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  • 1.
    Ali, Fuad
    Södertörn University College, School of Life Sciences.
    Developing electroporation as a method to obtain Stable Transformation in Drosophila melanogaster2008Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In this project I have tried to obtain stable transformants of Drosophila melanogaster flies using electroporation. I have completed approximately 200 tests using different DNA concentrations, voltages and cuvettes, including a novel Petri dish cuvette which I developed and manufactured myself. I also developed new and more efficient procedures of egg collection and egg dechorionation. Although I was not  successful in obtaining true stable transformants, control experiments indicate that electroporation of DNA into embryos could be accomplished under the conditions used. The lack of stable transformants was probably due to failure of the electroporated DNA to integrate into the host genome. The reasons for why the DNA did not integrate was not further investigated in this study.

  • 2. Archer, Amena
    et al.
    Lauter, Gilbert
    Södertörn University, School of Life Sciences.
    Hauptmann, Giselbert
    Södertörn University, School of Life Sciences.
    Mode, Agneta
    Gustafsson, Jan-Ake
    Transcriptional activity and developmental expression of liver X receptor (lxr) in zebrafish2008In: Developmental Dynamics, ISSN 1058-8388, E-ISSN 1097-0177, Vol. 237, no 4, p. 1090-1098Article in journal (Refereed)
    Abstract [en]

    Mammalian liver-X-receptors (LXRs) are transcription factors activated by oxysterols. They play an essential role in lipid and glucose metabolism. We have cloned the open reading frame of zebrafish lxr and describe its genomic organization. Zebrafish lxr encodes a 50-kDa protein with high sequence similarity to mammalian LXR alpha. In transfection assays, the encoded protein showed transcriptional activity in response to LXR-ligands. Treatment of adult zebrafish with the synthetic LXR ligand, GW3965, induced expression of genes involved in hepatic cholesterol and lipid pathways. Using qPCR and in situ hybridization, we found ubiquitous expression of lxr mRNA during the first 24 hr of development, followed by more restricted expression, particularly to the liver at 3dpf and the liver and intestine at 4dpf. In adult fish, all examined organs expressed lxr. In addition to a metabolic role of lxr, the temporal expression pattern suggests a developmental role in, e.g., the liver and CNS.

  • 3. Dubruille, R
    et al.
    Laurencon, A
    Vandaele, C
    Shishido, E
    Coulon-Bublex, M
    Swoboda, Peter
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Couble, P
    Kernan, M
    Durand, B
    Drosophila regulatory factor X is necessary for ciliated sensory neuron differentiation2002In: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 129, no 23, p. 5487-5498Article in journal (Refereed)
    Abstract [en]

    Ciliated neurons play an important role in sensory perception in many animals. Modified cilia at dendrite endings serve as sites of sensory signal capture and transduction. We describe Drosophila mutations that affect the transcription factor RFX and genetic rescue experiments that demonstrate its central role in sensory cilium differentiation. Rfx mutant flies show defects in chemosensory and mechanosensory behaviors but have normal phototaxis, consistent with Rfx expression in ciliated sensory neurons and neuronal precursors but not in photoreceptors. The mutant behavioral phenotypes are correlated with abnormal function and structure of neuronal cilia, as shown by the loss of sensory transduction and by defects in ciliary morphology and ultrastructure. These results identify Rfx as an essential regulator of ciliated sensory neuron differentiation in Drosophild.

  • 4.
    Efimenko, Evgeni
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Bubb, K
    Mak, H Y
    Holzman, T
    Leroux, M R
    Ruvkun, G
    Thomas, J H
    Swoboda, Peter
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Analysis of xbx genes in C-elegans2005In: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 132, no 8, p. 1923-1934Article in journal (Refereed)
    Abstract [en]

    Cilia and flagella are widespread eukaryotic subcellular components that are conserved from green algae to mammals. In different organisms they function in cell motility, movement of extracellular fluids and sensory reception. While the function and structural description of cilia and flagella are well established, there are many questions that remain unanswered. In particular, very little is known about the developmental mechanisms by which cilia are generated and shaped and how their components are assembled into functional machineries. To find genes involved in cilia development we used as a search tool a promoter motif, the X-box, which participates in the regulation of certain ciliary genes in the nematode Caenorhabditis elegans. By using a genome search approach for X-box promoter motif-containing genes (xbx genes) we identified a list of about 750 xbx genes (candidates). This list comprises some already known ciliary genes as well as new genes, many of which we hypothesize to be important for cilium structure and function. We derived a C elegans X-box consensus sequence by in vivo expression analysis. We found that xbx gene expression patterns were dependent on particular X-box nucleotide compositions and the distance from the respective gene start. We propose a model where DAF-19, the RFX-type transcription factor binding to the X-box, is responsible for the development of a ciliary module in C elegans, which includes genes for cilium structure, transport machinery, receptors and other factors.

