| 1. |
- Ekelund Ugge, Gustaf Magnus Oskar, 1990-
(författare)
-
Transcriptional biomarkers of toxicity – powerful tools or random noise? : An applied perspective from studies on bivalves
- 2023
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Aquatic organisms are constantly at risk of being exposed to potentially harmful chemical compounds of natural or anthropogenic origin. Biological life can for instance respond to chemical stressors by changes in gene expression, and thus, certain gene transcripts can potentially function as biomarkers, i.e. early warnings, of toxicity and chemical stress. A major challenge for biomarker application is the extrapolation of transcriptional data to potential effects at the organism level or above. Importantly, successful biomarker use also requires basal understanding of how to distinguish actual responses from background noise. The aim of this thesis is, based on response magnitude and variation, to evaluate the biomarker potential in a set of putative transcriptional biomarkers of general toxicity and chemical stress.Specifically, I addressed a selection of six transcripts involved in cytoprotection and oxidative stress: catalase (cat), glutathione-S-transferase (gst), heat shock proteins 70 and 90 (hsp70, hsp90), metallothionein (mt) and superoxide dismutase (sod). Moreover, I used metal exposures to serve as a proxy for general chemical stress, and due to their ecological relevance and nature as sedentary filter-feeders, I used bivalves as study organisms.In a series of experiments, I tested transcriptional responses in the freshwater duck mussel, Anodonta anatina, exposed to copper or an industrial wastewater effluent, to address response robustness and sensitivity, and potential controlled (e.g. exposure concentration) and random (e.g. gravidness) sources of variation. In addition, I performed a systematic review and meta-analysis on transcriptional responses in metal exposed bivalves to (1) evaluate what responses to expect from arbitrary metal exposures, (2) assess the influence from metal concentration (expressed as toxic unit), exposure time and analyzed tissue, and (3) address potential impacts from publication bias in the scientific literature.Response magnitudes were generally small in relationship to the observed variation, both for A. anatina and bivalves in general. The expected response to an arbitrary metal exposure would generally be close to zero, based on both experimental observations and on the estimated impact from publication bias. Although many of the transcripts demonstrated concentration-response relationships, large background noise might in practice obscure the small responses even at relatively high exposures. As demonstrated in A. anatina under copper exposure, this can be the case already for single species under high resolution exposures to single pollutants. As demonstrated by the meta-regression, this problem can only be expected to increase further upon extrapolation between different species and exposure scenarios, due to increasing heterogeneity and random variation. Similar patterns can also be expected for time-dependent response variation, although the meta-regression revealed a general trend of slightly increasing response magnitude with increasing exposure times.In A. anatina, gravidness was identified as a source of random variability that can potentially affect the baseline of most assessed biomarkers, particularly when quantified in gills. Response magnitudes and variability in this species were generally similar for selected transcripts as for two biochemical biomarkers included for comparison (AChE, GST), suggesting that the transcripts might not capture early warnings more efficiently than other molecular endpoints that are more toxicologically relevant. Overall, high concentrations and long exposure durations presumably increase the likelihood of a detectable transcriptional response, but not to an extent that justifies universal application as biomarkers of general toxicity and chemical stress. Consequently, without a strictly defined and validated application, this approach on its own appears unlikely to be successful for future environmental risk assessment and monitoring. Ultimately, efficient use of transcriptional biomarkers might require additional implementation of complementary approaches offered by current molecular techniques.
|
|
| 2. |
|
|
| 3. |
|
|
| 4. |
|
|
| 5. |
- Nandakumar, Mridula
(författare)
-
Pathogen-mediated selection in the immune system of rodents : Exploring selection targets, functional effects and trade-offs
- 2024
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Pathogens cause disease and play an important role in shaping evolution of the host immune system. They create pressure on host immunity to evolve in numerous ways, most commonly by increasing divergence between species (positive selection) or increasing polymorphisms within a population (balancing selection). Especially with balancing selection, trade-offs between different traits, for example responses to different pathogens, are essential. Across five papers, questions related to what immune genes are under selection, how this translates to an effect on the immune response and what trade-offs occur, are addressed using rodents as study system. Paper I utilised genomes from 30 rodent species to identify signatures of positive selection in immune genes. In general, function of immune genes was a significant determinant for signs of positive selection. This effect was significant even after accounting for potential confounding factors like gene expression and protein-protein interactions. In Paper II, the focus is on a local population of bank voles in Sweden, to look for signatures of balancing selection in the complement system – a branch of innate immunity. One complement gene, FCNA, was found to be under strong balancing selection. In Paper III, FCNA polymorphism was linked to associations with natural infections of Borrelia afzelii, a common pathogen for bank voles. Papers IV and V look at how the immune response of bank voles of various genotypes differ on stimulation with B. afzelii and the human pathogen Streptococcus pyogenes, captured with transcriptome sequencing of spleen cells. In Paper IV, the analysis is focused on various genotypes of TLR2, an immune gene under balancing selection in bank voles and associated with infection prevalence of B. afzelii in the wild. A stimulation-specific effect of TLR2 on immune response was found, where the magnitude of immune response to B. afzelii, but not S. pyogenes, depends on TLR2 expression level in a TLR2 genotype-specific way. In Paper V, tradeoffs at the cis-regulatory level between the response to B. afzelii and S. pyogenes was tested by searching for polymorphisms where the alleles are expressed differently to these two stimulations. Abundant cis-regulatory variation for responses to the two bacteria was found, but there was no evidence for trade-offs. In summary, this work pushes our knowledge of what immune genes can be expected to be under pathogen-mediated selection, as heretofore understudied categories of immune function showed signs of selection. A novel basis – the combination of genotype and expression – was uncovered for functional effects of polymorphic genes. Finally, there was no evidence for trade-offs between responses to different pathogens. Investigating the nature of trade-offs in the immune system further would be necessary towards understanding the causes and consequences of pathogen-mediated selection.
