Recently the EPA placed Aeromonas hydrophila on the Candidate Contaminant List (CCL). It has long been known to be a pathogen of cold blooded animals and now is a suspected human opportunistic pathogen as well. Among the various virulence factors produced by A. hydrophila, the cytolytic enterotoxin (AHCYTOEN) is by far one of the most important contributors to the pathogenicity of the organism. This factor is also produced by other pathogenic Aeromonas spp. In this study, PCR technology was used to detect AHCYTOEN gene from a simulated water distribution system. A set of primers was selected to amplify the unique sequence of a pathogenic island, AHCYTOEN gene. To examine the sensitivity of the PCR, serial dilutions of pure A. hydrophila culture were tested. The PCR technique used was sensitive enough to detect samples containing less than 10.0 cells/ml. Source water, bulk water, and simulated distribution biofilm samples were examined for the gene. Biofilm and bulk water samples exposed to raw source water were collected on 4 occasions during a 24-day period. PCR technology detected the AHCYTOEN gene from 100 % of the bulk water samples and 85% of tightly bound biofilm (TB) samples from a simulated water distribution system while no positive results were observed in loosely bound biofilm samples (LB). After the inlet line of the system was changed to normally treated distribution water, 11 biofilm samples were collected on 3 occasions during 15 day sampling period along with bulk water samples. No positive results were observed from the bulk water and LB samples while 91% of TB samples tested for the presence of the gene. No significant difference was observed in detection by PCR from biofilm samples before and after the switch to chloraminated water. / Department of Biology

Quality control procedures during food processing may involve either lengthy enrichment steps, precluding enumeration of bacteria in contaminated food, or direct inoculation of food samples onto appropriate selective media for subsequent enumeration. However, sublethally injured bacteria often fail to grow on selective media, enabling them to evade detection and intervention measures and ultimately threaten the health of consumers. This study compares traditional selective and nonselective agar-based overlays versus two commercial systems (Petrifilm and Easygel) for recovery of injured Escherichia coli B-41560, originally an isolate from ground beef. Bacteria were propagated in tryptic soy broth (TSB), ground beef, or infant milk formula (IMF) to a density of 106-108 CFU/mL, and stressed for six minutes either in lactic acid (pH of 4.5) or heat-shocked for 3 min. at 60°C. Samples were pour- plated in basal layers of either tryptic soy agar (TSA), Sorbitol MacConkey (SMAC), or Violet Red Bile (VRB) agar and resuscitated for 4h prior to addition of agar overlays. Other stressed bacteria were plated directly onto the commercial media Petrifilm and Easygel. Our results indicate that the use of selective and nonselective agar overlays for sensitive recovery and accurate enumeration of E. coli B-41560 is dependent on the stress treatment and food system. These data underscore the need to implement food safety measures that address sublethally- injured bacteria such as E. coli O157:H7, without the use of enrichment steps, in order to avoid underestimation of true densities for target pathogens. / Department of Biology

In some environmental situations, environmental effects caused by elevated metals resulting from past mining and smelting activities can be observed in nearby receiving water bodies several decades after mine and smelter closure. There is a growing need for managing the hazardous solid wastes such as mining wastes as well as for assessing water quality and for sustainable management of sediment quality. The work presented in this thesis examined the mobilization of metals from two metal sources: mining wastes from a mine site in Vietnam and sediments from a contaminated lake in Sweden in order to test the hypothesis that mobilization of metals will be increased, when the environmental conditions change by e.g. exposure of mining wastes to oxidative weathering, change of redox conditions at the water-sediment interface and resuspension of sediments. The results from this work under field and laboratory conditions have verified the hypothesis. The exposure of sulphidic mining wastes in oxidative weathering conditions may cause long-term production of ARD and the resultant long-term mobility of metals. The oxidation/resuspension of sediments is an important factor for the release of trace metals Zn, Cu and Cd into the solution and substantial amounts of particles and, hence, associated metals into overlying water. The concomitant changes in pH during oxidation/resuspension of sediment play a significant role in the metal release both to redox sensitive elements Fe and Mn and trace elements Zn, Cu and Cd. The concomitant change in DOC during oxidation/resuspension can also contribute to the increased mobility of study metals. The field study was coupled to intermittent operation of a hydropower plant. The mobility of the metals was higher under operation compared to non-operation and, thus, the potential impacts on dispersal of metal pollution to downstream aquatic environments. The sudden increase in water flow upon the hydropower plant upon shifts from inactive to active state could cause immediate release of particles and thus particulate metals in the overlying water. However, the magnitude and its integrated effects in fluxes of metals over the season call for further research. There is a need to further investigate the impacts of hydropower generation in a longer period of time and at a higher frequency of observations at the very start of the hydropower operation. The results from this multidisciplinary approach would give a basis for an optimal operation of the hydropower plant to minimize the metal pollution associated with the water flow. / <p>The series number is changed from 410 to 430 and the ISBN is changed from 978-91-85895-56-4 to 978-91-7393-926-3.</p>