  • 5.
    Gallio, Marco
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Stockholm University / Karolinska Institute.
    Englund, C
    Stockholm University / Umeå University.
    Kylsten, Per
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Samakovlis, C
    Stockholm University.
    Rhomboid 3 orchestrates Slit-independent repulsion of tracheal branches at the CNS midline2004In: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 131, no 15, p. 3605-3614Article in journal (Refereed)
    Abstract [en]

    EGF-receptor ligands act as chemoattractants for migrating epithelial cells during organogenesis and wound healing. We present evidence that Rhomboid 3/EGF signalling, which originates from the midline of the Drosophila ventral nerve cord, repels tracheal ganglionic branches and prevents them from crossing it. rho3 acts independently from the main midline repellent Slit, and originates from a different sub-population of midline cells: the VUM neurons. Expression of dominant-negative Egfr or Ras induces midline crosses, whereas activation of the Egfr or Ras in the leading cell of the ganglionic branch can induce premature turns away from the midline. This suggests that the level of Egfr intracellular signalling, rather than the asymmetric activation of the receptor on the cell surface, is an important determinant in ganglionic branch repulsion. We propose that Egfr activation provides a necessary switch for the interpretation of a yet unknown repellent function of the midline.

  • 6. Hao, Limin
    et al.
    Aspöck, Gudrun
    Bürglin, Thomas R
    Södertörn University, School of Life Sciences. Karolinska Institute.
    The hedgehog-related gene wrt-5 is essential for hypodermal development in Caenorhabditis elegans2006In: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 290, no 2, p. 323-336Article in journal (Refereed)
    Abstract [en]

    The Caenorhabditis elegans genome encodes a series of hedgehog-related genes, which are thought to have evolved and diverged from an ancestral Hh gene. They are classified into several families based on their N-terminal domains. Here, we analyze the expression and function of a member of the warthog gene family, wrt-5, that lacks the Hint/Hog domain. wrt-5 is expressed in seam cells, the pharynx, pharyngeal-intestinal valve cells, neurons, neuronal support cells, the excretory cell, and the reproductive system. WRT-5 protein is secreted into the extracelluar space during embryogenesis. Furthermore, during larval development, WRT-5 protein is secreted into the pharyngeal lumen and the pharyngeal expression changes in a cyclical manner in phase with the molting cycle. Deletion mutations in wrt-5 cause embryonic lethality, which are temperature sensitive and more severe at 15 degrees C than at 25 degrees C. Animals that hatch exhibit variable abnormal morphology, for example, bagging worms, blistering, molting defects, or Roller phenotypes. We examined hypodermal cell junctions using the AJM-1: :GFP marker in the wrt-5 mutant background and observed cell boundary abnormalities in the arrested embryos. AJM-1: :GFP protein is also misplaced in pharyngeal muscle cells in the absence of WRT-5. In conclusion, we show that wrt-5 is an essential gene that - despite its lack of a Hint domain - has multiple functions in C. elegans and is implicated in cell shape integrity.

  • 7. Hao, Limin
    et al.
    Mukherjee, Krishanu
    Liegeois, Samuel
    Baillie, David
    Labouesse, Michel
    Bürglin, Thomas R.
    Södertörn University, School of Life Sciences. Karolinska institutet.
    The hedgehog-related gene qua-1 is required for molting in Caenorhabditis elegans2006In: Developmental Dynamics, ISSN 1058-8388, E-ISSN 1097-0177, Vol. 235, no 6, p. 1469-1481Article in journal (Refereed)
    Abstract [en]

    The Caenorhabditis elegans genome encodes ten proteins that share similarity with Hedgehog through the C-terminal Hint/Hog domain. While most genes are members of larger gene families, qua-1 is a single copy gene. Here we show that orthologs of qua-1 exist in many nematodes, including Brugia malayi, which shared a common ancestor with C. elegans about 300 million years ago. The QUA-1 proteins contain an N-terminal domain, the Qua domain, that is highly conserved, but whose molecular function is not known. We have studied the expression pattern of qua-1 in C. elegans using a qua-1::GFP transcriptional fusion. qua-1 is mainly expressed in hyp1 to hyp11 hypodermal cells, but not in seam cells. It is also expressed in intestinal and rectal cells, sensilla support cells, and the P cell lineage in L1. The expression of qua-1::GFP undergoes cyclical changes during development in phase with the molting cycle. It accumulates prior to molting and disappears between molts. Disruption of the qua-1 gene function through an internal deletion that causes a frame shift with premature stop in the middle of the gene results in strong lethality. The animals arrest in the early larval stages due to defects in molting. Electron microscopy reveals double cuticles due to defective ecdysis, but no obvious defects are seen in the hypodermis. Qua domain-only::GFP and full-length QUA-1::GFP fusion constructs are secreted and associated with the overlying cuticle, but only QUA-1::GFP rescues the mutant phenotype. Our results suggest that both the Hint/Hog domain and Qua domain are critically required for the function of QUA-1.

