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Landsem A, Emblem Å, Lau C, Christiansen D, Gerogianni A, Karlsen BO, Mollnes TE, Nilsson PH, Brekke OL. Complement C3b contributes to Escherichia coli-induced platelet aggregation in human whole blood. Front Immunol 2022; 13:1020712. [PMID: 36591264 PMCID: PMC9797026 DOI: 10.3389/fimmu.2022.1020712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Introduction Platelets have essential functions as first responders in the immune response to pathogens. Activation and aggregation of platelets in bacterial infections can lead to life-threatening conditions such as arterial thromboembolism or sepsis-associated coagulopathy. Methods In this study, we investigated the role of complement in Escherichia coli (E. coli)-induced platelet aggregation in human whole blood, using Multiplate® aggregometry, flow cytometry, and confocal microscopy. Results and Discussion We found that compstatin, which inhibits the cleavage of complement component C3 to its components C3a and C3b, reduced the E. coli-induced platelet aggregation by 42%-76% (p = 0.0417). This C3-dependent aggregation was not C3a-mediated as neither inhibition of C3a using a blocking antibody or a C3a receptor antagonist, nor the addition of purified C3a had any effects. In contrast, a C3b-blocking antibody significantly reduced the E. coli-induced platelet aggregation by 67% (p = 0.0133). We could not detect opsonized C3b on platelets, indicating that the effect of C3 was not dependent on C3b-fragment deposition on platelets. Indeed, inhibition of glycoprotein IIb/IIIa (GPIIb/IIIa) and complement receptor 1 (CR1) showed that these receptors were involved in platelet aggregation. Furthermore, aggregation was more pronounced in hirudin whole blood than in hirudin platelet-rich plasma, indicating that E. coli-induced platelet aggregation involved other blood cells. In conclusion, the E. coli-induced platelet aggregation in human whole blood is partly C3b-dependent, and GPIIb/IIIa and CR1 are also involved in this process.
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Affiliation(s)
- Anne Landsem
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, Bodø, Norway,*Correspondence: Anne Landsem,
| | - Åse Emblem
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, Bodø, Norway
| | - Corinna Lau
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, Bodø, Norway
| | - Dorte Christiansen
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, Bodø, Norway
| | - Alexandra Gerogianni
- Linnaeus Centre for Biomaterials Chemistry, Linnaeus University, Kalmar, Sweden,Department of Chemistry and Biomedicine, Linnaeus University, Kalmar, Sweden
| | - Bård Ove Karlsen
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, Bodø, Norway
| | - Tom Eirik Mollnes
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, Bodø, Norway,Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway,Department of Immunology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Per H. Nilsson
- Linnaeus Centre for Biomaterials Chemistry, Linnaeus University, Kalmar, Sweden,Department of Chemistry and Biomedicine, Linnaeus University, Kalmar, Sweden,Department of Immunology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Ole-Lars Brekke
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, Bodø, Norway,Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
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Emblem Å, Knutsen E, Jørgensen TE, Fure H, Johansen SD, Brekke OL, Mollnes TE, Karlsen BO. Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene. Noncoding RNA 2022; 8:ncrna8020024. [PMID: 35447887 PMCID: PMC9027897 DOI: 10.3390/ncrna8020024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 12/04/2022] Open
Abstract
Many severe inflammation conditions are complement-dependent with the complement component C5a-C5aR1 axis as an important driver. At the RNA level, the blood transcriptome undergoes programmed expression of coding and long non-coding RNAs to combat invading microorganisms. Understanding the expression of long non-coding RNAs containing Alu elements in inflammation is important for reconstructing cell fate trajectories leading to severe disease. We have assembled a pipeline for computation mining of new Alu-containing long non-coding RNAs by intersecting immune genes with known Alu coordinates in the human genome. By applying the pipeline to patient bulk RNA-seq data with sepsis, we found immune genes containing 48 Alu insertion as robust candidates for further study. Interestingly, 1 of the 48 candidates was located within the complement system receptor gene C5aR1 and holds promise as a target for RNA therapeutics.
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Affiliation(s)
- Åse Emblem
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, 8005 Bodø, Norway; (Å.E.); (H.F.); (O.-L.B.); (T.E.M.)
| | - Erik Knutsen
- Department of Medical Biology, UiT The Arctic University of Norway, 9037 Tromsø, Norway;
| | - Tor Erik Jørgensen
- Genomics Division—FBA, Nord University, 8026 Bodø, Norway; (T.E.J.); (S.D.J.)
| | - Hilde Fure
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, 8005 Bodø, Norway; (Å.E.); (H.F.); (O.-L.B.); (T.E.M.)
| | | | - Ole-Lars Brekke
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, 8005 Bodø, Norway; (Å.E.); (H.F.); (O.-L.B.); (T.E.M.)
