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  • 1.
    Aktar, Farjana
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    ‘Hazaribagh’- development trajectory or trap? – A case study of a leather processing unit in Bangladesh2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The extensive alteration of global ecosystems, especially the changes caused by globalized and industrialized economic development activities over the last fifty years, have urged for a better understanding of the human-in-nature management system. Bangladesh, a densely populated developing country, is witnessing rapid environmental degradation while passing through different phases of industrial growth. Leather, one of the oldest industries in this country, provides a very positive picture in the country’s national economy and at the same time produces severe ecological and social crisis in a mutually reinforcing way. At first sight, it seems to fit the SES concept of social ecological trap. The previous scientific studies on ‘Hazaribagh’ leather processing unit in Bangladesh have investigated social, economic, ecological and stakeholder’s perspectives but did not address the pathway that has shaped the present situation. The objective of this case study was therefore to explore the reasons why change of this ‘Hazaribagh system’ has been impeded for so long and if the social-ecological trap concept could help to clarify the reasons for the chronic delay of the relocation of ‘Hazaribagh’ leather processing unit. This study has observed, through a historical investigation that a path dependent social ecological trap situation is persisting in the ‘Hazaribagh system’ where the economic opportunity is playing the role as a juncture between the phases of the process; and power mechanism and the disconnected SES has influenced and strengthened the claim. This study has also addressed some other underlying substantial social issues, which are influencing the process and might contribute to outline further research, and consequently provide insight to escape from the trap situation.

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  • 2.
    Azinas, Stavros
    et al.
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Carroni, Marta
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Cryo-EM uniqueness in structure determination of macromolecular complexes: A selected structural anthology2023In: Current opinion in structural biology, ISSN 0959-440X, E-ISSN 1879-033X, Vol. 81, article id 102621Article in journal (Refereed)
    Abstract [en]

    Cryogenic electron microscopy (cryo-EM) has become in the past 10 years one of the major tools for the structure determination of proteins. Nowadays, the structure prediction field is experiencing the same revolution and, using AlphaFold2, it is possible to have high-confidence atomic models for virtually any polypeptide chain, smaller than 4000 amino acids, in a simple click. Even in a scenario where all polypeptide chain folding were to be known, cryo-EM retains specific characteristics that make it a unique tool for the structure determination of macromolecular complexes. Using cryo-EM, it is possible to obtain near-atomic structures of large and flexible megacomplexes, describe conformational panoramas, and potentially develop a structural proteomic approach from fully ex vivo specimens.

  • 3. Baldwin, Lydia
    et al.
    Jones, Emily J.
    Iles, Alexander
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Carding, Simon R.
    Pamme, Nicole
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Dyer, Charlotte E.
    Greenman, John
    Development of a dual-flow tissue perfusion device for modeling the gastrointestinal tract-brain axis2023In: Biomicrofluidics, E-ISSN 1932-1058, Vol. 17, no 5, article id 054104Article in journal (Refereed)
    Abstract [en]

    Despite the large number of microfluidic devices that have been described over the past decade for the study of tissues and organs, few have become widely adopted. There are many reasons for this lack of adoption, primarily that devices are constructed for a single purpose or because they are highly complex and require relatively expensive investment in facilities and training. Here, we describe a microphysiological system (MPS) that is simple to use and provides fluid channels above and below cells, or tissue biopsies, maintained on a disposable, poly(methyl methacrylate), carrier held between polycarbonate outer plates. All other fittings are standard Luer sizes for ease of adoption. The carrier can be coated with cells on both sides to generate membrane barriers, and the devices can be established in series to allow medium to flow from one cell layer to another. Furthermore, the carrier containing cells can be easily removed after treatment on the device and the cells can be visualized or recovered for additional off-chip analysis. A 0.4 mu m membrane with cell monolayers proved most effective in maintaining separate fluid flows, allowing apical and basal surfaces to be perfused independently. A panel of different cell lines (Caco-2, HT29-MTX-E12, SH-SY5Y, and HUVEC) were successfully maintained in the MPS for up to 7 days, either alone or on devices connected in series. The presence of tight junctions and mucin was expressed as expected by Caco-2 and HT-29-MTX-E12, with Concanavalin A showing uniform staining. Addition of Annexin V and PI showed viability of these cells to be >80% at 7 days. Bacterial extracellular vesicles (BEVs) produced by Bacteroides thetaiotaomicron and labeled with 1,1 '-dioctadecyl-3,3,3 ',3 '-tetramethylindocarbo-cyanine perchlorate (DiD) were used as a model component of the human colonic microbiota and were visualized translocating from an apical surface containing Caco-2 cells to differentiated SH-SY5Y neuronal cells cultured on the basal surface of connected devices. The newly described MPS can be easily adapted, by changing the carrier to maintain spheroids, pieces, or slices of biopsy tissue and joined in series to study a variety of cell and tissue processes. The cell layers can be made more complex through the addition of multiple cell types and/or different patterning of extracellular matrix and the ability to culture cells adjacent to one another to allow study of cell:cell transfer, e.g., passive or active drug transfer, virus or bacterial entry or BEV uptake and transfer.

  • 4.
    Berckx, Fede
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    To be together or not to be together: Ca. 100 million years of evolutionary history of the earliest divergent Frankia clade2022Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Root nodule symbiosis evolved ca. 100 Mya between a nitrogen-fixing bacterium and the common ancestor to the Fabales, Fagales, Rosales, and Cucurbitales plant orders. Over time the majority of the lineages derived from this ancestor lost their symbiotic capability. While extant symbiotic members found in the Fabales order (legumes) all engage in symbiosis with rhizobia, extant symbiotic members of the latter three plant orders are referred to as actinorhizal plants. These engage in symbiosis with Frankia.

    Frankia is a genus of soil actinobacteria, which can be split into four phylogenetically distinct clades. The earliest divergent symbiotic clade, Frankia cluster-2, encompasses strains that have a broad host range and could not be cultured in vitro thus far with two exceptions. Based on Frankia enriched meta-genomes from whole nodules collected at different locations across the globe, it is clear there is very little diversity of Frankia cluster-2 in continental Eurasia, spanning from France to Japan. These strains are also closely related to strains found in North America. However, very little is known about strains occurring in the islands in the Pacific Ocean and the southern hemisphere.

    In short, this thesis aimed to investigate the biodiversity of the earliest divergent symbiotic Frankia clade and to understand how Frankia spread across the globe (Study 1 and Study 2). From nodules collected in study 1, a novel Streptomyces species was identified and declared (Study 3). The thesis also aimed to study genetic changes within Frankia cluster-2 which might be associated with their endosymbiotic lifestyle and low saprotrophic potential (Study 4 and Study 5).

