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  • 1.
    Asano, Masanari
    et al.
    Tokyo University of Science.
    Basieva, Irina
    Linnaeus University, Faculty of Technology, Department of Mathematics.
    Khrennikov, Andrei
    Linnaeus University, Faculty of Technology, Department of Mathematics.
    Ohya, Masanori
    Tokyo University of Science.
    Tanaka, Yoshiharu
    Tokyo University of Science.
    Yamato, Ichiro
    Tokyo University of Science.
    A model of epigenetic evolution based on theory of open quantum systems2013In: Systems and Synthetic Biology, ISSN 1872-5325, Vol. 7, no 4, p. 161-173Article in journal (Refereed)
    Abstract [en]

    We present a very general model of epigenetic evolution unifying (neo-)Darwinian and (neo-)Lamarckian viewpoints. The evolution is represented in the form of adaptive dynamics given by the quantum(-like) master equation. This equation describes development of the information state of epigenome under the pressure of an environment. We use the formalism of quantum mechanics in the purely operational framework. (Hence, our model has no direct relation to quantum physical processes inside a cell.) Thus our model is about probabilities for observations which can be done on epigenomes and it does not provide a detailed description of cellular processes. Usage of the operational approach provides a possibility to describe by one model all known types of cellular epigenetic inheritance.

  • 2.
    Bergman, Ingrid-Maria
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Polymorphism in pattern recognition receptor genes in pigs2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The mammalian immune defense consists of two systems, which are interconnected and co-operate to provide host defense. The innate immune system is always active and detects and responds to non-self without delay. The adaptive immune system has a lag phase, but is more specific and has got a memory.

    The innate immune system relies on pattern recognition receptors (PRRs) to detect molecular patterns signaling microbial presence. This thesis focuses on a centrally placed family of PRRs, namely the Toll-like receptors (TLRs), and on mannan-binding lectin (MBL), a PRR which initiates the lectin activation pathway of complement. TLRs are expressed on the cell surface and in intracellular compartments, while MBL is a soluble protein present in most body fluids.

    Polymorphism – literally ’many forms’ – refers to variation between individuals, at DNA level as well as in traits. A single nucleotide polymorphism (SNP) implicates that alternative nucleotides are present at a particular position in the genome. Mutations, together with phenomena like gene duplication and whole genome duplication, are the ultimate source of variation in nature and the fuel for evolution. Through natural selection and breeding, i.e. artificial selection, species are shaped and change over time.

    Domestic animals are well suited for genetic studies, since they enable comparisons of populations exposed to different selection criteria and environmental challenges. Also, in the case of pigs, comparisons to the wild ancestor – i.e. the wild boar – can shed light on the evolutionary process. Moreover, pigs are large animal models for humans.

    Paper I reports the refinement of previously identified quantitative trait loci for immune-related traits on pig chromosome 8.

    Papers II and III report differences in polymorphic patterns between wild boars and domestic pigs in the TLR1, TLR2, TLR6, and TLR10 genes. In TLR1 and TLR2, more SNPs were present in the domestic pigs than in the wild boars. In TLR6, SNP numbers were similar in both animal groups, but the level of heterozygosity was higher in the domestic pigs than in the wild boars. In TLR10, again, more SNPs were present in the domestic pigs, and a higher number of non-synonymous SNPs was detected in TLR10 compared to the other genes. This might suggest redundancy for TLR10 in pigs.

    Paper IV reports the presence of an SNP, previously detected in domestic pigs and assumed to affect MBL concentrations in serum, in European wild boars. Also, the connection between the presumed low-producing allele and low MBL concentration in serum was confirmed. Moreover, a novel SNP, with potential to be functionally important, was detected.

    Owing to the domestication process and differences in selection pressure, differences in polymorphic patterns between wild boars and domestic pigs are not surprising. However, since breeding means choosing among genotypes, the opposite pattern – more SNPs in wild boars than in domestic pigs – would have been expected. However, the result confirms other studies, which have shown that European wild boars went through a bottle neck before domestication started. The higher number of SNPs in domestic pigs may be due to relaxed purifying selection during the domestication process.

