| 1. |
- Lungu-Mitea, Sebastian
(författare)
-
Toxicity pathways in zebrafish cell lines : an ecotoxicological perspective on "toxicity testing in the 21st century"
- 2020
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Standard toxicological in vivo testing has been challenged as the procedures are time-consuming, expensive, and require a large number of animals; given the number of problematic chemicals. Novel toxicological frameworks, such as "toxicity testing in the 21st century", proposed the use of "new approach methods" (in vitro and in silico techniques), that can be applied in high-throughput setups and would allow for the testing of a large number of compounds. However, such new approach methods need to be designed and evaluated first. Especially within ecotoxicology, the coverage of species-specific bioanalytical tools, e.g. for fish, is rather scarce. Currently, mainly in vitro assays of mammalian and bacterial origin are used. This thesis outlines how to design and scrutinise fish transient reporter gene assays. We have established transient reporter gene assays in permanent zebrafish fibroblasts and hepatocytes of the oxidative stress response and the xenobiotic metabolism toxicity pathways. We identified non-specific effects caused by transient transfection itself and suggested preventive strategies. Further, we identified toxicity pathways’ cross-talk as a significant driver of uncertainty in regards to the assessment of receptor-mediated toxicity. Additionally, we evaluated the correlation between cytotoxicity in cultured zebrafish cells and the acute toxicity observed in zebrafish embryos. When using chemical distribution models to derive bioavailable concentrations, we observed a good positive correlation between the two test systems. The results advocate an intensified use of fish in vitro assays in integrated testing strategies. Conclusively, new approach methods, as developed and applied in this thesis, show great potential in future toxicity testing and environmental monitoring.
|
|
| 2. |
- Aboshady, Hadeer Moursy
(författare)
-
Genomic variation and molecular mechanisms of the host response to gastrointestinal nematodes in small ruminants
- 2020
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Gastrointestinal nematode (GIN) infections are one of the major constrains for sheep and goat production worldwide. One of the promising control strategies is the genetic selection for resistant animals as there are no issues due to anthelmintic resistance and it aligns to demands for chemical-free food. Exploring possible phenotypic and genomic markers that could be used in breeding scheme besides understanding the mechanisms responsible for resistance were the main goals of this thesis. Thesis consists of General introduction, a brief description of GIN biology and methods to control GIN with focus on phenotypic and genomic markers, four papers and General discussion. In paper Ⅰ, a systematic review and meta-analysis were conducted to re-analyse and summarize the findings on immunoglobulins response to GIN in the literature and discuss the potential to use immunoglobulins as biomarkers of the host resistance. A conceptual model summarizing the role of immunoglobulins in resistance to GIN is proposed. In paper Ⅱ, transcriptome profiling of the abomasal mucosa and lymph node tissues were compared between non-infected, resistant and susceptible Creole goats experimentally infected with Haemonchus contortus. Results indicated that the maintenance of the integrity of the mucosa has probably the priority for the host at late infection stage. In paper Ⅲ, the dynamics of the response of the abomasal mucosa of resistant and susceptible Creole goats experimentally infected with H. contortus were compared. The immune response was activated through many relevant pathways including the Th1 immune response at different time post-infection. Interestingly, the results showed a simultaneous time series activation of Th2 related genes in resistant compared to susceptible kids. In paper Ⅳ, the genomic variants of Creole goats resistant and susceptible to H. contortus were discovered from RNAsequencing data at four different times post-infection. Single nucleotide polymorphisms, insertions and deletions that distinguish the resistant and the susceptible groups were identified and characterized through functional analysis. The T cell receptor signalling pathway was one of the top significant pathways that distinguish the resistant from the susceptible group with genomic variants in 78% of genes in this pathway.