- Department of Clinical Medicine, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Tom Eirik Mollnes
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, 8005 Bodø, Norway; (Å.E.); (H.F.); (O.-L.B.); (T.E.M.)
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Department of Immunology, Oslo University Hospital Rikshospitalet, University of Oslo, 0372 Oslo, Norway
| | - Bård Ove Karlsen
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, 8005 Bodø, Norway; (Å.E.); (H.F.); (O.-L.B.); (T.E.M.)
- Correspondence:
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Chi SI, Dahl M, Emblem Å, Johansen SD. Giant group I intron in a mitochondrial genome is removed by RNA back-splicing. BMC Mol Biol 2019; 20:16. [PMID: 31153363 PMCID: PMC6545197 DOI: 10.1186/s12867-019-0134-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 05/23/2019] [Indexed: 01/29/2023] Open
Abstract
Background The mitochondrial genomes of mushroom corals (Corallimorpharia) are remarkable for harboring two complex group I introns; ND5-717 and COI-884. How these autocatalytic RNA elements interfere with mitochondrial RNA processing is currently not known. Here, we report experimental support for unconventional processing events of ND5-717 containing RNA. Results We obtained the complete mitochondrial genome sequences and corresponding mitochondrial transcriptomes of the two distantly related corallimorpharian species Ricordea yuma and Amplexidiscus fenestrafer. All mitochondrial genes were found to be expressed at the RNA-level. Both introns were perfectly removed by autocatalytic splicing, but COI-884 excision appeared more efficient than ND5-717. ND5-717 was organized into giant group I intron elements of 18.1 kb and 19.3 kb in A. fenestrafer and R. yuma, respectively. The intron harbored almost the entire mitochondrial genome embedded within the P8 peripheral segment. Conclusion ND5-717 was removed by group I intron splicing from a small primary transcript that contained a permutated intron–exon arrangement. The splicing pathway involved a circular exon-containing RNA intermediate, which is a hallmark of RNA back-splicing. ND5-717 represents the first reported natural group I intron that becomes excised by back-splicing from a permuted precursor RNA. Back-splicing may explain why Corallimorpharia mitochondrial genomes tolerate giant group I introns. Electronic supplementary material The online version of this article (10.1186/s12867-019-0134-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sylvia Ighem Chi
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Mikael Dahl
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Åse Emblem
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Steinar D Johansen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway. .,Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
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Urbarova I, Forêt S, Dahl M, Emblem Å, Milazzo M, Hall-Spencer JM, Johansen SD. Ocean acidification at a coastal CO2 vent induces expression of stress-related transcripts and transposable elements in the sea anemone Anemonia viridis. PLoS One 2019; 14:e0210358. [PMID: 31067218 PMCID: PMC6505742 DOI: 10.1371/journal.pone.0210358] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 04/05/2019] [Indexed: 12/17/2022] Open
Abstract
Ocean acidification threatens to disrupt interactions between organisms throughout marine ecosystems. The diversity of reef-building organisms decreases as seawater CO2 increases along natural gradients, yet soft-bodied animals, such as sea anemones, are often resilient. We sequenced the polyA-enriched transcriptome of adult sea anemone Anemonia viridis and its dinoflagellate symbiont sampled along a natural CO2 gradient in Italy to assess stress levels in these organisms. We found that about 1.4% of the anemone transcripts, but only ~0.5% of the Symbiodinium sp. transcripts were differentially expressed. Processes enriched at high seawater CO2 were mainly linked to cellular stress, including significant up-regulation of protective cellular functions and deregulation of metabolic pathways. Transposable elements were differentially expressed at high seawater CO2, with an extreme up-regulation (> 100-fold) of the BEL-family of long terminal repeat retrotransposons. Seawater acidified by CO2 generated a significant stress reaction in A. viridis, but no bleaching was observed and Symbiodinium sp. appeared to be less affected. These observed changes indicate the mechanisms by which A. viridis acclimate to survive chronic exposure to ocean acidification conditions. We conclude that many organisms that are common in acidified conditions may nevertheless incur costs due to hypercapnia and/or lowered carbonate saturation states.
