Research outputs

  1. Ontogeny of Hemidactylus (Gekkota, Squamata) with emphasis on the limbs

    Squamate reptiles constitute a major component of the world's terrestrial vertebrate diversity, encompassing many morphotypes related to ecological specialization. Specifically, Gekkota, the sister clade to most other squamates, have highly specialized autopodia, which have been linked to their ecological plasticity. In this study, a developmental staging table of the gecko Hemidactylus, housed at the Museum fur Naturkunde, is established. Twelve post-ovipositional stages are erected, monitoring morphological embryological transitions in eye, ear, nose, heart, limbs, pharyngeal arches, and skin structures. Ecomorphological specializations in the limbs include multiple paraphalanges, hypothesized to aid in supporting the strong muscles, that are situated adjacent to metacarpal and phalangeal heads. Furthermore, some phalanges are highly reduced in manual digits III and IV and pedal digits III, IV, and V. Development, composition, and growth of limb elements is characterized in detail via mu CT, histochemistry, and bone histological analysis. Using known life history data from two individuals, we found an average lamellar bone accretion rate in the humeral diaphysis comparable to that of varanids. Various adult individuals also showed moderate to extensive remodeling features in their long bone cortices, indicating that these animals experience a highly dynamic bone homeostasis during their growth, similar to some other medium-sized to large squamates. This study of in-ovo development of the gecko Hemidactylus and its ecomorphological specializations in the adult autopodia, enlarges our knowledge of morphological trait evolution and of limb diversity within the vertebrate phylum.

    General information

    StatePublished
    Ministry of Education publication typeA1 Journal article-refereed
    OrganisationsInstitute of Biotechnology, Vertebrate Evolution, Development and Regeneration Group, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Vrije Universiteit Brussel , Royal Belgian Institute of Natural Sciences, Leibniz Institute for Evolution and Biodiversity Science, Berlin
    Contributorsvan der Vos, W., Stein, K., Di-Poi, N., Bickelmann, C.
    Number of pages15
    Pages195-209
    Publication date9 Mar 2018
    Peer-reviewedYes

    Publication information

    JournalZoosystematics and evolution
    Volume94
    Issue number1
    ISSN (Print)1860-0743
    Original languageEnglish
    Fields of ScienceGecko, in-ovo development, staging table, limb development, bone histology, mu CT, immunohistochemistry, ossification, ecomorphological specialization, EMBRYONIC-DEVELOPMENT, DEVELOPMENTAL-STAGES, INTEGRATIVE BIOLOGY, LIZARDS, EVOLUTION, GECKO, MORPHOLOGY, REPTILIA, SETAE, HETEROCHRONY, 1181 Ecology, evolutionary biology
    Electronic versions
    DOIs
    SourceWOS
    Source-ID000427301100002

    Research output: Contribution to journalArticle

  2. Anatomical recovery of the GABAergic system after a complete spinal cord injury in lampreys

    Lampreys recover locomotion spontaneously several weeks after a complete spinal cord injury. Dysfunction of the GABAergic system following SCI has been reported in mammalian models. So, it is of great interest to understand how the GABAergic system of lampreys adapts to the post-injury situation and how this relates to spontaneous recovery. The spinal cord of lampreys contains 3 populations of GABAergic neurons and most of the GABAergic innervation of the spinal cord comes from these local cells. GABAB receptors are expressed in the spinal cord of lampreys and they play important roles in the control of locomotion. The aims of the present study were to quantify: 1) the changes in the number of GABAergic neurons and innervation of the spinal cord and 2) the changes in the expression of the gabab receptor subunits b1 and b2 in the spinal cord of the sea lamprey after SCI. We performed complete spinal cord transections at the level of the fifth gill of mature larval lampreys and GABA immunohistochemistry or gabab in situ hybridization experiments. Animals were analysed up to 10 weeks post lesion (wpl), when behavioural analyses showed that they recovered normal appearing locomotion (stage 6 in the Ayer's scale of locomotor recovery). We observed a significant decrease in the number of GABA-ir cells and fibres 1 h after lesion both rostral and caudal to the lesion site. GABA-ir cell numbers and innervation were recovered to control levels 1 to 2 wpl. At 1, 4 and 10 wpl the expression of gabab1 and gabab2 transcripts was significantly decreased in the spinal cord compared to control un-lesioned animals. This is the first study reporting the quantitative long-term changes in the number of GABAergic cells and fibres and in the expression of gabab receptors in the spinal cord of any vertebrate following a traumatic SCI. Our results show that in lampreys there is a full recovery of the GABAergic neurons and a decrease in the expression of gabab receptors when functional recovery is achieved. (C) 2018 Elsevier Ltd. All rights reserved.

