| 1. |
- Ekelund Ugge, Gustaf Magnus Oskar, 1990-
(författare)
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Transcriptional biomarkers of toxicity – powerful tools or random noise? : An applied perspective from studies on bivalves
- 2023
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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.
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| 2. |
- Jelenkovic, A., et al.
(författare)
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Genetic and environmental influences on adult human height across birth cohorts from 1886 to 1994
- 2016
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Ingår i: eLIFE. - Cambridge, United Kingdom : eLife Sciences Publications. - 2050-084X. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Human height variation is determined by genetic and environmental factors, but it remains unclear whether their influences differ across birth-year cohorts. We conducted an individual-based pooled analysis of 40 twin cohorts including 143,390 complete twin pairs born 1886-1994. Although genetic variance showed a generally increasing trend across the birth-year cohorts, heritability estimates (0.69-0.84 in men and 0.53-0.78 in women) did not present any clear pattern of secular changes. Comparing geographic-cultural regions (Europe, North America and Australia, and East Asia), total height variance was greatest in North America and Australia and lowest in East Asia, but no clear pattern in the heritability estimates across the birth-year cohorts emerged. Our findings do not support the hypothesis that heritability of height is lower in populations with low living standards than in affluent populations, nor that heritability of height will increase within a population as living standards improve.
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| 3. |
- Karim, Sazzad, et al.
(författare)
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Improved drought tolerance without undesired side effects in transgenic plants producing trehalose
- 2007
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Ingår i: Plant Molecular Biology. - : Springer Science and Business Media LLC. - 0167-4412 .- 1573-5028. ; 64:4, s. 371-386
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Tidskriftsartikel (refereegranskat)abstract
- Most organisms naturally accumulating trehalose upon stress produce the sugar in a two-step process by the action of the enzymes trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP). Transgenic plants overexpressing TPS have shown enhanced drought tolerance in spite of minute accumulation of trehalose, amounts believed to be too small to provide a protective function. However, overproduction of TPS in plants has also been found combined with pleiotropic growth aberrations. This paper describes three successful strategies to circumvent such growth defects without loosing the improved stress tolerance. First, we introduced into tobacco a double construct carrying the genes TPS1 and TPS2 (encoding TPP) from Saccharomyces cerevisiae. Both genes are regulated by an Arabidopsis RuBisCO promoter from gene AtRbcS1A giving constitutive production of both enzymes. The second strategy involved stress-induced expression by fusing the coding region of ScTPS1 downstream of the drought-inducible Arabidopsis AtRAB18 promoter. In transgenic tobacco plants harbouring genetic constructs with either ScTPS1 alone, or with ScTPS1 and ScTPS2 combined, trehalose biosynthesis was turned on only when the plants experienced stress. The third strategy involved the use of AtRbcS]A promoter together with a transit peptide in front of the coding sequence of ScTPS1, which directed the enzyme to the chloroplasts. This paper confirms that the enhanced drought tolerance depends on unknown ameliorated water retention as the initial water status is the same in control and transgenic plants and demonstrates the influence of expression of heterologous trehalose biosynthesis genes on Arabidopsis root development.
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| 4. |
- Sernland, Emma
(författare)
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Optimal strategies and information in foraging theory
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis, I present both theoretical and empirical work where we have studied how humans and animals use information in situations where they need to continually update their information on the density of a resource. We have found that the amount of information, and the way the information is presented, are important factors for how well decisions are adapted to current circumstances. In an empirical study on humans, we found that humans seem to have a default idea of the distribution of a resource. This default idea seems to be plastic, i.e. it is adjusted according to incoming information. The way additional information was presented, as well as the information content, was important for how well the default idea was adjusted to current circumstances.By using mathematical models, we have also studied whether access to information from group members, so called public information, is one of the reasons why some species live in groups. When group members aim to maximize its intake rate of food and share both information and food items found equally, and when each individual has to pay all the cost for travelling between foraging patches, the intake rate of food will decrease with increasing group size. The animals will spend a larger proportion of the time on travelling between patches and less time on foraging the larger the group size. In this case, information sharing on food density in patches is not a reason why animals live in groups.We have also used mathematical models to study the information dynamics in a group of foraging animals that cannot both search for food and information at the same time. The animals aim to maximize their survival, and are given three behavioural choices in each time step: stay and search for food, stay and scan for information, or leave the current patch. The results show that the choice of behaviour depends on the energy reserves of the individual. An animal with low energy reserves searches for food and leaves the patch if its assessment of potential patch quality decreases to a certain level. An animal with high energy reserves chooses to stay in the patch and scan for information. In our model we assume that when one individual leaves the patch, the rest of the group also leaves. This means that it is those individuals that have low energy reserves that will make the leaving decisions for the group.In the end, we use these theories on Bayesian foraging, information updating and decision-making in order to develop a new type of effort-based quota for sustainable fisheries management: an effort-based dynamic quota (EDQ). We show that by using information from ongoing fishing combined with fishing data from earlier years, we can reach a higher maximum sustainable yield compared to using a total allowable catch (TAC).