    Download full text (pdf)
    Ingrid-Maria Bergman, Doctoral Thesis (Kappa)
  • 3.
    Bergman, Ingrid-Maria
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Edman, Kjell
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Nilsson Ekdahl, Kristina
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Uppsala University.
    Rosengren, K. Johan
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. The University of Queensland, Australia.
    Edfors, Inger
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Extensive polymorphism in the porcine Toll-like receptor 10 gene2012In: International Journal of Immunogenetics, ISSN 1744-3121, E-ISSN 1744-313X, Vol. 39, no 1, p. 68-76Article in journal (Refereed)
    Abstract [en]

    The great importance of the Toll-like receptors (TLRs) in innate immunity is well established, but one family member – TLR10 – remains elusive. TLR10 is expressed in various tissues in several species, but its ligand is not known and its function is still poorly understood. The open reading frame of TLR10 was sequenced in 15 wild boars, representing three populations, and in 15 unrelated domestic pigs of Hampshire, Landrace and Large White origin. Amino acid positions corresponding to detected nonsynonymous single nucleotide polymorphisms (SNPs) were analysed in the crystal structures determined for the human TLR1–TLR2–lipopeptide complex and the human TLR10 Toll/Interleukin 1 receptor (TIR) dimer. SNP occurrence in wild boars and domestic pigs was compared, and haplotypes for the TLR10 gene and the TLR6-1-10 gene cluster were reconstructed. Despite the limited number of animals sequenced in the present study (N = 30), a larger number of SNPs were found in TLR10 than recently reported for TLR1, TLR6 and TLR2. Thirty-three SNPs were detected, of which 20 were nonsynonymous. The relative frequency of nonsynonymous (dN) and synonymous (dS) SNPs between wild boars and domestic pigs was higher in TLR10 than recently reported for TLR1, TLR6 and TLR2. However, the polymorphism reported in the present study seems to leave the function of the TLR10 molecule unaffected. Furthermore, no nonsynonymous SNPs were detected in the part of the gene corresponding to the hinge region of the receptor, probably reflecting rigorously acting functional constraint. The total number of SNPs and the number of nonsynonymous SNPs were significantly lower (< 0.05) in the wild boars than in the domestic pigs, and fewer TLR10 haplotypes were present in the wild boars. The majority of the TLR6-1-10 haplotypes were specific for either wild boars or domestic pigs, probably reflecting differences in microbial environment and population history.

  • 4.
    Bergman, Ingrid-Maria
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Edman, Kjell
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Rosengren, K. Johan
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Edfors, Inger
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    European wild boars and domestic pigs display different polymorphic patterns in the Toll-like receptor (TLR)1, TLR2, TLR6, and TLR10 genes.2010In: International Symposium on Animal Genomics for Animal Health Paris, France, 31 May – 2 June 2010: The AGAH 2010 Abstract Book, 2010, p. 35-Conference paper (Other academic)
    Abstract [en]

    The Toll-like receptors (TLR) are vitally important pattern recognition receptors linking innate and adaptive immunity. Several single nucleotide polymorphisms (SNP) in human TLR genes have been associated with disease. There are few studies on associations between polymorphisms in TLR genes and disease in pigs, but the TLR2/TLR6 heterodimer is activated by Mycoplasma hyopneumoniae, and the expression of TLR2, TLR4, and TLR9 is modulated in the presence of different Salmonella serovars. Porcine TLR1, TLR6, and TLR10 are located in a cluster on the p arm of chromosome 8, while TLR2 resides on the q arm. Previously, we identified quantitative trait loci (QTL) for immune-related traits on pig chromosome 8, close to the KIT gene and the microsatellite S0225, respectively. In order to explore polymorphism in some TLR genes in European wild boars and domestic pigs, TLR1, TLR2, and TLR6 were sequenced in 25 wild boars, representing three populations, and in 15 domestic pigs of Hampshire, Landrace, and Large White origin. Similarly, TLR10 was sequenced in 15 wild boars and 15 domestic pigs. In TLR1 and TLR2, more SNP were present in the domestic pigs than in the wild boars. In TLR6, SNP numbers were similar in both animal groups, but the level of heterozygosity was higher in the domestic pigs than in the wild boars. In TLR10, again, more SNP were present in the domestic pigs, and a higher number of nonsynonymous SNP were detected in TLR10 compared to the other genes. This may suggest redundancy for TLR10 in pigs. 