|
|
| 6. |
- Pendrill, Ann-Marie, 1952
(författare)
-
Students compete in European Union Science Olympiad 2010
- 2010
-
Ingår i: Physics Education. - 0031-9120 .- 1361-6552. ; 45:4, s. 318-320
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- In April 2010, young students from 21 countries competed in EUSO - the European Union Science Olympiad. Each country sent two teams of three students to an experimental science competition. The first day, the teams helped an alien find water on Earth, and the second day, the solved a criminal case.
|
|
| 7. |
|
|
| 8. |
- Pilesjö, Petter, et al.
(författare)
-
Analys av geografiska data
- 2020. - 7:1
-
Ingår i: Geografisk informationsbehandling: : teori, metoder och tillämpningar - teori, metoder och tillämpningar. - 9789144131740 ; , s. 215-272
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- I detta kapitel i boken Geografisk information Behandling beskrivs och behandlas metoder för hur geografisk data analyseras. Kapitlet omfattar såväl geografisk teori som exempel på tillämpningar. Geografisk informationsbehandling baseras på insamling, lagring, analys och visualisering av geografiska data. Denna indelning utgör också grunden för bokens disposition. Boken är i första hand avsedd för introducerande kurser vid universitet och högskolor men vissa delar är lämpliga även på avancerad nivå. Den är också utmärkt för yrkesverksamma inom GIS som vill öka sina teoretiska kunskaper.Boken innehåller både teoretiska och praktiska delar, där de senare beskriver tillämpningar som exempelvis samhällsplanering, miljöövervakning och kommersiella tjänster. I insamlingsdelen beskrivs hur man anger en position genom att koppla ett koordinatsystem till jordytan. Därefter beskrivs de vanligaste metoderna att samla in geografiska data som satellitbaserade positioneringssystem, flygfotografering, satellitbaserad fjärranalys och laserskanning. Lagringsdelen behandlar hur dessa data lagras i databaser och distribueras via webben. Analysdelen innehåller beskrivningar av de vanligaste analysmetoderna samt kvalitetsfrågor. Resultatet av en geografisk analys visualiseras oftast i form av kartor, vilket är temat för den sista delen av boken.Denna sjunde upplaga har uppdaterats med nya aktuella tillämpningsexempel. Dessa är i denna upplaga beskrivna tillsammans med de teoretiska beskrivningarna för att stärka kopplingen mellan teori och tillämpningar. Dessutom har beskrivningen av webbtillämpningar utökats och utgör nu ett eget kapitel, och även texten om webbvisualiseringar har stärkts i kartografikapitlet. Vidare har det tillkommit beskrivningar av nya mättekniker samt texter om lagring, analys och visualisering av 3D geografiska data.
|
|
| 9. |
- Shevela, Dmitriy, et al.
(författare)
-
Oxygenic photosynthesis
- 2013
-
Ingår i: Natural and Artificial Photosynthesis. - Hoboken, NJ, USA : John Wiley & Sons Inc.. - 9781118160060 - 9781118659892 ; , s. 13-63
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- This chapter is intended as a background on natural photosynthesis for those interested in artificial photosynthesis. It describes how light is used for creating positive and negative charges, and how these charges are transferred through the molecular assemblies in the membranes. Next, the chapter also describes how the charge transport leads to creation of a pH difference across the photosynthetic membrane, and how charge and pH differences lead to the production of high-energy phosphate that can be used in chemical synthesis. The chapter overviews photophosphorylation in chromatophores of photosynthetic bacteria and, discusses carbon dioxide assimilation systems in oxygenic organisms. Finally, it describes how the type of photosynthesis present today has evolved over billions of years, and what can we expect of the future that we are ourselves able to influence. In addition, in the end, the chapter considers some interesting photosynthesis-related questions relevant to whole land and aquatic plants.
|
|
| 10. |
|
|
