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Alternative Splicing and Transcriptome Profiling of Experimental Autoimmune Encephalomyelitis Using Genome-Wide Exon Arrays
Alan Gillett,Klio Maratou,Chris Fewings,Robert A. Harris,Maja Jagodic,Tim Aitman,Tomas Olsson
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0007773
Abstract: Multiple Sclerosis (MS) is a chronic inflammatory disease causing demyelination and nerve loss in the central nervous system. Experimental autoimmune encephalomyelitis (EAE) is an animal model of MS that is widely used to investigate complex pathogenic mechanisms. Transcriptional control through isoform selection and mRNA levels determines pathway activation and ultimately susceptibility to disease.
Cytokine responses during chronic denervation
Saku Ruohonen, Mohsen Khademi, Maja Jagodic, Hanna-Stiina Taskinen, Tomas Olsson, Matias R?ytt?
Journal of Neuroinflammation , 2005, DOI: 10.1186/1742-2094-2-26
Abstract: Transected rat sciatic nerve was sutured and ligated to prevent reinnervation. The samples were collected from the left sciatic nerve distally and proximally from the point of transection. The endoneurium was separated from the surrounding epi- and perineurium to examine the expression of cytokines in both of these compartments. Macrophage invasion into endoneurium was investigated and Schwann cell proliferation was followed as well as the expression of cytokines IL-1β, IL-10, IFN-γ and TNF-α mRNA. The samples were collected from 1 day up to 5 weeks after the primary operation.At days 1 to 3 after injury in the epi-/perineurium of the proximal and distal stump, a marked expression of the pro-inflammatory cytokines TNF-α and IL-1β and of the anti-inflammatory cytokine IL-10 was observed. Concurrently, numerous macrophages started to gather into the epineurium of both proximal and distal stumps. At day 7 the number of macrophages decreased in the perineurium and increased markedly in the endoneurium of both stumps. At this time point marked expression of TNF-α and IFN-γ mRNA was observed in the endo- and epi-/perineurium of the proximal stump. At day 14 a marked increase in the expression of IL-1β could be noted in the proximal stump epi-/perineurium and in the distal stump endoneurium. At that time point many macrophages were observed in the longitudinally sectioned epineurium of the proximal 2 area as well as in the cross-section slides from the distal stump. At day 35 TNF-α, IL-1β and IL-10 mRNA appeared abundantly in the proximal epi-/perineurium together with macrophages.The present studies show that even during chronic denervation there is a cyclic expression pattern for the studied cytokines. Contrary to the previous findings on reinnervating nerves the studied cytokines show increased expression up to 35 days. The high expressions of pro-inflammatory and anti-inflammatory cytokines in the proximal epi-/perineurial area at day 35 may be involved in the formatio
A Silent Exonic SNP in Kdm3a Affects Nucleic Acids Structure but Does Not Regulate Experimental Autoimmune Encephalomyelitis
Alan Gillett, Petra Bergman, Roham Parsa, Andreas Bremges, Robert Giegerich, Maja Jagodic
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0081912
Abstract: Defining genetic variants that predispose for diseases is an important initiative that can improve biological understanding and focus therapeutic development. Genetic mapping in humans and animal models has defined genomic regions controlling a variety of phenotypes known as quantitative trait loci (QTL). Causative disease determinants, including single nucleotide polymorphisms (SNPs), lie within these regions and can often be identified through effects on gene expression. We previously identified a QTL on rat chromosome 4 regulating macrophage phenotypes and immune-mediated diseases including experimental autoimmune encephalomyelitis (EAE). Gene analysis and a literature search identified lysine-specific demethylase 3A (Kdm3a) as a potential regulator of these phenotypes. Genomic sequencing determined only two synonymous SNPs in Kdm3a. The silent synonymous SNP in exon 15 of Kdm3a caused problems with quantitative PCR detection in the susceptible strain through reduced amplification efficiency due to altered secondary cDNA structure. Shape Probability Shift analysis predicted that the SNP often affects RNA folding; thus, it may impact protein translation. Despite these differences in rats, genetic knockout of Kdm3a in mice resulted in no dramatic effect on immune system development and activation or EAE susceptibility and severity. These results provide support for tools that analyze causative SNPs that impact nucleic acid structures.
