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1.
  • Gómez-Martínez, Daniela, et al. (författare)
  • Phenotypic and transcriptomic acclimation of the green microalga Raphidocelis subcapitata to high environmental levels of the herbicide diflufenican
  • 2023
  • Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 875
  • Tidskriftsartikel (refereegranskat)abstract
    • Herbicide pollution poses a worldwide threat to plants and freshwater ecosystems. However, the understanding of how organisms develop tolerance to these chemicals and the associated trade-off expenses are largely unknown. This study aims to investigate the physiological and transcriptional mechanisms underlying the acclimation of the green microalgal model species Raphidocelis subcapitata (Selenastraceae) towards the herbicide diflufenican, and the fitness costs associated with tolerance development. Algae were exposed for 12 weeks (corresponding to 100 generations) to diflufenican at the two environmental concentrations 10 and 310 ng/L. The monitoring of growth, pigment composition, and photosynthetic performance throughout the experiment revealed an initial dose-dependent stress phase (week 1) with an EC50 of 397 ng/L, followed by a time-dependent recovery phase during weeks 2 to 4. After week 4, R. subcapitata was acclimated to diflufenican exposure with a similar growth rate, content of carotenoids, and photosynthetic performance as the unexposed control algae. This acclimation state of the algae was explored in terms of tolerance acquisition, changes in the fatty acids composition, diflufenican removal rate, cell size, and changes in mRNA gene expression profile, revealing potential fitness costs associated with acclimation, such as up-regulation of genes related to cell division, structure, morphology, and reduction of cell size. Overall, this study demonstrates that R. subcapitata can quickly acclimate to environmental but toxic levels of diflufenican; however, the acclimation is associated with trade-off expenses that result in smaller cell size.
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2.
  • Airaud, M, et al. (författare)
  • Biologie - Les manuels visuels pour la Licence
  • 2018
  • Bok (övrigt vetenskapligt/konstnärligt)abstract
    • En couleurs et très illustré, ce manuel a été conçu pour vous qui débutez un cursus scientifique universitaire. Il vous permettra d’acquérir les connaissances fondamentales en biologie, mais aussi la démarche et la rigueur scientifiques indispensables aux études supérieures. De multiples rubriques vous garantissent un apprentissage progressif et complet : un cours visuel avec de nombreux exemples concrets pour introduire et illustrer les notions et concepts clés ; des encadrés méthodologiques pour vous guider vers les bonnes pratiques et vous faire découvrir les grandes méthodes expérimentales ; des focus sur des applications, sujets de recherche ou thèmes d’actualité ; des repères historiques ; de nombreux QCM et exercices (tous corrigés) pour tester vos acquis et vous entraîner.
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3.
  • Subhash, Santhilal, 1987, et al. (författare)
  • Sperm Originated Chromatin Imprints and LincRNAs in Organismal Development and Cancer
  • 2020
  • Ingår i: iScience. - : Elsevier BV. - 2589-0042. ; 23:6
  • Tidskriftsartikel (refereegranskat)abstract
    • Importance of sperm-derived transcripts and chromatin imprints in organismal development is poorly investigated. Here using an integrative approach, we show that human sperm transcripts are equally important as oocyte. Sperm-specific and sperm-oocyte common transcripts carry distinct chromatin structures at their promoters correlating with corresponding transcript levels in sperm. Interestingly, sperm-specific H3K4me3 patterns at the lincRNA promoters are not maintained in the germ layers and somatic tissues. However, bivalent chromatin at the sperm-specific protein-coding gene promoters is maintained throughout the development. Sperm-specific transcripts reach their peak expression during zygotic genome activation, whereas sperm-oocyte common transcripts are present during early preimplantation development but decline at the onset of zygotic genome activation. Additionally, there is an inverse correlation between sperm-specific and sperm-oocyte lincRNAs throughout the development. Sperm-lincRNAs also show aberrant activation in tumors. Overall, our observations indicate that sperm transcripts carrying chromatin imprints may play an important role in human development and cancer.
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6.
  • Tapani, Sofia, 1982 (författare)
  • Stochastic modelling and analysis of early mouse development
  • 2011
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • The aim of this thesis is to model and describe dynamical events for biological cells using statistical and mathematical tools. The thesis includes five papers that all relate to stochastic modelling of cells. In order to understand the development and patterning of the early mammalian embryo, stochastic modelling has become a more important tool than ever. It allows for studying the processes that mediate the transition from pluripotency of the embryonic cells to their differentiation. It is still unclear whether the positions of cells determine their future fates. One alternative possibility is that cells are pre-specified at random positions and then sort according to a already set fate. Mouse embryonic cells are thought to be equivalent in their developmental properties until approaching the eight-cell stage. Some biological studies show, in comparison, that patterning can be present already at sperm entry and in the pronuclei migration. We investigate in Paper I the dynamics of the pronuclei migration by analysing their trajectories and find that not only do the pronuclei follow a noise corrupted path towards the centre of the egg but they also have some attraction to each other which affects their dynamics. Continuing in Paper II and III, we use these results to model this behaviour with a coupled stochastic differential equation model. This enables us to simulate distributions that describe the meeting plane between pronuclei which in turn can be related to the orientation of the first cleavage of the egg. Our results show that adding randomness in sperm entry point is different from the randomness added through the environment of the egg. We are also able to show that data sets with normal eggs and eggs treated with an actin growth inhibitor give rise to considerably different model dynamics, suggesting that the treatment is affecting the migration in an invasive way. Altering the pronuclei dynamics can alter the polarity of the egg and may transfer into the later axis-formation process. Invasiveness of experimental procedures is a difficult issue to handle. The alternative to invasive procedures is not appealing since it means that important developmental features may not be discovered because of individual variability and noise, leading to guesswork of the underlying mechanisms. The embryonic cells are easily affected by treatments performed to make the measuring, made by hand, easier or by the light exposure of the microscope. Treatments as such are used for example for producing flourescent proteins in membranes or slowing processes down. Paper IV and Paper V serve to analyse how light induced stress affects yeast cells and we employ a method for analysing the noisy non-stationary time series, which are a result of the yeast experiments, using wavelet decomposition.
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7.
  • Förlin, Lars, 1950, et al. (författare)
  • mRNA Expression and Biomarker Responses in Perch at a Biomonitoring Site in the Baltic Sea - Possible Influence of Natural Brominated Chemicals
  • 2019
  • Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 6
  • Tidskriftsartikel (refereegranskat)abstract
    • Perch (Perca fluviatilis) has been used in biological effect monitoring in a program for integrated coastal fish monitoring at the reference site Kvadofjarden along the Swedish east coast, which is a site characterized by no or minor local anthropogenic influences. Using a set of physiological and biochemical endpoints (i.e., biomarkers), clear time trends for "early warning" signs of impaired health were noted in the perch from this site, possibly as a result of increased baseline pollution. The data sets also showed relatively large variations among years. To identify additional temporal variation in biological parameters, global mRNA expression studies using RNA sequencing was performed. Perch collected in 2010 and 2014 were selected, as they showed variations in several biomarkers, such as the activity of the detoxification enzyme CYP1A (EROD), the plasma levels of vitellogenin, markers for oxidative stress, white blood cells count and gonad sizes. The RNA sequencing study identified approximately 4800 genes with a significantly difference in mRNA expression levels. A gene ontology enrichment analysis showed that these differentially expressed genes were involved in biological processes such as complement activation, iron ion homeostasis and cholesterol biosynthetic process. In addition, differences in immune system parameters and responses to the exposure of toxic substances have now been verified in two different biological levels (mRNA and protein) in perch collected in 2010 and 2014. Markedly higher mRNA expression of the membrane transporter (MATE) and the detoxification enzyme COMT, together with higher concentrations of bioactive naturally produced brominated compounds, such as brominated indoles and carbazoles, seem to indicate that the perch collected in 2014 had been exposed to macro- and microalga blooming to a higher degree than did perch from 2010. These results and the differential mRNA expression between the 2 years in genes related to immune and oxidative stress parameters suggest that attention must be given to algae blooming when elucidating the well-being of the perch at Kvadofjarden and other Baltic coastal sites.
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8.