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  • 5. Bergström, Anna
    et al.
    Ljungros, Kristina
    Forsberg Nilsson, Karin
    Ericson, Emilia
    Lindenfors, Patrik
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Humanities, Centre for Cultural Evolution.
    Larhammar, Dan
    Nu hotas kvinnors rätt till sina kroppar2014In: Aftonbladet, ISSN 0349-1145Article in journal (Other (popular science, discussion, etc.))
  • 6.
    Boalt, Elin
    Stockholm University, Faculty of Science, Department of Botany.
    Ecology and evolution of tolerance in two cruciferous species2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Tolerance to herbivory is the ability of plants to maintain fitness in spite of damage. The goal of this thesis is to investigate the genetic variation and expression of tolerance within species, determine whether and in what conditions tolerance has negative side-effects, and how tolerance is affected by different ecological factors. Tolerance is investigated with special focus on the effects of different damage types, competitive regimes, history of herbivory, and polyploidization in plants. Studies are conducted as a literature review and three experiments on two cruciferous species Raphanus raphanistrum and Cardamine pratensis.

    In the tolerance experiments, plants are subjected to artificial damage solely, or in a combination with natural damage. A literature review was conducted in order to investigate the effects of damage method. We found that traits related to tolerance, such as growth and fitness were not as sensitive in regard to damage method as measures of induced chemical traits, or measures of secondary herbivory.

    Genetic variation of tolerance was demonstrated within populations of R. raphanistrum and between subspecies of C. pratensis. In R. raphanistrum, traits involved in floral display and male fitness were positively associated with plant tolerance to herbivore damage. A potential cost of tolerance was demonstrated as a negative correlation between levels of tolerance in high and low competitive regimes. I found no evidence of other proposed costs of tolerance in terms of highly tolerant plants suffering of reduced fitness in the absence of herbivores or trade-offs in terms of a negative association between tolerance to apical and leaf damage, or between tolerance and competitive ability. In C. pratensis, higher ploidy level in plants involved higher levels of tolerance measured as clonal reproduction. Furthermore, populations exposed to higher levels of herbivory had better tolerance than populations exposed to lower levels of herbivory. In this thesis, I demonstrate evidence of different components for the evolution of tolerance in plants: genotypic variation, selective factors in terms of costs and ploidization, and selective agents in terms of changing environment or herbivore pressure.

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    FULLTEXT01
  • 7.
    Brandt, Knut M.
    Stockholm College.
    The metabolic effect and the binding of carbon dioxide in baker's yeast1945Doctoral thesis, monograph (Other academic)
  • 8.
    Britton, Tom
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics.
    Lindenstrand, David
    Stockholm University, Faculty of Science, Department of Mathematics.
    Inhomogeneous epidemics on weighted networks2012In: Mathematical Biosciences, ISSN 0025-5564, E-ISSN 1879-3134, Vol. 240, no 2, p. 124-131Article in journal (Refereed)
    Abstract [en]

    A social (sexual) network is modeled by an extension of the configuration model to the situation where edges have weights, e.g., reflecting the number of sex-contacts between the individuals. An epidemic model is defined on the network such that individuals are heterogeneous in terms of how susceptible and infectious they are. The basic reproduction number R-0 is derived and studied for various examples, but also the size and probability of a major outbreak. The qualitative conclusion is that R-0 gets larger as the community becomes more heterogeneous but that different heterogeneities (degree distribution, weight, susceptibility and infectivity) can sometimes have the cumulative effect of homogenizing the community, thus making R-0 smaller. The effect on the probability and final size of an outbreak is more complicated.

  • 9.
    Cheng, Lei
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Factors modifying cellular response to ionizing radiation2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Many physical factors influence the biological effect of exposure to ionizing radiation, including radiation quality, dose rate and temperature. This thesis focuses on how these factors influence the outcome of exposure and the mechanisms behind the cellular response. 

    Mixed beam exposure, which is the combination of different ionizing radiations, occurs in many situations and the effects are important to understand for radiation protection and effect prediction. Recently, studies show that the effect of simultaneous irradiation with different qualities is greater than simple additivity of single radiation types, which is called a synergistic effect. But its mechanism is unclear. In Paper I, II and III, alpha particles and X-rays were used to study the effect of mixed beams. Paper I shows that mixed exposure induced a synergistic effect in generating double strand breaks (DSB), and these DSB were repaired by slow kinetics in U2OS cells. In Paper II, alkaline comet assay was applied to investigate the induction and repair of DNA lesions including DSB, single strand breaks and alkali labile sites in peripheral blood lymphocytes (PBL). We demonstrate that mixed beams interact in inducing DNA damage and influencing DNA damage response (DDR), which result in a delay of DNA repair. Both in Paper I and II, mixed beams showed a capability in inducing higher activity of DDR proteins than expected from additivity. Paper III investigates selected DDR-related gene expression levels after exposure to mixed beams in PBL from 4 donors. Synergy was present for all donors but the results suggested individual variability in the response to mixed beams, most likely due to life style changes.

    Low temperature at exposure is radioprotective at the level of cytogenetic damage. In Paper IV, data indicate that this effect is through promotion of DNA repair, which leads to reduced transformation of DNA damage into chromosomal aberrations.  

    Paper V aims to compare the biological effectiveness of gamma radiation delivered at a very high dose rate (VHDR) with that of a high dose rate (HDR) in order to optimize chronic exposure risk prediction based on the data of atomic bomb survivors. The results suggest that VHDR gamma radiation is more effective in inducing DNA damage than HDR.     

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  • 10. Dahl, Leo
    et al.
    Kotliar, Ilana B.
    Bendes, Annika
    Dodig-Crnkovic, Tea
    Fromm, Samuel
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Elofsson, Arne
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Uhlen, Mathias
    Sakmar, Thomas P.
    Schwenk, Jochen M.
    Multiplexed selectivity screening of anti-GPCR antibodies2023In: Science Advances, E-ISSN 2375-2548, Vol. 9, no 18, article id eadf9297Article in journal (Refereed)
    Abstract [en]

    G protein-coupled receptors (GPCRs) control critical cellular signaling pathways. Therapeutic agents including anti-GPCR antibodies (Abs) are being developed to modulate GPCR function. However, validating the selectivity of anti-GPCR Abs is challenging because of sequence similarities among individual receptors within GPCR sub-families. To address this challenge, we developed a multiplexed immunoassay to test >400 anti-GPCR Abs from the Human Protein Atlas targeting a customized library of 215 expressed and solubilized GPCRs representing all GPCR subfamilies. We found that-61% of Abs tested were selective for their intended target,-11% bound off -target, and-28% did not bind to any GPCR. Antigens of on-target Abs were, on average, significantly longer, more disordered, and less likely to be buried in the interior of the GPCR protein than the other Abs. These results provide important insights into the immunogenicity of GPCR epitopes and form a basis for designing therapeu-tic Abs and for detecting pathological auto-Abs against GPCRs.