|
|
| 3. |
- Adler, Karl
(författare)
-
Digital soil mapping and portable X-ray fluorescence prediction of cadmium, copper and zinc concentrations as decision support for crop production
- 2022
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Trace element concentrations in agricultural soil are important for crop production. Certain trace elements, e.g. copper (Cu) and zinc (Zn), are essential for crops to complete their life cycle. Other trace elements, e.g. cadmium (Cd), can be harmful to crops or the end-consumer. Hence, it is important to have maps of soil concentrations of trace elements or methods for determining concentrations in soil samples. This thesis investigated the possibility of predicting trace element concentrations (Zn, Cu, Cd) in soil samples using portable X-ray fluorescence (PXRF) measurements. It also examined usefulness of digital soil mapping (DSM) to create maps of Cu and Cd concentrations in agricultural topsoil in Sweden.Portable X-ray fluorescence models were validated at national and farm level. Predicted Zn concentrations were found to be comparable to those obtained in conventional laboratory analysis, while predicted Cd and Cu concentrations were less accurate. The most accurate PXRF models were created using non-linear machine learning algorithms, e.g. random forest.Digital soil mapping of Cd concentrations in Skåne County, combined with data from grain sampling, revealed that low Cd concentrations in winter wheat grain were associated with predicted low concentrations in soil. The map could thus be used to identify arable soils suitable for producing winter wheat for products with strict quality criteria, e.g. baby food. Digital soil mapping of Cu concentrations at national level revealed that 47% of arable soils are highly likely not at risk of Cu deficiency. Covariate importance analysis indicated importance of airborne gamma radiation measurement data in DSM of Cu and Cd concentrations.
|
|
| 4. |
- Agstam, Oskar
(författare)
-
Restoration of Nutrient Rich Lakes - Towards Better Understanding of Sediment Phosphorus Availability and Management
- 2022
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Lakes are important for many reasons as they provide valuable ecological and human services, such as drinking water and recreational use. Eutrophication, a result of excess nutrients (e.g. phosphorus (P)) in lakes, is a threat to these resources, causing impairment of water quality. Excess P loading to lakes accumulates in the sediment, consequently making sediment a potential source of P via release (internal loading). One way of counteracting effects caused by internal loading is to inactivate the pool of potentially available P in the sediment. Better information is needed for optimizing most in-lake P reduction methods, including aluminum (Al)-treatment. One of these areas is better knowledge about the availability of different P fractions, and which fractions to target with a specific dose of Al under certain environmental conditions such as bioturbation (e.g. sediment mixing by carp). We also need to deepen the knowledge about modern Altreatment methods, with respect to both treatment techniques and dosing. Knowledge about factors affecting how long the positive effects from an Al-treatment last also needs to be improved. This thesis presents results concerning optimization of Al application methods, where a novel application method that injects Al into the sediment was evaluated and a model for optimal Al dose determination is presented. Factors affecting treatment longevity were evaluated, using historical water quality records and knowledge about a previously assumed recalcitrant P form being bioavailable due to bioturbation by benthic feeding fish like carp and bream. Al-treatment methods, including practical Al application methods as well as dosing methods are developing rapidly and being applied in the field, and further work is needed to keep up with evaluating the progress of lake restoration results using methods like Al-treatment.
|
|
| 5. |
- Aguilera Nuñez, Guillermo
(författare)
-
Local and landscape-level impacts of agricultural intensification on arthropod communities and their interaction networks
- 2020
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Arthropods play a central role in agricultural landscapes being responsible for the delivery of many ecosystem services such as pollination, biological pest control, and nutrient cycling. But the current global decline of arthropods is intensified by habitat modification, loss and fragmentation, pesticide use and other intensive management practices. Thus, it is crucial to understand how such impacts affect ecosystem services provisioning. In this thesis, I aim to explore how the management of local crop fields and landscape composition affect beneficial arthropod communities at different levels, including abundances and diversity of species and species interaction networks. I focus on predaceous and parasitic insects that provide biological pest control and pollinators. I assess i) how crop diversity affects arthropod diversity, ii) how fertilisation affects the local predator community and pest control, iii) how crop type (annual vs perennial) and landscape composition affect the predator-prey and host-parasitoid interaction networks and the implications for pest control. I found that increasing crop diversity in landscapes with a high proportion of seminatural habitats can enhance the diversity of beneficial arthropods. I also detected that organic fertilisation can benefit the abundance of local predators while specialist predators that move into the crop from the surrounding habitats boost biological pest control. I also found that crop type and landscape composition have effects beyond community species composition as also the interaction networks were altered, modifying the network stability and pest control potential. My findings suggest that the main drivers of change in agricultural landscapes affect arthropod communities at different levels. Effects of habitat type and local management can be observed not only in the community composition, but some of the consequences were also reflected in the species interaction networks. Finally, I show that food web ecology can link community composition and ecosystem service provisioning.