  • Edelbroek, Bart (författare)
  • Function and Evolution of Small Regulatory RNAs and their Associated Proteins : A Journey from Genome to Proteome
  • 2024
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Organisms throughout the tree of life have evolved distinct ways to regulate gene expression. Some of these processes involve non-coding RNAs (ncRNAs), which are not translated but functional nonetheless. These ncRNAs are of utmost importance, with dysregulation of some causing severe developmental effects or even being lethal.In order to get a better fundamental understanding of gene regulation, and the ncRNAs that evolved to regulate gene expression, we study this in Amoebozoa. Members of this taxon vary greatly in lifestyle and organismal complexity. Some are strictly unicellular, free-living, whereas others, such as the social amoeba Dictyostelium discoideum can transition between unicellular and multicellular lifestyles. D. discoideum features a variety of small ncRNAs. Among these are the microRNAs. microRNAs have mostly been studied in plants and animals, where they are believed to have evolved convergently, and hypothesized to have played a role when these taxa evolved multicellular lifestyles. At what point the D. discoideum microRNAs evolved, how they function, and if they are involved in its multicellular lifestyle are fundamental questions addressed in this thesis. Here, we studied the evolution and function of microRNAs in a broad set of species belonging to Amoebozoa. We could identify microRNAs in all studied amoebae, and concluded that they are probably not involved in the evolution of multicellularity. To in detail investigate the evolution of microRNAs, we performed comparative genomics using D. discoideum and the close relative Dictyostelium firmibasis. For this, we sequenced, assembled and annotated the genome of the latter. At this point, our findings suggest that the microRNAs evolved several times in Amoebozoa, although we cannot rule out if they have a deep evolutionary history.The Class I RNAs are another type of ncRNAs. These, on the other hand, are only present in the social amoebae. They are hypothesized to regulate the transition from unicellular to multicellular in these species, potentially in a post-transcriptional manner. In order to investigate this, it is essential to understand to what extent the proteome and transcriptome correlate. Hence, we performed paired transcriptomics and proteomics in a time-series during multicellular development. By including a strain in which a specific Class I RNA is knocked out, we have initiated studies of its role during the transition to multicellularity.In conclusion, we were able to answer broad evolutionary and functional questions about gene regulation and ncRNAs by studying Amoebozoa from genome to proteome. 
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9.
  • Arcot Jayaram, Satish, 1979- (författare)
  • New roles for apical secretion and extracellular matrix assembly in Drosophila epithelial morphogenesis
  • 2010
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Branched tubular organs, such as the lung and vascular system fulfill the respiratory needs of most animals. Optimal tissue function relies on the uniform sizes and shapes of the constituting branches in each organ. The Drosophila tracheal airways provide a recognized genetic model system for identification and characterization of tube size regulators. We found that the programmed secretion and assembly of the apical extracellular matrix (ECM) is required for the expansion of the trachea and salivary glands (SG) tubes. We have characterized Vermiform (Verm) and Serpentine (Serp), two chitin-binding proteins with predicted polysaccharide deacetylase domains (ChLDs). Verm and Serp mutants show overelongated tubes, suggesting that luminal ECM modification restricts tracheal tube elongation. The luminal deposition of ChLDs, but not other secreted components, depends on paracellular septate junction integrity (SJs) in the tracheal epithelium. Deletion of the deacetylase domain renders Serp-GFP intracellular, arguing that the deacetylase domain harbors uncharacterized secretion signals. To explore this possibility we transferred the deacetylase domain from Serp to Gasp, another tracheal luminal protein, which requires the Emp24 adaptor for ER exit. The Gasp-Deac-GFP chimera was normally secreted in emp24 mutants indicating that the deacetylase domain contains potential ER-exit signals. To identify such signals we characterized conserved sequence motifs in the Serp deacetylase domain. Mutations of the N-glycosylation sites gradually reduced Serp-GFP luminal deposition suggesting that increased glycosylation enhances apical Serp secretion. By contrast, substitutions in three conserved amino acid stretches completely blocked the ER-exit of Serp-GFP. The mutated proteins were N-glycosylated suggesting that the motifs may be involved in a subsequent protein-folding step or facilitate ER exit through interactions with unidentified specific adaptors.
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10.
  • Barsoum, Emad, 1979- (författare)
  • Mating type switching and transcriptional silencing in Kluyveromyces lactis
  • 2010
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • To explore the similarities and differences of regulatory circuits among budding yeasts, we characterized the role of unscheduled meiotic gene expression 6 (UME6) and a novel mating type switching pathway in Kluyveromyces lactis. We found that Ume6 was required for transcriptional silencing of the cryptic mating-type loci HMLα and HMRa. Ume6 acted directly at these loci by binding to the cis-regulatory silencers. Ume6 also served as a block to polyploidy and was required for repression of three meiotic genes, independently of the Rpd3 and Sin3 corepressors. Mating type switching from MATα to MATa required the α3 protein. The α3 protein was similar to transposases of the mutator like elements (MULEs). Mutational analysis showed that the DDE-motif in α3, which is conserved in MULEs was necessary for switching. During switching α3 mobilizes from the genome in the form of a DNA circle. The sequences encompassing the α3 gene circle junctions in the MATα locus were essential for switching from MATα to MATa. Switching also required a DNA binding protein, Mating type switch 1 (Mts1), whose binding sites in MATα were important. Expression of Mts1 was repressed in MATa/MATα diploids and by nutrients, limiting switching to haploids in low nutrient conditions. In a genetic selection for strains with increased switching rates we found a mutation in the RAS1 gene. By measuring the levels of the MTS1 mRNA and switching rates in ras1, pde2 and msn2 mutant strains we show that mating type switching in K. lactis was regulated by the RAS/cAMP pathway and the transcription factor Msn2. ras1 mutants contained 20-fold higher levels of MTS1 mRNA compared to wild type whereas pde2 and msn2 expressed less MTS1 mRNA and had decreased switching rates. Furthermore we found that MTS1 contained several potential Msn2 binding sites upstream of its ORF. We suggest that these observations explain the nutrient regulation of switching.
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11.
  • Carter, Sidney D., et al. (författare)
  • Nej1 recruits the Srs2 helicase to DNA double-strand breaks and supports repair by a single-strand annealing-like mechanism
  • 2009
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 106:29, s. 12037-12042
  • Tidskriftsartikel (refereegranskat)abstract
    • Double-strand breaks (DSBs) represent the most severe DNA lesion a cell can suffer, as they pose the risk of inducing loss of genomic integrity and promote oncogenesis in mammals. Two pathways repair DSBs, nonhomologous end joining (NHEJ) and homologous recombination (HR). With respect to mechanism and genetic requirements, characterization of these pathways has revealed a large degree of functional separation between the two. Nej1 is a cell-type specific regulator essential to NHEJ in Saccharomyces cerevisiae. Srs2 is a DNA helicase with multiple roles in HR. In this study, we show that Nej1 physically interacts with Srs2. Furthermore, mutational analysis of Nej1 suggests that the interaction was strengthened by Dun1-dependent phosphorylation of Nej1 serines 297/298. Srs2 was previously shown to be recruited to replication forks, where it promotes translesion DNA synthesis. We demonstrate that Srs2 was also efficiently recruited to DSBs generated by the HO endonuclease. Additionally, efficient Srs2 recruitment to this DSB was dependent on Nej1, but independent of mechanisms facilitating Srs2 recruitment to replication forks. Functionally, both Nej1 and Srs2 were required for efficient repair of DSBs with 15-bp overhangs, a repair event reminiscent of a specific type of HR called single-strand annealing (SSA). Moreover, absence of Rad51 suppressed the SSA-defect in srs2 and nej1 strains. We suggest a model in which Nej1 recruits Srs2 to DSBs to promote NHEJ/SSA-like repair by dismantling inappropriately formed Rad51 nucleoprotein filaments. This unexpected link between NHEJ and HR components may represent cross-talk between DSB repair pathways to ensure efficient repair.
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13.
  • Forsman, Anders, et al. (författare)
  • Fitness benefits of diverse offspring in pygmy grasshoppers
  • 2007
  • Ingår i: Evolutionary Ecology Research. ; 9:8, s. 1305-1318
  • Tidskriftsartikel (refereegranskat)abstract
    • Question: Do females obtain fitness benefits from an increase in offspring diversity?Hypotheses: Polyandry increases offspring diversity within a clutch. Increased offspring diversity will reduce competition among siblings (manifested as increased mean survival in more diverse families) and the probability that all offspring might be ill-suited to future conditions (manifested as lower variance in survival in diverse families).Organisms: Pygmy grasshoppers, Tetrix subulata and Tetrix: undulata, that are polymorphic for colour pattern.Field site: South-central Sweden.Methods: We varied the number of mates provided to colour polymorphic pygmy grasshoppers. We reared families in either warm or cold conditions using a split-brood design.Conclusions: The colour morph diversity of broods increased with the number of experimentally provided mates. Colour morphs represent alternative strategies that differ in body size, physiology, behaviour, and life history. Survival increased with increasing sibling diversity, supporting the hypothesis that different morphs avoid competition by using different subsets of available resources. Homogeneous families (in which all siblings belong to the same or only a few colour morphs) varied more in survival than did families with diverse siblings, supporting the hypothesis that morphs vary in their ability to cope with and utilize different resources.
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14.
  • Grebe, Markus, 1967- (författare)
  • Plant biology : Unveiling the Casparian strip.
