Validation of miRNA genes suitable as Reference genes in qPCR analyses of miRNA gene expression in Atlantic salmon (Salmo salar)

Background MicroRNAs (miRNAs) are an abundant class of endogenous small RNA molecules that downregulate gene expression at the post-transcriptional level. They play important roles by regulating genes that control multiple biological processes, and recent years there has been an increased interest in studying miRNA genes and miRNA gene expression. The most common method applied to study gene expression of single genes is quantitative PCR (qPCR). However, before expression of mature miRNAs can be studied robust qPCR methods (miRNA-qPCR) must be developed. This includes identification and validation of suitable reference genes. We are particularly interested in Atlantic salmon (Salmo salar). This is an economically important aquaculture species, but no reference genes dedicated for use in miRNA-qPCR methods has been validated for this species. Our aim was, therefore, to identify suitable reference genes for miRNA-qPCR methods in Salmo salar. Results We used a systematic approach where we utilized similar studies in other species, some biological criteria, results from deep sequencing of small RNAs and, finally, experimental validation of candidate reference genes by qPCR to identify the most suitable reference genes. Ssa-miR-25-3p was identified as most suitable single reference gene. The best combinations of two reference genes were ssa-miR-25-3p and ssa-miR-455-5p. These two genes were constitutively and stably expressed across many different tissues. Furthermore, infectious salmon anaemia did not seem to affect their expression levels. These genes were amplified with high specificity, good efficiency and the qPCR assays showed a good linearity when applying a simple cybergreen miRNA-PCR method using miRNA gene specific forward primers. Conclusions We have identified suitable reference genes for miRNA-qPCR in Atlantic salmon. These results will greatly facilitate further studies on miRNA genes in this species. The reference genes identified are conserved genes that are identical in their mature sequence in many aquaculture species. Therefore, they may also be suitable as reference genes in other teleosts. Finally, the systematic approach used in our study successfully identified suitable reference genes, suggesting that this may be a useful strategy to apply in similar validation studies in other aquaculture species

Similar but not the same: Comparing Norwegian and Swedish teachers’ influence on textbook selection and involvement in text discussions

The present study compares Norwegian and Swedish teachers ? influence on textbook selection and the impact of this on teachers ? involvement in textbook discussions(discussions with colleagues and the principal). For this purpose we conducted a survey with Norwegian (n = 236) and Swedish (n = 340) teachers in grade 0 to 9(which compromises pupils at approximately ages 6 to 15). The core argument is thateven though Norway and Sweden have very similar welfare and education systems,they nevertheless differ in teachers ? influence on textbook selection and involvement in textbook discussions. Factor analysis was used to develop two new measures of teaching: influence on textbook selection and involvement in textbook discussions. First, the study shows there is a mean difference between the countries in both influence on textbook selection and involvement in textbook discussions indices. Second, OLS regression was used to demonstrate a curvilinear effect of age on influence on textbookselection in both countries. A curvilinear relationship was also found between teachingyears and the influence on textbook selection in both countriesEl presente estudio compara la influencia de profesores noruegos y suecos en laseleccio?n de libros dida?cticos y el impacto de este factor en la participacio?n de los docentes en los debates sobre los libros dida?cticos (debates con colegas y el Director). Para ello, realizamos una investigacio?n de maestros noruegos (n = 236) y suecos (n = 340), nivel K-9 de ensen?anza. El argumento central es que mientras Noruega y Sueciatienen sistemas sociales y educativos muy similares, difieren en la influencia de losmaestros en la seleccio?n de los libros dida?cticos y su participacio?n en las discusiones sobre los libros dida?cticos. El ana?lisis de factores fue utilizado para desarrollar dosnuevas medidas de ensen?anza: influencia en la seleccio?n de libros dida?cticos y laparticipacio?n en las discusiones sobre los libros dida?cticos. En primer lugar, el estudiomuestra que existe una diferencia relativa entre los pai?ses, en los i?ndices de influenciaen la seleccio?n de libros dida?cticos asi? como en la participacio?n en la discusio?n delos libros dida?cticos. En segundo lugar, la regresio?n a trave?s del me?todo mi?nimos cuadrados ordinarios (MQO) fue utilizada para demostrar un efecto curvili?neo de laedad en te?rminos de influencia en la seleccio?n de libros dida?cticos en ambos pai?ses. Tambie?n se encontro? una relacio?n curvili?nea con respecto a la influencia de los an?osde ensen?anza en la seleccio?n de libros dida?cticos en ambos pai?sesO presente estudo compara a influe?ncia dos professores noruegueses e suecos sobrea selec?a?o de livros dida?ticos e o impacto desse fator no envolvimento dos professores nas discusso?es sobre livros dida?ticos (discusso?es com colegas e o diretor). Para isto, realizamos uma pesquisa com professores noruegueses (n = 236) e suecos (n = 340), noni?vel K-9 do ensino. O argumento central e? que, embora a Noruega e a Sue?cia tenhamsistemas sociais e educacionais muito semelhantes, eles diferem quanto a? influe?nciados professores sobre a selec?a?o de livros dida?ticos e quanto ao seu envolvimento nas discusso?es sobre livros dida?ticos. A ana?lise de fatores foi utilizada para desenvolver duasnovas medidas de ensino: influe?ncia na selec?a?o de livros dida?ticos e envolvimento nas discusso?es sobre livros dida?ticos. Primeiro, o estudo mostra que ha? uma diferenc?a me?dia entre os pai?ses, tanto nos i?ndices de influe?ncia na selec?a?o de livros dida?ticos quanto nosde envolvimento em discussa?o sobre livros dida?ticos. Em segundo lugar, a regressa?opelo me?todo dos Mi?nimos Quadrados Ordina?rios (MQO) foi utilizada para demonstrar um efeito curvili?neo da idade no que se refere a? influe?ncia na selec?a?o de livros dida?ticos em ambos os pai?ses. Um relacionamento curvili?neo tambe?m foi encontrado quanto a? influe?ncia dos anos de ensino na selec?a?o de livros dida?ticos em ambos os pai?se