  • 8.
    Hench, Jürgen
    et al.
    Södertörn University, School of Life Sciences.
    Henriksson, Johan
    Södertörn University, School of Life Sciences, Molecular biology.
    Lüppert, Martin
    Södertörn University, School of Life Sciences.
    Bürglin, Thomas R.
    Södertörn University, School of Life Sciences, Molecular biology.
    Spatio-temporal reference model of Caenorhabditis elegans embryogenesis with cell contact maps2009In: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 333, no 1, p. 1-13Article in journal (Refereed)
    Abstract [en]

    The nematode Caenorhabditis elegans has been used as a model for developmental biology for decades. Still, the few publicly available spatio-temporal (4D) data sets have conflicting information regarding variability of cell positions and are not well-suited for a standard 4D embryonic model, due to compression. We have recorded six uncompressed embryos, and determined their lineage and 4D coordinates, including nuclear radii, until the end of gastrulation. We find a remarkable degree of stability in the cell positions, as well as little rotational movement, which allowed us to combine the data into a single reference model of C. elegans embryogenesis. Using Voronoi decomposition we generated the list of all predicted cell contacts during early embryogenesis and calculated these contacts up to the similar to 150 cell stage, and find that about 1500 contacts last 2.5 min or longer. The cell contact map allows for comparison of multiple 4D data sets, e. g., mutants or related species, at the cellular level. A comparison of our uncompressed 4D model with a compressed embryo shows that up to 40% of the cell contacts can be different. To visualize the 4D model interactively we developed a software utility. Our model provides an anatomical resource and can serve as foundation to display 4D expression data, a basis for developmental systems biology.

  • 9.
    Kitambi, Satish S.
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet / Harvard Medical School/MEEI, Boston, Massachusetts, USA.
    Malicki, Jarema J.
    Harvard Medical School/MEEI, Boston, Massachusetts, USA.
    Spatiotemporal Features of Neurogenesis in the Retina of Medaka, Oryzias latipes2008In: Developmental Dynamics, ISSN 1058-8388, E-ISSN 1097-0177, Vol. 237, no 12, p. 3870-3881Article in journal (Refereed)
    Abstract [en]

    The vertebrate retina is very well conserved in evolution. Its structure and functional features are very similar in phyla as different as primates and teleost fish. Here, we describe the spatiotemporal characteristics of neurogenesis in the retina of a teleost, medaka, and compare them with other species, primarily the zebrafish. Several intriguing differences are observed between medaka and zebrafish. For example, photoreceptor differentiation in the medaka retina starts independently in two different areas, and at more advanced stages of differentiation, medaka and zebrafish retinae display obviously different patterns of the photoreceptor cell mosaic. Medaka and zebrafish evolutionary lineages are thought to have separated from each other 110 million years ago, and so the differences between these species are not unexpected, and may be exploited to gain insight into the architecture of developmental pathways. Importantly, this work highlights the benefits of using multiple teleost models in parallel to understand a developmental process.

  • 10.
    Kitambi, Satish S.
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet / Harvard Medical School/MEEI, Boston, USA.
    McCulloch, Kyle J.
    Harvard Medical School/MEEI, Boston, USA.
    Peterson, Randall T.
    Massachusetts General Hospital, USA.
    Malicki, Jarema J.
    Harvard Medical School/MEEI, Boston, USA.
    Small molecule screen for compounds that affect vascular development in the zebrafish retina2009In: Mechanisms of Development, ISSN 0925-4773, E-ISSN 1872-6356, Vol. 126, no 5-6, p. 464-477Article in journal (Refereed)
    Abstract [en]

    Blood vessel formation in the vertebrate eye is a precisely regulated process. in the human retina, both an excess and a deficiency of blood vessels may lead to a loss of vision. To gain insight into the molecular basis of vessel formation in the vertebrate retina and to develop pharmacological means of manipulating this process in a living organism, we further characterized the embryonic zebrafish eye vasculature, and performed a small molecule screen for compounds that affect blood vessel morphogenesis. The screening of approximately 2000 compounds revealed four small molecules that at specific concentrations affect retinal vessel morphology but do not produce obvious changes in trunk vessels, or in the neuronal architecture of the retina. Of these, two induce a pronounced widening of vessel diameter without a substantial loss of vessel number, one compound produces a loss of retinal blood vessels accompanied by a mild increase of their diameter, and finally one other generates a severe loss of retinal vessels. This work demonstrates the utility of zebrafish as a screening tool for small molecules that affect eye vasculature and presents several compounds of potential therapeutic importance.