The development of a scum in a commercial sports drink is of concern because the product would be of poor quality, which may result in financial losses due to consumer rejection of the product and hence a decrease in the firm’s market share. The scum could be harmful to health and as such the firm could be litigated. Several factors, including microbial proliferation, may be the cause of the development of a scum in sports drink, but the actual cause seems not to have been established. The aim of this study was to characterise the scum in sports drink and determine the effects of preservation factors (pasteurisation, chemical preservatives and refrigeration) on its development. Samples of the sports drink were taken at different stages of processing to determine the effect of preservatives, pasteurisation and storage temperature on scum development. Some samples were kept at room temperature (approx. 25°C) and others were kept in the refrigerator (approx. 4ºC) during the study. A total of 150 samples were analysed over a period of four months. The structural characteristics of the scum that developed in the sports drink were determined by scanning electron microscopy (SEM) and elemental analysis. The sports drink samples were analysed for their microbial load and microbial types. Consumer acceptability of pasteurised and non-pasteurised drink was compared by conducting sensory evaluation using a consumer panel of 60 panellists. Customer complaints recorded by the sports drink manufacture that were due to scum development in the drink were also reviewed to establish the impact of scum development on consumer acceptability of the drink. The results of the study indicated that scum development was due to microbial contamination of the drink. The causative organism of the scum was identified as Acinetobacter baumanii. Acinetobacter baumanii is a gram negative non-spore forming coccobacilli and does not ferment sucrose. Acinetobacter baumanii forms the scum in sports drink as a means of protection from environmental stresses. The scum was found to be a compound of C, Si and O. The non-pasteurised samples were slightly more acceptable to consumers compared to the pasteurised samples. The consumer acceptability of pasteurised drink samples was negatively affected by the loss of aroma and flavour during pasteurisation. The preservation factors (chemical preservatives, pasteurisation and refrigeration) had no effect on scum development. To prevent post pasteurisation contamination, it is recommended that the pasteurisation process be done at the filling stage instead of at the holding stage. The frequency of changing rubbers and gaskets on the filling line should be at least every two months. The drink is pasteurised at 90ºC for 20 seconds, this needs to be reduced to a level where it will not have an influence on the loss of taste and aroma of the pasteurised drink, but without reducing the effectiveness of pasteurisation. / Thesis (M.Sc.Agric.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

The genotoxicity of energetic compounds (i.e., explosives) that are known to be present in contaminated soils at military training sites has not been extensively investigated. Thus, the Salmonella mutagenicity and Muta(TM)Mouse assays were employed as in vitro assays to examine the mutagenic activity of twelve explosive compounds, as well as three soil samples from Canadian Forces Base Petawawa. Salmonella analyses employed strains TA98 (frameshift mutations) and TA100 (base-pair substitution mutations), as well as the metabolically-enhanced YG1041 (TA98 background) and YG1042 (TA100 background), with and without exogenous metabolic activation (S9). For Salmonella analyses, the results indicate that ten of the explosive compounds were mutagenic, and consistently elicited direct-acting, base-pair substitution activity. All three soil samples were also observed to be mutagenic, eliciting direct-acting, frameshift activity. Mutagenic potencies were significantly higher on the metabolically-enhanced strains for all compounds and soil samples. For Muta(TM)Mouse analyses on FE1 cells, the results indicate that the majority of explosive compounds did not exhibit mutagenic activity. All three soil samples elicited significant positive responses (PET 1 and PET 3 without S9, and PET 2 with S9), and although there is some evidence of a concentration-related trend, the responses were weak. Correspondence of the mutagenic activity observed with the two assay systems, for both the explosive compounds and soil samples, was negligible. The differential response is likely due to differences in metabolic capacity between the two assay systems. Furthermore, it is likely that there are unidentified compounds present in these soil samples that are, at least in part, responsible for the observed mutagenic activity. Additional testing of other explosive compounds, as well as soil samples from other military training sites, using a variety of in vitro and in vivo assays, is warranted in order to reliably estimate mutagenic hazard and subsequently assess risk to human health.

