Hvað eru HeLa-frumur? Arnar Pálsson. „Hvað eru HeLa-frumur?“. Vísindavefurinn 9.3.2015. http://visindavefur.is/?id=69338. Árið 1951 innritaðist rúmlega þrítug kona, Henrietta Lacks (1920–1951), á John Hopkins-spítalann í Baltimore sem á þessum tíma var einn fárra spítala sem meðhöndluðu blökkufólk. Ástæða spítalavistarinnar var hnútur í kviðarholi sem læknar greindu síðan sem krabbamein á leginu. Því miður dugði meðferð ekki til að bjarga lífi hennar en hún lést október þetta sama ár. Seinna kom í ljós að orsökin var HPV-sýking sem er ein algengasta orsök leghálskrabbameins. Á meðan á meðferð Henríettu stóð voru frumur fjarlægðar úr æxlinu og setti vísindamaðurinn George Gey (1899-1970) þær í rækt, að Henríettu forspurðri.
Submitted to Plos One: The developmental transcriptome of contrasting Arctic charr (Salvelinus alpinus) morphs
We just sent this manuscript to PLoS One, after G3 decided they did not like it. (Main sticking point is that they wanted de novo assembly - but we argued it was not a good idea with the 36bp non paired end reads) At any rate, I like PLoS One, and would like to publish one paper there a year...
Posted in Publications
Ég heiti Hekla, ef ég set DNA úr mér í plöntu verður þá plantan Hekluplanta?
Ég heiti Hekla, ef ég set DNA úr mér í plöntu verður þá plantan Hekluplanta? Afkvæmi líkjast foreldrum sínum því þau fá erfðaefni (DNA) frá þeim. Þetta á við um öll afkvæmi, hvort sem þau eru börn, dýr, plöntur eða aðrar lífverur enda er DNA erfðaefni allra lífvera á jörðinni. Í náttúrunni getur DNA flust á milli einstaklinga, en það er frekar sjaldgæft. Dæmi eru um að DNA og gen flytjist á milli ólíkra tegunda baktería, og nokkur dæmi eru um flutning inn í dýr eða plöntur.
Posted in Vísindavefur - svör
Í hvaða landi eða landsvæði eru rauðhærðir algengastir?
Í hvaða landi eða landsvæði eru rauðhærðir algengastir? Hvar er Ísland í röðinni hvað varðar hlutfall rauðhærðra? Er hægt að sjá með DNA-rannsókn hvaðan rauðhærðir Íslendingar koma? Rautt hár er algengast meðal Vesturlandabúa, en nær óþekkt hjá upprunalegum ættbálkum Afríku, Ameríku og Ástralíu. Rautt hár finnst að auki í nokkrum asískum ættbálkum. Í Vestur-Evrópu er það algengast á Bretlandseyjum.
Posted in Vísindavefur - svör
(Icelandic) Tilviljun og tilgangur í lífi og eilífð: Um Tilviljun og nauðsyn eftir Jacques Monod
Posted in Publications
Academic advisor for Dr. Sara Sigurbjornsdottir
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.
Posted in General biology
The developmental transcriptome of contrasting Arctic charr (Salvelinus alpinus) morphs
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.
Posted in Publications
Transcriptional dynamics of a conserved gene expression network associated with craniofacial divergence in Arctic charr
Transcriptional dynamics of a conserved geneexpression network associated with craniofacial divergence in Arctic charr. Ehsan Pashay Ahi et al. Evodevo
Background
Understanding the molecular basis of craniofacial variation can provide insights into key developmental mechanisms of adaptive changes and their role in trophic divergence and speciation. Arctic charr (Salvelinus alpinus) is a polymorphic fish species, and, in Lake Thingvallavatn in Iceland, four sympatric morphs have evolved distinct craniofacial structures. We conducted a gene expression study on candidates from a conserved gene coexpression network, focusing on the development ofcraniofacial elements in embryos of two contrasting Arctic charr morphotypes (benthic and limnetic).
Results
Four Arctic charr morphs were studied: one limnetic and two benthic morphs from Lake Thingvallavatn and a limnetic reference aquaculture morph. The presence of morphological differences at developmental stages before the onset of feeding was verified by morphometric analysis. Following up on our previous findings that Mmp2 and Sparc were differentially expressed between morphotypes, we identified a network of genes with conserved coexpression across diverse vertebrate species. A comparative expression study of candidates from this network in developing heads of the four Arctic charr morphs verified the coexpression relationship of these genes and revealed distinct transcriptional dynamics strongly correlated with contrasting craniofacial morphologies (benthic versus limnetic). A literature review and Gene Ontology analysis indicated that a significant proportion of the network genes play a role in extracellular matrix organization and skeletogenesis, and motif enrichment analysis of conserved noncoding regions of network candidates predicted a handful of transcription factors, including Ap1 and Ets2, as potential regulators of the gene network. The expression of Ets2 itself was also found to associate with network gene expression. Genes linked to glucocorticoid signalling were also studied, as both Mmp2 and Sparc are responsive to this pathway. Among those, several transcriptional targets and upstream regulators showed differential expression between the contrasting morphotypes. Interestingly, although selected network genes showed overlapping expression patterns in situ and no morph differences, Timp2 expression patterns differed between morphs.
Conclusion
Our comparative study of transcriptional dynamics in divergent craniofacial morphologies of Arctic charr revealed a conserved network of coexpressed genes sharing functional roles in structural morphogenesis. We also implicate transcriptional regulators of the network as targets for future functional studies.
Posted in Publications