Clostridium difficile is a pathogen for both humans and animals and is often associated with antibiotic-associated diarrhea. Recently, several human cases of C. difficile-infection with increased mortality and morbidity have been reported. In studies performed in different countries C. difficile has been found in meat. Therefore the question whether C. difficile can be a zoonotic agent has been raised. The aim of this study was to optimize a method for isolation of C. difficile from faeces. When C. difficile is isolated from animals that do not have diarrhea the sample must be cultivated in an enrichment broth. Parameters influencing the enrichment were tested such as enrichment before and after spore selection, enrichment time, alcohol and heat chock for spore selection and if the samples had to be centrifuged or not before cultivation on agar plates. Enrichment in broth before spore selection was better than after. Heat and alcohol chock showed similar results, therefore you can chose which method you want. Cultivation from the pellet after centrifugation of the sample was better than cultivating directly from the inoculated broth. When the sample had low concentration of bacteria long enrichment time, 7 days or more, was best. The next step will be isolation of C. difficile from food-producing animals and humans and the strains will then be compared to se if the same strain is found in humans and in animals, to se if C. difficile-infection can be a zoonoz.

Microarray technology allows measurement of the expression levels of thousand of genes simultaneously. Several gene set analysis (GSA) methods are widely used for extracting useful information from microarrays, for example identifying differentially expressed pathways associated with a particular biological process or disease phenotype. Though GSA methods like Gene Set Enrichment Analysis (GSEA) are widely used for pathway analysis, these methods are solely based on statistics. Such methods can be awkward to use if knowledge of specific pathways involved in particular biological processes are the aim of the study. Here we present a novel method (Knowledge Based Gene Set Analysis: KB-GSA) which integrates knowledge about user-selected pathways that are known to be involved in specific biological processes. The method generates an easy to understand graphical visualization of the changes in expression of the genes, complemented with some common statistics about the pathway of particular interest.

It is well known that photosynthetic health impacts the overall fitness of the mature plant. This study aims to determine photosynthetic vigour of spring wheat cultivars during field development as well as their biomass composition at maturity to determine which cultivars/varieties would be optimum for cellulosic ethanol production. Additionally, specimens were grown at non-acclimating (20˚C), cold acclimating (5˚C), non-acclimating high CO2 (20˚C/750 µmol mol-1 CO2) and cold-acclimating high CO2 (5˚C/750 µmol mol-1 CO2) to resolve photosynthetic responses to different environments. Plants were photoinhibited under high irradiance (5 fold growth irradiance) and low temperature (5˚C) while photochemical efficiency of PSII was monitored throughout using chlorophyll fluorescence imaging. Vegetative production was monitored using normalised difference vegetation index. De-epoxidation of xanthophyll photoprotective pigments were also recorded using HPLC and photochemical reflectance index. Additionally, carbon assimilation rate was recorded with infra-red gas analysis methods. It was discovered that no one wheat cultivar demonstrated any photosynthetic advantage in the field or under photoinhibitory conditions. However, photosynthetic differences were observed between wheat grown in different environments. Plants that were cold-acclimated or grown under high CO2 were more resilient to photoinhibitory stress. This was also reflected by most cold-acclimated cultivars having increased triose phosphate utilization, electron transport and zeaxanthin induction. Plants acclimated to high CO2 at room temperature also displayed increased electron transport and triose phosphate utilization but had decreased zeaxanthin induction. It is hypothesized increased excitation pressure in cold acclimated and high CO2 cultivars allowed for their increase in the development of photoinhibitory tolerance.