  • 2011
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 473:7347, s. 294-5
  • Tidskriftsartikel (refereegranskat)
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15.
  • Jafari, Gholamali, et al. (författare)
  • Genetics of extracellular matrix remodeling during organ growth using the Caenorhabditis elegans pharynx model.
  • 2010
  • Ingår i: Genetics. - : Oxford University Press (OUP). - 1943-2631. ; 186:3, s. 969-82
  • Tidskriftsartikel (refereegranskat)abstract
    • The organs of animal embryos are typically covered with an extracellular matrix (ECM) that must be carefully remodeled as these organs enlarge during post-embryonic growth; otherwise, their shape and functions may be compromised. We previously described the twisting of the Caenorhabditis elegans pharynx (here called the Twp phenotype) as a quantitative mutant phenotype that worsens as that organ enlarges during growth. Mutations previously known to cause pharyngeal twist affect membrane proteins with large extracellular domains (DIG-1 and SAX-7), as well as a C. elegans septin (UNC-61). Here we show that two novel alleles of the C. elegans papilin gene, mig-6(et4) and mig-6(sa580), can also cause the Twp phenotype. We also show that overexpression of the ADAMTS protease gene mig-17 can suppress the pharyngeal twist in mig-6 mutants and identify several alleles of other ECM-related genes that can cause or influence the Twp phenotype, including alleles of fibulin (fbl-1), perlecan (unc-52), collagens (cle-1, dpy-7), laminins (lam-1, lam-3), one ADAM protease (sup-17), and one ADAMTS protease (adt-1). The Twp phenotype in C. elegans is easily monitored using light microscopy, is quantitative via measurements of the torsion angle, and reveals that ECM components, metalloproteinases, and ECM attachment molecules are important for this organ to retain its correct shape during post-embryonic growth. The Twp phenotype is therefore a promising experimental system to study ECM remodeling and diseases.
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16.
  • Kodandaramaiah, Ullasa (författare)
  • Vagility - the neglected component in historical biogeography
  • 2009
  • Ingår i: Evolutionary biology. - New York : Springer. - 0071-3260 .- 1934-2845. ; 36:3, s. 327-335
  • Tidskriftsartikel (refereegranskat)abstract
    • The conceptual gap between ecological and historical biogeography is wide, although both disciplines are concerned with explaining how distributions have been shaped. A central aim of modern historical biogeography is to use a phylogenetic framework to reconstruct the geographic history of a group in terms of dispersals and vicariant events, and a number of analytical methods have been developed to do so. To date the most popular analytical methods in historical biogeography have been parsimony-based. Such methods can be classified into two groups based on the assumptions used. The first group assumes that vicariance between two areas creates common patterns of disjunct distributions across several taxa whereas dispersals and extinctions generate clade specific patterns. The second group of methods assumes that passive vicariance and within-area speciation have a higher probability of occurrence than active dispersal events and extinction. Typically, none of these methods takes into account the ecology of the taxa in question. I discuss why these methods can be potentially misleading if the ecology of the taxon is ignored. In particular, the vagility or dispersal ability of taxa plays a pivotal role in shaping the distributions and modes of speciation. I argue that the vagility of taxa should be explicitly incorporated in biogeographic analyses. Likelihood-based methods with models in which more realistic probabilities of dispersal and modes of speciation can be specified are arguably the way ahead. Although objective quantification will pose a challenge, the complete ignorance of this vital aspect, as has been done in many historical biogeographic analyses, can be dangerous. I use worked examples to show a simple way of utilizing such information, but better methods need to be developed to more effectively use ecological knowledge in historical biogeography.
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17.
  • Leneveu, Julien, et al. (författare)
  • Varying rates of diversification in the genus Melitaea (Lepidoptera: Nymphalidae) during the past 20 million years
  • 2009
  • Ingår i: Biological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4066 .- 1095-8312. ; 97:2, s. 346-361
  • Tidskriftsartikel (refereegranskat)abstract
    • The influence of Quarternary glacial cycles on the extant diversity of Holarctic species has been intensively studied. It has been hypothesized that palaeoclimatic changes are responsible for divergence events in lineages. A constant improvement in DNA sequencing and modeling methods, as well as palaeoclimatic reconstruction, permit a deeper exploration of general causes of speciation in geological time. In the present study, we sampled, as exhaustively as possible, the butterflies belonging to the genus Melitaea (Lepidoptera: Nymphalidae), which are widely spread in the Palaearctic region. We conducted analyses to assess the phylogeny of the genus and estimated the timing of divergence and the most likely distribution of ancestral populations. The results obtained indicate that the systematics of the genus is in need of revision and that the diversity of the genus has been profoundly shaped by palaeoenvironmental changes during its evolutionary history. The present study also emphasizes that, when employed with caveats, major palaeoenvironmental events could represent very powerful tools for the calibration of the dating of divergences using molecular data.
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18.
  • Ueberschär, Malin, 1991-, et al. (författare)
  • BEN-solo proteins regulate genome accessibility
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Active and silent transcriptional domains are established in parallel with the activation of the genome of a developing animal. Chromatin insulator elements separate transcription units and form barriers to limit the spread of different histone modifications. In contrast to other insulator binding proteins the BEN-solo proteins are expressed ubiquitously only at the stage of mid-blastula transition. They interact with other insulators and can partition the densely spaced transcription units in Drosophila ensuring their correct transcription, but their effect on chromatin architecture has never been explored. Here we show that the ELBA complex and Insv both regulate chromatin accessibility during genome activation. Many regions gain or lose signal in ATAC-seq in the mutants which is accompanied by changes in nascent transcription genome-wide. While ELBA contributes to the silencing of a reporter on the y chromosome, Insv appears to limit the spread of heterochromatin observed by the formation of HP1a-GFP foci. We conclude that ELBA and Insv act as chromatin barriers at a set of common target loci, but also diverge in their regulatory functions on heterochromatin, possibly via different interactors.
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19.
  • Ueberschär, Malin, 1991-, et al. (författare)
  • Insulator activity of paused promoters is independent of active transcription
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Insulators are a class of cis-regulatory elements that organize genome architecture and separate transcription units. Recent evidence suggests that highly transcribed genes co-localize with insulators at chromatin boundaries. However, whether active transcription contributes to chromatin insulation remains unclear. In this study we address whether highly transcribed promoters, which are also in a paused state in the Drosophila embryo, function as insulators with the ability to block enhancer-promoter interaction. Using a transgenic reporter assay, we show that some, but not all, paused promoters act as insulators. To further dissect functional contribution of promoter pausing to enhancer-blocking activity, we focus on an insulator containing the paused wingless (wg) promoter, and find that depleting RNA polymerase II (Pol II) binding has no effect on its insulator function; instead, the insulator binding proteins GAF and ELBA as well as their cognate DNA motifs are essential. We therefore conclude that active transcription or Pol II pausing is not a general mechanism required for enhancer blocking and that the insulator activity is mainly conferred by insulator proteins.
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20.
  • Wang, Shenqiu, 1979- (författare)
  • Grainy head target genes in epithelial morphogenesis and wound healing
  • 2010
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • grainy head (grh) genes encode a family of transcription factors conserved from fly to human. Drosophila grh is the founding member of this gene family and has multiple functions, including tracheal tube size control, epidermal barrier formation and reconstruction after wounding. To understand the underlying molecular mechanism of grh functions, we tried to isolate its direct targets and analyze their function. We identified ten grh targets by combining bioinformatics and genetics. Grh directly controls the expression of stitcher (stit), which encodes a Ret family receptor tyrosine kinase (RTK), during both development and wound healing. Stit promotes actin cable assembly and induces extracellular signal-regulated kinase (ERK) phosphorylation around the wound edges upon injury. Stit also activates barrier repair genes and its own expression at the wound sites in a Grh-dependent manner. This positive feedback loop ensures efficient epidermal wound repair. In addition, Grh regulates the expression of multiple genes involved in chitin biosynthesis or modification. Most of the genes are required for tracheal tube size control. Two of them, verm and serp, encode related putative luminal chitin deacetylases. The functional analysis of verm and serp identifies an important role of luminal chitin matrix modification in limiting tracheal tube elongation. Therefore, it is very likely that Grh controls tracheal tube size through regulating multiple targets involved in the assembly or modification of luminal chitin matrix. Grh also directly activates the epidermal expression of Peptidoglycan recognition protein LC (PGRP-LC) gene that is required for the induction of antimicrobial peptides (AMPs) upon infection. Furthermore, ectopically expressing Grh is sufficient to induce AMP Cecropin A lacZ reporter (CecA-LacZ) in the embryonic epidermis. These results suggest a new function of Grh in the local immune responses in Drosophila barrier epithelia.
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22.