  • 11. Fortes-Lima, Cesar A.
    et al.
    Burgarella, Concetta
    Hammarén, Rickard
    Eriksson, Anders
    Vicente, Mário
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Jolly, Cecile
    Semo, Armando
    Gunnink, Hilde
    Pacchiarotti, Sara
    Mundeke, Leon
    Matonda, Igor
    Muluwa, Joseph Koni
    Coutros, Peter
    Nyambe, Terry S.
    Cikomola, Justin Cirhuza
    Coetzee, Vinet
    de Castro, Minique
    Ebbesen, Peter
    Delanghe, Joris
    Stoneking, Mark
    Barham, Lawrence
    Lombard, Marlize
    Meyer, Anja
    Steyn, Maryna
    Malmström, Helena
    Rocha, Jorge
    Soodyall, Himla
    Pakendorf, Brigitte
    Bostoen, Koen
    Schlebusch, Carina M.
    The genetic legacy of the expansion of Bantu-speaking peoples in Africa2024In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 625, no 7995, p. 540-547Article in journal (Refereed)
    Abstract [en]

    The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent1-7. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals8. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods9 and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies10 and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations. We gathered genetic data for 1,763 individuals from 147 populations across 14 African countries, and 12 Late Iron Age individuals, to trace the expansion of Bantu-speaking peoples over the past 6,000 years.

  • 12.
    Gustafsson, Anders
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Lindenfors, Patrik
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Human size evolution: no allometric relationship between male and female stature2004In: Journal of Human Evolution, ISSN 0047-2484, E-ISSN 1095-8606, Vol. 47, no 4, p. 253-266Article in journal (Refereed)
    Abstract [en]

    In many animal groups, sexual size dimorphism tends to be more pronounced in species with large body size. Similarly, in a previous cross-cultural analysis, male and female stature in humans were shown to be positively allometrically related, indicating a similar relationship where populations with larger stature were more dimorphic. In this study, we re-examine the hypothesis of an allometric relationship between the sexes using phylogenetic methodology. First, however, we tested whether there exist phylogenetic signals in male and female stature. Data on mean stature from 124 human populations was gathered from the literature. A phylogenetic test showed that male and female stature were significantly associated with phylogeny. These results indicate that comparative methods that to some degree incorporate genetic relatedness between populations are crucial when analyzing human size evolution in a cross-cultural context. Further, neither non-phylogenetic nor phylogenetic analyses revealed any allometric relationship between male and female stature. Thus, we found no support for the idea that sexual dimorphism increases with increasing stature in humans

  • 13. Hagman, Mattias
    Att odla riktigt små kryp hemma2001In: Terrariet, Vol. 8, no 7, p. 9-12Article in journal (Other (popular science, discussion, etc.))
  • 14. Hagman, Mattias
    Costa Rica - den rika kusten2000In: Terrariet, Vol. 7, no 4, p. 3-12Article in journal (Other (popular science, discussion, etc.))
  • 15. Hagman, Mattias
    Odling av en stor pilgiftsgroda - Dendrobates tinctorius ”Taffelberg”2000In: Terrariet, Vol. 7, no 7, p. 4-8Article in journal (Other (popular science, discussion, etc.))
  • 16. Hagman, Mattias
    Pilgiftsgrodor1999In: Terrariet, ISSN 1404-7519, Vol. 6, no 12, p. 4-18Article in journal (Other (popular science, discussion, etc.))
  • 17. Hagman, Mattias
    Terrarieteknik och växter2001In: Terrariet, Vol. 8, no 10, p. 3-12Article in journal (Other (popular science, discussion, etc.))
  • 18.
    Hagman, Mattias
    Stockholm University, Faculty of Science, Department of Zoology.
    Vergiftigd door Oophaga pumilio : (Dutch translation by Peter de Jong)2012In: Dendrobatidae Nederland, ISSN 1574-3640, no 30 juni, p. 5-Article in journal (Other (popular science, discussion, etc.))
  • 19.
    Helleberg, Hans
    Stockholm University.
    Biomarkers aiming at cancer risk estimation of polycyclic aromatic hydrocarbons2001Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Polycyclic aromatic hydrocarbons (PAH), a family of compounds that are formed in incomplete combustion of organic matter, occur as general pollutants in air and food. Exposure to PAH is, according to preliminary estimates, associated with non-acceptable cancer risks showing the need for improved data to be used in risk estimation. Risk assessment of PAH is a complex matter, i.a. because certain PAH could increase cancer risk by more than one mechanism, with different dose-response.

    This study deals mainly with development and evaluation of biomarkers for dose. Benzo[a]pyrene (BaP), and fluoranthene in the early experiments, were chosen as indicators of PAH exposure. Among BaP metabolites, ± (anti)r-7,t-8-dihydroxy-t-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) is regarded to be the predominant cancer initiator. In mice with deficient DNA repair, given BaP by gavage, the dGuo-N2 adduct levels in DNA, reflecting doses of BPDE, were approximately the same in different tissues. The results indicate that BPDE markers in blood could be used to measure the average target dose. The large amounts of blood proteins (serum-albumin (SA) and hemoglobin (Hb)) and the well defined in vivo turnover kinetics, without repair, make blood proteins more suitable dose monitors than DNA.

    A new way of isolating and measuring histidine (His) adducts of BPDE in SA and Hb has been developed. His adducts were released from the proteins by treatment with hydrazine. After derivatization and enrichment with C18 and cation solid phase extraction the His adduct was obtained in a form suitable for analysis by liquid chromatography/mass spectrometry. The hydrazinolysis of BPDE-treated human Hb and SA released both new and earlier known adducts from the proteins. The level observed of His adducts in the SA and Hb corresponded to 70 and 10 %, respectively, of the total adduct level in the in vitro-treated proteins.

    Following acute treatment (i.p.) of mice with radiolabelled BaP the adducts in SA, Hb and DNA were determined. In the SA samples the His adducts from BPDE were quantified, as well as two other so far unidentified products from BaP metabolites. The levels of the His adduct were roughly 10 times higher in SA than in Hb. The dGuo-N2 adduct levels in liver and lung DNA were 14 - 40 times higher than the His adduct in SA per unit of weight.

    The mutagenic effectiveness of BPDE and g-radiation were determined in V79 cells. An incremental formation of one dGuo-N2 adduct per 108 nucleotides was found to have a mutagenic potency corresponding to that of about 1 cGy.

    The usefulness of biomarkers for genotoxic and immunotoxic effects in mice exposed to low levels of diesel exhaust (10 mg PAH per kg body weight) were examined. Ethoxyresorufin O-deethylase activity was used to measure induction status of CYP1 isoenzymes and it was concluded that exposure to ambient levels of diesel exhaust would probably not lead to induction.

    On the basis of the results obtained some gaps in quantitative knowledge necessary in risk estimation of BaP has been filled and remaining gaps could be defined. It is indicated that the present methods together with other sensitive techniques are applicable in risk estimation of PAH at current exposure levels, that is in the low-dose range, below exposure levels leading to enzyme induction including promotion.

