| 1. |
- Meadows, J R S, et al.
(författare)
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Haplogroup relationships between domestic and wild sheep resolved using a mitogenome panel
- 2011
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 106:4, s. 700-706
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Tidskriftsartikel (refereegranskat)abstract
- Five haplogroups have been identified in domestic sheep through global surveys of mitochondrial (mt) sequence variation, however these group classifications are often based on small fragments of the complete mtDNA sequence; partial control region or the cytochrome B gene. This study presents the complete mitogenome from representatives of each haplogroup identified in domestic sheep, plus a sample of their wild relatives. Comparison of the sequence successfully resolved the relationships between each haplogroup and provided insight into the relationship with wild sheep. The five haplogroups were characterised as branching independently, a radiation that shared a common ancestor 920,000 ± 190,000 years ago based on protein coding sequence. The utility of various mtDNA components to inform the true relationship between sheep was also examined with Bayesian, maximum likelihood and partitioned Bremmer support analyses. The control region was found to be the mtDNA component, which contributed the highest amount of support to the tree generated using the complete data set. This study provides the nucleus of a mtDNA mitogenome panel, which can be used to assess additional mitogenomes and serve as a reference set to evaluate small fragments of the mtDNA.
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| 2. |
- Höppner, Marc P., et al.
(författare)
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An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:3, s. e91172-
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Tidskriftsartikel (refereegranskat)abstract
- The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now covers 99.8% of the euchromatic portion of the genome. We also present multiple RNA-Sequencing data sets from 10 different canine tissues to catalog similar to 175,000 expressed loci. While about 90% of the coding genes previously annotated by EnsEMBL have measurable expression in at least one sample, the number of transcript isoforms detected by our data expands the EnsEMBL annotations by a factor of four. Syntenic comparison with the human genome revealed an additional similar to 3,000 loci that are characterized as protein coding in human and were also expressed in the dog, suggesting that those were previously not annotated in the EnsEMBL canine gene set. In addition to,20,700 high-confidence protein coding loci, we found,4,600 antisense transcripts overlapping exons of protein coding genes, similar to 7,200 intergenic multi-exon transcripts without coding potential, likely candidates for long intergenic non-coding RNAs (lincRNAs) and,11,000 transcripts were reported by two different library construction methods but did not fit any of the above categories. Of the lincRNAs, about 6,000 have no annotated orthologs in human or mouse. Functional analysis of two novel transcripts with shRNA in a mouse kidney cell line altered cell morphology and motility. All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts.
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| 3. |
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| 4. |
- Ordovas, Karen G., et al.
(författare)
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Impaired regional left ventricular strain after repair of tetralogy of fallot
- 2012
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Ingår i: Journal of Magnetic Resonance Imaging. - : Wiley. - 1522-2586 .- 1053-1807. ; 35:1, s. 79-85
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: To test the potential of magnetic resonance imaging (MRI) in early detection of left ventricular (LV) dysfunction in patients with pulmonary regurgitation and normal LV ejection fraction after repair of tetralogy of Fallot. Materials and Methods: Patients (n = 18) with repaired tetralogy of Fallot and pulmonary regurgitation were prospectively recruited. Healthy volunteers (n = 10) were used as control. Tagging MR images were acquired at the base, mid, and apical LV levels for assessing segmental rotation and circumferential strain. Cine MR images and velocity- encoded MR images were also acquired for assessment of biventricular volumes and biventricular function and pulmonary regurgitant fraction, respectively. Mean values were compared between groups using unpaired Student's t- test. Results: Patients presented with preserved global LV function (LVEF of 59 +/- 5%). A significant decrease in LV peak circumferential strain was seen in patients compared with normal volunteers at the basilar (-15.6 +/- 4.5% vs. -17.6 +/- 4.4%; P < 0.01) and apical (-14.46 +/- 6.1% vs. -17.3 +/- 5.1%, P < 0.01) slices. LV peak rotation was also delayed in patients compared with volunteers at the basilar (6.1 +/- 2.6 degrees vs. 4.2 +/- 0.6 degrees; P < 0.01) and mid (8.0 +/- 1.7 degrees vs. 4.9 +/- 1.0 degrees; P < 0.01) slices. Conclusion: MRI can detect early regional LV dysfunction in patients with preserved LVEF after repair of tetralogy of Fallot. MR may be a useful technique for guiding clinical decisions in these patients in order to prevent future global LV deterioration.
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| 5. |
- Zamani, Neda, et al.
(författare)
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A universal genomic coordinate translator for comparative genomics
- 2014
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 15, s. 227-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N-2 with the number of available genomes, N. Results: Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across species. Conclusions: Kraken is a computational genome coordinate translator that facilitates cross-species comparisons, distinguishes orthologs from paralogs, and does not require costly all-to-all whole genome mappings. Kraken is freely available under LPGL from http://github.com/nedaz/kraken.
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