  • Davoine, Celine, et al. (författare)
  • Functional metabolomics as a tool to analyze Mediator function and structure in plants
  • 2017
  • Ingår i: PLOS ONE. - : Public Library Science. - 1932-6203. ; 12:6
  • Tidskriftsartikel (refereegranskat)abstract
    • Mediator is a multiprotein transcriptional co-regulator complex composed of four modules; Head, Middle, Tail, and Kinase. It conveys signals from promoter-bound transcriptional regulators to RNA polymerase II and thus plays an essential role in eukaryotic gene regulation. We describe subunit localization and activities of Mediator in Arabidopsis through metabolome and transcriptome analyses from a set of Mediator mutants. Functional metabolomic analysis based on the metabolite profiles of Mediator mutants using multivariate statistical analysis and heat-map visualization shows that different subunit mutants display distinct metabolite profiles, which cluster according to the reported localization of the corresponding subunits in yeast. Based on these results, we suggest localization of previously unassigned plant Mediator subunits to specific modules. We also describe novel roles for individual subunits in development, and demonstrate changes in gene expression patterns and specific metabolite levels in med18 and med25, which can explain their phenotypes. We find that med18 displays levels of phytoalexins normally found in wild type plants only after exposure to pathogens. Our results indicate that different Mediator subunits are involved in specific signaling pathways that control developmental processes and tolerance to pathogen infections.
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23.
  • Axäng, Claes, 1977, et al. (författare)
  • Developmental genetics of the C. elegans pharyngeal neurons NSML and NSMR.
  • 2008
  • Ingår i: BMC Developmental Biology. - 1471-213X. ; 8
  • Tidskriftsartikel (refereegranskat)abstract
    • Background We are interested in understanding how the twenty neurons of the C. elegans pharynx develop in an intricate yet reproducible way within the narrow confines of the embryonic pharyngeal primordium. To complement an earlier study of the pharyngeal M2 motorneurons, we have now examined the effect of almost forty mutations on the morphology of a bilateral pair of pharyngeal neurosecretory-motor neurons, the NSMs. Results A careful description of the NSM morphology led to the discovery of a third, hitherto unreported process originating from the NSM cell body and that is likely to play a proprioceptive function. We found that the three NSM processes are differently sensitive to mutations. The major dorsal branch was most sensitive to mutations that affect growth cone guidance and function (e.g. unc-6, unc-34, unc-73), while the major sub-ventral branch was more sensitive to mutations that affect components of the extracellular matrix (e.g. sdn-1). Of the tested mutations, only unc-101, which affects an adaptin, caused the loss of the newly described thin minor process. The major processes developed synaptic branches post-embryonically, and these exhibited activity-dependent plasticity. Conclusion By studying the effects of nearly forty different mutations we have learned that the different NSM processes require different genes for their proper guidance and use both growth cone dependent and growth cone independent mechanisms for establishing their proper trajectories. The two major NSM processes develop in a growth cone dependent manner, although the sub-ventral process relies more on substrate adhesion. The minor process also uses growth cones but uniquely develops using a mechanism that depends on the clathrin adaptor molecule UNC-101. Together with the guidance of the M2 neuron, this is the second case of a pharyngeal neuron establishing one of its processes using an unexpected mechanism.
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24.
  • Mörck, Catarina, 1972, et al. (författare)
  • C. elegans ten-1 is synthetic lethal with mutations in cytoskeleton regulators, and enhances many axon guidance defective mutants.
  • 2010
  • Ingår i: BMC developmental biology. - 1471-213X. ; 10
  • Tidskriftsartikel (refereegranskat)abstract
    • Teneurins are transmembrane proteins that assist morphogenetic processes in many organisms. ten-1 is the C. elegans teneurin homolog with two transcripts, ten-1a and ten-1b, that respectively encode a long (TEN-1L) and short (TEN-1S) form of the protein. We previously isolated a C. elegans mutant where one pharyngeal neuron was frequently misplaced, and now show that it corresponds to a novel allele of ten-1.
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25.
  • Vizlin-Hodzic, Dzeneta, et al. (författare)
  • Developmental studies of Xenopus shelterin complexes: the message to reset telomere length is already present in the egg
  • 2009
  • Ingår i: FASEB Journal. - : Wiley. - 0892-6638 .- 1530-6860. ; 23:8, s. 2587-2594
  • Tidskriftsartikel (refereegranskat)abstract
    • The 6-protein complex shelterin protects the telomeres of human chromosomes. The recent discovery that telomeres are important for epigenetic gene regulation and vertebrate embryonic development calls for the establishment of model organisms to study shelterin and telomere function under normal developmental conditions. Here, we report the sequences of the shelterin-encoding genes in Xenopus laevis and its close relation Xenopus tropicalis. In vitro expression and biochemical characterization of the Xenopus shelterin proteins TRF1, TRF2, POT1, TIN2, RAP1, TPP1, and the shelterin accessory factor PINX1 indicate that all main functions of their human orthologs are conserved in Xenopus. The XlTRF1 and XtTRF1 proteins bind double-stranded telomeric DNA sequence specifically and interact with XlTIN2 and XtTIN2, respectively. Similarly, the XlTRF2 and XtTRF2 proteins bind double-stranded telomeric DNA and interact with XlRAP1 and XtRAP1, respectively, whereas the XlPOT1 and XtPOT1 proteins bind single stranded telomeric DNA. Real-time PCR further reveals the gene expression profiles for telomerase and the shelterin genes during embryogenesis. Notably, the composition of shelterin and the formation of its subcomplexes appear to be temporally regulated during embryonic development. Moreover, unexpectedly high telomerase and shelterin gene expression during early embryogenesis may reflect a telomere length resetting mechanism, similar to that reported for induced pluripotent stem cells and for animals cloned through somatic nuclear transfer.
  •  
26.
  • Bélteky, Johan (författare)
  • Chicken domestication : Effects of tameness on brain gene expression and DNA methylation
  • 2016
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Domestication greatly increases phenotypic variation in a short time span, with selection for a single phenotype and a plethora of associated phenotypic changes as an outcome of the process. The domestication process influences the underlying genomic architecture of a species, and the success and speed of the process is likely influenced by it. The main aims of my thesis was to study how domestication affects the brain of chickens: specifically changes in morphology, gene expression, and DNA methylation. Differences in gene expression and DNA methylation between White Leghorn and Red Junglefowl chickens were mapped, and inheritance of these patterns were quantified, indicating a faithful transmission of breed-specific epigenetic markers. Selection on the behavioral trait fearfulness, generated high and low fearful lines of Red Junglefowl. Both the parental population and the fifth selected generation were used for the analyses in this thesis. One experiment studied morphological changes in the brain and other vital organs, and found that relative total brain size increased in high fearful birds, as a consequence of an increase in cerebral hemisphere size in high fearful birds and not in low fearful birds. Also, the relative heart, liver, spleen and testis size increased in high fearful birds, indicating correlated morphological changes with selection for fearfulness. Two additional experiments examined differential gene expression in the hypothalamus and the anterior cerebral hemisphere. The hypothalamus differed in expression of genes with reproductive and immunological functions, whilst the cerebral hemisphere differed in expression of genes related to social behaviors and neurological functions especially those upregulated in low fearful birds.  These results indicate the occurrence of tissue- and species-specific changes in gene expression as overlap with other domestication events were nearly nonexistent. A fourth experiment sought to associate the change in fear levels and gene expression differences with DNA methylation. Chromosomal regions with differential DNA methylation between high and low fearful birds were identified, and genes in these regions had annotated functions relevant to phenotypic differences between the selection lines. This thesis is the first to study the genetic alterations of domestication using the wild ancestor of an already domesticated species to repeat the domestication process selecting against fear of humans. The findings corroborate results from previous comparisons of wild and domestic animals, and further support the theory that rigorous selection for a behavioral trait can cause a cascade of genetic and epigenetic changes facilitating the domestication of a population.
  •  
27.
  • André, Carl, 1958, et al. (författare)
  • Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus) : direct, simultaneous evaluation of neutral vs putatively selected loci
  • 2011
  • Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 106:2, s. 270-280
  • Tidskriftsartikel (refereegranskat)abstract
    • In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species.
  •  
28.
  • Bromhead, D., et al. (författare)
  • The potential impact of ocean acidification on eggs and larvae of the Yellowfin Tuna.