  • 20.
    Holmström, Therese E.
    et al.
    Stockholm University, Faculty of Science, The Wenner-Gren Institute.
    Mattsson, Charlotte L.
    Stockholm University, Faculty of Science, The Wenner-Gren Institute.
    Wang, Yanling
    Stockholm University, Faculty of Science, The Wenner-Gren Institute.
    Iakovleva, Irina
    Stockholm University, Faculty of Science, The Wenner-Gren Institute.
    Petrovic, Natasa
    Stockholm University, Faculty of Science, The Wenner-Gren Institute.
    Nedergaard, Jan
    Stockholm University, Faculty of Science, The Wenner-Gren Institute.
    Non-transactivational, dual pathways for LPA-induced Erk1/2 activation in primary cultures of brown pre-adipocytes2010In: Experimental Cell Research, ISSN 0014-4827, E-ISSN 1090-2422, Vol. 316, no 16, p. 2664-75Article in journal (Refereed)
    Abstract [en]

    In many cell types, G-protein-coupled receptor (GPCR)-induced Erk1/2 MAP kinase activation is mediated via receptor tyrosine kinase (RTK) transactivation, in particular via the epidermal growth factor (EGF) receptor. Lysophosphatidic acid (LPA), acting via GPCRs, is a mitogen and MAP kinase activator in many systems, and LPA can regulate adipocyte proliferation. The mechanism by which LPA activates the Erk1/2 MAP kinase is generally accepted to be via EGF receptor transactivation. In primary cultures of brown pre-adipocytes, EGF can induce Erk1/2 activation, which is obligatory and determinant for EGF-induced proliferation of these cells. Therefore, we have here examined whether LPA, via EGF transactivation, can activate Erk1/2 in brown pre-adipocytes. We found that LPA could induce Erk1/2 activation. However, the LPA-induced Erk1/2 activation was independent of transactivation of EGF receptors (or PDGF receptors) in these cells (whereas in transformed HIB-1B brown adipocytes, the LPA-induced Erk1/2 activation indeed proceeded via EGF receptor transactivation). In the brown pre-adipocytes, LPA instead induced Erk1/2 activation via two distinct non-transactivational pathways, one G(i)-protein dependent, involving PKC and Src activation, the other, a PTX-insensitive pathway, involving PI3K (but not Akt) activation. Earlier studies showing LPA-induced Erk1/2 activation being fully dependent on RTK transactivation have all been performed in cell lines and transfected cells. The present study implies that in non-transformed systems, RTK transactivation may not be involved in the mediation of GPCR-induced Erk1/2 MAP kinase activation

  • 21.
    Joandi, Linnéa
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    The impact of climate change on aquatic systems and phytoplankton communities: A quantitative study of the impacts of altering food-quality on microzooplankton growth rate2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    A global increase in atmospheric CO2 and temperature is assumed to affect the marine ecosystems in numerous ways, e.g. by altering ocean circulation patterns and changing nutrient regimes. The changes are expected to impact heavily on both phytoplankton communities as well as the rest of the marine food-web. Based on previous experimental studies that have investigated the impacts of varied algae food-quality on zooplankton, this quantitative study hypothesizes that (i) the tested microzooplankton species Brachionus plicatilis (rotifer) and Euplotes sp. (ciliate) will show high population growth rates (g) when fed with Nannochloropsis sp. grown under nutrient replete conditions, (ii) that the species will show a population growth rate close to zero when fed with algae grown on phosphorous-deficient media and (iii) that microzooplankton will be negatively affected by the algae grown in nitrogen-deficient media. The study thus aims to investigate how changes in the balance of energy and several chemical elements in ecological interactions, ecological stoichiometry, affect the growth rates of algal grazers. The results show that food-independent factors had a large impact on growth rates and resulted in unexpected, deviating trends. However, as the growth rates for B. plicatilis fed with phosphorous-deficient algae were lower than those of B. plicatilis fed with nitrogen-deficient algae, there is some support for the

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  • 22.
    Johansson, Christer
    Stockholm University.
    Exchange of nitrogen oxides between the atmosphere and terrestrial surfaces1988Doctoral thesis, comprehensive summary (Other academic)
  • 23.
    Kohler, Andreas
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. University of Graz, Graz, Austria.
    Barrientos, Antoni
    Fontanesi, Flavia
    Ott, Martin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. University of Gothenburg, Gothenburg, Sweden.
    The functional significance of mitochondrial respiratory chain supercomplexes2023In: EMBO Reports, ISSN 1469-221X, E-ISSN 1469-3178, article id e57092Article, review/survey (Refereed)
    Abstract [en]

    The mitochondrial respiratory chain (MRC) is a key energy transducer in eukaryotic cells. Four respiratory chain complexes cooperate in the transfer of electrons derived from various metabolic pathways to molecular oxygen, thereby establishing an electrochemical gradient over the inner mitochondrial membrane that powers ATP synthesis. This electron transport relies on mobile electron carries that functionally connect the complexes. While the individual complexes can operate independently, they are in situ organized into large assemblies termed respiratory supercomplexes. Recent structural and functional studies have provided some answers to the question of whether the supercomplex organization confers an advantage for cellular energy conversion. However, the jury is still out, regarding the universality of these claims. In this review, we discuss the current knowledge on the functional significance of MRC supercomplexes, highlight experimental limitations, and suggest potential new strategies to overcome these obstacles. Mitochondrial respiratory chain complexes can associate into supramolecular structures termed respiratory supercomplexes. This review discusses their structure, assembly and potential physiological functions.image

  • 24.
    Konn, Cécile
    et al.
    Stockholm University, Faculty of Science, Department of Geology and Geochemistry.
    Charlou, Jean-Luc
    Laboratoire de géochimie et métallogénie, Ifremer, Brest, France.
    Testemale, Denis
    Institut Néel, Grenoble, France.
    Querellou, Joel
    UMR6197 LM2E, Ifremer, Brest, France.
    Holm, Nils
    Stockholm University, Faculty of Science, Department of Geology and Geochemistry.
    New insight on the origin of organic compounds in fluids from ultramafic-hosted hydrothermal systemsManuscript (preprint) (Other academic)
    Abstract [en]

    Hydrocarbons gases (C1-C4) as well as larger organic compounds were reported elsewhere in fluids from the Rainbow and the Lost City ultramafic-hosted hydrothermal fields. Whereas hydrocarbon gases are likely abiogenic (Fischer-Tropsch Type reaction), the origin of larger molecules remains unclear. Our ability to differentiate between biotic and abiotic sources of organic compounds in deep-sea hydrothermal systems may give clues to the understanding of organic geochemistry on the early Earth. Here, we report a series of experiments of hydrothermal degradation (40 MPa / 200, 350 and 450°C) of the piezophile archaea Pyrococcus abyssi biomass, which provides supporting lines of evidence of the abiogenic origin of saturated hydrocarbons as well as of the possible biogenic origin of alkylated aromatic hydrocarbons, Polycyclic Aromatic Hydrocarbons (PAH) and C12:0-C16:0 fatty acids in fluids from ultramafic-hosted hydrothermal systems.