  • 5.
    Bergman, Ingrid-Maria
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Johansson, Amelie
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Wattrang, Eva
    Fossum, Caroline
    Andersson, Leif
    Edfors, Inger
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Refined analysis of quantitative trait loci (QTLs) for immune capacity related traits on pig chromosome 8Manuscript (preprint) (Other academic)
  • 6.
    Bergman, Ingrid-Maria
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Rosengren, K. Johan
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Edman, Kjell
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Edfors, Inger
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    European wild boars and domestic pigs display different polymorphic patterns in the Toll-like receptor (TLR) 1, TLR2, and TLR6 genes2010In: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 62, no 1, p. 49-58Article in journal (Refereed)
    Abstract [en]

    During the last decade, the Toll-like receptors (TLRs) have been extensively studied and their immense importance in innate immunity is now being unveiled. Here, we report pronounced differences – probably reflecting the domestication process and differences in selective pressure – between wild boars and domestic pigs regarding single nucleotide polymorphisms (SNPs) in TLR genes. The open reading frames of TLR1, TLR2, and TLR6 were sequenced in 25 wild boars, representing three populations, and in 15 unrelated domestic pigs of Hampshire, Landrace, and Large White origin. In total, 20, 27, and 26 SNPs were detected in TLR1, TLR2, and TLR6, respectively. In TLR1 and TLR2, the numbers of SNPs detected were significantly lower (P ≤ 0.05, P ≤ 0.01) in the wild boars than in the domestic pigs. In the wild boars, one major high frequency haplotype was found in all three genes, while the same pattern was exhibited only by TLR2 in the domestic pigs. The relative frequency of non-synonymous (dN) and synonymous (dS) SNPs was lower for the wild boars than for the domestic pigs in all three genes. In addition, differences in diversity between the genes were revealed: the mean heterozygosity at the polymorphic positions was markedly lower in TLR2 than in TLR1 and TLR6. Because of its localization – in proximity of the bound ligand – one of the non-synonymous SNPs detected in TLR6 may represent species-specific function on the protein level. Furthermore, the codon usage pattern in the genes studied deviated from the general codon usage pattern in Sus scrofa.

  • 7.
    Bergman, Ingrid-Maria
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Sandholm, Kerstin
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Juul-Madsen, Helle R.
    Heegaard, Peter M.
    Nilsson Ekdahl, Kristina
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Edfors, Inger
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    MBL-A concentrations and MBL1 genotypes in European wild boars, Large White pigs, and wild boar/Large White crossbreds2010In: 8th European Colloquium on Acute Phase Proteins in Helsinki, 2010.08.25-2010.08.27, 2010, p. 25-26Conference paper (Refereed)
  • 8.
    Bergman, Ingrid-Maria
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Aarhus University, Denmark.
    Sandholm, Kerstin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Nilsson Ekdahl, Kristina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Uppsala university.
    Okumura, Naohiko
    Institute of Society for Techno-innovation of Agriculture, Japan.
    Uenishi, Hirohide
    National Institute of Agrobiological Sciences, Japan.
    Guldbrandtsen, Bernt
    Aarhus University, Denmark.
    Essler, Sabine
    Univ of Veterinary Medicine, Austria.
    Knoll, Ales
    Mendel University, Czech Republic.
    Heegaard, Peter
    Technical University of Denmark, Denmark.
    Edfors, Inger
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Juul-Madsen, Helle
    Aarhus University, Denmark.
    MBL1 genotypes in wild boar populations from Sweden, Austria, the Czech Republic and Japan2013In: International Journal of Immunogenetics, ISSN 1744-3121, E-ISSN 1744-313X, Vol. 40, no 2, p. 131-139Article in journal (Refereed)
    Abstract [en]