  • 2015
  • Ingår i: Deep-sea research. Part II, Topical studies in oceanography. - : Elsevier BV. - 0967-0645. ; 113, s. 268-279
  • Tidskriftsartikel (refereegranskat)abstract
    • Anthropogenic carbon dioxide (CO2) emissions are resulting in increasing absorption of CO2 by the earth's oceans, which has led to a decline in ocean pH, a process known as ocean acidification (OA). Evidence suggests that OA may have the potential to affect the distribution and population dynamics of many marine organisms. Early life history processes (e.g. fertilization) and stages (eggs, larvae, juveniles) may be relatively more vulnerable to potential OA impacts, with implications for recruitment in marine populations. The potential impact of OA upon tuna populations has not been investigated, although tuna are key components of pelagic ecosystems and, in the Pacific Ocean, form the basis of one of the largest and most valuable fisheries in the world. This paper reviews current knowledge of potential OA impacts on fish and presents results from a pilot study investigating how OA may affect eggs and larvae of yellowfin tuna, Thunnus albacares. Two separate trials were conducted to test the impact of pCO2 on yellowfin egg stage duration, larval growth and survival. The pCO2 levels tested ranged from present day ($400 μatm) to levels predicted to occur in some areas of the spawning habitat within the next 100 years (o2500 μatm) to 300 years ($ o5000 μatm) to much more extreme levels ($10,000 μatm). In trial 1, there was evidence for significantly reduced larval survival (at mean pCO2 levelsZ4730 μatm) and growth (at mean pCO2 levels Z 2108 μatm), while egg hatch time was increased at extreme pCO2 levelsZ10,000 μatm (nintermediate levels were not tested). In trial 2, egg hatch times were increased at mean pCO2 levelsZ1573 μatm, but growth was only impacted at higher pCO2 (Z8800 μatm) and there was no relationship with survival. Unstable ambient conditions during trial 2 are likely to have contributed to the difference in results between trials. Despite the technical challenges with these experiments, there is a need for future empirical work which can in turn support modeling-based approaches to assess how OA will affect the ecologically and economically important tropical tuna resources.
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29.
  • Fagman, Henrik, 1975, et al. (författare)
  • Morphogenetics of early thyroid development.
  • 2010
  • Ingår i: Journal of molecular endocrinology. - 1479-6813.
  • Forskningsöversikt (refereegranskat)abstract
    • The thyroid develops from the foregut endoderm. Yet uncharacterized inductive signals specify endoderm progenitors to a thyroid cell fate that assemble in the pharyngeal floor from which the primordium buds and migrates to the final position of the gland. The morphogenetic process is regulated by both cell-autonomous (activated by e.g. Nkx2-1, Foxe1, Pax8 and Hhex) and mesoderm-derived (mediated by e.g. Tbx1 and Fgf) mechanisms acting in concert to promote growth and survival of progenitor cells. The developmental role of thyroid-stimulating hormone is limited to thyroid differentiation set to work after the gross anatomy of the gland is already sculptured. This review summarizes recent advances on the molecular genetics of thyroid morphogenesis put into context of endoderm developmental traits and highlights established and potentially novel mechanisms of thyroid dysgenesis of relevance to congenital hypothyroidism in man.
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30.
  • Friberg, Urban, et al. (författare)
  • No evidence of mitochondrial genetic variation for sperm competition within a population of Drosophila melanogaster
  • 2008
  • Ingår i: Journal of Evolutionary Biology. - : Wiley. - 1010-061X .- 1420-9101. ; 21:6, s. 1798-1807
  • Tidskriftsartikel (refereegranskat)abstract
    • Cytoplasmic, Drosophila melanogaster, genetic variation, mtDNA, offence/k Recent studies have advocated a role for mitochondrial DNA (mtDNA) in sperm competition. This is controversial because earlier theory and empirical work suggested that mitochondrial genetic variation for fitness is low. Yet, such studies dealt only with females and did not consider that variation that is neutral when expressed in females, might be non-neutral in males as, in most species, mtDNA is never selected in males. We measured male ability to compete for fertilizations, at young and late ages, across 25 cytoplasms expressed in three different nuclear genetic backgrounds, within a population of Drosophila melanogaster. We found no cytoplasmic (thus no mtDNA) genetic variation for either male offence or offensive sperm competitiveness. This contrasts with previous findings demonstrating cytoplasmic genetic variation for female fitness and female ageing across these same lines. Taken together, this suggests that mitochondrial genes do not contribute to variation in sperm competition at the within-population level.
  •  
31.
  • Frommel, Andrea, et al. (författare)
  • Effect of ocean acidification on marine fish sperm (Baltic cod: Gadus morhua)
  • 2011
  • Ingår i: Biogeosiences. - 1726-4170. ; 7:12, s. 3915-3919
  • Tidskriftsartikel (refereegranskat)abstract
    • Ocean acidification, as a consequence of increasing marine pCO(2), may have severe effects on the physiology of marine organisms. However, experimental studies remain scarce, in particular concerning fish. While adults will most likely remain relatively unaffected by changes in seawater pH, early life-history stages are potentially more sensitive - particularly the critical stage of fertilization, in which sperm motility plays a central role. In this study, the effects of ocean acidification (decrease of pH(T) to 7.55) on sperm motility of Baltic cod, Gadus morhua, were assessed. We found no significant effect of decreased pH on sperm speed, rate of change of direction or percent motility for the population of cod analyzed. We predict that future ocean acidification will probably not pose a problem for sperm behavior, and hence fertilization success, of Baltic cod.
  •  
32.
  • Kradolfer, David, et al. (författare)
  • Increased Maternal Genome Dosage Bypasses the Requirement of the FIS Polycomb Repressive Complex 2 in Arabidopsis Seed Development
  • 2013
  • Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 9
  • Tidskriftsartikel (refereegranskat)abstract
    • Seed development in flowering plants is initiated after a double fertilization event with two sperm cells fertilizing two female gametes, the egg cell and the central cell, leading to the formation of embryo and endosperm, respectively. In most species the endosperm is a polyploid tissue inheriting two maternal genomes and one paternal genome. As a consequence of this particular genomic configuration the endosperm is a dosage sensitive tissue, and changes in the ratio of maternal to paternal contributions strongly impact on endosperm development. The FERTILIZATION INDEPENDENT SEED (FIS) Polycomb Repressive Complex 2 (PRC2) is essential for endosperm development; however, the underlying forces that led to the evolution of the FIS-PRC2 remained unknown. Here, we show that the functional requirement of the FIS-PRC2 can be bypassed by increasing the ratio of maternal to paternal genomes in the endosperm, suggesting that the main functional requirement of the FIS-PRC2 is to balance parental genome contributions and to reduce genetic conflict. We furthermore reveal that the AGAMOUS LIKE (AGL) gene AGL62 acts as a dosage-sensitive seed size regulator and that reduced expression of AGL62 might be responsible for reduced size of seeds with increased maternal genome dosage.
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33.
  • Kvarnryd, Moa, et al. (författare)
  • Early life progestin exposure causes arrested oocyte development, oviductal agenesis and sterility in adult Xenopus tropicalis frogs
  • 2011
  • Ingår i: Aquatic Toxicology. - : Elsevier BV. - 0166-445X .- 1879-1514. ; 103:1-2, s. 18-24
  • Tidskriftsartikel (refereegranskat)abstract
    • Levonorgestrel (LNG) is a commonly used pharmaceutical progestin found in the environment. Information on the long-term toxicity of progestins following early life exposure is scant. We investigated the effects of developmental LNG exposure on sex differentiation, reproductive organ development and fertility in the model frog Xenopus tropicalis. Tadpoles were exposed to 0, 0.06 or 0.5 nM LNG via the water from hatching until metamorphosis. At metamorphosis effects on gonadal differentiation were evaluated using a subsample of frogs. Remaining animals were held unexposed for nine months, at which time reproductive organ structure, function and fertility were determined. LNG exposure severely impaired oviduct and ovary development and fertility. All adult females in the 0.5 nM group (n = 10) completely lacked oviducts. They also displayed a significantly larger fraction of immature oocytes, arrested in meiotic prophase, than control females. Upon mating with unexposed males, only one of 11 LNG-exposed females laid eggs, whereas all control females did. No effects on testicular development, sperm count or male fertility were observed. At metamorphosis, no effects on sex ratio or gonadal histology were evident. The effects on ovarian and oviductal development were detected at adult age but not at metamorphosis, emphasising the importance of investigating the long-term consequences of developmental exposure. This is the first developmental reproductive toxicity study of a progestin in an aquatic vertebrate. Considering that several progestins are present in contaminated surface waters, further investigation into the sensitivity of frogs to progestins is warranted to understand the risk such compounds may pose to wild frog populations.
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34.