  • 25.
    Kotova, Natalia
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Vare, Daniel
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Schultz, Niklas
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Gradecka Meesters, Dobrosława
    Stępnik, Maciej
    Grawé, Jan
    Helleday, Thomas
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Jenssen, Dag
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Genotoxicity of alcohol is linked to DNA replication-associated damage and homologous recombination repairIn: Carcinogenesis, ISSN 0143-3334, E-ISSN 1460-2180Article in journal (Refereed)
  • 26.
    Lasselin, Julie
    et al.
    Stockholm University, Faculty of Social Sciences, Stress Research Institute. Karolinska Institutet, Sweden; University Hospital Essen, Germany.
    Petrovic, Predrag
    Olsson, Mats J.
    Paues Göranson, Sofie
    Lekander, Mats
    Stockholm University, Faculty of Social Sciences, Stress Research Institute. Karolinska Institutet, Sweden.
    Jensen, Karin B.
    Axelsson, John
    Stockholm University, Faculty of Social Sciences, Stress Research Institute. Karolinska Institutet, Sweden.
    Sickness behavior is not all about the immune response: Possible roles of expectations and prediction errors in the worry of being sick2018In: Brain, behavior, and immunity, ISSN 0889-1591, E-ISSN 1090-2139, Vol. 74, p. 213-221Article in journal (Refereed)
    Abstract [en]

    Background

    People react very differently when sick, and there are only poor correlations between the intensity of the immune response and sickness behavior. Yet, alternative predictors of the individual differences in sickness are under-investigated. Based on the predictive coding model of placebo responses, where health outcomes are function of bottom-up sensory information and top-down expectancies, we hypothesized that individual differences in behavioral changes during sickness could be explained by individual top-down expectancies and prediction errors.

    Methods

    Twenty-two healthy participants were made sick by intravenously administering lipopolysaccharide (2 ng/kg body weight). Their expectations of becoming sick were assessed before the injection.

    Results

    Participants having lower expectations of becoming sick before the injection reacted with more emotional distress (i.e., more negative affect and lower emotional arousal) than those with high expectations of becoming sick, despite having similar overall sickness behavior (i.e., a combined factor including fatigue, pain, nausea and social withdrawal). In keeping with a predictive coding model, the “prediction error signal”, i.e., the discrepancy between the immune signal and sickness expectancy, predicted emotional distress (reduction in emotional arousal in particular).

    Conclusion

    The current findings suggest that the emotional component of sickness behavior is, at least partly, shaped by top-down expectations. Helping patients having a realistic expectation of symptoms during treatment of an illness may thus reduce aggravated emotional responses, and ultimately improve patients’ quality of life and treatment compliance.

    Registration

    “Endotoxin-induced Inflammatory and Behavioral Responses and Predictors of Individual Differences”, https://clinicaltrials.gov/ct2/show/NCT02529592, registration number: NCT02529592.

  • 27.
    Leduc, Jean
    Stockholm University.
    Catecholamine production and release in exposure and acclimation to cold.1961Doctoral thesis, monograph (Other academic)
  • 28.
    Lindenfors, Patrik
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Humanities, Centre for Cultural Evolution.
    Ericson, Emilia
    Twana, Tara
    Johnsson, Cecilia
    Dannefjord, Per
    Sturmark, Christer
    Aborträtt och trafficking hör ihop2014In: Aftonbladet, ISSN 0349-1145Article in journal (Other (popular science, discussion, etc.))
  • 29.
    Lindquist, Armin
    Stockholm University.
    Über die Morphologie und Biologie von Limnocalanus im Ostseebecken.1961Doctoral thesis, comprehensive summary (Other academic)
  • 30.
    López Clinton, Samantha
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden; Centre for Palaeogenetics, Sweden; Metropolitan Autonomous University, Mexico.
    Microcosmos explorers: foldscope workshop for science outreach in Mexican schools2023In: Biology Methods & Protocols, E-ISSN 2396-8923, Vol. 8, no 1, article id bpad035Article in journal (Refereed)
    Abstract [en]

    Foldscopes are ultra-low-cost paper microscopes invented by Manu Prakash and Jim Cybulski at Stanford University. They are about as light as a pencil and waterproof, all whilst offering similar optic quality to traditional microscopes. Foldscopes do not require electricity or glass slides to be used, which increases the possibilities of their use in education and outreach activities with children or people with disabilities. In 2019, thanks to a material grant of 100 foldscopes from One World Science and additional purchased foldscopes, I designed and implemented a science workshop called Exploradores del Microcosmos, or Explorers of Microcosmos in English. The aim of the workshop was to help make microscopy more accessible, in particular at underfunded schools, and stimulate active learning about ecosystems and evolution in the participants. Within this article, I describe the workshop and relay my personal insights and reflections on its execution across multiple schools and groups in Mexico.

  • 31.
    Löfroth, Göran
    Stockholm University.
    Studies on γ-radiation induced changes in compounds and systems of biological importance1967Doctoral thesis, comprehensive summary (Other academic)
  • 32. Mahajan, Shauna L.
    et al.
    Tanner, Lydia
    Ahmadia, Gabby
    Becker, Hannah
    DeMello, Nicole
    Fidler, Robert
    Harborne, Alastair R.
    Jagadish, Arundhati
    Mills, Morena
    Cairney, Paul
    Cheng, Samantha
    Fariss, Brandie
    Masuda, Yuta J.
    Pabari, Mine
    Tengö, Maria
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    Wyborn, Carina
    Glew, Louise
    Accelerating evidence-informed decision-making in conservation implementing agencies through effective monitoring, evaluation, and learning2023In: Biological Conservation, ISSN 0006-3207, E-ISSN 1873-2917, Vol. 286, article id 110304Article in journal (Refereed)
    Abstract [en]

    Evidence-informed decision-making can help catalyze the development and implementation of effective conservation actions. Yet despite decades of research on evidence-informed conservation, its realization within conservation implementing agencies and organizations still faces challenges. First, conservation decisions are shaped by individual, organizational, and systemic factors that operate and interact across different temporal and spatial scales. Second, the different cultures and value systems within conservation implementing agencies fuels continued debate on what can and should count as evidence for decision-making, and ultimately shapes how evidence is used in practice. While the importance of evidence-informed conservation is increasingly recognized, we have witnessed few changes within conservation implementing agencies that could enable better engagement with diverse types of evidence and knowledge holders. Based on our experience supporting monitoring, evaluation and learning systems in conservation implementing agencies, we argue that to realize evidence-informed conservation we need a better understanding of the process and context of conservation decision-making within organizations, an alignment of institutional systems and processes that generate evidence relevant to information needs, and changes that help conservation organizations become learning organizations. These actions could help transform how conservation practitioners and organizations learn to enable more evidence-informed decision-making within the complex systems they work in.

  • 33. Masrati, Gal
    et al.
    Mondal, Ramakanta
    Rimon, Abraham
    Kessel, Amit
    Padan, Etana
    Lindahl, Erik
    Stockholm University, Science for Life Laboratory (SciLifeLab).
    Ben-Tal, Nir
    An angular motion of a conserved four-helix bundle facilitates alternating access transport in the TtNapA and EcNhaA transporters2020In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 117, no 50, p. 31850-31860Article in journal (Refereed)
    Abstract [en]

    There is ongoing debate regarding the mechanism through which cation/proton antiporters (CPAs), like Thermus thermophilus NapA (TtNapA) and Escherichia coli NapA (EcNhaA), alternate between their outward- and inward-facing conformations in the membrane. CPAs comprise two domains, and it is unclear whether the transition is driven by their rocking-bundle or elevator motion with respect to each other. Here we address this question using metadynamics simulations of TtNapA, where we bias conformational sampling along two axes characterizing the two proposed mechanisms: angular and translational motions, respectively. By applying the bias potential for the two axes simultaneously, as well as to the angular, but not the translational, axis alone, we manage to reproduce each of the two known states of TtNapA when starting from the opposite state, in support of the rocking-bundle mechanism as the driver of conformational change. Next, starting from the inward-facing conformation of EcNhaA, we sample what could be its long-sought-after outward-facing conformation and verify it using cross-linking experiments.