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Affiliation(s)
- Ilona Urbarova
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- * E-mail: (IU); (SDJ)
| | - Sylvain Forêt
- Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Mikael Dahl
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Åse Emblem
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Marco Milazzo
- Department of Earth and Marine Sciences, University of Palermo, Palermo, Italy
| | - Jason M. Hall-Spencer
- School of Biological and Marine Science, University of Plymouth, Plymouth, United Kingdom
- Shimoda Marine Research Center, University of Tsukuba, Shimoda City, Shizuoka, Japan
| | - Steinar D. Johansen
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- Genomics Research Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- * E-mail: (IU); (SDJ)
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Dubin A, Chi SI, Emblem Å, Moum T, Johansen SD. Deep-water sea anemone with a two-chromosome mitochondrial genome. Gene 2019; 692:195-200. [PMID: 30641219 DOI: 10.1016/j.gene.2018.12.074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/10/2018] [Accepted: 12/20/2018] [Indexed: 10/27/2022]
Abstract
Mitochondrial genome organization of sea anemones appears conserved among species and families, and is represented by a single circular DNA molecule of 17 to 21 kb. The mitochondrial gene content corresponds to the same 13 protein components of the oxidative phosphorylation (OxPhos) system as in vertebrates. Hallmarks, however, include a highly reduced tRNA gene repertoire and the presence of autocatalytic group I introns. Here we demonstrate that the mitochondrial genome of the deep-water sea anemone Protanthea simplex deviates significantly from that of other known sea anemones. The P. simplex mitochondrial genome contains a heavily scrambled order of genes that are coded on both DNA strands and organized along two circular mito-chromosomes, MCh-I and MCh-II. We found MCh-I to be representative of the prototypic sea anemone mitochondrial genome, encoding 12 OxPhos proteins, two ribosomal RNAs, two transfer RNAs, and a group I intron. In contrast, MCh-II was found to be a laterally transferred plasmid-like DNA carrying the conserved cytochrome oxidase II gene and a second allele of the small subunit ribosomal RNA gene.
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Affiliation(s)
- Arseny Dubin
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
| | - Sylvia Ighem Chi
- Department of Medical Biology, Faculty of Health Sciences, UiT - Arctic University of Norway, Tromsø, Norway.
| | - Åse Emblem
- Department of Medical Biology, Faculty of Health Sciences, UiT - Arctic University of Norway, Tromsø, Norway; Research Laboratory and Department of Laboratory Medicine, Nordland Hospital, Bodø, Norway.
| | - Truls Moum
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
| | - Steinar D Johansen
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway; Department of Medical Biology, Faculty of Health Sciences, UiT - Arctic University of Norway, Tromsø, Norway.
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Jørgensen TE, Karlsen BO, Emblem Å, Jakt LM, Nordeide JT, Moum T, Johansen SD. A mitochondrial long noncoding RNA in atlantic cod harbors complex heteroplasmic tandem repeat motifs. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:307-311. [PMID: 30198386 DOI: 10.1080/24701394.2018.1502281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A heteroplasmic tandem repeat (HTR) array occupies 100 to 300 bp of the mitochondrial DNA control region in the Atlantic cod, and recently we noted that the repeat appeared integrated in a polyadenylated mitochondrial long noncoding RNA. Here we provide a more detailed analysis of the mitochondrial HTR in the mitochondrial genome of 134 Atlantic cod specimens. We report all specimens to harbor mitochondrial HTRs in the control region, and identified 26 distinct variants among the 402 repeat motifs assessed. Whereas most specimens contained HTR profiles of 2-5 copies consisting of the same 40-bp motif, 22 specimens showed compound HTR arrays of at least two types of motifs present in the same mitochondrial DNA molecule. We found HTR profiles to be highly conserved between different tissue types of a single individual, and strictly maternally inherited in a mating experiment between parental Atlantic cod expressing different HTR profiles and array motifs. We conclude that mitochondrial heteroplasmy in the control region is very common in Atlantic cod, and results in length heterogenity of the long noncoding RNA lncCR-H.