Devan Jagodic
Eesti ja soome-ugri keeleteaduse ajakiri , 2011,
Abstract: The paper focuses on the processes of language maintenance and shift among the Slovenian community in north-eastern Italy, from both the present and future perspectives, and presents the results of two empirical studies. The first offers a quantitative analysis of the linguistic behaviour of the Slovenian community members,in order to provide information about the level of minority language maintenance or the gradual shift towards Italian. The intergenerational comparison brings into focus some divergences among two different age groups and indicates the variables that cooperate to establish them. The second study explores the challenges that the Slovenian community must face in order to encourage the use of the minority language among non-Slovenian speakers. Relying on qualitative data obtained by a series of in-depth interviews with representatives of Slovenian political, cultural and economic organizations in Italy, the study aims to identify some possible strategies for the spread and promotion of the Slovenian language among the wider society.
Expression of Ccl11 Associates with Immune Response Modulation and Protection against Neuroinflammation in Rats
Milena Z. Adzemovic, Johan ?ckinger, Manuel Zeitelhofer, Sonja Hochmeister, Amennai Daniel Beyeen, Atul Paulson, Alan Gillett, Melanie Thessen Hedreul, Ruxandra Covacu, Hans Lassmann, Tomas Olsson, Maja Jagodic
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0039794
Abstract: Multiple sclerosis (MS) is a polygenic disease characterized by inflammation and demyelination in the central nervous system (CNS), which can be modeled in experimental autoimmune encephalomyelitis (EAE). The Eae18b locus on rat chromosome 10 has previously been linked to regulation of beta-chemokine expression and severity of EAE. Moreover, the homologous chemokine cluster in humans showed evidence of association with susceptibility to MS. We here established a congenic rat strain with Eae18b locus containing a chemokine cluster (Ccl2, Ccl7, Ccl11, Ccl12 and Ccl1) from the EAE- resistant PVG rat strain on the susceptible DA background and utilized myelin oligodendrocyte glycoprotein (MOG)-induced EAE to characterize the mechanisms underlying the genetic regulation. Congenic rats developed a milder disease compared to the susceptible DA strain, and this was reflected in decreased demyelination and in reduced recruitment of inflammatory cells to the brain. The congenic strain also showed significantly increased Ccl11 mRNA expression in draining lymph nodes and spinal cord after EAE induction. In the lymph nodes, macrophages were the main producers of CCL11, whereas macrophages and lymphocytes expressed the main CCL11 receptor, namely CCR3. Accordingly, the congenic strain also showed significantly increased Ccr3 mRNA expression in lymph nodes. In the CNS, the main producers of CCL11 were neurons, whereas CCR3 was detected on neurons and CSF producing ependymal cells. This corresponded to increased levels of CCL11 protein in the cerebrospinal fluid of the congenic rats. Increased intrathecal production of CCL11 in congenic rats was accompanied by a tighter blood brain barrier, reflected by more occludin+ blood vessels. In addition, the congenic strain showed a reduced antigen specific response and a predominant anti-inflammatory Th2 phenotype. These results indicate novel mechanisms in the genetic regulation of neuroinflammation.
Fine-Mapping Resolves Eae23 into Two QTLs and Implicates ZEB1 as a Candidate Gene Regulating Experimental Neuroinflammation in Rat
Pernilla Stridh,Melanie Thessen Hedreul,Amennai Daniel Beyeen,Milena Z. Adzemovic,Hannes Laaksonen,Alan Gillett,Johan ?ckinger,Monica Marta,Hans Lassmann,Kristina Becanovic,Maja Jagodic,Tomas Olsson
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0012716
Abstract: To elucidate mechanisms involved in multiple sclerosis (MS), we studied genetic regulation of experimental autoimmune encephalomyelitis (EAE) in rats, assuming a conservation of pathogenic pathways. In this study, we focused on Eae23, originally identified to regulate EAE in a (LEW.1AV1xPVG.1AV1)F2 cross. Our aim was to determine whether one or more genes within the 67 Mb region regulate EAE and to define candidate risk genes.