  • 34.
    Mattsson, Emma
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Importance of Fucus vesiculosus (bladderwrack) for coastal fish communities in the Baltic Sea2019Independent thesis Advanced level (degree of Master (Two Years)), 80 credits / 120 HE creditsStudent thesis
    Abstract [en]

    Within temperate coastal seascapes, macroalgae provide habitats for different organisms such as invertebrates and fish. In analogy to seagrass meadows, macroalgae beds are known for their importance as fish nurseries. However, within the Baltic Sea the importance of the canopy forming macroalgae Fucus vesiculosus for coastal fish communities, especially the juveniles, is unclear. In order to address this knowledge gap, fish communities in areas with and without F. vesiculosus were investigated around Askö, an island in the archipelago of the Baltic Sea. Sites were subjected to different exposures (sheltered, exposed or very exposed) and three different methods were used for sampling (underwater visual census (UVCs), beach seine netting and remote underwater videos (RUVs)). Overall, fish community composition differed significantly among locations and fish abundance and fish biomass were significantly higher in sites with F. vesiculosus than sites without. There was no significant relationship between algae cover or habitat complexity and fish abundance/biomass in sites with F. vesiculosus. Fish behaviour differed between sites with and without F. vesiculosus, with fish feeding more in sites with F. vesiculosus and traveling more in sites without F. vesiculosus. Only one location, Knabberskär, had significantly higher species richness in F. vesiculosus than in sites without F. vesiculosus. There were no differences in juvenile abundance among sites with or without F. vesiculosus and abundance of adult fish was higher than juvenile fish, regardless of location, site or species. Mean invertebrate abundance was a twice as high in the sheltered location Husbåtsviken than in Knabberskär. Higher fish abundance, fish biomass and species richness in sites with F. vesiculosus compared to sites without, suggest that macroalgae may play an important role in the Baltic Sea, however it might not be as important for juvenile fishes as predicted. The three different sampling methods provided similar results for fish abundance, but not for fish biomass. Continued studies where the relationship between fish communities and aspects of F. vesiculosus structure (such as canopy height) as well as linkage with other habitats is recommended for further understanding and better protection of F. vesiculosus habitats.

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  • 35.
    McComas, Sarah
    et al.
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Reichenbach, Tom
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Mitrovic, Darko
    Alleva, Claudia
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Bonaccorsi, Marta
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Delemotte, Lucie
    Drew, David
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Stockbridge, Randy B.
    Determinants of sugar-induced influx in the mammalian fructose transporter GLUT52023In: eLIFE, E-ISSN 2050-084X, Vol. 12, article id e84808Article in journal (Refereed)
    Abstract [en]

    In mammals, glucose transporters (GLUT) control organism-wide blood-glucose homeostasis. In human, this is accomplished by 14 different GLUT isoforms, that transport glucose and other monosaccharides with varying substrate preferences and kinetics. Nevertheless, there is little difference between the sugar-coordinating residues in the GLUT proteins and even the malarial Plasmodium falciparum transporter PfHT1, which is uniquely able to transport a wide range of different sugars. PfHT1 was captured in an intermediate 'occluded' state, revealing how the extracellular gating helix TM7b has moved to break and occlude the sugar-binding site. Sequence difference and kinetics indicated that the TM7b gating helix dynamics and interactions likely evolved to enable substrate promiscuity in PfHT1, rather than the sugar-binding site itself. It was unclear, however, if the TM7b structural transitions observed in PfHT1 would be similar in the other GLUT proteins. Here, using enhanced sampling molecular dynamics simulations, we show that the fructose transporter GLUT5 spontaneously transitions through an occluded state that closely resembles PfHT1. The coordination of D-fructose lowers the energetic barriers between the outward- and inward-facing states, and the observed binding mode for D-fructose is consistent with biochemical analysis. Rather than a substrate-binding site that achieves strict specificity by having a high affinity for the substrate, we conclude GLUT proteins have allosterically coupled sugar binding with an extracellular gate that forms the high-affinity transition-state instead. This substrate-coupling pathway presumably enables the catalysis of fast sugar flux at physiological relevant blood-glucose concentrations.

  • 36.
    Meher, Prabodha Kumar
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Lundholm, Lovisa
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Wojcik, Andrzej
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Jan Kochanowski University, Poland.
    Fluorescence in situ hybridisation for interphase chromosomal aberration-based biological dosimetry2023In: Radiation Protection Dosimetry, ISSN 0144-8420, E-ISSN 1742-3406, Vol. 199, no 14, p. 1501-1507Article in journal (Refereed)
    Abstract [en]

    Metaphase spreads stained with Giemsa or painted with chromosome-specific probes by fluorescence in situ hybridisation (FISH) have been in use since long for retrospective dose assessment (biological dosimetry). However, in cases of accidental exposure to ionising radiation, the culturing of lymphocytes to obtain metaphase chromosomes and analysis of chromosomal aberrations is time-consuming and problematic after high radiation doses. Similarly, analysing chromosomal damage in G0/G1 cells or nondividing cells by premature chromosome condensation is laborious. Following large-scale radiological emergencies, the time required for analysis is more important than precision of dose estimate. Painting of whole chromosomes using chromosome-specific probes in interphase nuclei by the FISH technique will eliminate the time required for cell culture and allow a fast dose estimate, provided that a meaningful dose-response can be obtained by scoring the number of chromosomal domains visible in interphase nuclei. In order to test the applicability of interphase FISH for quick biological dosimetry, whole blood from a healthy donor was irradiated with 8 Gy of gamma radiation. Irradiated whole blood was kept for 2 h at 37°C to allow DNA repair and thereafter processed for FISH with probes specific for Chromosomes-1 and 2. Damaged chromosomal fragments, distinguished by extra color domains, were observed in interphase nuclei of lymphocytes irradiated with 8 Gy. These fragments were efficiently detected and quantified by the FISH technique utilising both confocal and single plane fluorescence microscopy. Furthermore, a clear dose-response curve for interphase fragments was achieved following exposure to 0, 1, 2, 4 and 8 Gy of gamma radiation. These results demonstrate interphase FISH as a promising test for biodosimetry and for studying cytogenetic effects of radiation in nondividing cells.