|
|
| 6. |
- Ajal, James
(författare)
-
Growth and nitrogen economy of cereal-legume sole- and intercrops, and their effects on weed suppression
- 2021
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Crop production currently faces the dilemma of using methods that increase crop yield but with adverse environmental effects, or attaining lower yields with less environmental impacts. Applying ecological principles has shown potential in finding a middle-ground of maintaining crop yield with less inputs. In this thesis, I evaluated the role of intra– and interspecific functional diversity of cereal–legume intercrops in increasing nitrogen accumulation efficiency, competition against weeds, and improving the productivity of the mixture compared to sole crops. Peabarley and faba bean-wheat species combinations were grown in the field in Uppsala, Sweden and Taastrup, Denmark as sole crops and two-species mixtures. In addition, a pot experiment with various combinations of faba bean, wheat, and a common weed was set up under semi-controlled conditions in Sweden. Both crops and weeds were evaluated for nitrogen economy, biomass accumulation, and grain yields. Using trait space analysis, I demonstrated that intercropping, cultivar identity, and environmental differences influence trait space through phenotypic plasticity. Furthermore, intercropping facilitated more N acquisition in the cereals compared to when grown in sole crop. For crop-weed interaction, pea-barley intercrop reduced weed biomass compared to the sole-cropped pea, and the weed species’ competitiveness and dominance was influenced by nitrogen availability in the soil. Based on the results presented in this thesis, there is need to pay more attention to the functional traits of species components when designing mixtures. The weed species composition should be taken into account before nitrogen addition, otherwise, the additional nitrogen may favour mostly weed growth, at the expense of the crops. This study is timely considering the current emphasis on crop production methods that use ecological principles to address challenges in arable farming.
|
|
| 7. |
- Al-Sarraj, Razaw
(författare)
-
Analysis of factorial experiments using mixed-effects models: options for estimation, prediction and inference
- 2022
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In linear mixed-effects modelling of experiments, estimation of variance components, prediction of random effects, and computation of denominator degrees of freedom associated with inference on fixed effects, are important elements of the analysis. This thesis investigates alternatives to the likelihoodbased procedures for analysis of factorial experiments with normally distributed observations. Consistent methods, such as the maximum likelihood method, can be disadvantageous in cases where only small samples are available. Moreover, the algorithms used in linear mixed-effects models can be computationally demanding in large datasets. In this thesis, Henderson’s method 3, a non-iterative variance component estimation method, was considered for estimation of the variance components in a two-way mixed linear model with three variance components. The variance component estimator corresponding to one of the random effects was improved by perturbing the standard unbiased estimator. The improved variance component estimator performed better in terms of mean square error. In an application on a quantitative trait loci (QTL) study, the modified estimator was compared to the restricted maximum likelihood estimator on data from European wild boar × domestic pig intercross. The modified estimator was shown to approximate the results obtained from the restricted maximum likelihood (REML) method very closely. For balanced and unbalanced data in two-way with and without interaction models, the generalized prediction intervals for the random effects were derived. The coverage probabilities of the proposed intervals were compared with those based on the REML method and the approximate methods of Satterthwaite (1946) and Kenward and Roger (1997). The coverage of the proposed intervals was closer to the chosen nominal level than coverage of prediction intervals based on the REML method. With focus on Type I error, the implications of the available options in the mixed procedure of SAS and the lmer function of R for the inference on the fixed effects were examined. With the default setting of SAS, the frequency of Type I error was higher than with R. The Type I error rate in SAS was close to the nominal value when negative estimates of the variance components were allowed. Both software packages occasionally produced inaccurate results.
