I had the great fortune of serving as the academic advisor of Sara Sigurbjornsdottir, who defended her Ph.D thesis Monday the 5th of January. The thesis is titled: Complex cell shape: Molecular mechanisms of tracheal terminal cell development in Drosophila melanogaster.
Sara worked on development of terminal cells in the tracheal system of the fruitfly, focusing on characterizing gene function and pathways that affect both formation and maturation of the cells.
She worked at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany in the laboratory of dr. Maria Leptin, EMBO Director. The doctoral committee also includes our gentle selves, and two great molecular biologists dr. Marko Kaksonen, and dr. Stefano De Renzis, both group leaders at the European Molecular Biology Laboratory, Heidelberg, Germany.
Official opponents were dr. Stefan Luschnig, Senior Research Associate, Institute of Molecular Life Sciences, University of Zurich, Switzerland and dr.
Thorarinn Gudjonsson, Professor at the Faculty of Medicine, School of Health Sciences, University of Iceland.
See abstract of her talk and further details.
Her published paper on Molecular mechanisms of de novo lumen formation.
We just submitted a paper to G3, and deposited the manuscript on BioRxiv.
The developmental transcriptome of contrasting Arctic charr (Salvelinus alpinus) morphs
Jóhannes Gudbrandsson, Ehsan P Ahi, Kalina H Kapralova, Sigrídur R Franzdottir, Bjarni K Kristjánsson, Sophie S Steinhaeuser, Ísak M Jóhannesson, Valerie H Maier, Sigurdur S Snorrason, Zophonías O Jónsson, Arnar Pálsson
Species showing repeated evolution of similar traits can help illuminate the molecular and developmental basis of diverging traits and specific adaptations. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several landlocked Arctic charr (Salvelinus alpinus) populations in Iceland.
In order to study the genetic divergence between small benthic morphs and larger morphs with limnetic morphotype, we conducted an RNA-seq transcriptome analysis of developing charr. We sequenced mRNA from whole embryos at four stages in early development of two stocks with very different morphologies, the small benthic (SB) charr from Lake Thingvallavatn and Holar aquaculture (AC) charr. The data reveal significant differences in expression of several biological pathways during charr development. There is also a difference between SB- and AC-charr in mitochondrial genes involved in energy metabolism and blood coagulation genes. We confirmed expression difference of five genes in whole embryos with qPCR, including lysozyme and natterin which was previously identified as a fish-toxin of a lectin family that may be a putative immunopeptide. We verified differential expression of 7 genes in developing heads, and the expression associated consistently with benthic v.s. limnetic charr (studied in 4 morphs total). Comparison of Single nucleotide polymorphism (SNP) frequencies reveals extensive genetic differentiation between the SB- and AC-charr (60 fixed SNPs and around 1300 differing more than 50% in frequency). In SB-charr the high frequency derived SNPs are in genes related to translation and oxidative processes. Curiously, several derived SNPs reside in the 12s and 16s mitochondrial ribosomal RNA genes, including a base highly conserved among fishes.
The data implicate multiple genes and molecular pathways in divergence of small benthic charr and/or the response of aquaculture charr to domestication. Functional, genetic and population genetic studies on more freshwater and anadromous populations are needed to confirm the specific loci and mutations relating to specific ecological or domestication traits in Arctic charr.
Sorry, this entry is only available in Icelandic.
Sorry, this entry is only available in Icelandic.
Sorry, this entry is only available in Icelandic.
Sorry, this entry is only available in Icelandic.
We co-authored a manuscript submitted recently to a special issue of Developmental dynamics.
Bones in motion: Ontogeny of craniofacial development in sympatric Arctic charr morphs Kalina H. Kapralova, Zophonías O. Jónsson, Arnar Palsson, Sigrídur Rut Franzdóttir, Soizic Le Deuff, Bjarni K. Kristjanson, Sigurður S. Snorrason
Our recent paper on deletion polymorphism in the eve stripe 3+7 enhancer was covered by the Global medical discovery website.
Palsson A, Wesolowska N, Reynisdóttir S, Ludwig MZ, Kreitman M (2014) Naturally Occurring Deletions of Hunchback Binding Sites in the Even-Skipped Stripe 3+7 Enhancer. PLoS ONE 9(5): e91924. doi:10.1371/journal.pone.0091924
Transcription factors (TF) bind to specific DNA sequence to regulate expression of genes. Evolutionary studies of enhancers show that some TF binding sites are well conserved while others are less constrained. The regulatory elements of the even-skipped (eve) gene in Drosophila are a textbook example of regulatory function, as specific activating and repressing TFs bind to specific binding sites and control the spatio-temporal expression of the gene. These enhancers are also a textbook example of TF binding site “turn-over” and compensatory evolution within regulatory elements.
In this study we examine natural sequence polymorphism in characterized enhancers in Drosophila melanogaster, and find the TF binding sites to be preserved by selection. Curiously we find two exceptions, both in the same enhancer of eve (that forms stripes 3 and 7 in the embryo). Both mutations are large deletions (larger than 45 bp) and both remove conserved binding sites for the same transcription factor. Hunchback is an important developmental regulator that affects expression of eve in the embryo. Both deletions are at high frequency in fly populations, and thus do not seem to be harmful for the flies. By analogy one might say that a tree is struck twice by lighting, but doesnt catch fire.
The most puzzling result of this study is that both Hb binding sites are conserved and the two deletions removing them are at up to 35% frequency in the population.
Furthermore, one of the Hb sites was not noticed earlier, because the Drosophila reference genome is homozygous for the deletion allele.
We postulate that coevolution between Hb function and its target sequences best explains the data. In other words, this could reflect compensatory evolution of cis and trans factors, that is developmental system drift in the gene regulatory network controlling stripe formation in fruitfly embryos.
The charr group had one paper accepted in BMC EvoDevo last week. The title is:
Ehsan P Ahi, Kalina H Kapralova, Arnar Palsson, Valerie H Maier, Johannes Gudbrandsson, Sigurdur S Snorrason, Zophonias O Jonsson and Sigridur R Franzdottir Transcriptional dynamics of a conserved gene expression network associated with benthic-limnetic craniofacial divergence in Arctic charr. Abstract to follow.