  • 37.
    Nguyen, Thi Thanh Van
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    The actinorhizal symbiosis of the earliest divergent Frankia cluster2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In recent years, the need to reduce reliance on synthetic nitrogen fertilizer has led to extensive research on biological nitrogen fixation, especially on root nodule symbioses. My study focuses on actinorhizal symbioses, the symbiotic interactions between members of nitrogen-fixing soil actinobacteria from the genus Frankia and a diverse group of plants from eight families, collectively called actinorhizal plants. Frankia cluster II has been shown to be sister to all other clusters. Thus, one of my aims was to gain insight into this cluster to get more information about the evolution of actinorhizal symbioses. The first sequenced genome of a member from this cluster Candidatus Frankia datiscae Dg1 originated from Pakistan. This strain contains the canonical nod genes nodABC responsible for the synthesis of lipochitooligosaccharide Nod factors. In this thesis, we obtained three Frankia inocula from North America (USA), one from Europe (France), one from Asia (Japan) and one from Oceania (Papua New Guinea). Thirteen metagenomes were sequenced based on gDNA isolated from root nodules of Datisca glomerata (Datiscaceae), Ceanothus thyrsiflorus (Rhamnaceae), Coriaria myrtifolia and Coriaria arborea (Coriariaceae). This study shows that members of Frankia cluster II come in teams, helping to explain the ability of cluster II to nodulate a wide host range, four families from two orders. The inoculum from Papua New Guinea, the only sequenced strain from the Southern Hemisphere so far, contains a new Frankia species, which was proposed as Candidatus Frankia meridionalis. All cluster II strains in this study contain the canonical nod genes nodABC, with the exception of the strain from Papua New Guinea which contains only nodB’C. All North American metagenomes also contain the sulfotransferase gene nodH. This gene shows host plant-specific expression in that it was expressed in nodules of C. thyrsiflorus but not in D. glomerata. Phylogenetic analysis and transposase frequencies of the new genomes strongly support the hypothesis that the extension of the cluster II host range from Coriaria to Datisca occurred in Eurasia and that cluster II strains came to North America via the Bering Strait. To acquire more information of the influence of the host plant on the behavior of the microsymbionts, the bacterial metabolism in nodules of D. glomerata (Cucurbitales) and C. thyrsiflorus (Rosales) were compared at the level of transcription. The system to protect nitrogenase from oxygen in Ceanothus nodules seems to be more efficient than in Datisca nodules, whereas the bacterial nitrogen metabolism is likely to be similar in both host plants. The amino acid profile of D. glomerata nodules shows that the nitrogenous solutes are dominated by glutamate and arginine, supporting the suggestion that Frankia in D. glomerata nodules exports an assimilated form of nitrogen, most likely arginine. Thus, our data show that cluster II Frankia strains differ from all other Frankia clusters with regard to the presence of the canonical nod genes and their nitrogen metabolism in symbiosis. 

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  • 38.
    Nguyen, Thi Thanh Van
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Hilker, Rolf
    Wibberg, Daniel
    Battenberg, Kai
    Berry, Alison
    Kalinowski, Jörn
    Pawlowski, Katharina
    Cucurbitales vs. Rosales: Analysis of bacterial metabolism based on candidate gene expression profiling in root nodules of Datisca glomerata and Ceanothus thyrsiflorusManuscript (preprint) (Other academic)
  • 39.
    Nguyen, Thi Thanh Van
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Wibberg, Daniel
    Vigil-Stenman, Theoden
    Battenberg, Kai
    Demchenko, Kirill
    Blom, Jochen
    Fernandez, Maria
    Yamanaka, Takashi
    Berry, Alison
    Kalinowski, Jörn
    Brachmann, Andreas
    Pawlowski, Katharina
    Metagenomes from the earliest divergent Frankia cluster: They come in teamsManuscript (preprint) (Other academic)
  • 40.
    Nuppenau, Jan-Niklas
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Höglund, Elsa
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Minadakis, Nikolaos
    Stockholm Univ, Dept Ecol Environm & Plant Sci, Stockholm, Sweden.
    Kainulainen, Kent
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum.
    Humphreys, Aelys M.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).
    Phylogeography of Icelandic Agrostis (Poaceae) Reveals a New Geothermal Lineage2023In: International journal of plant sciences, ISSN 1058-5893, E-ISSN 1537-5315, Vol. 184, no 6, p. 413-428Article in journal (Refereed)
    Abstract [en]

    Premise of research. Geothermal areas create living conditions strikingly different from their surroundings, providing opportunities for studying organisms' thermal adaptations and responses to climate warming. However, the origins of geothermal organisms are poorly known, limiting our ability to design and interpret experimental studies. To address this, we tested whether geothermal populations of Agrostis (Poaceae) in Iceland represent a single lineage (clade) and, if so, whether that lineage originated in adjacent, nonthermal areas or elsewhere.Methodology. We studied the phylogeography of A. stolonifera and A. vinealis from geothermally heated and nonheated areas in Iceland, using whole plastome data and Bayesian and likelihood phylogenetic analyses. Having identified an exclusively geothermal clade for A. stolonifera, we performed a common-garden experiment to test for heritable phenotypic differences between geothermal and nonthermal plants.Pivotal results. At least two lineages of A. stolonifera have colonized Iceland independently, one being exclusively geothermal and the other exclusively nonthermal. The geothermal lineage is phylogenetically isolated, and its geographical origin could not be determined. Grown in a common garden, geothermal A. stolonifera produced significantly shorter stolons than nonthermal plants. In contrast, geothermal A. vinealis did not form a clade. Instead, all Icelandic A. vinealis formed a clade with nonthermal A. vinealis from outside of Iceland, plus geothermal A. rossiae and A. scabra.Conclusions. We demonstrate the existence of an exclusively geothermal lineage of A. stolonifera, which also shows heritable phenotypic differences, but not of A. vinealis. These contrasting findings possibly reflect different growth forms and life histories. Our results provide a phylogenetic hypothesis to be tested with nuclear data and a framework for future experimental studies, highlighting the importance of a historical perspective for understanding the peculiar plant communities that thrive in geothermal areas. Finally, our results suggest A. vinealis is in need of taxonomic revision.