  • Mattsson, Anna, et al. (författare)
  • Metabolic Profiling of Chicken Embryos Exposed to Perfluorooctanoic Acid ( PFOA) and Agonists to Peroxisome Proliferator-Activated Receptors
  • 2015
  • Ingår i: PLOS ONE. - : Public Library Science. - 1932-6203. ; 10:12
  • Tidskriftsartikel (refereegranskat)abstract
    • Untargeted metabolic profiling of body fluids in experimental animals and humans exposed to chemicals may reveal early signs of toxicity and indicate toxicity pathways. Avian embryos develop separately from their mothers, which gives unique possibilities to study effects of chemicals during embryo development with minimal confounding factors from the mother. In this study we explored blood plasma and allantoic fluid from chicken embryos as matrices for revealing metabolic changes caused by exposure to chemicals during embryonic development. Embryos were exposed via egg injection on day 7 to the environmental pollutant perfluorooctanoic acid (PFOA), and effects on the metabolic profile on day 12 were compared with those caused by GW7647 and rosiglitazone, which are selective agonists to peroxisome-proliferator activated receptor a (PPAR alpha) and PPAR gamma, respectively. Analysis of the metabolite concentrations from allantoic fluid by Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) showed clear separation between the embryos exposed to GW7647, rosiglitazone, and vehicle control, respectively. In blood plasma only GW7647 caused a significant effect on the metabolic profile. PFOA induced embryo mortality and increased relative liver weight at the highest dose. Sublethal doses of PFOA did not significantly affect the metabolic profile in either matrix, although single metabolites appeared to be altered. Neonatal mortality by PFOA in the mouse has been suggested to be mediated via activation of PPAR alpha. However, we found no similarity in the metabolite profile of chicken embryos exposed to PFOA with those of embryos exposed to PPAR agonists. This indicates that PFOA does not activate PPAR pathways in our model at concentrations in eggs and embryos well above those found in wild birds. The present study suggests that allantoic fluid and plasma from chicken embryos are useful and complementary matrices for exploring effects on the metabolic profile resulting from chemical exposure during embryonic development.
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35.
  • Nakano, Hiroaki, 1977, et al. (författare)
  • Developmental Studies of Xenoturbella
  • 2008
  • Ingår i: Journal of Morphology. - 0362-2525. ; 269, s. 1477-1478
  • Konferensbidrag (övrigt vetenskapligt/konstnärligt)
  •  
36.
  • Rebernig, Carolin, et al. (författare)
  • Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus Are Established in the Endosperm
  • 2015
  • Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • The transition to selfing in Capsella rubella accompanies its recent divergence from the ancestral outcrossing C. grandiflora species about 100,000 years ago. Whether the change in mating system was accompanied by the evolution of additional reproductive barriers that enforced species divergence remained unknown. Here, we show that C. rubella and C. grandiflora are reproductively separated by an endosperm-based, non-reciprocal postzygotic hybridization barrier. While hybridizations of C. rubella maternal plants with C. grandiflora pollen donors resulted in complete seed abortion caused by endosperm cellularization failure, the reciprocal hybridization resulted in the formation of small seeds with precociously cellularized endosperm. Strikingly, the transcriptomic response of both hybridizations mimicked respectively the response of paternal and maternal excess hybridizations in Arabidopsis thaliana, suggesting unbalanced genome strength causes hybridization failure in both species. These results provide strong support for the theory that crosses between plants of different mating systems will be unbalanced, with the outcrosser behaving like a plant of increased ploidy, evoking a response that resembles an interploidy-type seed failure. Seed incompatilibity of C. rubella pollinated by C. grandiflora followed the Bateson-Dobzhansky-Muller model, involving negative genetic interaction of multiple paternal C. grandiflora loci with at least one maternal C. rubella locus. Given that both species only recently diverged, our data suggest that a fast evolving mechanism underlies the post-zygotic hybridization barrier(s) separating both species.
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37.
  • Tavoosidana, Gholamreza, 1975- (författare)
  • Epigenetic Regulation of Genomic Imprinting and Higher Order Chromatin Conformation
  • 2006
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • The genetic information encoded by the DNA sequence, can be expressed in different ways. Genomic imprinting is an epigenetic phenomenon that results in monoallelic expression of imprinted genes in a parent of origin-dependent manner. Imprinted genes are frequently found in clusters and can share common regulatory elements. Most of the imprinted genes are regulated by Imprinting Control Regions (ICRs). H19/Igf2 region is a well known imprinted cluster, which is regulated by insulator function of ICR located upstream of the H19 gene. It has been proposed that the epigenetic control of the insulator function of H19 ICR involves organization of higher order chromatin interactions. In this study we have investigated the role of post-translational modification in regulating insulator protein CTCF (CCCTC-binding factor). The results indicated novel links between poly(ADP-ribosyl)ation and CTCF, which are essential for regulating insulators function. We also studied the higher order chromatin conformation of Igf2/H19 region. The results indicated there are different chromatin structures on the parental alleles. We identified CTCF-dependent loop on the maternal allele which is different from the paternal chromatin and is essential for proper imprinting of Igf2 and H19 genes. The interaction of H19 ICR with Differentially Methylated Regions (DMRs) of Igf2 in a parent-specific manner maintains differential epigenetic marks on maternal and paternal alleles. The results indicate that CTCF occupies specific sites on highly condensed mitotic chromosomes. CTCF-dependent long-range key interaction on the maternal allele is maintained during mitosis, suggesting the possible epigenetic memory of dividing cells. In this study, we developed a new method called Circular Chromosome Conformation Capture (4C) to screen genome-wide interactions with H19 ICR. The results indicated there are wide intra- and inter-chromosomal interactions which are mostly dependent on CTCF-binding site at H19 ICR. These observations suggest new aspects of epigenetic regulation of the H19/Igf2 imprinted region and higher order chromatin structure.
  •  
38.
  • Achurra, A., et al. (författare)
  • DNA barcoding and species delimitation: the Stylodrilus heringianus case (Annelida : Clitellata : Lumbriculidae)
  • 2013
  • Ingår i: Invertebrate Systematics. - 1445-5226. ; 27:1, s. 118-128
  • Tidskriftsartikel (refereegranskat)abstract
    • Individuals of the aquatic oligochaete species Stylodrilus heringianus Claparède, 1862 were collected across a part of this species’ distribution range in Sweden, Estonia, Great Britain and Spain to test whether they represent a single metapopulation or several separately evolving lineages. Using sequences of the barcoding gene cytochrome c oxidase subunit I (COI) and two nuclear genes (internal transcribed spacer region and histone 3), three different approaches were conducted: pairwise distance-method, Bayesian inference and network analysis. Both the COI phylogeny and network analyses were concordant in recovering six haplotype clusters, which showed a maximum genetic distance of 7.7% (K2P) among each other. Nevertheless, nuclear genes failed to confirm any lineage separation, and we conclude that the sampled specimens all belong to the same species. A phylogeographic history with allopatric divergence and secondary contact is suggested to explain this intraspecific pattern of mitochondrial divergence and nuclear non-divergence. The study shows that a mitochondrial single-locus approach can be problematic for the accurate delimitation of species, and we emphasise the need for nuclear genes as supplementary markers, when taxonomic resolution is assessed with COI barcodes.
  •  
39.
  •  
40.
  • Mohammad, Faizaan (författare)
  • Long Noncoding RNA Mediated Regulation of Imprinted Genes
  • 2010
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Genomic imprinting is an epigenetic phenomenon that causes a subset of mammalian genes to be expressed from only one allele in a parent-of-origin manner. The defects in the imprinting regulation result in disorders that affect development, growth and metabolism. We have used the Kcnq1 imprinted cluster as a model to understand the mechanism of imprinted gene regulation. The imprinting at the Kcnq1 locus is regulated by a long noncoding RNA, Kcnq1ot1, whose transcription on the paternal chromosome is associated with the silencing of at least eight neighboring genes. By destabilizing Kcnq1ot1 in an episomal system, we have conclusively shown that it is the RNA and not the process of transcription that is required for the gene silencing in cis. Kcnq1ot1 RNA interacts with the chromatin modifying enzymes such as G9a and Ezh2 and recruits them to imprinted genes to establish repressive chromatin compartment and gene silencing. Using the episomal system, we have identified an 890 bp silencing domain (SD) at the 5’ end of Kcnq1ot1 RNA, which is required for silencing of neighboring reporter genes. The deletion of the SD in the mouse resulted in the relaxation of imprinting of ubiquitously imprinted genes (Cdkn1c, Kcnq1, Slc22a18, and Phlda2) as well as reduced DNA methylation over the somatic DMRs associated with the ubiquitously imprinted genes. Moreover, Kcnq1ot1 RNA interacts with Dnmt1 and recruits to the somatic DMRs and this recruitment was significantly affected in the SD mutant mice. By using a transgenic mouse, we have conditionally deleted Kcnq1ot1 promoter at different developmental stages and demonstrated that Kcnq1ot1 maintains imprinting of the ubiquitously imprinted genes by regulating DNA methylation over the somatic DMRs. Kcnq1ot1 is dispensable for the maintenance of repressive histone marks and the imprinting of placental-specific imprinted genes (Tssc4 and Osbpl5). In conclusion, we have described the mechanisms by which Kcnq1ot1 RNA establishes and maintains expression of multiple imprinted genes in cis.
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41.