    The single nucleotide polymorphism (SNP) G949T in the mannose-binding lectin (MBL) 1 gene has been associated with low MBL-A concentration in serum and detected at different frequencies in various European pig populations. However, the origin of this SNP is not known. Part of the MBL1 gene was sequenced in 12 wild boar/Large White crossbred pigs from the second backcross (BC 2) generation in a family material originating from two wild boar x Large White intercrosses. Also, MBL-A serum concentration was measured in the entire BC 2 generation (n = 45). Furthermore, the genotypes of 68 wild boars from Sweden, Austria, the Czech Republic, and Japan were determined in regard to five previously described SNPs in MBL1. The T allele of G949T was present among the BC 2 animals. MBL-A serum concentration in the BC 2 animals showed a bimodal distribution, with one-third of the animals at levels between 0.7 and 1.6 μg mL−1 and the remaining pigs at levels around 13 μg mL−1. There was a co-variation between the presence of the T allele and low MBL-A concentration in serum. The genotyping of the wild boars revealed differences between populations. The T allele of G949T was not detected in the Austrian and Japanese samples and is thus unlikely to be an original feature of wild boars. In contrast, it was present at high frequency (0.35) among the Swedish wild boars, probably representing a founder effect. Five MBL1 haplotypes were resolved. Only two of these were present among the Japanese wild boars compared to four in each of the European populations. This difference may reflect differences in selection pressure and population history.

  • 9.
    Dragan, Smiljic
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Studies of small bicoid knock-down and overexpression at early and late stage of development in Drosophila melanogaster.2016Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
  • 10. Holmgren, G
    et al.
    Drugge, Ulf
    University of Kalmar, School of Human Sciences.
    Haettner, E
    Lundgren, E
    Sandgren, O
    Steen, L
    Wahlqvist, J
    Four Swedish cases with Homozygoty for the FAP-MET30-gene1990Other (Other academic)
  • 11.
    Högberg, Anders
    Linnaeus University, Faculty of Arts and Humanities, Department of Cultural Sciences.
    Migration är inte den enda förklaringen till genflöden2018In: Respons : recensionstidskrift för humaniora & samhällsvetenskap, ISSN 2001-2292, no 2, p. 19-23Article in journal (Other (popular science, discussion, etc.))
    Abstract [sv]

    Resultat från DNA-analyser de senaste tio åren har fått stor betydelse för tolkningar av människans utveckling, rörelsemönster och interaktion. Men samtidigt kännetecknas flera studier av svagt underbyggda tolkningar. DNA-analyser visar att något har hänt, men säger inte mycket om hur eller varför. En alltför enkel tolkningsram begränsar förståelsen av människans förhistoria. Denna forskning behöver integreras med humanvetenskapernas kunskap om släktskap, mobilitet och kulturmöten för att nå sin fulla potential.

  • 12. Jacobsen, M
    et al.
    Kracht, SS
    Esteso, G
    Cirera, S
    Edfors, Inger
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Archibald, AL
    Bendixen, C
    Anderson, L
    Fredholm, M
    Jorgensen, CB
    Refined candidate region specified by haplotype sharing for Escherichia coli F4ab/F4ac susceptibility alleles in pigs.2010In: Animal Genetics, ISSN 0268-9146, E-ISSN 1365-2052, Vol. 41, p. 21-25Article in journal (Refereed)
    Abstract [en]

    P>Infection of the small intestine by enterotoxigenic Escherichia coli F4ab/ac is a major welfare problem and financial burden for the pig industry. Natural resistance to this infection is inherited as a Mendelian recessive trait, and a polymorphism in the MUC4 gene segregating for susceptibility/resistance is presently used in a selection programme by the Danish pig breeding industry. To elucidate the genetic background involved in E. coli F4ab/ac susceptibility in pigs, a detailed haplotype map of the porcine candidate region was established. This region covers approximately 3.7 Mb. The material used for the study is a three generation family, where the founders are two Wild boars and eight Large White sows. All pigs have been phenotyped for susceptibility to F4ab/ac using an adhesion assay. Their haplotypes are known from segregation analysis using flanking markers. By a targeted approach, the candidate region was subjected to screening for polymorphisms, mainly focusing on intronic sequences. A total of 18 genes were partially sequenced, and polymorphisms were identified in GP5, CENTB2, APOD, PCYT1A, OSTalpha, ZDHHC19, TFRC, ACK1, MUC4, MUC20, KIAA0226, LRCH3 and MUC13. Overall, 227 polymorphisms were discovered in the founder generation. The analysis revealed a large haplotype block, spanning at least 1.5 Mb around MUC4, to be associated with F4ab/ac susceptibility.