In this study we evaluated the use of microarray technology in Bacterial Source Tracking (BST), with the intent of identifying candidate genes to be used to differentiate between closely related strains of Escherichia coli. We anticipate that genes differentially expressed in response to stress by both a laboratory strain and environmental isolate could be used as marker genes on a microarray in BST. Using microarrays we characterized the transcriptional response of E. coli K12 MG1655 (K12), maintained for about 80 years in an artificial environment versus E. coli 43(C)-4A or E43, a strain recently isolated from the natural environment. The responses were to a temperature decrease from 37°C to 21°C, and to growth in a diluted LB broth (dLB). Overall we found that there were more genes differentially expressed between the strains than either strain's response to the stresses. At the 4-fold threshold, at reduced temperature there were only 26 genes differentially regulated by K12 and 9 by E43, respectively. In K12 the functions of some differentially expressed genes were linked to the general stress response and biofilm formation. A few genes differentially expressed by E43 were involved in the stress response. Similarly, in response to dLB there were 46 and 11 genes differentially expressed by K12 and E43 respectively. While it appeared that genes differentially expressed by K12 were involved in dealing with nutrient deficiencies, the genes differentially expressed by E43 did not show a similar pattern. Of these genes, none were obvious candidate genes for a microarray to be used in BST. However, we did find that 169, 286 and 254 genes were differentially expressed between K12 and E43 at 37°C, 21°C, and in dLB, respectively. Many of these genes were differentially expressed under all 3 growth conditions. Several of the genes differentially expressed between the strains were in the O-antigen-lipopolysaccharide gene family and are genes that could potentially be used on a microarray in BST. We found that E43, isolated from the natural environment, did not respond to the growth conditions in the same way as the model strain, E. coli K12, indicating that strains of E. coli isolated from the natural environment may not be identical to the model strain K12. It is suggested that other strains isolated from the natural environment be investigated. Such studies could also reveal genes differentially expressed between the strains that could be used on a microarray for use in BST.

Food production in urban areas has been conducted worldwide as a subsistence strategy and source of income. Recently, however, it is recognized that urban agriculture has the potential to contribute to the development of sustainable urban environments. This study examines the benefits of urban food production in North American cities, as well as focusing on some of the critical barriers to its widespread expansion and acceptance. It also explores the potential for contamination of produce from the ambient atmosphere in mid-sized urban centres. Through interviewing nine urban farmers and one urban planner, in the city of Victoria, British Columbia, I documented each producer’s knowledge of the benefits and limitations associated with urban food production. Each interviewee impressed upon me the numerous benefits that can be accrued through the practice of urban agriculture, but they also painted a picture of the struggles that urban farmers face. Issues identified included: a real and perceived risk of contamination, problems with land ownership and access, and lack of meaningful support for urban farmers. Although urban agriculture has been accepted in principle by the City of Victoria and other Canadian cities, there are many challenges that must be overcome for urban food production to truly produce a viable, sustained food system. A coordinated, comprehensive government policy for involvement in the urban food system is critical to effectively addressing urban food issues. Investigations of heavy metal levels in lettuce (Lactuca sativa) grown in sampling sites across an urban/rural gradient showed that atmospheric contamination by heavy metals is greatest at urban sites, but also affects residential and rural sites. Sampling site types included: a control area (rural farms and properties outside of Victoria); residential sites (yards in residential neighbourhoods in the City of Victoria); and, industrial/business sites (heavily trafficked and industrialized areas in downtown Victoria). Site types were intended to reflect areas perceived as safe, probably safe, and probably not safe, and were selected based on expert opinion and land use. Results indicate that caution should be exercised in growing leafy greens at downtown sites, and that growing food in most residential neighbourhoods and green spaces is typically no worse than growing greens in rural Victoria. In fact, due to the proximity of urban agriculture to the market, growing food locally eliminates the need for transportation and extra processing; reducing the extra exposure crops otherwise might face during these phases. Urban food production requires the support of communities and governments in order to contribute to both urban food security and urban sustainability. The City of Victoria has started on a path to ensuring that this food system receives the required support, but it requires concerted effort and action. Further research into urban food systems is necessary to ensure that urban food production is able to become a viable, sustained food system. / Graduate