    General information

    StatePublished
    Ministry of Education publication typeA1 Journal article-refereed
    OrganisationsUniversity of Santiago de Compostela
    ContributorsRomaus-Sanjurjo, D., Valle-Maroto, S. M., Barreiro-Iglesias, A., Fernandez-Lopez, B., Rodicio, M. C.
    Number of pages14
    Pages389-402
    Publication date15 Mar 2018
    Peer-reviewedYes

    Publication information

    JournalNeuropharmacology
    Volume131
    ISSN (Print)0028-3908
    Original languageEnglish
    Fields of ScienceGABA, GABAB, Complete spinal cord injury, Cerebrospinal fluid contacting-cell, Sea lamprey, Spinal cord plasticity, GAMMA-AMINOBUTYRIC-ACID, LARVAL SEA LAMPREY, PROMOTES AXON REGENERATION, GABA-IMMUNOREACTIVE CELLS, DORSAL-HORN, BRAIN-STEM, NEUROPATHIC PAIN, NEUROTRANSMITTER COLOCALIZATION, PRESYNAPTIC INHIBITION, PATTERN GENERATORS, 3112 Neurosciences
    DOIs
    SourceWOS
    Source-ID000427316000034

    Research output: Contribution to journalArticle

  3. An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations

    Protein-protein interactions govern almost all cellular functions. These complex networks of stable and transient associations can be mapped by affinity purification mass spectrometry (AP-MS) and complementary proximity-based labeling methods such as BioID. To exploit the advantages of both strategies, we here design and optimize an integrated approach combining AP-MS and BioID in a single construct, which we term MAC-tag. We systematically apply the MAC-tag approach to 18 subcellular and 3 sub-organelle localization markers, generating a molecular context database, which can be used to define a protein's molecular location. In addition, we show that combining the AP-MS and BioID results makes it possible to obtain interaction distances within a protein complex. Taken together, our integrated strategy enables the comprehensive mapping of the physical and functional interactions of proteins, defining their molecular context and improving our understanding of the cellular interactome.

    General information

    StatePublished
    Ministry of Education publication typeA1 Journal article-refereed
    OrganisationsInstitute of Biotechnology, Helsinki Institute of Life Science HiLIFE
    ContributorsLiu, X., Salokas, K., Tamene, F., Jiu, Y., Weldatsadik, R. G., öhman, T., Varjosalo, M.
    Number of pages16
    Publication date22 Mar 2018
    Peer-reviewedYes

    Publication information

    JournalNature Communications
    Volume9
    Article number in E-publication (not DOI)1188
    ISSN (Print)2041-1723
    Original languageEnglish
    Fields of ScienceRNA-POLYMERASE-II, MASS SPECTROMETRY DATA, AFFINITY-PURIFICATION, CROSS-LINKING, SUBSTRATE-SPECIFICITY, RECOMBINANT PROTEINS, INTERACTION NETWORKS, BIOTIN LIGASE, KINASE, TFIIH, 1182 Biochemistry, cell and molecular biology
    Electronic versions
    DOIs
    SourceWOS
    Source-ID000428039500006

    Research output: Contribution to journalArticle

  4. Absence Seizures as a Feature of Juvenile Myoclonic Epilepsy in Rhodesian Ridgeback Dogs

    Myoclonic epilepsy in Rhodesian Ridgeback (RR) dogs is characterized by myoclonic seizures occurring mainly during relaxation periods, a juvenile age of onset and generalized tonic-clonic seizures in one-third of patients. An 8-month-old female intact RR was presented for myoclonic seizures and staring episodes that both started at 10 weeks of age. Testing for the DIRAS1 variant indicated a homozygous mutant genotype. Unsedated wireless video-electroencephalography (EEG) identified frequent, bilaterally synchronous, generalized 4 Hz spike-and-wave complexes (SWC) during the staring episodes in addition to the characteristic myoclonic seizures with generalized 4-5 Hz SWC or 4-5 Hz slowing. Photic stimulation did not evoke a photoparoxysmal response. Repeat video-EEG 2 months after initiation of levetiracetam treatment disclosed a >95% decrease in frequency of myoclonic seizures, and absence seizures were no longer evident. Absence seizures represent another seizure type in juvenile myoclonic epilepsy (JME) in RR dogs, which reinforces its parallels to JME in humans.