|
|
| 8. |
- Alexandersson, Elin
(författare)
-
Reducing signal interference in complex NMR spectra : characterization and quantification of metabolites in mixtures
- 2024
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Nuclear magnetic resonance (NMR) spectroscopy is a versatile analytical technique that can be used for identification, characterization, and quantification of various compounds. However, many sample types, including most biological samples, are mixtures of numerous different compounds with large differences in concentration and physico-chemical properties. When such samples are studied with NMR spectroscopy, they typically give rise to complicated NMR spectra that are difficult to analyse due to large dynamic range and extensive signal overlap. Methods are therefore needed that reduce signal overlap and other interferences in NMR spectra of complex mixtures so that individual compounds can be characterized and quantified. The work in this thesis revolves around two such methods. One common form of signal interference is caused by intense, unwanted signals that overlap with, and sometimes obscure, signals of interest. Here, an NMR experiment was developed that enables selective suppression of the unwanted signals so that other signals can be studied. After evaluation and optimization of the experiment, it was used in the first complete NMR spectral assignment of the minor furanose forms of glucose. Broad signals from lipids or macromolecules is another type of interference. Such signals are frequently encountered in NMR spectra of metabolomics samples, where they prevent accurate quantification of certain metabolites. In this thesis, an automated workflow was devised and optimized that first eliminates the interference from broad signals and then calculates absolute metabolite concentrations. The entire workflow was performed in less than one second per spectrum.
|
|
| 9. |
- Almqvist, Viktor
(författare)
-
Who you gonna call? Examining the possibilities of remote veterinary meat inspection
- 2021
-
Doktorsavhandling (refereegranskat)abstract
- Demand for locally produced meat from small-scale slaughterhouses and game-handling facilities brings severe logistical challenges in meat inspection, since such facilities are often situated in rural areas and the costs and time associated with inspection visits to remote establishments are significant. With advances in technology, it might be possible to conduct meat inspections remotely via video link. This thesis aims to determine the performance of remote inspections, both ante mortem and post mortem, where a guided, untrained assistant present at the slaughterhouse relays video and sensory impressions to a veterinarian off-site. Performance was evaluated based on agreement between remote and on-site inspections. As part of this, a practical technological solution, with emphasis on a less-is-more approach, was conceived, assembled and tested in practical use. Comparisons between methods were conducted using Cohen’s kappa-based statistics. On directly comparing findings under 26 different inspection codes or classifications recorded by two veterinarians conducting inspections on 400 carcasses and organs of pigs at a Swedish large-scale slaughterhouse, it was found that the level of agreement between the two methods was generally high, with most findings scoring ‘almost perfect agreement’. When ante mortem inspections were evaluated in a similar way, it was concluded that, due to extremely low prevalence of findings, ante mortem inspections are difficult to perform remotely under current conditions. In conclusion, remote post mortem veterinary inspections appear very promising, but the method needs to be evaluated further.
|
|
| 10. |
- Alsing Johansson, Todd
(författare)
-
How clean is clean enough? : infection prevention and control in animal healthcare
- 2024
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Microorganisms in the environment and on equipment in animal healthcare facilities may constitute a risk of healthcare-associated infections (HAIs). Knowledge of the bacterial load as well as factors influencing the bacterial load is helpful in establishing infection prevention and control (IPC) routines to reduce the risk of HAIs. Cleaning and disinfection of environmental surfaces and equipment is an important IPC measure to reduce the risk of environmental spread of pathogens and incidence of HAIs.The overall aim of the thesis was to improve IPC in animal healthcare by studying the bacterial load, before and after cleaning and disinfection, in the environment and on equipment, by passive air and surface sampling.The bacterial load was generally low in air and on high-touch and near-patient surfaces in the operating room (OR) and the ultrasound room (UR). On near-patient surfaces in dog cages the bacterial load was generally low after decontamination, except after microfibre cleaning of the floor. The bacterial load was high on nearpatient surfaces and dental handpieces after equine dental care, and after decontamination the bacterial load on near-patient surfaces was generally low, but on dental handpieces the bacterial load was still high. Genes conveying resistance to chlorhexidine and quaternary ammonium compounds were identified in environmental staphylococci from the OR and the UR.In conclusion, this thesis present a generally low bacterial load, except after microfibre-cleaning of the floor in dog cages and after decontamination of dental handpieces. This indicates a need for evidence-based cleaning and disinfection routines for environmental surfaces and equipment in animal healthcare, to reduce the risk of HAIs.
|
|