  • 13.
    Yildirim, Yeserin
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Tinnert, Jon
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Forsman, Anders
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Contrasting patterns of neutral and functional genetic diversity in stable and disturbed environments2018In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 8, no 23, p. 12073-12089Article in journal (Refereed)
    Abstract [en]

    Genetic structure among and diversity within natural populations is influenced by acombination of ecological and evolutionary processes. These processes can differentlyinfluence neutral and functional genetic diversity and also vary according toenvironmental settings. To investigate the roles of interacting processes as drivers ofpopulation‐level genetic diversity in the wild, we compared neutral and functionalstructure and diversity between 20 Tetrix undulata pygmy grasshopper populations indisturbed and stable habitats. Genetic differentiation was evident among the differentpopulations, but there was no genetic separation between stable and disturbedenvironments. The incidence of long‐winged phenotypes was higher in disturbedhabitats, indicating that these populations were recently established by flight‐capablecolonizers. Color morph diversity and dispersion of outlier genetic diversity, estimatedusing AFLP markers, were higher in disturbed than in stable environments,likely reflecting that color polymorphism and variation in other functionally importanttraits increase establishment success. Neutral genetic diversity estimated usingAFLP markers was lower in disturbed habitats, indicating stronger eroding effects onneutral diversity of genetic drift associated with founding events in disturbed comparedto stable habitats. Functional diversity and neutral diversity were negativelycorrelated across populations, highlighting the utility of outlier loci in genetics studiesand reinforcing that estimates of genetic diversity based on neutral markers donot infer evolutionary potential and the ability of populations and species to copewith environmental change.

  • 14.
    Yurova Axelsson, Ekaterina
    Linnaeus University, Faculty of Technology, Department of Mathematics.
    On the representation of the genetic code by the attractors of 2-adic function2015In: Physica scripta. T, ISSN 0281-1847, Vol. 2015, no T 165, article id 014043Article in journal (Refereed)
    Abstract [en]

    The genetic code is a map which gives the correspondence between codons in DNA and amino acids. As a continuation of the study made by Khrennikov and Kozyrev on the genetic code, we consider a construction, where amino acids are associated to the attractors of some two-adic function. In this paper, we give an explicit form of representations for the standard nuclear and vertebrate mitochondrial genetics codes. To set these functions we use a van der Put representation. The usage of the van der Put series reduces the complexity of computation for explicit form of the functions for the genetic codes.

  • 15.
    Zoabi, Muhammad
    et al.
    Technion, Israel.
    Nadar-Ponniah, Prathamesh T.
    Technion, Israel.
    Khoury-Haddad, Hanan
    Technion, Israel.
    Ušaj, Marko
    Technion, Israel.
    Budowski-Tal, Inbal
    Technion, Israel.
    Haran, Tali
    Technion, Israel.
    Henn, Arnon
    Technion, Israel.
    Mandel-Gutfreund, Yael
    Technion, Israel.
    Ayoub, Nabieh
    Technion, Israel.
    RNA-dependent chromatin localization of KDM4D lysine demethylase promotes H3K9me3 demethylation2014In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 42, no 21, p. 13026-13038Article in journal (Refereed)
    Abstract [en]

    The JmjC-containing lysine demethylase, KDM4D, demethylates di-and tri-methylation of histone H3 on lysine 9 (H3K9me3). How KDM4D is recruited to chromatin and recognizes its histone substrates remains unknown. Here, we show that KDM4D binds RNA independently of its demethylase activity. We mapped two non-canonical RNA binding domains: the first is within the N-terminal spanning amino acids 115 to 236, and the second is within the C-terminal spanning amino acids 348 to 523 of KDM4D. We also demonstrate that RNA interactions with KDM4D N-terminal region are critical for its association with chromatin and subsequently for demethylating H3K9me3 in cells. This study implicates, for the first time, RNA molecules in regulating the levels of H3K9 methylation by affecting KDM4D association with chromatin.

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