| 1. |
- McGinn, Steven, et al.
(author)
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New Technologies for DNA analysis-A review of the READNA Project.
- 2016
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In: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784.
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Research review (peer-reviewed)abstract
- The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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| 2. |
- Oskolkov, Nikolay, et al.
(author)
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High-throughput muscle fiber typing from RNA sequencing data
- 2022
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In: Skeletal Muscle. - : Springer Science and Business Media LLC. - 2044-5040. ; 12, s. 1-9
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Journal article (peer-reviewed)abstract
- Background: Skeletal muscle fiber type distribution has implications for human health, muscle function, and performance. This knowledge has been gathered using labor-intensive and costly methodology that limited these studies. Here, we present a method based on muscle tissue RNA sequencing data (totRNAseq) to estimate the distribution of skeletal muscle fiber types from frozen human samples, allowing for a larger number of individuals to be tested. Methods: By using single-nuclei RNA sequencing (snRNAseq) data as a reference, cluster expression signatures were produced by averaging gene expression of cluster gene markers and then applying these to totRNAseq data and inferring muscle fiber nuclei type via linear matrix decomposition. This estimate was then compared with fiber type distribution measured by ATPase staining or myosin heavy chain protein isoform distribution of 62 muscle samples in two independent cohorts (n = 39 and 22). Results: The correlation between the sequencing-based method and the other two were rATPas = 0.44 [0.13–0.67], [95% CI], and rmyosin = 0.83 [0.61–0.93], with p = 5.70 × 10–3 and 2.00 × 10–6, respectively. The deconvolution inference of fiber type composition was accurate even for very low totRNAseq sequencing depths, i.e., down to an average of ~ 10,000 paired-end reads. Conclusions: This new method (https://github.com/OlaHanssonLab/PredictFiberType) consequently allows for measurement of fiber type distribution of a larger number of samples using totRNAseq in a cost and labor-efficient way. It is now feasible to study the association between fiber type distribution and e.g. health outcomes in large well-powered studies.
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| 3. |
- Ekström, Curt, et al.
(author)
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Nuclear Spins of Neutron-deficient Promethium, Samarium, Europium and Gadolinium Isotopes
- 1972
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In: Physica scripta. T. - : IOP Publishing. - 0281-1847 .- 0031-8949 .- 1402-4896. ; 6:4, s. 181-190
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Journal article (peer-reviewed)abstract
- Spin-measurements have been performed on some neutron-deficient promethium, samarium, europium and gadolinium isotopes using conventional atomic-beam magnetic resonance techniques. The results are: 141Pm (20.9 min) I=5/2, 140Sm (14.8 min) I=0, 141Sm (11.3 min) I=1/2, 141mSm (22.9 min) I=11/2, 142Sm (72.5 min) I=0, 143Sm (8.8 min) I=3/2, 145Eu (5.93 d) I=5/2, 146Eu (4.65 d) I=4, 147Eu (22 d) I=5/2, 148Eu (54 d) I=5, 149Eu (93.1 d) I=5/2, 150Eu (12.6 h) I=0, 145Gd (22.9 min) I=1/2, 147Gd (38.5 h) I=7/2, 149Gd (9.4 d) I=7/2, 151Gd (120 d) I=7/2. The investigated nuclei appear close to the shell closure at neutron number N=82. A systematic review of the low-lying states of odd-even and doubly-odd nuclei in this region is presented.
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| 4. |
- Jónsdóttir, Kristín
(author)
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Studies of Unusual Seismicity and Long Period Events at the Glacier Overlain Katla Volcano, Iceland
- 2009
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Doctoral thesis (other academic/artistic)abstract
- Earthquake catalogues are usually dominated by diffusive behaviour consistent with the Omori law of aftershocks. This is investigated in terms of waiting times, i.e. the time between successive events in a time-sorted earthquake catalogue. The theoretical waiting time probability distribution for the Omori law is derived and shown to predict the numerically produced Omori aftershock sequence well. These results enhance our understanding of aftershock processes and demonstrate that previous waiting time interpretations were severely flawed.Iceland earthquake catalogues are studied in terms of waiting times. Omori aftershock sequences are shown to predict most datasets well but there are some significant exceptions. One of these is data from the glacier covered Katla volcano in South Iceland, with few aftershocks. This dataset can be further split into two geographical groups: Several hundred volcano-tectonic earthquakes occurring within the caldera, reaching depths down to 15 km, and thousands of emergent low frequency earthquakes with a poorly defined shallow source in Goðabunga, in the western part of Katla. These events are investigated further.The lp events at Goðabunga have been recorded for decades and show a clear seasonal and climate-related correlation where their number increases in the autumn as well as during warmer years. Many of them form groups with very with similar waveforms. New broad-band seismic data suggests that the lp events originate in a steep outlet glacier covering Katla. Here, ice movement leads to ice falls over the steep escarpment, and we now believe that the lp events are generated by large ice falls rather than being related to gas or magma movements within the volcano, and are not precursors to an eruption as previously suspected. This observation probably has major significance for hazard estimation at the many ice-covered volcanoes around the world.We report near-field (vlp) signals simultaneous with the largest lp events. Our data is partly consistent in character with surface deformation (displacement and tilt) due to the ice movements. However, in line with results from elsewhere, the magnitudes of the observed effects are large relative to those from mathematical modelling. Our analysis suggests that the signal is not an instrumental artefact. Possible explanations are discussed.
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| 5. |
- Petursdottir, Dagbjort H., et al.
(author)
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Early-Life Human Microbiota Associated With Childhood Allergy Promotes the T Helper 17 Axis in Mice
- 2017
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In: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 8
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Journal article (peer-reviewed)abstract
- The intestinal microbiota influences immune maturation during childhood, and is implicated in early-life allergy development. However, to directly study intestinal microbes and gut immune responses in infants is difficult. To investigate how different types of early-life gut microbiota affect immune development, we collected fecal samples from children with different allergic heredity (AH) and inoculated germ-free mice. Immune responses and microbiota composition were evaluated in the offspring of these mice. Microbial composition in the small intestine, the cecum and the colon were determined by 16S rRNA sequencing. The intestinal microbiota differed markedly between the groups of mice, but only exposure to microbiota associated with AH and known future allergy in children resulted in a T helper 17 (Th17)-signature, both systemically and in the gut mucosa in the mouse offspring. These Th17 responses could be signs of a particular microbiota and a shift in immune development, ultimately resulting in an increased risk of allergy.
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