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| 5. |
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| 6. |
- Sutkowska, Agnieszka, et al.
(författare)
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Refugial pattern of Bromus erectus in Central Europe based on ISSR fingerprinting
- 2013
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Ingår i: Acta Biologica Cracoviensia. Series Botanica. - Cracow : Polish Academy of Sciences. - 0001-5296 .- 1898-0295. ; 55:2, s. 107-119
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Tidskriftsartikel (refereegranskat)abstract
- We studied the thermophilous grass Bromus erectusin Central Europe to determine its pattern of populationgenetic structure and genetic diversity, using ISSR-PCR fingerprinting to analyze 200 individuals from 37 popu-lations. We found three genetic groups with a clear geographic structure, based on a Bayesian approach. Thefirst group occurred west and south of the Alps, the second east and north of the Alps, and the third was formedby four genetically depauperated populations in Germany. The populations from Germany formed a subset ofthe Bohemian-Moravian populations, with one private allele. Two differentiation centers, one in the Atlantic-Mediterranean and the second in the Pannonian-Balkan area, were recognized by species distribution modeling.The geographic distribution of the genetic groups coincides with the syntaxonomic split of the Festuco-Brometeaclass into the Festucetalia valesiaceae and Brometalia erecti orders. We found a statistically significant decreasein mean ISSR bands per individual from south to north, and to a lesser extent from the east to west. The for-mer was explained by Holocene long-distance migrations from southern refugia, the latter by the difference inthe gradient of anthropopression. We hypothesize a cryptic northern shelter of the species in Central Europe inthe putative Moravian-Bohemian refugium.
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| 7. |
- Backström, Tobias, et al.
(författare)
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CRF and urotensin I effects on aggression and anxiety-like behavior in rainbow trout
- 2011
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Ingår i: Journal of Experimental Biology. - : The Company of Biologists. - 0022-0949 .- 1477-9145. ; 214:6, s. 907-914
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Tidskriftsartikel (refereegranskat)abstract
- Corticotropin-releasing factor (CRF) is central in the stress response but also modulates several behaviors including anxiety-related behaviors and aggression. In this study, juvenile rainbow trout (Oncorhynchus mykiss) were tested for competitive ability, determined during dyadic fights for dominance, after intracerebroventricular (i.c.v.) administration of CRF, urotensin I (UI), the non-specific CRF antagonist alpha-helical RF9-41 (ahCRF) or the CRF receptor subtype 1-specific antagonist antalarmin, when paired with a mass-matched con-specific injected with saline. In addition, isolated fish received the same substances. Plasma cortisol and brain monoamines were monitored in all fish. Most fish receiving CRF showed a conspicuous behavior consisting of flaring the opercula, opening the mouth and violent shaking of the head from side to side. When this occurred, the fish immediately forfeited the fight. Similar behavior was observed in most fish receiving UI but no effect on outcome of dyadic fights was noted. This behavior seems similar to non-ambulatory motor activity seen in rats and could be anxiety related. Furthermore, fish receiving CRF at a dose of 1000. ng became subordinate, whereas all other treatments had no effects on the outcome of dyadic fights. In addition, isolated fish receiving ahCRF had lower brain stem concentrations of 5-hydroxyindoleacetic acid, serotonin, 3,4-dihydroxyphenylacetic acid and dopamine. In conclusion, CRF seems to attenuate competitive ability, and both CRF and UI seem to induce anxiety-like behavior.
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| 8. |
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| 9. |
- Futo, M., et al.
(författare)
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Embryo-Like Features in Developing Bacillus subtilis Biofilms
- 2021
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Ingår i: Molecular Biology and Evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 38:1, s. 31-47
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Tidskriftsartikel (refereegranskat)abstract
- Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.
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| 10. |
- Shumkova, Ekaterina, et al.
(författare)
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Draft Genome Sequence of Rhodococcus ruber Strain P25 : an Active Polychlorinated Biphenyl Degrader
- 2015
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Ingår i: Genome Announcements. - : ASM International. - 2169-8287. ; 3:5
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Tidskriftsartikel (refereegranskat)abstract
- We report the 5,728,255-bp draft genome sequence of Rhodococcus ruber P25, isolated from a soil polluted with halogenated aromatic compounds in the city of Perm, Russia. The strain degrades polychlorinated biphenyls and a broad range of aromatic compounds. It possesses genes that mediate the degradation of biphenyls/polychlorinated biphenyls, naphthalene, and monoaromatic compounds.
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