  • Arvola, Marie (författare)
  • Immunological aspects of maternal-foetal interactions in mice
  • 2001
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Mammalian pregnancy is an immunological paradox. The foetus, which expresses both paternal and maternal cell-surface molecules, has to be protected from rejection by the maternal immune system. At the same time, the mother has to have an efficient immune defence and must provide her offspring with antibodies.The first part of this thesis investigates some of the mechanisms involved in the foetal avoidance of maternal rejection reactions. Placental absence of MHC class II expression, as well as a bias for Th2-cytokines at the maternal-foetal interface are suggested to be important for foetal survival. The results showed that placental MHC class II expression cannot be induced in vivo. Transfections of trophoblast cells with MHC class II genes, however, resulted in detectable MHC class II cell-surface expression, indicating that a post-transcriptional block does not exist in these cells.By using IL-4- and IL-10-double deficient mice, it was shown that neither maternal nor foetal expression of these cytokines were crucial for completion of allogeneic pregnancy.In the second part of the thesis, the effect of transmission of immunoglobulin G (IgG) from the mother to the offspring was studied. It was observed that viable maternal Ig-secreting cells occasionally infiltrated the B cell-deficient offspring and remained functional for long periods. In this study "green fluorescent mice" were used as a tool. Furthermore, neonatal ingestion of wild type milk increased the survival of adoptively transferred B-lineage cells in B cell-deficient mice, suggesting that suckling of IgG-containing milk could be used to facilitate B cell-reconstitution in B cell-deficient mice. Finally, results from studies on normal mice showed that absence of maternal IgG-transmission during their neonatal development resulted in elevated serum-IgG production, as well as enhanced immune reactions upon immunisations in adult life. This showed that maternal IgG can have long-term immunoregulatory effects in the offspring.
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42.
  • Barsoum, Emad, 1979-, et al. (författare)
  • {alpha}3, a transposable element that promotes host sexual reproduction
  • 2010
  • Ingår i: Genes & Development. - : Cold Spring Harbor Laboratory. - 0890-9369 .- 1549-5477. ; 24:15, s. 33-44
  • Tidskriftsartikel (refereegranskat)abstract
    • Theoretical models predict that selfish DNA elements require host sex to persist in a population. Therefore, a transposon that induces sex would strongly favor its own spread. We demonstrate that a protein homologous to transposases, called alpha3, was essential for mating type switch in Kluyveromyces lactis. Mutational analysis showed that amino acids conserved among transposases were essential for its function. During switching, sequences in the 5' and 3' flanking regions of the alpha3 gene were joined, forming a DNA circle, showing that alpha3 mobilized from the genome. The sequences encompassing the alpha3 gene circle junctions in the mating type alpha (MATalpha) locus were essential for switching from MATalpha to MATa, suggesting that alpha3 mobilization was a coupled event. Switching also required a DNA-binding protein, Mating type switch 1 (Mts1), whose binding sites in MATalpha were important. Expression of Mts1 was repressed in MATa/MATalpha diploids and by nutrients, limiting switching to haploids in low-nutrient conditions. A hairpin-capped DNA double-strand break (DSB) was observed in the MATa locus in mre11 mutant strains, indicating that mating type switch was induced by MAT-specific DSBs. This study provides empirical evidence for selfish DNA promoting host sexual reproduction by mediating mating type switch.
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43.
  • Barsoum, Emad, 1979-, et al. (författare)
  • Regulation of mating type switching in Kluyveromyces lactis by the RAS/cAMP pathway and the transcription factor Msn2
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • We explored the regulation of mating type switching in Kluyveromyces lactis. Using an assay dependent on loss of a URA3 gene inserted into the MATa locus, we determined that the switching rate of a wild type strain grown in rich media was ~6X10-4 events/generation. In a genetic selection for identifying strains with increased switching rates, we found a strain with an insertion in the K. lactis RAS1 gene, encoding a small GTPase with a central role in growth regulation. Compromised Ras1 function leads to a lower cAMP level suggesting a role for cAMP in promoting switching. Consistent with this idea, a strain lacking the PDE2 gene, which encodes an enzyme that degrades cAMP, resulted in decreased switching rates. To explore how cAMP regulated switching, we investigated the transcription of the MTS1 gene, encoding an inducer of switching. The ras1 mutant strain contained 20-fold higher levels of the MTS1 mRNA compared to wild type, but in the pde2 mutant strain MTS1 transcription was repressed 5-fold. In addition, strains lacking the MSN2 gene, which encodes a transcription factor that binds the stress response element (STRE), expressed less MTS1 mRNA and had decreased switching rates. We suggest a model in which nutrient limitation induces switching through cAMP and Msn2-dependent transcriptional induction of the MTS1 gene.
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44.
  • Barsoum, Emad, 1979-, et al. (författare)
  • Ume6 is required for the MATa/MATα cellular identity and transcriptional silencing in Kluyveromyces lactis
  • 2010
  • Ingår i: Genetics. - : The Genetics Society of America. - 0016-6731 .- 1943-2631. ; 184:4, s. 999-1011
  • Tidskriftsartikel (refereegranskat)abstract
    • To explore the similarities and differences of regulatory circuits among budding yeasts, we characterized the role of the unscheduled meiotic gene expression 6 (UME6) gene in Kluyveromyces lactis. We found that Ume6 was required for transcriptional silencing of the cryptic mating-type loci HMLα and HMRa. Chromatin immunoprecipitation (ChIP) suggested that Ume6 acted directly by binding the cis-regulatory silencers of these loci. Unexpectedly, a MATa ume6 strain was mating proficient, whereas a MATα ume6 strain was sterile. This observation was explained by the fact that ume6 derepressed HMLα2 only weakly, but derepressed HMRa1 strongly. Consistently, two a/α-repressed genes (MTS1 and STE4) were repressed in the MATα ume6 strain, but were expressed in the MATa ume6 strain. Surprisingly, ume6 partially suppressed the mating defect of a MATa sir2 strain. MTS1 and STE4 were repressed in the MATa sir2 ume6 double-mutant strain, indicating that the suppression acted downstream of the a1/α2-repressor. We show that both STE12 and the MATa2/HMRa2 genes were overexpressed in the MATa sir2 ume6 strain. Consistent with the idea that this deregulation suppressed the mating defect, ectopic overexpression of Ste12 and a2 in a MATa sir2 strain resulted in efficient mating. In addition, Ume6 served as a block to polyploidy, since ume6/ume6 diploids mated as pseudo a-strains. Finally, Ume6 was required for repression of three meiotic genes, independently of the Rpd3 and Sin3 corepressors.
  •  
45.
  • Crona, Filip, 1977-, et al. (författare)
  • Gene regulation by the lysine demethylase KDM4A in Drosophila
  • 2013
  • Ingår i: Developmental Biology. - : Elsevier BV. - 0012-1606 .- 1095-564X. ; 373:2, s. 453-463
  • Tidskriftsartikel (refereegranskat)abstract
    • Lysine methylation of histones is associated with both transcriptionally active chromatin and with silent chromatin, depending on what residue is modified. Histone methyltransferases and demethylases ensure that histone methylations are dynamic and can vary depending on cell cycle- or developmental stage. KDM4A demethylates H3K36me3, a modification enriched in the 3' end of active genes. The genomic targets and the role of KDM4 proteins in development remain largely unknown. We therefore generated KDM4A mutant Drosophila, and identified 99 mis-regulated genes in first instar larvae. Around half of these genes were down-regulated and the other half up-regulated in dKDM4A mutants. Although heterochromatin protein 1a (HP1a) can stimulate dKDM4A demethylase activity in vitro, we find that they antagonize each other in control of dKDM4A-regulated genes. Appropriate expression levels for some dKDM4A-regulated genes rely on the demethylase activity of dKDM4A, whereas others do not. Surprisingly, although highly expressed, many demethylase-dependent and independent genes are devoid of H3K36me3 in wild-type as well as in dKDM4A mutant larvae, suggesting that some of the most strongly affected genes in dKDM4A mutant animals are not regulated by H3K36 methylation. By contrast, dKDM4A over-expression results in a global decrease in H3K36me3 levels and male lethality, which might be caused by impaired dosage compensation. Our results show that a modest increase in global H3K36me3 levels is compatible with viability, fertility, and the expression of most genes, whereas decreased H3K36me3 levels are detrimental in males.
  •  
46.