Recreational drug use peaks in the developmental stage of adolescence in humans. In this dissertation, we used a rodent model of adolescence and behavioral assessments of intravenous (i.v.) cocaine self-administration and reinstatement of cocaine-seeking to explore age differences in these cocaine-related behaviors, and then tested for the influence of environmental enrichment and for correlations between behavior and expression of plasticity genes. Although taking similar amount of cocaine, male rats trained to self-administer cocaine during adolescence (adolescent-onset) showed attenuated cue-induced reinstatement of cocaine seeking compared with adults. This attenuated cue-induced reinstatement did not generalize to a natural reward, sucrose pellets. Then we asked whether the attenuated reinstatement may be due to rapid developmental re-organization of reinforcement circuits (high plasticity) in adolescent-onset groups. To stimulate or inhibit neuroplasticity, subjects experienced environmental enrichment or impoverishment during abstinence. Environmental manipulations had no effect in adolescent-onset groups, whereas the enriched environment attenuated cue-induced reinstatement in adults compared with their impoverished counterparts. Thus, we turned to internal factors that may contribute to age-differences in reinstatement of cocaine seeking. Using in situ hybridization to quantify the mRNA for two neuroplasticity-related genes, activity-regulated cytoskeletal-associated gene (arc) and brain-derived neurotrophic factor (bdnf), we identified that overall, arc expression in the nucleus accumbens (NAc) and bdnf expression in the medial prefrontal cortex (mPFC) was higher in adolescent-onset than in adult groups. Together our data suggest that adolescence in rodents may be a period of relative biological resistance to some long-term drug effects.

Genetic regulatory networks are of great importance in terms of scientific interests and practical medical importance. Since a number of high-throughput measurement devices are available, such as microarrays and sequencing techniques, regulatory networks have been intensively studied over the last decade. Based on these high-throughput data sets, statistical interpretations of these billions of bits are crucial for biologist to extract meaningful results. In this thesis, we compare a variety of existing regression models and apply them to construct regulatory networks which span trancription factors and microRNAs. We also propose an extended algorithm to address the local optimum issue in finding the Maximum A Posterjorj estimator. An E. coli mRNA expression microarray data set with known bona fide interactions is used to evaluate our models and we show that our regression networks with a properly chosen prior can perform comparably to the state-of-the-art regulatory network construction algorithm. Finally, we apply our models on a p53-related data set, NCI-60 data. By further incorporating available prior structural information from sequencing data, we identify several significantly enriched interactions with cell proliferation function. In both of the two data sets, we select specific examples to show that many regulatory interactions can be confirmed by previous studies or functional enrichment analysis. Through comparing statistical models, we conclude from the project that combining different models with over-representation analysis and prior structural information can improve the quality of prediction and facilitate biological interpretation. Keywords: regulatory network, variable selection, penalized maximum likelihood estimation, optimization, functional enrichment analysis.

Stereotypes in captive elephants is a widespread issue. Ways to tackle this is with social and feedenrichment among others. The aim of this study was to investigate if extra feed supply wouldaffect stereotypic behaviour in Asian elephants held in captivity. Three elephant cows wereprovided with extra feed and recorded during the night and morning. The results showed asignificant decrease in stereotypic behavior for one of the elephants, from 31% to 9,5% (P =0,003). While the second elephant did not engage in stereotypic behaviour, the third elephantshowed the same frequency of stereotypic behavior, 9%, during both baseline and treatment. Thethird elephant did increase her foraging significantly, from 31% to 54% (P = 0,02). Waken timespent foraging increased for all three elephants to 64-80% which is in the same range as in wildAsian elephants. Additional enrichment in the form of extra feed supply can be used both todecrease stereotypic behaviours and to increase foraging.

It is well known that photosynthetic health impacts the overall fitness of the mature plant. This study aims to determine photosynthetic vigour of spring wheat cultivars during field development as well as their biomass composition at maturity to determine which cultivars/varieties would be optimum for cellulosic ethanol production. Additionally, specimens were grown at non-acclimating (20˚C), cold acclimating (5˚C), non-acclimating high CO2 (20˚C/750 µmol mol-1 CO2) and cold-acclimating high CO2 (5˚C/750 µmol mol-1 CO2) to resolve photosynthetic responses to different environments. Plants were photoinhibited under high irradiance (5 fold growth irradiance) and low temperature (5˚C) while photochemical efficiency of PSII was monitored throughout using chlorophyll fluorescence imaging. Vegetative production was monitored using normalised difference vegetation index. De-epoxidation of xanthophyll photoprotective pigments were also recorded using HPLC and photochemical reflectance index. Additionally, carbon assimilation rate was recorded with infra-red gas analysis methods. It was discovered that no one wheat cultivar demonstrated any photosynthetic advantage in the field or under photoinhibitory conditions. However, photosynthetic differences were observed between wheat grown in different environments. Plants that were cold-acclimated or grown under high CO2 were more resilient to photoinhibitory stress. This was also reflected by most cold-acclimated cultivars having increased triose phosphate utilization, electron transport and zeaxanthin induction. Plants acclimated to high CO2 at room temperature also displayed increased electron transport and triose phosphate utilization but had decreased zeaxanthin induction. It is hypothesized increased excitation pressure in cold acclimated and high CO2 cultivars allowed for their increase in the development of photoinhibitory tolerance.