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Affiliation(s)
- Tor Erik Jørgensen
- a Genomics group, Faculty of Biosciences and Aquaculture , Nord University , Bodø , Norway
| | - Bård Ove Karlsen
- b Research Laboratory and Department of Laboratory Medicine , Nordland Hospital , Bodø , Norway
| | - Åse Emblem
- c Department of Medical Biology Faculty of Health Sciences , UiT - Arctic University of Norway , Tromsø , Norway
| | - Lars Martin Jakt
- a Genomics group, Faculty of Biosciences and Aquaculture , Nord University , Bodø , Norway
| | - Jarle T Nordeide
- a Genomics group, Faculty of Biosciences and Aquaculture , Nord University , Bodø , Norway
| | - Truls Moum
- a Genomics group, Faculty of Biosciences and Aquaculture , Nord University , Bodø , Norway
| | - Steinar D Johansen
- a Genomics group, Faculty of Biosciences and Aquaculture , Nord University , Bodø , Norway.,c Department of Medical Biology Faculty of Health Sciences , UiT - Arctic University of Norway , Tromsø , Norway
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Jørgensen TE, Karlsen BO, Emblem Å, Breines R, Andreassen M, Rounge TB, Nederbragt AJ, Jakobsen KS, Nymark M, Ursvik A, Coucheron DH, Jakt LM, Nordeide JT, Moum T, Johansen SD. Mitochondrial genome variation of Atlantic cod. BMC Res Notes 2018; 11:397. [PMID: 29921324 PMCID: PMC6009815 DOI: 10.1186/s13104-018-3506-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/15/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The objective of this study was to analyse intraspecific sequence variation of Atlantic cod mitochondrial DNA, based on a comprehensive collection of completely sequenced mitochondrial genomes. RESULTS We determined the complete mitochondrial DNA sequence of 124 cod specimens from the eastern and western part of the species' distribution range in the North Atlantic Ocean. All specimens harboured a unique mitochondrial DNA haplotype. Nine hundred and fifty-two polymorphic sites were identified, including 109 non-synonymous sites within protein coding regions. Eighteen variable sites were identified as indels, exclusively distributed in structural RNA genes and non-coding regions. Phylogeographic analyses based on 156 available cod mitochondrial genomes did not reveal a clear structure. There was a lack of mitochondrial genetic differentiation between two ecotypes of cod in the eastern North Atlantic, but eastern and western cod were differentiated and mitochondrial genome diversity was higher in the eastern than the western Atlantic, suggesting deviating population histories. The geographic distribution of mitochondrial genome variation seems to be governed by demographic processes and gene flow among ecotypes that are otherwise characterized by localized genomic divergence associated with chromosomal inversions.
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Affiliation(s)
- Tor Erik Jørgensen
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Bård Ove Karlsen
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital, Bodø, Norway
| | - Åse Emblem
- Department of Medical Biology, Faculty of Health Sciences, UiT-Arctic University of Norway, Tromsø, Norway
| | - Ragna Breines
- Department of Medical Biology, Faculty of Health Sciences, UiT-Arctic University of Norway, Tromsø, Norway
| | - Morten Andreassen
- Department of Medical Biology, Faculty of Health Sciences, UiT-Arctic University of Norway, Tromsø, Norway
| | - Trine B Rounge
- Centre for Ecological and Evolutionary Syntheses (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Alexander J Nederbragt
- Centre for Ecological and Evolutionary Syntheses (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Syntheses (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Marianne Nymark
- Department of Medical Biology, Faculty of Health Sciences, UiT-Arctic University of Norway, Tromsø, Norway
| | - Anita Ursvik
- Department of Medical Biology, Faculty of Health Sciences, UiT-Arctic University of Norway, Tromsø, Norway
| | - Dag H Coucheron
- Department of Medical Biology, Faculty of Health Sciences, UiT-Arctic University of Norway, Tromsø, Norway
| | - Lars Martin Jakt
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Jarle T Nordeide
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Truls Moum
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Steinar D Johansen
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway.