  • Dai, Qi, 1976- (författare)
  • Chromatin regulators and transcriptional control of Drosophila development
  • 2007
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • The development of a multicellular organism is programmed by complex patterns of gene expression. In eukaryotic cells, genes are packaged by histone proteins into chromatin. Chromatin regulators often function as transcription co-factors. In this study, we have investigated the function of four co-factors, dAda2b, Reptin, Ebi and Brakeless during development of the fruit fly Drosophila melanogaster. dAda2b and Reptin belong to histone acetyl transferase (HAT) complexes, a SAGA-like complex and the Tip60 complex, respectively. We generated dAda2b mutants and found that lack of dAda2b strongly affects global histone acetylation and viability. We further propose that Ada2 may be involved in DNA repair. Our studies revealed new roles of Reptin and other Tip60 complex components in Polycomb Group mediated repression and heterochromatin formation, thereby promoting generation of silent chromatin.During embryogenesis, transcriptional repressors establish localized and tissue-specific patterns of gene expression. In this thesis, we identified two novel co-repressors in the early embryo, Ebi and Brakeless. Ebi genetically and physically interacts with the Snail repressor. The Ebi-interaction motif in the Snail protein is essential for Snail function in vivo and is evolutionarily conserved in insects. We further demonstrated that Ebi associates with histone deacetylase 3 (HDAC3) and that histone deacetylation is part of the mechanism by which Snail mediates transcriptional repression. We isolated Brakeless in a genetic screen for novel regulators of gene expression during embryogenesis. We found that mutation of brakeless impairs function of the Tailless repressor. Brakeless associates with Atrophin, another Tailless corepressor, and they function together in Tailless-mediated repression. In summary, transcription co-factors, including chromatin regulators, are selectively required in distinct processes during development.
  •  
47.
  • Ericsson, Rolf (författare)
  • A Comparative Study of Head Development in Mexican Axolotl and Australian Lungfish: Cell Migration, Cell Fate and Morphogenesis
  • 2003
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • The development of the vertebrate head is a complex process involving interactions between a multitude of cell types and tissues. This thesis describes the development of the cranial neural crest and of the visceral arch muscles in the head of two species. One, the Mexican axolotl (Ambystoma mexicanum), is a basal tetrapod, whereas the other, the Australian lungfish (Neoceratodus forsteri), belongs to the Dipnoi, the extant sister group of the Tetrapoda. The migration of neural crest cells, which form most of the bones and connective tissues in the head, and the morphogenesis of the jaw, was determined in the Mexican axolotl. It was shown that both the upper and lower jaws form from ventral condensations of neural crest cells in the mandibular arch. The dorsal condensation, earlier considered to give rise to the upper jaw, was shown to form the trabecula cranii.The normal spatio-temporal development of visceral arch muscles was investigated in both the Mexican axolotl and the Australian lungfish. In axolotl, the muscles tended to start forming almost simultaneously in all visceral arches at their future origins and extend towards their future insertions at the onset of muscle fibre formation. In lungfish, fibres formed simultaneously throughout most of each muscle anlage in the first and second visceral arch, but were delayed in the branchial arches. The anlagen were first observed at their future insertion, from which they developed towards future origins. To test the ability of neural crest cells to pattern the visceral arch muscles, migrating crest cells were extirpated from axolotl embryos, which resulted in a wide range of muscle malformations. In most cases, the muscles appeared in the right position but were small and extended in abnormal directions. This shows that neural crest cells are responsible not for the position of the muscles but for their correct anatomical pattern. Fate mapping showed that connective tissue surrounding myofibers is, at least partly, neural crest derived.In conclusion, the work presented in this thesis shows that although early development may map out the patterns of later development, the differences between axolotl and lungfish head development are not seen until during morphogenesis. Further investigation of morphogenesis is needed to explain the great variation of head morphology seen in vertebrates today.
  •  
48.
  • Estefa, Jordi, 1987- (författare)
  • Long bone growth and evolution revealed by three-dimensional imaging
  • 2020
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Propagation phase-contrast synchrotron radiation microtomography is a non-destructive method used for studying histology in three dimensions (3D). Using it, the 3D organization of the diaphyseal cortical vascularization in the humerus of two seymouriamorphs was analyzed in this thesis. Their vascularization suggests a combination of active growth and a long pre-reproductive period, an intermediate condition between that of Devonian tetrapods and early amniotes, reflecting a gradual change in evolution. The focus of the thesis then shifts to the metaphysis of long bones. The latter possesses complex 3D structures difficult to capture in 2D images. Observations in extant tetrapods have shown that hematopoiesis in long-bones requires the presence of tubular marrow processes opening onto an open medullary cavity with a centralized vascular system. A network of tubular marrow processes was found in connection with interconnected small cavities in the metaphyses of seymouriamorphs which may have acted as open spaces containing a centralized vascular mesh. Based on this interpretation, the long-bone marrow cavity of the Permian stem-amniotes studied here could have been the oldest evidence of possible hematopoiesis among tetrapods. As a third focus, both computer simulations (Finite Element Analysis) and empirical experiments were conducted to investigate the role of Secondary Ossification Centers (SOCs) within the epiphyses of mammals. The results indicate that the presence of a SOC protects the growth plate from mechanical stresses, allowing the cells there to withstand six times more stress. Finally, the 3D microanatomy of the metaphyses and epiphyses in the humeri of monotreme, marsupial and placental extant mammals were investigated at different developmental stages. The data were used to produce a nomenclature based on the degree of epiphyseal ossification encompassing the entire development of all the condyles within a single epiphysis. This nomenclature was used to describe the epiphyseal development in a large group of mammals and highlight differences in ossification timing between groups. These results offer a unique glimpse into the development and evolution of long-bones. They highlight the value of visualizing long-bone microstructure in both 2D and 3D, and the need to develop new nomenclatures that reflect the 3D nature of the data.
  •  
49.
  • Fallahshahroudi, Amir, 1981- (författare)
  • Domestication Effects on the Stress Response in Chickens : Genetics, Physiology, and Behaviour
  • 2017
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Animal domestication, the process where animals become adapted to living in proximity to humans, is associated with the alteration of multiple traits, including decreased fearfulness and stress response. With an estimated population of 50 billion, the domesticated chicken is the most populous avian species in the world. Hundreds of chicken breeds have been developed for meat and egg production, hobby or research purposes. Multidirectional selection and the relaxation of natural selection in captivity have created immense phenotypic diversity amongst domesticates in a relatively short evolutionary time. The extensive phenotypic diversity, existence of the wild ancestor, and feasibility of intercrossing various breeds makes the chicken a suitable model animal for deciphering genetic determinants of complex traits such as stress response. We used chicken domestication as a model to gain insights about the mechanisms that regulate stress response in an avian species. We studied behavioural and physiological stress response in the ancestral Red Junglefowl and one of its domesticated progenies, White Leghorn. An advanced intercross between the aforementioned breeds was later used to map genetic loci underlying modification of stress response. The general pattern of the stress response in chickens was comparable with that reported in mammals, however we identified distinctive differences in the stress modulatory pathways in chickens. We showed that changes in the expression levels of several stress modulatory genes in the brain, the pituitary and the adrenal glands underlie the observed modified stress response in domesticated chickens. Using quantitative trait loci (QTL) mapping, several QTL underlying stress induced corticosterone, aldosterone and baseline dehydroepiandrosterone (DHEA) levels were detected. As a next step, we combined QTL mapping with gene expression (eQTL) mapping and narrowed two QTL down to the putative causal genes, SERPINA10 and PDE1C. Both of these genes were differentially expressed in the adrenal glands of White Leghorn and the Red Junglefowl, had overlapping eQTL with hormonal QTL, and their expression levels in the adrenal glands were correlated with plasma levels of corticosterone and al-dosterone. These two genes thus serve as strong candidates for further functional investigation concerning modification of the stress response during domestication. This dissertation increase the knowledge about genetics and physiology of the stress response in an avian species and its modification during domestication. Our findings expand the basic knowledge about the stress response in chicken, which can potentially be used to improve welfare through appropriate genetic selection.
  •  
50.
  • Friberg, Magne, et al. (författare)
  • Generation-dependent female choice: behavioral polyphenism in a bivoltine butterfly
  • 2007
  • Ingår i: Behavioral Ecology. - : Oxford University Press (OUP). - 1045-2249 .- 1465-7279. ; 18:4, s. 758-763
  • Tidskriftsartikel (refereegranskat)abstract
    • Climatic and biotic circumstances vary as seasons shift, and different cohorts of multivoltine species are likely subjected to different selection regimes. The bivoltine butterfly Leptidea reali (Re´al’s wood white; Lepidoptera: Pieridae) appears during May and June in central Sweden and has a partial second generation in late July. We manipulated both generations to appear simultaneously and performed laboratory mating experiments that showed the presence of a behavioral polyphenism in mating propensity, which is induced during the developmental stages. Females of the summer generation expressed higher mating propensities than spring generation females. Spring females showed an increase in mating propensity with increasing age, whereas summer females accepted most matings already when they were only 1 or 2 days old. It is likely that larval time constraints, a lower abundance of males and a lower risk of accepting a male of their univoltine sister species Leptidea sinapis (wood white), have relaxed selection on mate discrimination among summer generation females. A major challenge for future research is to further investigate the developmental pathways causing the polyphenism and the adaptive implications of cohort dependent behaviors.
  •  
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