A widespread problem in the housing of captive animals is the occurrence and development of abnormal behaviors. In the pig breeding industry the abnormal behaviors causing the biggest welfare problems are stereotypies such as tail-biting, ear-biting, equipment-biting and belly-nosing. In this study a rope and an activation ball were tested as curative treatments to reduce the performance of these stereotypies by inducing the underlying innate behaviors. A total of 141 pigs spread over 18 pens were used as test-subjects. They were divided into three groups which were introduced to one of the two enrichments or no enrichment at all. Both the enrichments contained characteristics which mostly targeted exploratory and foraging needs and, if functional, were thought to mainly have an effect on tail-biting, ear-biting and equipment-biting. The pigs were observed both at initial contact with the enrichments and after having familiarized with them for three days, and the amount of registered enrichment interaction and performed stereotypies were used to evaluate the effect of the enrichment objects. In both enrichment treatments the enrichments occupied the pigs both on day one and after three days. The presence of equipment-biting was successfully reduced on both day one and day three while the presence of tail-biting and ear-biting only were initially reduced. No effect was found on belly-nosing in either enrichment treatment. This suggests that both enrichments are functional over time and efficient in reducing some types of harmful social behaviors. However, belly-nosing would need to be targeted with a different kind of object.

Due to the expansion of the human population we are an increasing threat to all wild animals. They are driven to exist in smaller areas and in the worst case scenario extinction. Zoos are being encouraged to improve the animal’s physical and social surroundings. Environmental enrichment is a term used for such improvements. In this behavioural study, the enrichment introduced to two Pallas cats (Felis manul) at Parken Zoo in Eskilstuna, Sweden, consisted of a fishing rod and a clothes peg with a dead mouse or chick attached. The intention was to see if the feeding enrichment could increase activity levels and how the cats were using their enclosure. The enclosure was divided into seven zones which have a varying degree of opportunities for the animals to climb, hide and rest above ground level. The environmental enrichment effects on the Pallas cats´ behaviour, activity levels and use of the enclosure were measured and recorded using instantaneous scan sampling, and the mean value was calculated for each individual. The behavioural and enclosure results proved that enrichment benefits the cats activity levels. The behaviours that showed a variation when presented with enrichment were: walking, climbing, grooming, aggressive behaviour, out of sight behaviour, crouching position, sitting and standing still.  The results showed that the cats preferred the zones in the enclosure that offered a larger view of the nearby enclosures. This study shows that providing captive felids with inexpensive, easy to administer enrichment objects can have profound effects on activity behaviours and their enclosure.

Environmental enrichment (EE) is used to improve the wellbeing of animals in human care. One way of testing what resources an animal prefers to have access to, is to make it pay a price. The price is in the form of time or energy spent to get access to the resource. When measuring the motivation of animals it is useful to compare the resource which is to be evaluated to a resource with a known value. Food is often the comparator. The maximum price paid approach measures the highest price an animal is willing to pay for access to a resource. In this study the motivation of a grey seal (Halichoerus grypus) for getting access to artificial kelp and live fish was measured. Food was used as the comparator. A large net cage with a weighted entrance and a nonweighted exit gate was used as the test arena. The seal had to enter it by opening the entrance gate which had increasing weights every day, in 10 steps up to 65 kg. The seal was not willing to pay any price for the live fish. The maximum price paid for the food was 60kg, and for the artificial kelp 10kg, i.e. 17% of the maximum price paid for food. The results suggest that neither live fish nor artificial kelp was an attractive EE for this seal. However, the study also shows that spring (reproductive period) is not a good time to test motivation in grey seals.