  • 41.
    Palmé, Anna
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Wennerström, Lovisa
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Guban, Peter
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Stopping compensatory releases of salmon in the Baltic Sea. Good or bad for Baltic salmon gene pools?: Report from the Baltic Salmon 2012 symposium and workshop, Stockholm university February 9-102012Report (Other academic)
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    Workshop report
  • 42.
    Palmé, Anna
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Wennerström, Lovisa
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Guban, Peter
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Compromising Baltic salmon genetic diversity: Conservation genetic risks associated with compensatory releases of salmon in the Baltic Sea2012Report (Other academic)
  • 43.
    Palmé, Anna
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Wennerström, Lovisa
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Guban, Peter
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Conclusions on conservation genetic risks associated with compensatory releases of salmon in the Baltic Sea.: A brief summary of a synthesis report to the Swedish Agency for Marine and Water Management.2012Report (Other academic)
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    Summary report
  • 44.
    Perry, Diana
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Spatial risk assessment of global change impacts on Swedish seagrass ecosystemsManuscript (preprint) (Other academic)
  • 45.
    Raj, Bhoj
    Stockholm University.
    Pollen morphological studies in the Acanthaceae1961Doctoral thesis, monograph (Other academic)
  • 46.
    Rasmusson, Lina M.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Seagrass Respiration: An assessment of oxygen consumption patterns of temperate marine macrophytes2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In coastal seas, the abundance of marine macrophytes has profound influence on the flows of oxygen and inorganic carbon through the water. Vast amounts of carbon dioxide are taken up by photosynthesis and part of this is respired back into the water column. The photosynthetic carbon uptake of the most common seagrasses of the northern hemisphere is nowadays extensively studied at both community- and individual levels, and its impact on coastal carbon- and oxygen fluxes is quite well defined. However, the coinciding release of carbon dioxide and consumption of oxygen by the processes of mitochondrial respiration and photorespiration in these organisms has as yet not been given much attention, especially concerning how these processes are affected by external factors. For estimations of the rates of mitochondrial respiration, the common approach has been to use values obtained during darkness and treat them as being constant over the day. This approach is questioned in this thesis where the effects of different abiotic and biotic factors on oxygen consumption were examined to elucidate possible variations of seagrass respiration rates (with primary focus on the species Zostera marina), explored mainly using gas exchange techniques. The initial aim was to investigate whether the rates of respiration are at all fluctuating. This was found to be the case. Secondly, impacts of various factors on the respiration process were examined on Z. marina, with additional studies on the seagrass Ruppia maritima and the common green alga Ulva intestinalis. It was found that respiration rates were lower in the light for all three species. Specific investigations on Z. marina showed that respiration rates also varied with time of the day. Moreover, the rates of both respiration and photosynthesis differed between Z. marina shoots of different age as well as among different parts of the leaves. These differences were observed at both ambient (19.1oC) and elevated (29.1oC) temperatures. Photorespiration, previously considered insignificant in seagrasses, was found to have a profound role, as high rates were observed in productive bays, i.e. in settings with low inorganic carbon availability and high oxygen. Overall, this thesis has identified important external and developmental factors influencing the patterns of oxygen consumption and associated carbon dioxide release of two common temperate seagrasses. Clearly, respiration in seagrasses is a dynamic process that responds to a variety of external and developmental factors, which should be carefully considered when assessing the carbon budget of coastal vegetated areas.

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  • 47.
    Rasmusson, Lina M.
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Björk, Mats
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Gullström, Martin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Effects of increased temperature on respiration and photosynthesis differ among different leaf parts and with tissue age of the seagrass Zostera marinaManuscript (preprint) (Other academic)
  • 48.
    Rasmusson, Lina M.
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Lauritano, Chiara
    Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy.
    Procaccini, Gabriele
    Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy.
    Gullström, Martin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Björk, Mats
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Respiratory oxygen consumption in the seagrass Zostera marina is affected by light and varies on a diel basis: a combined gas exchange and gene expression studyManuscript (preprint) (Other academic)
  • 49. Robuchon, Marine
    et al.
    da Silva, Jessica
    Dubois, Grégoire
    Gumbs, Rikki
    Hoban, Sean
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Owen, Nisha R.
    Perino, Andrea
    Conserving species' evolutionary potential and history: Opportunities under the Kunming–Montreal Global Biodiversity Framework2023In: Conservation Science and Practice, E-ISSN 2578-4854, Vol. 5, no 6, article id e12929Article in journal (Refereed)
    Abstract [en]

    Genetic diversity (GD) and phylogenetic diversity (PD) respectively represent species' evolutionary potential and history, and support most of the biodiversity benefits to humanity. Yet, these two biodiversity facets have been overlooked in previous biodiversity policies. As the Parties to the Convention on Biological Diversity (CBD) adopted the Kunming–Montreal Global Biodiversity Framework (GBF) in December 2022, we analyze how GD and PD are considered in this new framework and discuss how their incorporation in the GBF could strengthen their conservation. Although the inclusion of certain indicators could be elevated, both GD and PD are an integral part of the recently adopted GBF. This represents a significant improvement compared to the CBD strategic plan 2011–2020 and an unprecedented opportunity to bring species' evolutionary potential and history to the core of public biodiversity policies. We urge the scientific community to leverage this opportunity to actually improve the conservation of species' evolutionary potential and history. 

  • 50.
    Roufidou, Chrysoula
    Stockholm University, Faculty of Science, Department of Zoology.
    Reproductive physiology of the female three-spined stickleback, Gasterosteus aculeatus2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Reproduction in vertebrates, including fishes, is under control of the brain-pituitary-gonad (BPG) axis. The female three-spined stickleback, Gasterosteus aculeatus, produces egg clutches at intervals of a few days and spawns them in a nest built by male. Following ovulation, eggs are stored in the ovarian cavity surrounded by the ovarian fluid (OF). If spawning or spontaneous release do not occur, the eggs can undergo overripening, a phenomenon occurring both in nature and captivity.

    In this PhD thesis, the changes of reproductive hormones and vitellogenesis were studied at overripening of eggs and over the natural spawning cycle. OF properties were also examined at overripening of eggs and after treatment with sex steroids.

    Plasma levels of steroids: testosterone (T), estradiol (E2), 17,20β-dihydroxypregn-4-en-3-one (17,20β-P) and 17,20β,21-trihydroxypregn-4-en-3-one (17,20β,21-P) were measured by radioimmunoassay, and relative mRNA levels of the pituitary gonadotropins (fsh-β/lh-β), brain gonadotropin-releasing hormones (gnrh2/gnrh3) and kisspeptin and its receptor (kiss2/gpr54) by qPCR. Overripening of eggs was accompanied with a significant reduction in most of endocrine parameters of BPG axis (T, E2, 17,20β-P; lh-β; kiss2, gpr54). Low level of hormones could be advantageous for the overripe egg-bound females, since this would reduce further ovulations giving higher chances to survive and reproduce again. Over the 3-day spawning cycle, T and E2 were highly correlated, showed cyclicity with low levels at ovulation and increasing from 24 and 6 hours post-spawning (hps), respectively. Spawning may give rise to this increase as these rises did not occur if release of the eggs does not happen (overripe females). A peak at pituitary lh-β mRNA levels appeared 48 hps, a day before the next ovulation. No significant changes were found for the other studied hormones.

    Vitellogenesis was studied by measurement of the vitellogenin mRNA levels in the liver by qPCR. The levels were highest at 24 and 48 hps and were positively correlated to both E2 and T over the cycle. However, changes were small suggesting a rather continuous vitellogenesis over the stickleback spawning cycle which could be an advantage for a multiple spawner with a limited spawning season. Overripening reduced vitellogenin mRNA levels but did not abolish it.

    OF amount was diminished in overripe females and had a lower viscocity but higher dry weight and protein levels than in non-overripe ovulated females, suggesting that changes in OF properties are related to the egg overripening. The effects of steroids were studied using Silastic capsules. T and 17,20β-P induced an increase of OF amount, but protein levels were only increased in 17,20β-P-treated females, proposing a role of this steroid in the control of OF secretion. 1-D SDS-PAGE showed that OF contained several proteins, some of them came from eggs, but no consistent differences between groups.

    Concluding, the knowledge of the reproductive physiological changes is important for understanding their essential roles in the production of viable eggs in this species but also in the reproductive physiology of female fishes in general.

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