    General information

    StatePublished
    Ministry of Education publication typeA1 Journal article-refereed
    OrganisationsMedicum, Research Programme for Molecular Neurology, Hannes Tapani Lohi / Principal Investigator, Veterinary Genetics, Veterinary Biosciences, Research Programmes Unit, University of Munich, University of Guelph, University of Toronto, Paracelsus Medical University Salzburg, University of Veterinary Medicine Hannover, Folkhälsan Research Centre
    ContributorsWielaender, F., James, F. M. K., Cortez, M. A., Kluger, G., Nessler, J. N., Tipold, A., Lohi, H., Fischer, A.
    Number of pages5
    Pages428-432
    Publication date2018
    Peer-reviewedYes

    Publication information

    JournalJournal of Veterinary Internal Medicine
    Volume32
    Issue number1
    ISSN (Print)1939-1676
    Original languageEnglish
    Fields of ScienceCanine, DIRAS1, Electroencephalography (EEG), Wireless video-EEG, IDIOPATHIC GENERALIZED EPILEPSY, OPERATIONAL CLASSIFICATION, LONG-TERM, ELECTROENCEPHALOGRAPHY, PHOTOSENSITIVITY, PATHOPHYSIOLOGY, LEVETIRACETAM, MANAGEMENT, DISORDER, EEG, 413 Veterinary science
    DOIs
    URLs
    SourceWOS
    Source-ID000425814500052

    Research output: Contribution to journalArticle

  5. Explanation

    An explanation is an answer to an explanation‐seeking why or how question. Explanation is interest‐relative in the sense that which why questions are asked depends on the interests and background knowledge of the audience, but what is the right answer to the posed question is an objective matter. Explanation provides information of relations of dependence. Typically, this dependence is causal, but there are also constitutive explanations. Intentional and functional explanations are subspecies of causal explanation.

    General information

    StatePublished
    Ministry of Education publication typeB2 Book chapter
    OrganisationsFaculty Common Matters, Sociology
    ContributorsYlikoski, P. K.
    Publication date4 Dec 2017

    Host publication information

    Title of host publicationThe Wiley‐Blackwell Encyclopedia of Social Theory
    PublisherWiley Blackwell
    EditorTurner, B. S.
    ISBN (Print)9781118430866
    ISBN (Electronic)9781118430873
    Fields of Science611 Philosophy
    DOIs

    Research output: Chapter in Book/Report/Conference proceedingChapter

  6. Viperin Restricts Zika Virus and Tick-Borne Encephalitis Virus Replication by Targeting NS3 for Proteasomal Degradation

    Flaviviruses are arthropod-borne viruses that constitute a major global health problem, with millions of human infections annually. Their pathogenesis ranges from mild illness to severe manifestations such as hemorrhagic fever and fatal encephalitis. Type I interferons (IFNs) are induced in response to viral infection and stimulate the expression of interferon-stimulated genes (ISGs), including that encoding viperin (virus-inhibitory protein, endoplasmic reticulum associated, IFN inducible), which shows antiviral activity against a broad spectrum of viruses, including several flaviviruses. Here we describe a novel antiviral mechanism employed by viperin against two prominent flaviviruses, tick-borne encephalitis virus (TBEV) and Zika virus (ZIKV). Viperin was found to interact and colocalize with the structural proteins premembrane (prM) and envelope (E) of TBEV, as well as with nonstructural (NS) proteins NS2A, NS2B, and NS3. Interestingly, viperin expression reduced the NS3 protein level, and the stability of the other interacting viral proteins, but only in the presence of NS3. We also found that although viperin interacted with NS3 of mosquito-borne flaviviruses (ZIKV, Japanese encephalitis virus, and yellow fever virus), only ZIKV was sensitive to the antiviral effect of viperin. This sensitivity correlated with viperin's ability to induce proteasome-dependent degradation of NS3. ZIKV and TBEV replication was rescued completely when NS3 was overexpressed, suggesting that the viral NS3 is the specific target of viperin. In summary, we present here a novel antiviral mechanism of viperin that is selective for specific viruses in the genus Flavivirus, affording the possible availability of new drug targets that can be used for therapeutic intervention.

