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- Nyberg, Lena, 1979, et al.
(författare)
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A single-step competitive binding assay for mapping of single DNA molecules
- 2012
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Ingår i: Biochemical and Biophysical Research Communications - BBRC. - : Elsevier BV. - 0006-291X .- 1090-2104. ; 417:1, s. 404-408
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Tidskriftsartikel (refereegranskat)abstract
- Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification cif pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.
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- Wiklund-Hörnkvist, Carola, et al.
(författare)
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The neural mechanisms underlying test-enhanced learning: An event-related functional magnetic resonance imaging study
- 2012
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Ingår i: Earli-SIG 22: Neuroscience and Education" 24th-26th May 2012, Institute of Education, London. ; , s. 9-9
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Konferensbidrag (refereegranskat)abstract
- Considerable research in cognitive psychology has demonstrated that testing improves the performance on later retention tests, a phenomenon called the testing-effect. However, the neural mechanisms of test-enhanced learning are not well understood. The current study examined changes in functional brain networks in relation to repeated retrieval (i.e. test-enhanced learning).Participants (n=20) first studied 60 Swahili-Swedish word-pairs. Subsequently, they underwent functional magnetic resonance imaging while being tested on each study item three times.Successful repeated retrieval was characterized by decreased activity in prefrontal and premotor regions and in the right caudate, compared to items not successfully retrieved at consecutive tests. Successful repeated retrieval was also characterized by increased activity in right middle temporal cortex (BA 37 & 21).Tentatively, these results imply that the benefits of test-enhanced learning in part is due to decreased need for executive processing along with strengthening of semantic representations.The current results generate novel information on the effectiveness of testing as a learning method and thus contribute to bridge the current gap between cognitive neuroscience and educational research.
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- Wiklund-Hörnqvist, Carola, 1972-
(författare)
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Brain-based teaching : behavioral and neuro-cognitive evidence for the power of test-enhanced learning
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- A primary goal of education is the acquisition of durable knowledge which challenges the use of efficient pedagogical methods of how to best facilitate learning. Research in cognitive psychology has demonstrated that repeated testing during the learning phase improves performance on later retention tests compared to restudy of material. This empirical phenomenon is called the testing effect. The testing effect has shown to be robust across different kinds of material and when compared to different pedagogical methods. Despite the extensive number of published papers on the testing effect, the majority of the studies have been conducted in the laboratory. More specific, few studies have examined the testing effect in authentic settings when using course material during the progress of a course. Further, few studies have investigated the beneficial effects with test-enhanced learning by the use of neuroimaging methods (e.g. fMRI). The aim with the thesis was to investigate the effects of test-enhanced learning in an authentic educational context and how this is related to individual differences in working memory capacity (Study I and II) as well as changes in brain activity involved in successful repeated testing and long term retention (Study III).In study I, we examined whether repeated testing with feedback benefitted learning compared to rereading of introductory psychology key concepts in a sample of undergraduate students. The results revealed that repeated testing with feedback was superior compared to rereading both immediate after practice and at longer delays. The effect of repeated testing was beneficial for students irrespectively of WMC. In Study II, we investigated test-enhanced learning in relation to the encoding variability hypothesis for the learning of mathematics in a sample of fifth-grade children. Learning was examined in relation to both practiced and transfer tasks. No differences were found for the practiced tasks. Regarding the transfer tasks, the results gave support for the encoding variability hypothesis, but only at the immediate test. In contrast, when we followed up the durability of learning across time, the results showed that taking the same questions over and over again during the intervention resulted in better performance across time compared to variable encoding. Individual differences in WMC predicted performance on the transfer tasks, but only at the immediate test, regardless of group.Together, the results from Study I and Study II clearly indicate that testenhanced learning is effective in authentic settings, across age-groups and also produces transfer. Integrate current findings from cognitive science, in terms of test-enhanced learning, by the use of authentic materials and assessments relevant for educational goals can be rather easily done with vi computer based tasks. The observed influence of individual differences in WMC between the studies warrant further study of its specific contribution to be able to optimize the learning procedure.In Study III, we tested the complementary hypothesis regarding the mechanisms behind memory retrieval. Recurrent retrieval may be efficient because it induces representational consistency or, alternatively, because it induces representational variability - the altering or adding of underlying representations as a function of successful repeated retrieval. A cluster in right superior parietal cortex was identified as important for items successfully repeatedly retrieved Day 1, and also correctly remembered Day 7, compared to those successfully repeatedly retrieved Day 1 but forgotten Day 7. Representational similarity analysis in this region gave support for the theoretical explanations that emphasis semantic elaboration.
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- Zaghlool, Ammar, 1980-, et al.
(författare)
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Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues
- 2013
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Ingår i: BMC Biotechnology. - : Springer Science and Business Media LLC. - 1472-6750. ; 13, s. 99-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The starting material for RNA sequencing (RNA-seq) studies is usually total RNA or polyA+ RNA. Both forms of RNA represent heterogeneous pools of RNA molecules at different levels of maturation and processing. Such heterogeneity, in addition to the biases associated with polyA+ purification steps, may influence the analysis, sensitivity and the interpretation of RNA-seq data. We hypothesize that subcellular fractions of RNA may provide a more accurate picture of gene expression. Results: We present results for sequencing of cytoplasmic and nuclear RNA after cellular fractionation of tissue samples. In comparison with conventional polyA+ RNA, the cytoplasmic RNA contains a significantly higher fraction of exonic sequence, providing increased sensitivity in expression analysis and splice junction detection, and in improved de novo assembly of RNA-seq data. Conversely, the nuclear fraction shows an enrichment of unprocessed RNA compared with total RNA-seq, making it suitable for analysis of nascent transcripts and RNA processing dynamics. Conclusion: Our results show that cellular fractionation is a more rapid and cost effective approach than conventional polyA+ enrichment when studying mature RNAs. Thus, RNA-seq of separated cytosolic and nuclear RNA can significantly improve the analysis of complex transcriptomes from mammalian tissues.
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