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Karlsen BO, Emblem Å, Jørgensen TE, Klingan KA, Nordeide JT, Moum T, Johansen SD. Mitogenome sequence variation in migratory and stationary ecotypes of North-east Atlantic cod. Mar Genomics 2014; 15:103-8. [DOI: 10.1016/j.margen.2014.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/11/2013] [Accepted: 01/06/2014] [Indexed: 11/25/2022]
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Emblem Å, Okkenhaug S, Weiss ES, Denver DR, Karlsen BO, Moum T, Johansen SD. Sea anemones possess dynamic mitogenome structures. Mol Phylogenet Evol 2014; 75:184-93. [DOI: 10.1016/j.ympev.2014.02.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/31/2014] [Accepted: 02/17/2014] [Indexed: 11/24/2022]
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Karlsen BO, Klingan K, Emblem Å, Jørgensen TE, Jueterbock A, Furmanek T, Hoarau G, Johansen SD, Nordeide JT, Moum T. Genomic divergence between the migratory and stationary ecotypes of Atlantic cod. Mol Ecol 2013; 22:5098-111. [DOI: 10.1111/mec.12454] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 06/30/2013] [Accepted: 07/09/2013] [Indexed: 01/15/2023]
Affiliation(s)
- Bård O. Karlsen
- Faculty of Biosciences and Aquaculture; University of Nordland; N-8049 Bodø Norway
- Department of Medical Biology; Faculty of Health Sciences; University of Tromsø; N-9037 Tromsø Norway
- Division of Molecular Diagnostics; Department of Laboratory Medicine; Nordland Hospital Trust; N-8092 Bodø Norway
| | - Kevin Klingan
- Faculty of Biosciences and Aquaculture; University of Nordland; N-8049 Bodø Norway
| | - Åse Emblem
- Department of Medical Biology; Faculty of Health Sciences; University of Tromsø; N-9037 Tromsø Norway
| | - Tor E. Jørgensen
- Faculty of Biosciences and Aquaculture; University of Nordland; N-8049 Bodø Norway
| | - Alexander Jueterbock
- Faculty of Biosciences and Aquaculture; University of Nordland; N-8049 Bodø Norway
| | - Tomasz Furmanek
- Institute of Marine Research; PO Box 1870 Nordnesgaten 50 5817 Bergen Norway
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture; University of Nordland; N-8049 Bodø Norway
| | - Steinar D. Johansen
- Faculty of Biosciences and Aquaculture; University of Nordland; N-8049 Bodø Norway
- Department of Medical Biology; Faculty of Health Sciences; University of Tromsø; N-9037 Tromsø Norway
| | - Jarle T. Nordeide
- Faculty of Biosciences and Aquaculture; University of Nordland; N-8049 Bodø Norway
| | - Truls Moum
- Faculty of Biosciences and Aquaculture; University of Nordland; N-8049 Bodø Norway
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Urbarova I, Karlsen BO, Okkenhaug S, Seternes OM, Johansen SD, Emblem Å. Digital marine bioprospecting: mining new neurotoxin drug candidates from the transcriptomes of cold-water sea anemones. Mar Drugs 2012; 10:2265-2279. [PMID: 23170083 PMCID: PMC3497022 DOI: 10.3390/md10102265] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/08/2012] [Accepted: 10/10/2012] [Indexed: 11/16/2022] Open
Abstract
Marine bioprospecting is the search for new marine bioactive compounds and large-scale screening in extracts represents the traditional approach. Here, we report an alternative complementary protocol, called digital marine bioprospecting, based on deep sequencing of transcriptomes. We sequenced the transcriptomes from the adult polyp stage of two cold-water sea anemones, Bolocera tuediae and Hormathia digitata. We generated approximately 1.1 million quality-filtered sequencing reads by 454 pyrosequencing, which were assembled into approximately 120,000 contigs and 220,000 single reads. Based on annotation and gene ontology analysis we profiled the expressed mRNA transcripts according to known biological processes. As a proof-of-concept we identified polypeptide toxins with a potential blocking activity on sodium and potassium voltage-gated channels from digital transcriptome libraries.
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Affiliation(s)
- Ilona Urbarova
- RNA and Transcriptomics Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N9037 Tromsø, Norway; (I.U.); (B.O.K.); (S.O.); (A.E.)
| | - Bård Ove Karlsen
- RNA and Transcriptomics Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N9037 Tromsø, Norway; (I.U.); (B.O.K.); (S.O.); (A.E.)
| | - Siri Okkenhaug
- RNA and Transcriptomics Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N9037 Tromsø, Norway; (I.U.); (B.O.K.); (S.O.); (A.E.)
| | - Ole Morten Seternes
- Pharmacology Group, Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, N9037 Tromsø, Norway;
| | - Steinar D. Johansen
- RNA and Transcriptomics Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N9037 Tromsø, Norway; (I.U.); (B.O.K.); (S.O.); (A.E.)
- Marine Genomics Group, Faculty of Biosciences and Aquaculture, University of Nordland, N8049 Bodø, Norway
| | - Åse Emblem
- RNA and Transcriptomics Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N9037 Tromsø, Norway; (I.U.); (B.O.K.); (S.O.); (A.E.)
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Johansen SD, Emblem Å, Karlsen BO, Okkenhaug S, Hansen H, Moum T, Coucheron DH, Seternes OM. Approaching marine bioprospecting in hexacorals by RNA deep sequencing. N Biotechnol 2010; 27:267-75. [DOI: 10.1016/j.nbt.2010.02.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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