    IMPORTANCE Flaviviruses are a group of enveloped RNA viruses that cause severe diseases in humans and animals worldwide, but no antiviral treatment is yet available. Viperin, a host protein produced in response to infection, effectively restricts the replication of several flaviviruses, but the exact molecular mechanisms have not been elucidated. Here we have identified a novel mechanism employed by viperin to inhibit the replication of two flaviviruses: tick-borne encephalitis virus (TBEV) and Zika virus (ZIKV). Viperin induced selective degradation via the proteasome of TBEV and ZIKV non-structural 3 (NS3) protein, which is involved in several steps of the viral life cycle. Furthermore, viperin also reduced the stability of several other viral proteins in a NS3-dependent manner, suggesting a central role of NS3 in viperin's antiflavivirus activity. Taking the results together, our work shows important similarities and differences among the members of the genus Flavivirus and could lead to the possibility of therapeutic intervention.

    General information

    StatePublished
    Ministry of Education publication typeA1 Journal article-refereed
    OrganisationsUmeå University
    ContributorsPanayiotou, C., Lindqvist, R., Kurhade, C., Vonderstein, K., Pasto, J., Edlund, K., Upadhyay, A. S., Overby, A. K.
    Number of pages13
    Publication dateApr 2018
    Peer-reviewedYes

    Publication information

    JournalJournal of Virology
    Volume92
    Issue number7
    Article number in E-publication (not DOI)ARTN e02054-17
    ISSN (Print)0022-538X
    Original languageEnglish
    Fields of ScienceISG, viperin, NS3, flavivirus, proteasomal degradation, interferons, HEPATITIS-C VIRUS, INTERFERON-STIMULATED GENES, WEST NILE VIRUS, PROTEIN VIPERIN, PATHOGENESIS, IDENTIFICATION, INFECTION, INHIBIT, RNA, COMPLEX, 3111 Biomedicine, 1183 Plant biology, microbiology, virology
    DOIs
    SourceWOS
    Source-ID000428409800027

    Research output: Contribution to journalArticle

  7. Social Simulation

    Simulation is a particular type of modeling. In simulation the behavior of one system is studied to make inferences about the behavior of another system. Computer simulations can be classified as equation‐based and agent‐based simulations. In agent‐based simulations macro‐dynamics are emergent products of local individual interactions. Agent‐based simulations are very flexible with respect to the characteristics of the agents. Instead of assuming the hyper‐rational and all‐knowing agents of economic theory, the modeler can decide the cognitive architecture of the agents. The agents in agent‐based simulations are autonomous, interdependent, and heterogeneous, which makes it possible to model how macro social patterns are created and maintained as the intended and unintended outcomes of individual actions.

    General information

    StatePublished
    Ministry of Education publication typeB2 Book chapter
    OrganisationsFaculty Common Matters, Sociology
    ContributorsYlikoski, P. K.
    Publication date4 Dec 2017

    Host publication information

    Title of host publicationThe Wiley‐Blackwell Encyclopedia of Social Theory
    PublisherWiley Blackwell
    EditorTurner, B. S.
    ISBN (Print)9781118430866
    ISBN (Electronic)9781118430873
    Fields of Science611 Philosophy, 5141 Sociology
    DOIs