Studien har gjorts mot bakgrund av den pågående diskussionen gällande införandet av sprutbytesverksamhet i Jönköpings län och vill till den diskussionen tillföra de skilda erfarenheterna som finns i fyra olika existerande sprutbytesprogrammen i Sverige, att jämföra likheter och skillnader i praxis och att relatera dessa erfarenheter till deras mål och resurser. Trots att lagen om sprutbyte trädde i kraft år 2006 är sprutbyte fortfarande ett kontroversiellt ämne i Sverige. I denna omtvistade form av preventiv verksamhet finns det dock en viktig del som gör ämnet mer relevant och det är de goda, sociala bieffekter som programmen medför. Dessa omnämns i studien som paramedicinsk vård. Metoden som ligger till grund för studien är kvalitativa, semistrukturerade intervjuer. Materialet har sedan analyserats för betydelsen av sitt innehåll och genom organisationsteori. Utgångspunkten är avhandlingar, vetenskapliga artiklar och litteratur i ämnet sprutbyte. Vid sprutbytesprogrammen i Sverige skiljer sig uppfattningarna åt gällande behovet och implementeringen av den paramedicinska vården i verksamheten. Likaså går åsikterna isär mellan de forskare, politiker och professionellt verksamma som intervjuats. En gemensam nämnare är dock synen på paramedicin i stort som något betydelsefullt för personer i aktivt missbruk, oavsett om det är landstinget eller socialtjänsten som bedriver den. Studiens konklusion blir således att denna form av verksamhet kräver ett holistiskt perspektiv av den vård som ska bedrivas. Samarbete utanför landstingens och kommunens gränser verkar gynnande. Landstinget har större inflytande än kommunen men kommunen har å andra sidan större resurser när det gäller paramedicinska vårdinsatser. I de landsting där eventuella sprutbytesverksamheter diskuteras kan studien ge exempel på goda respektive mindre goda paramedicinska insatser vid de program som idag är verksamma. / In light of the ongoing discussion regarding the possible introduction of needle exchange programs in Jönköping county, this study aims to compare similarities and differences in practice at four different needle exchange programs in Sweden and to relate these experiences to their objectives and resources. Despite the fact that the law of needle exchange entered into force 2006, needle exchange programs are still a controversial subject of discussion in Sweden. In this contested form of infection care there is an important part though which makes the subject more legitimate. That is the positive social side effects which come as a result of the programs. These effects are mentioned in the study as paramedic care. The method underlying the study is qualitative, semi structured interviews. The material has been analyzed for the relevance of its content and also through organization theory. The starting point is theses, scientific articles and literature on the subject of needle exchange. At the needle exchange programs in Sweden the perceptions regarding the need for and the implementation of paramedical care differs as well as the views of researchers, politicians and professionally active that we interviewed on the subject. A common denominator, however, is the perception of paramedical care at large as something significant for people in active addiction, whether it is the country council or the social services that engaged in it. The conclusion of the study is thus that this form of activities requires a holistic perspective of the care that should be conducted. Cooperation outside the county and municipal boundaries seems favorable. The county councils have more influence than the municipalities but the municipalities on the other hand have greater resources in terms of paramedical care efforts. In the county councils where any needle exchange activities are up for discussion this study could give examples on favorable and less favorable paramedical activities at programs that are currently active.

This thesis addresses gaps that exist in the theory and knowledge of ancient DNA (aDNA). Much of the underlying basis of the field has been neglected in the excitement that followed the first aDNA studies. Therefore the results of many studies have been based on untested assumptions about the nature of post mortem DNA damage, sample preservation, contamination, and the efficacy of sample decontamination techniques. The validity of such results is questionable if the assumptions prove false. Hydrolytic post mortem DNA damage may modify recovered aDNA sequences. This thesis reports new insights into the biochemical basis of, predisposition of certain sequences and nucleotide positions towards, and subsequent effects of, such damage. Parallels of post mortem damage with in vivo mutation also enable insights into DNA sequence evolution. The long-term survival of DNA, and contamination of samples with exogenous DNA are two related problems characteristic to aDNA. The survival of endogenous DNA within bone, teeth and hair samples, the susceptibility of such samples to contamination, and the efficacy of decontamination techniques used to remedy such problems are investigated. The results highlight serious flaws in using bone and teeth as a DNA source. In contrast, the results demonstrate that hair may present a valuable DNA source for future studies. Numerous studies have reported the retrieval of ancient pathogen DNA from human samples. Analyses of the DNA content within teeth extracted from putative victims of the 2^nd plague argue that such studies are at great risk from DNA degradation, and contamination arising due to environmental microorganisms. An extrapolation of these results using basic physical and chemical theory is used to evaluate the potential survival of aDNA in ancient Egyptian remains. This suggests that positive results from such samples are unlikely.

Lietuvos žaliavinio pieno užterštumo B grupės teršalais analizė 2005-2010 metais. Tyrimo metu gautų rodiklių palyginimas su Europos Sąjungos šalių narių rodiklių palyginimas. / Lithuania milk contamination Group B contamination analysis in 2005-2010 years. The study of performance comparison with the European Union member states are shown.