Targeted SNP discovery in Atlantic salmon (Salmo salar) genes using a 3'UTR-primed SNP detection approach

<p>Abstract</p> <p>Background</p> <p>Single nucleotide polymorphisms (SNPs) represent the most widespread type of DNA variation in vertebrates and may be used as genetic markers for a range of applications. This has led to an increased interest in identification of SNP markers in non-model species and farmed animals. The <it>in silico </it>SNP mining method used for discovery of most known SNPs in Atlantic salmon (<it>Salmo salar</it>) has applied a global (genome-wide) approach. In this study we present a targeted 3'UTR-primed SNP discovery strategy that utilizes sequence data from <it>Salmo salar </it>full length sequenced cDNAs (FLIcs). We compare the efficiency of this new strategy to the <it>in silico </it>SNP mining method when using both methods for targeted SNP discovery.</p> <p>Results</p> <p>The SNP discovery efficiency of the two methods was tested in a set of FLIc target genes. The 3'UTR-primed SNP discovery method detected novel SNPs in 35% of the target genes while the <it>in silico </it>SNP mining method detected novel SNPs in 15% of the target genes. Furthermore, the 3'UTR-primed SNP discovery strategy was the less labor intensive one and revealed a higher success rate than the <it>in silico </it>SNP mining method in the initial amplification step. When testing the methods we discovered 112 novel bi-allelic polymorphisms (type I markers) in 88 salmon genes [dbSNP: ss179319972-179320081, ss250608647-250608648], and three of the SNPs discovered were missense substitutions.</p> <p>Conclusions</p> <p>Full length insert cDNAs (FLIcs) are important genomic resources that have been developed in many farmed animals. The 3'UTR-primed SNP discovery strategy successfully utilized FLIc data to detect novel SNPs in the partially tetraploid Atlantic salmon. This strategy may therefore be useful for targeted SNP discovery in several species, and particularly useful in species that, like salmonids, have duplicated genomes.</p

Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar)

<p>Abstract</p> <p>Background</p> <p>Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs) are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP), the number of sequences where the full-length of the cDNA insert has been determined has been small.</p> <p>Results</p> <p>High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank: <ext-link ext-link-type="gen" ext-link-id="BT043497">BT043497</ext-link> - <ext-link ext-link-type="gen" ext-link-id="BT044056">BT044056</ext-link>]. Five hundred and ten (91%) of the transcripts were annotated using Gene Ontology (GO) terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS). The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. Finally, conserved 7-mers in the 3'UTRs were identified, of which some were identical to miRNA target sequences.</p> <p>Conclusion</p> <p>This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We have demonstrated that many FLIcs contained a complete coding sequence (cCDS). This suggests that the remaining cDNA libraries generated by SGP represent a valuable cCDS FLIc source. The conservation of 7-mers in 3'UTRs indicates that these motifs are functionally important. Identity between some of these 7-mers and miRNA target sequences suggests that they are miRNA targets in <it>Salmo salar </it>transcripts as well.</p

The invisible minority: why do textbook authors avoid people with disabilities in their books?