    Research output: Chapter in Book/Report/Conference proceedingChapter

  8. Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce

    Seasonal cues influence several aspects of the secondary growth of tree stems, including cambial activity, wood chemistry, and transition to latewood formation. We investigated seasonal changes in cambial activity, secondary cell wall formation, and tracheid cell death in woody tissues of Norway spruce (Picea abies) throughout one seasonal cycle. RNA sequencing was performed simultaneously in both the xylem and cambium/phloem tissues of the stem. Principal component analysis revealed gradual shifts in the transcriptomes that followed a chronological order throughout the season. A notable remodeling of the transcriptome was observed in the winter, with many genes having maximal expression during the coldest months of the year. A highly coexpressed set of monolignol biosynthesis genes showed high expression during the period of secondary cell wall formation as well as a second peak in midwinter. This midwinter peak in expression did not trigger lignin deposition, as determined by pyrolysis-gas chromatography/mass spectrometry. Coexpression consensus network analyses suggested the involvement of transcription factors belonging to the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES and MYELOBLASTOSIS-HOMEOBOX families in the seasonal control of secondary cell wall formation of tracheids. Interestingly, the lifetime of the latewood tracheids stretched beyond the winter dormancy period, correlating with a lack of cell death-related gene expression. Our transcriptomic analyses combined with phylogenetic and microscopic analyses also identified the cellulose and lignin biosynthetic genes and putative regulators for latewood formation and tracheid cell death in Norway spruce, providing a toolbox for further physiological and functional assays of these important phase transitions.

    General information

    StatePublished
    Ministry of Education publication typeA1 Journal article-refereed
    OrganisationsUmeå University, Sveriges lantbruksuniversitet
    ContributorsJokipii-Lukkari, S., Delhomme, N., Schiffthaler, B., Mannapperuma, C., Prestele, J., Nilsson, O., Street, N. R., Tuominen, H.
    Number of pages20
    Pages2851-2870
    Publication dateApr 2018
    Peer-reviewedYes

    Publication information

    JournalPlant Physiology
    Volume176
    Issue number4
    ISSN (Print)0032-0889
    Original languageEnglish
    Fields of SciencePROGRAMMED CELL-DEATH, PINUS-TAEDA L., GENE REGULATORY NETWORKS, LOBLOLLY-PINE, ARABIDOPSIS-THALIANA, LIGNIN BIOSYNTHESIS, CYSTEINE PROTEASES, VASCULAR DEVELOPMENT, XYLEM DEVELOPMENT, WALL FORMATION, 1183 Plant biology, microbiology, virology
    DOIs
    SourceWOS
    Source-ID000429089100021

    Research output: Contribution to journalArticle

  9. Majorana neutrinos in the seesaw mechanism and Bogoliubov quasiparticles

    General information

    StatePublished
    Ministry of Education publication typeA1 Journal article-refereed
    OrganisationsDepartment of Physics
    ContributorsFujikawa, K., Tureanu, A.
    Publication date28 Mar 2018
    Peer-reviewedYes

    Publication information

    JournalPhysical Review D
    Volume97
    Issue number5
    ISSN (Print)2470-0010
    Original languageEnglish
    Fields of Science114 Physical sciences
    Electronic versions
    DOIs
    SourceRIS
    Source-IDurn:FB37F2C33F5DEB5609135643906002EE

    Research output: Contribution to journalArticle

  10. Ejaculated boar spermatozoa displaying a rare multivesicular defect

    Two cases of a previously unreported sperm defect appearing in boar studs in Finland are presented. Spermatozoa showed small particles scattered on their surface with a prevalence decreasing with boar age. Semen samples, either stained with eosin-nigrosin or examined with phase contrast optics on formaldehyde-fixed spermatozoa, revealed the presence of multiple particles attached to the surface of spermatozoa counted as dead cells at fixation. Transmission electron microscopy revealed these were multivesicular and multilamellar vesicles, built up by phospholipid membranes. The case is classified as a post-epididymal multivesicular sperm defect with a favorable prognosis.

    General information

    StatePublished
    Ministry of Education publication typeA1 Journal article-refereed
    OrganisationsDepartments, Production animal medicine, Faculty of Veterinary Medicine, Production Animal Medicine , University of Pannonia, Linköping University
    ContributorsNagy, S., Tamminen, T., Andersson, M., Rodriguez-Martinez, H.
    Number of pages4
    Publication date27 Mar 2018
    Peer-reviewedYes

    Publication information

    JournalActa Veterinaria Scandinavica
    Volume60
    Article number in E-publication (not DOI)21
    ISSN (Print)0044-605X
    Original languageEnglish
    Fields of ScienceCLSM, Exosomes, Pig, Semen morphology, TEM, ACROSOME REACTION, PROSTASOMES, GRANULES, 413 Veterinary science
    DOIs
    URLs
    SourceWOS
    Source-ID000428941800001

    Research output: Contribution to journalArticle

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