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TIA1-muutosten vaikutus stressigranuloiden muodostumiseen
Get PDFWelander Distal Myopathy (WDM) is caused by the p.E384K mutation in the TIA1 gene. The mutation supposedly causes the disease by a gain-of-function mechanism related to the formation of stress granules (Hackman et al. 2013). Also environmental factors have been proposed to affect the development of the disease: an increased number of stress granules has been observed in cells treated with cold shock compared to cells kept in 37 °C (Hofmann et al. 2012).
When patients with WDM-like symptoms have been screened for changes in TIA1, an p.N357S-change has been found enriched in these patients. The p.N357S-change has earlier been reported as a polymorphism. The change in question is located in the same prion-like domain in exon 5, in which the p.E384K-mutation also lies. Therefore, the p.N357S-change could affect the predisposition to aggregation.
The pro gradu project is divided into two parts:
• The effect of the p.N357S polymorphism on stress granule formation in arsenite and possibly other stress treated cells
• The effect of cold shock on stress granule formation on wild type and p.E384K TIA1
The results indicate, that the p.N357S change in TIA1 causes a change in the translated protein’s behavior. Similarly to the p.E384K change, the p.N357S change also induces an increased amount of stress granules in arsenite treated cells. However, the results also show that the stress granules recover faster in fluorescence recovery after photobleaching (FRAP) studies p.N357S transfected cells as compared to TIA1 p.E384K and wild type transfected cells.
The cold shock experiment indicates that there is a difference in the stress granule formation between cells transfected with p.E384K and wild type TIA1. This supports previously published results of the effect of the p.E384K change on the stress response and stress granule formation, and also the use of cold shock as a stress inducing treatment.
Used methods: PCR, transformation, DNA-extraction, cell culture, transfection, induction of stress granule formation by arsenite treatment and cold shock. The cells are cultivated on well plates, imaged and the data is analyzed with an automatized high content image analysis method (the CellInsight-platform). p.N357S cells were also analyzed with FRAP.Welanders distala myopati (WDM) orsakas av mutationen p.E384K i genen TIA1. Mutationen antas vara sjukdomsalstrande på grund av en ökad produktion av protein, som relaterats till formationen av stressgranuler (Hackman et al. 2013). Även omgivningsfaktorer har föreslagits verka i sjukdomens utveckling: en ökad mängd stressgranuler har observerats i celler som behandlats med köldshock jämfört med celler som förvarats i 37°C (Hofmann et al. 2012).
I patienter med WDM-liknande symptom som undersökts för förändringar i TIA1 har en p.N357S-förändring noterats förrikad. Denna förändring har tidigare anmälts som en polymorfism. Förändringen i fråga ligger i samma prionliknande domän i exon 5 som WDM-orsakande förändringen p.E384K. Därmed kunde p.N357S-förändringen öka predispositionen till aggregering.
Pro gradu –arbetet är uppdelat i två delar:
• p.N357S-polymorfismens effekt på stressgranulsbildningen i arsenitbehandle celler
• Köldshockens effekt på stressgranulsbildningen
Resultaten påvisar, att förändringen p.N357S i TIA1 orsakar en förändring i det translaterade proteinets beteende. I likhet med p.E384K-förändringen orsakar även p.N357S en ökad mängd stressgranuler i arsenitbehandlade celler. Däremot tyder resultaten på att stressgranulerna återbildas snabbare i fluorescence recovery after photobleaching-studier (FRAP) I p.N357S-transfekterade celler än i celler som transfekterats med TIA1 p.E384K och vildtyp.
Köldshocksexperimenten tyder på att det finns en viss skillnad mellan bildningen av stressgranuler i celler transfekterade med p.E384K och vildtyps-TIA1. Detta stöder tidigare publicerade resultat om p.E384K-förändringens påverkan på stressresponsen och stressgranulsbildningen, och även köldshock som stressinducerande behandling.
Använda metoder: PCR, transformation, DNA-ekstraktion, cellkultur, transfektion, induktion av stressgranulsformation med arsenitbehandling och köldshock. Cellerna kultiveras på brunnsplattor, fotograferas och datat analyseras med en automatiserad High Content biildanalysmetod (CellInsight-platform). p.N357S-celler analyserades även med FRAP
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Copy number variants in genes causing neuromuscular disorders
No full textThe aim of this thesis project was to improve the methods of molecular genetic mutation analysis in neuromuscular disorders, mainly focusing on challenging repetitive intragenic regions and making these methods more accessible.
The large skeletal muscle genes nebulin and titin contain large repetitive, i.e., segmental duplication regions. These regions cause hurdles for standard copy number variation detection methods and are therefore often omitted from analysis. The segmental duplication region of nebulin has been previously shown to harbor pathogenic copy number variants; when the number of duplicated blocks deviates by two or more blocks per allele from the normal number, the alteration is considered a pathogenic recessive mutation.