  • 11.
    Kitambi, Satish Srinivas
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Hauptmann, Giselbert
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    The zebrafish orphan nuclear receptor genes nr2e1 and nr2e3 are expressed in developing eye and forebrain2007In: Gene Expression Patterns, ISSN 1567-133X, E-ISSN 1872-7298, Vol. 7, no 4, p. 521-528Article in journal (Refereed)
    Abstract [en]

    Mammalian Nr2e1 (Tailless, Mtll or Tlx) and Nr2e3 (photoreceptor-specific nuclear receptor, Pnr) are highly related orphan nuclear receptors, that are expressed in eye and forebrain-derived structures. In this study, we analyzed the developmental expression patterns of zebrafish nr2e1 and nr2e3. RT-PCR analysis showed that nr2e1 and nr2e3 are both expressed during embryonic and post-embryonic development. To examine the spatial distribution of nr2e1 and nr2e3 during development whole-mount in situ hybridization was performed. At tailbud stage, initial nr2e1 expression was localized to the rostral brain rudiment anterior to pax2.1 and eng2 expression at the prospective midbrain-hindbrain boundary. During Subsequent stages, nr2e1 became widely expressed in fore- and midbrain primordia, eye and olfactory placodes. At 24 hpf, strong nr2e1 expression was detected in telencephalon, hypothalamus, dorsal thalamus, pretectum, midbrain tectum, and retina. At 2 dpf, the initially widespread nr2e1 expression became more restricted to distinct regions within the fore- and midbrain and to the retinal ciliary margin, the germinal zone which gives rise to retina and presumptive iris. Express on of nr2e3 was exclusively found in the developing retina and epiphysis. In both structures, nr2e3 expression was found in photoreceptor cells. The developmental expression profile of zebrafish nr2e1 and nr2e3 is consistent with evolutionary conserved functions in eye and rostral brain structures.

  • 12.
    Para, Alessia
    et al.
    Södertörn University, Avdelning Naturvetenskap. Uppsala University.
    Sundås-Larsson, Annika
    Södertörn University, Avdelning Naturvetenskap.
    The pleiotropic mutation dar1 affects plant architecture in Arabidopsis thaliana2003In: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 254, no 2, p. 215-225Article in journal (Refereed)
  • 13. Scherfer, Christoph
    et al.
    Qazi, Mousumi R.
    Takahashi, Kuniaki
    Ueda, Ryu
    Dushay, Mitchell S.
    Södertörn University, School of Life Sciences.
    Theopold, Ulnich
    Lemaitre, Bruno
    The Toll immune-regulated Drosophila protein Fondue is involved in hemolymph clotting and puparium formation2006In: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 295, no 1, p. 156-163Article in journal (Refereed)
    Abstract [en]

    Clotting is critical in limiting hemolymph loss and initiating wound healing in insects as in vertebrates. It is also an important immune defense, quickly forming a secondary barrier to infection, immobilizing bacteria and thereby promoting their killing. However, hemolymph clotting is one of the least understood immune responses in insects. Here, we characterize fondue (fon; CG15825), an immune-responsive gene of Drosophila melanogaster that encodes an abundant hemolymph protein containing multiple repeat blocks. After knockdown of fon by RNAi, bead aggregation activity of larval hemolymph is strongly reduced, and wound closure is affected. Jon is thus the second Drosophila gene after hemolectin (hml), for which a knockdown causes a clotting phenotype. In contrast to hml-RNAi larvae, clot fibers are still observed in samples from fon-RNAi larvae. However, clot fibers from fon-RNAi larvae are more ductile and longer than in wt hemolymph samples, indicating that Fondue might be involved in cross-linking of fiber proteins. In addition, fon-RNAi larvae exhibit melanotic tumors and constitutive expression of the antifungal peptide gene Drosomycin (Drs), while fon-RNAi pupae display an aberrant pupal phenotype. Altogether, our studies indicate that Fondue is a major hemolymph protein required for efficient clotting in Drosophila.

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