Parent-of-Origin Effects Implicate Epigenetic Regulation of Experimental Autoimmune Encephalomyelitis and Identify Imprinted Dlk1 as a Novel Risk Gene
Pernilla Stridh equal contributor,Sabrina Ruhrmann equal contributor,Petra Bergman,Mélanie Thessén Hedreul,Sevasti Flytzani,Amennai Daniel Beyeen,Alan Gillett,Nina Krivosija,Johan ?ckinger,Anne C. Ferguson-Smith,Maja Jagodic
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004265
Abstract: Parent-of-origin effects comprise a range of genetic and epigenetic mechanisms of inheritance. Recently, detection of such effects implicated epigenetic mechanisms in the etiology of multiple sclerosis (MS), a chronic inflammatory disease of the central nervous system. We here sought to dissect the magnitude and the type of parent-of-origin effects in the pathogenesis of experimental neuroinflammation under controlled environmental conditions. We investigated inheritance of an MS-like disease in rat, experimental autoimmune encephalomyelitis (EAE), using a backcross strategy designed to identify the parental origin of disease-predisposing alleles. A striking 37–54% of all detected disease-predisposing loci depended on parental transmission. Additionally, the Y chromosome from the susceptible strain contributed to disease susceptibility. Accounting for parent-of-origin enabled more powerful and precise identification of novel risk factors and increased the disease variance explained by the identified factors by 2-4-fold. The majority of loci displayed an imprinting–like pattern whereby a gene expressed only from the maternal or paternal copy exerts an effect. In particular, a locus on chromosome 6 comprises a well-known cluster of imprinted genes including the paternally expressed Dlk1, an atypical Notch ligand. Disease-predisposing alleles at the locus conferred lower Dlk1 expression in rats and, together with data from transgenic overexpressing Dlk1 mice, demonstrate that reduced Dlk1 drives more severe disease and modulates adaptive immune reactions in EAE. Our findings suggest a significant epigenetic contribution to the etiology of EAE. Incorporating these effects enables more powerful and precise identification of novel risk factors with diagnostic and prognostic implications for complex disease.
Monuments and Counter-Monument Sights in Post-Conflict Bosnia and Herzegovina: A Case Study of Gavrilo Princip’s Monuments  [PDF]
Maja Slijepcevic
Sociology Mind (SM) , 2016, DOI: 10.4236/sm.2016.63010
Abstract: The ever-present need of remembering and reimagining the memory through the culture of building memorial sights, as markers of identity, at the places of extreme violence in the immediate aftermaths of the conflict deescalation was a light motive for writing this paper. By allocating the empirical research on the ground of Bosnia and Herzegovina, there is a great opportunity to re-examine the dense perplexity of issues that are enhancing the momentum of the memory juxtaposed with the counter-memory, whereas different interest groups (political or civil) are simultaneously producing competing memories. The case study of BiH allows us to notice and highlight the multidimensionality of memory and counter-memoryalong the way of Bosnian postwar society towards the reconciliation, how it enables the identity building and the nation re-building during the processes of political consolidation and its didactic use for further conflict prevention. Using the discourses, visual materials and interviews from the field research adjusted on the post-conflict memory sites in Federation of Bosnia and Herzegovina vs Republika Srpska(case study monuments of Gavrilo Principe in Sarajevo vs East Sarajevo), I would like to pinpoint the chasm between the actual purpose of memory sites that are built there after the conflict and the danger of them miscommunicating the conflict inflicted past that could possibly lead to a restoration of that latent conflict. Therefore, my research is concentrated on the coupled counter-memorial sites, which are of enormous importance for the process of reconciliation because of their role of keeping balance to the official narratives and memorials, despite of the fact that this role of them is usually neglected by scholars.