We developed a custom comparative genomic hybridization array for the detection of copy number variants in neuromuscular disorder-causing genes. The array covers all 11 known nemaline myopathy genes and 176 additional known and potential neuromuscular disorder genes. The genes are divided by coverage into three groups, all of which allow copy number variant detection at the exon level. Using the array, we detected the largest nebulin deletion (loss of genetic material) hitherto in a patient presenting with an asymmetric distal myopathy. We were also able to determine that the deletion was present in the patient in a mosaic state, which may contribute to the asymmetric phenotype of the patient. The deletion is the first causative dominant de novo deletion described in nebulin.
We have previously used the comparative genomic hybridization array for routine screening of samples from patients in whom a copy number variant in the nebulin segmental duplication region is suspected to be a causative mutation. Moreover, the array detected previously unrecorded recurrent copy number variation in the segmental duplication region of titin. The array, however, is both relatively costly and laborious to run and yields far more data than necessary. In addition, the repetitive nature of the titin segmental duplication region does not allow for exact copy number determination by the comparative genomic hybridization array alone. We, therefore, set out to develop custom droplet digital PCR assays for routine screening of the nebulin segmental duplication region and assays to verify the copy number variation of the titin segmental duplication region.
Using the droplet digital PCR assays targeting the nebulin segmental duplication region, we were able to determine the copy number of the region adequately. The droplet digital PCR assays targeting the titin segmental duplication region confirmed that the region is subject to copy number variation, revealing a novel putative pathogenic or modifying mechanism in the gene.Målet med detta doktorsavhandlingsarbete var att förbättra de molekylärgenetiska metoderna för mutationsanalys vid neuromuskulära sjukdomar med speciellt fokus på repetitiva regioner inom gener, och att göra dessa metoder lättare tillgängliga.
De stora skelettmuskelgenerna nebulin och titin innehåller stora segmentella duplikationsregioner. Dessa regioner utmanar standardmetoderna inom analysen av förändringar i antalet segmentkopior, och lämnas därför ofta bort vid analyser. Den segmentala duplikationsregionen i nebulin har tidigare visats vara föremål för sjukdomsorsakande varianter i antalet segmentkopior; när antalet duplicerade block avviker med två eller fler stycken per allel från det normala antalet, anses förändringen vara en recessiv sjukdomsorsakande mutation.
Vi utvecklade en komparativ genomisk hybridisations-mikromatris för att påvisa förändringar i antalet kopior av gener för neuromuskulära sjukdomar. Mikromatrisen täcker alla 11 kända nemalinmyopatiorsakande gener, tillsammans med 176 andra kända eller möjliga gener för neuromuskulära sjukdomar, populärt kallade muskelsjukdomar. Generna är indelade i tre grupper på basis av täckning, varav alla möjliggör bestämning av förändringar i antalet kopior på exonnivå.
Med hjälp av mikromatrisen kunde vi hitta den största nebulindeletionen (det största bortfallet av genetiskt material) hittills i en patient med en asymmetrisk distal myopati. Vi kunde också se att deletionen var närvarande i mosaiktillstånd, vilket kan bidra till den asymmetriska muskelsvagheten hos patienten. Deletionen uppstod som en nymutation och är den första sjukdomsorsakande dominanta de novo deletion som beskrivits i nebulingenen.
Vi har tidigare använt mikromatrisen för rutinanalys av prover från patienter hos vilka en förändring i antalet nebulinsegmentkopior har misstänkts vara sjukdomsorsakande. Ytterligare upptäckte vi med hjälp av mikromatrisen tidigare okänd kopieantalsvariation i titinets segmentala duplikationsområdet. Mikromatrisen är dock både såväl förhållandevis dyrt som arbetsdrygt, och producerar mycket mer data än vad som är nödvändigt. Dessutom tillåter inte den repetitiva naturen av titinets segmentala duplikationsregion inte exakt bestämning av antalet kopior med hjälp av endast mikromatrisen. Därmed satsade vi på att utveckla målspecifika droplet-digital-PCR-primers och hydrolysprober för rutinsållning och kopieantalsbestämning av nebulinets segmentala duplikationsregion, och primers och hydrolysprober i ett försök att verifiera variationen i antalet segmentkopior i titinets segmentala duplikationsregion.
Droplet-digital-PCR primer-hydrolysprobparen för nebulinets segmentala duplikationsområde kunde adekvat bestämma antalet kopior i regionen. Droplet-digital-PCR-primer-hydrolysprobparen för titinets segmentala duplikationsområdet bekräftade förekomsten av förändringar i antalet kopior i området, och avslöjade därmed en möjlig ny sjukdomsorsakande eller modifierande mekanism hos genen.ei saavutettav
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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