Representation of disability in school textbooks may influence pupils’ knowledge and perceptions of people with disabilities. The aim of this study was to investigate representation of people with disabilities in school textbooks. The study employed a mixed-methods approach. Quantitative frequency analysis was used to investigate the extent of representation of disabilities in texts and pictures in 78 Norwegian textbooks for Grades 5–10. Regarding texts, the results showed that people with disabilities were represented in less than half of these textbooks (49%). Concerning pictures, people with disabilities were even less represented, appearing in only 29% of the textbooks. These quantitative findings were supplemented by a qualitative survey of textbook authors, who were asked to explain the marked absence of disability references in their own books and in school textbooks in general. The two most frequent explanations were that textbook authors had either overlooked people with disabilities, or that the Norwegian National Curriculum (Kunnskapsdepartementet 2006. Lærerplanverket for Kunnskapsløftet (LK06) [The Norwegian National Curriculum]. https://www.udir.no/lk20/overordnet-del/) did not explicitly mention this minority. We discuss these explanations as expressions of conscious considerations rather than unconscious omissions.publishedVersio

Comparing Swedish and Norwegian teachers' professional development: How human capital and social capital factor into teachers' reading habits

The present study compares how Swedish (n = 340) and Norwegian (n = 236) teachers' human capital and social capital support reading habits as an aspect of professional development. The overall aim was to describe how teachers' human and social capital support their professional development as measured by the aspect of reading habits during leisure time. Our research questions were: To what extent do Swedish and Norwegian teachers differ in their reading habits during leisure time? To what extent do young and old Swedish and Norwegian teachers differ in their reading habits during leisure time? To what extent does Swedish and Norwegian teachers' social capital (collegial talk, principal talk) predict their reading habits during leisure time? To what extent does Swedish and Norwegian teachers' human capital (based on their age, education, and work years) predict their reading habits during leisure time? We compared teachers' reading habits between countries. Older teachers read, on average, more fiction, nonfiction, and newspapers. However, younger teachers in both countries are more prone to read digital texts than older teachers. By contrast, teachers' social capital only seemed to matter in Sweden, while talks with the principal had no effect in either country.publishedVersio

Studiestrategier hos første års bachelorstudenter med dysleksi

Nyere forskning viser til at flere studenter med diagnosen dysleksi tar fatt på høyere utdanning og at overgangen innebærer en rekke utfordringer. Gjennom denne undersøkelsen ønsker vi kunnskap om anvendelse og opplevd utbytte av kontekstuelle, selvregulerte studiestrategier til norske, første års høyskolestudenter med dysleksi. Vår teori tar utgangspunkt i teori om selvregulert læring. Vårt utvalg bestod av 17 førsteårsstudenter med dysleksi fra seks ulike studieprogram. Undersøkelsesmetoden var daglig loggføring av studiestrategier i form av nettbasert dagbok med lukkede spørsmål om strategibruk, gjennomført fortløpende i 12 dager. Deretter ble seks av studentene, tre med høy og tre med lav strategisk aktivitet, valgt ut til individuelle intervjuer for å utdype og begrunne sin strategibruk.Vår undersøkelse samsvarer med andre studier som viser at studenter med dysleksi er en heterogen gruppe som varierer både når det gjelder anvendelse og utbytte av selvregulerte studiestrategier. Studentene har en tendens til å bruke et fåtall studiestrategier som fungerer som nøkkelstrategier, og som de opplever å ha godt utbytte av. Begrenset repertoar av strategier tilsier at studenter med dysleksi kan tjene på å få opplæring i hensiktsmessige studiestrategier som kan kompensere for svake leseferdigheter. Så vidt vi vet er studenters bruk av selvregulerte studiestrategier knyttet til bestemte studiekontekster ikke tidligere studert i Norge. Daglig loggføring er også internasjonalt lite brukt for å måle strategibruk.publishedVersio

Expression Analysis of Moritella viscosa-Challenged Atlantic Salmon Identifies Disease-Responding Genes, MicroRNAs and Their Predicted Target Genes and Pathways

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A Longitudinal Mixed Methods Study of Norwegian Preservice Teachers’ Beliefs About Sources of Teaching Knowledge and Motivation to Learn From Theory and Practice

We set out to investigate preservice teachers’ beliefs about sources of teaching knowledge and their motivation to learn from practice and theory in teacher education in a longitudinal study (n = 96, at the beginning of the study). Participants placed more trust in experiential knowledge sources compared with formalized sources and participants’ beliefs about sources of teaching knowledge generally predicted their motivation to learn from different sources. Quantitative results were further supported and elaborated by qualitative interview data that suggested development of preservice teachers’ beliefs about sources of teaching knowledge and their understanding of the relation between theoretical and practical knowledge over time. The findings extend existing literature by providing a window on how (preservice) teachers may articulate their views about sources of teaching knowledge and relations between theory and practice, with expected consequences for teaching practice. Implications for teacher educators’ practice are also discussed.publishedVersio