with Rosalina leei

In order to develop a viable foraminiferal proxy for heavy metal pollutants, juvenile specimens of Rosalina leei were subjected to different mercury concentrations (0-180 ng/l). Initially considerable growth was observed in specimens kept in saline water having a mercury concentration up to 100 ng/l. But with the gradual increase in concentration of mercury the growth rate started decreasing. Total growth achieved was significantly lower in case of specimens kept at relatively higher mercury concentrations then those maintained in normal saline water. The most significant result of this experiment was the addition of abnormal chambers in the specimens kept at higher mercury concentration. Later the specimens kept at highest concentration (180 ng/l) were subjected to progressively increasing concentration of mercury to see the further effects and it was found that the specimens were still living at as high a mercury concentration as 260 ng/l although there was no growth.

Antibacterial potentiality ofMesua ferrea Linn. flowers

The antibacterial efficacy of the methanol extract of whole flowers of Mesua ferrea Linn. was studied against various strains of bacteria. It could inhibit a large number of Gram-positive and Gram-negative bacteria at concentration ranges of 100 to 50 microg/ml, or even lower, as against vibrios and Escherichia coli. In in vivo tests, used at concentrations of 100 and 200 microg/g of body weight, it offered significant protection to Swiss strain of albino mice when challenged with 50 MLD of a virulent strain Sulmonella typhimurium ATCC 6539. Mortality in mice due to these two dosages of the extract alone was insignificant. The extract at 200 microg/g body weight dosage, could significantly reduce the viable count of the strain Sulmonella typhimurium ATCC 6539 in liver, spleen and heart blood of the extract treated challenged mice.

Emergence of mesua ferrea linn. Leaf extract as a potent bactericide

The methanolic extract of leaves of Mesua ferrea Linn. were tested for its antibacterial potentiality against 103 various strains of bacteria including Staphylococcus aureus, Bacillus spps. Klebsiella spps., Streptococus pneumoniae, Sarcina lutea, Lactobacilus arabinosus, Escherichia coli, shigellae, salmonellae, Proteus spps., Pseudomonas spps. and the vibrios. Significant antibacterial effects were produced by the extract against Staphylococcus aureus, Bacillus sppa., lactobacilli, Escherichia coli, shigellae and salmonellae and the results were compared with standard antibiotic ciprofloxacin. Further the extract was proved to be bacterial in its action.

Antimicrobial potentiality of a phenothiazine group of antipsychotic drug-prochlorperazine

The antipsychotic drug, prochlorperazine (Pcp), was tested for its antimicrobial efficacy against 103 strains belonging to both gram positive and gram negative bacteria. The drug was found to possess maximum activity against Staphylococcus aureus, Vibrio cholerae and Shigella spp. Pcp was moderately active against E. coli but most of the strains belonging to Bacillus spp, Klebsiella spp, Salmonella spp and Lactobacillus spp were found to be resistant to this drug. The drug was tested for its mode of antibacterial activity against Shigella dysenteriae 1 and it was found to be bacteriostatic in action. In in vivo studies, Pcp offered significant protection to Swiss albino mice at concentrations of 0.75 micro g/g (P < 0.01) and 1.5 microg/g (P < 0.001) body weight when challenged with 50 median lethal dose of Salmonella typhimurium NCTC 74. Thus the result depicts that prochlorperazine may emerge as a strong antimicrobial drug to replace the conventional antibiotics and to overcome the problem of drug resistance.

Antimicrobial activity of the mycotoxin citrinin obtained from the fungus penicillium citrinum

The mycotoxin Citrinin was obtained from the fungus Penicillium citrinum. It was tested for it's Minimum Inhibitory Concentration (MIC) against some gram positive strains viz. Staphylococcus aureus, Bacillus pumilus, Bacillus subtillis, Bacillus cereus, Klebsiella pneumoniae, Streptococcus pneumoniae, Lactobacillus arabinosus and gram negative strains E.Coli, Shigella dysenteriae, shigella sonnei, shigella boydii, Salmonella typhimurium, Proteus mirabilis and Vibrio cholerae. Further the zones of inhibition produced by the fungal extract against the bacterial strains were assayed and compared with those produced by the standard antibiotic ciprofloxacin.