Natural Polymorphisms in Tap2 Influence Negative Selection and CD4∶CD8 Lineage Commitment in the Rat
Jonatan Tuncel ,Sabrina Haag,Anthony C. Y. Yau,Ulrika Norin,Amelie Baud,Erik L?nnblom,Klio Maratou,A. Jimmy Ytterberg,Diana Ekman,Soley Thordardottir,Martina Johannesson,Alan Gillett,EURATRANS Consortium,Pernilla Stridh,Maja Jagodic,Tomas Olsson,Alberto Fernández-Teruel,Roman A. Zubarev,Richard Mott,Timothy J. Aitman,Jonathan Flint,Rikard Holmdahl
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004151
Abstract: Genetic variation in the major histocompatibility complex (MHC) affects CD4:CD8 lineage commitment and MHC expression. However, the contribution of specific genes in this gene-dense region has not yet been resolved. Nor has it been established whether the same genes regulate MHC expression and T cell selection. Here, we assessed the impact of natural genetic variation on MHC expression and CD4:CD8 lineage commitment using two genetic models in the rat. First, we mapped Quantitative Trait Loci (QTLs) associated with variation in MHC class I and II protein expression and the CD4:CD8 T cell ratio in outbred Heterogeneous Stock rats. We identified 10 QTLs across the genome and found that QTLs for the individual traits colocalized within a region spanning the MHC. To identify the genes underlying these overlapping QTLs, we generated a large panel of MHC-recombinant congenic strains, and refined the QTLs to two adjacent intervals of ~0.25 Mb in the MHC-I and II regions, respectively. An interaction between these intervals affected MHC class I expression as well as negative selection and lineage commitment of CD8 single-positive (SP) thymocytes. We mapped this effect to the transporter associated with antigen processing 2 (Tap2) in the MHC-II region and the classical MHC class I gene(s) (RT1-A) in the MHC-I region. This interaction was revealed by a recombination between RT1-A and Tap2, which occurred in 0.2% of the rats. Variants of Tap2 have previously been shown to influence the antigenicity of MHC class I molecules by altering the MHC class I ligandome. Our results show that a restricted peptide repertoire on MHC class I molecules leads to reduced negative selection of CD8SP cells. To our knowledge, this is the first study showing how a recombination between natural alleles of genes in the MHC influences lineage commitment of T cells.
Temporal Processing of Vibratory Communication Signals at the Level of Ascending Interneurons in Nezara viridula (Hemiptera: Pentatomidae)
Maja Zorovi?
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0026843
Abstract: During mating, males and females of N. viridula (Heteroptera: Pentatomidae) produce sex- and species-specific calling and courtship substrate-borne vibratory signals, grouped into songs. Recognition and localization of these signals are fundamental for successful mating. The recognition is mainly based on the temporal pattern, i.e. the amplitude modulation, while the frequency spectrum of the signals usually only plays a minor role. We examined the temporal selectivity for vibratory signals in four types of ascending vibratory interneurons in N. viridula. Using intracellular recording and labelling technique, we analyzed the neurons' responses to 30 pulse duration/interval duration (PD/ID) combinations. Two response arrays were created for each neuron type, showing the intensity of the responses either as time-averaged spike counts or as peak instantaneous spike rates. The mean spike rate response arrays showed preference of the neurons for short PDs (below 600 ms) and no selectivity towards interval duration; while the peak spike rate response arrays exhibited either short PD/long ID selectivity or no selectivity at all. The long PD/short ID combinations elicited the weakest responses in all neurons tested. No response arrays showed the receiver preference for either constant period or duty cycle. The vibratory song pattern selectivity matched the PD of N. viridula male vibratory signals, thus pointing to temporal filtering for the conspecific vibratory signals already at level of the ascending interneurons. In some neurons the responses elicited by the vibratory stimuli were followed by distinct, regular oscillations of the membrane potential. The distance between the oscillation peaks matched the temporal structure of the male calling song, indicating a possible resonance based mechanism for signal recognition.
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