| 51. |
- Barrio, Alvaro Martinez, et al.
(författare)
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The First Sequenced Carnivore Genome Shows Complex Host-Endogenous Retrovirus Relationships
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:5, s. e19832-
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Tidskriftsartikel (refereegranskat)abstract
- Host-retrovirus interactions influence the genomic landscape and have contributed substantially to mammalian genome evolution. To gain further insights, we analyzed a female boxer (Canis familiaris) genome for complexity and integration pattern of canine endogenous retroviruses (CfERV). Intriguingly, the first such in-depth analysis of a carnivore species identified 407 CfERV proviruses that represent only 0.15% of the dog genome. In comparison, the same detection criteria identified about six times more HERV proviruses in the human genome that has been estimated to contain a total of 8% retroviral DNA including solitary LTRs. These observed differences in man and dog are likely due to different mechanisms to purge, restrict and protect their genomes against retroviruses. A novel group of gammaretrovirus-like CfERV with high similarity to HERV-Fc1 was found to have potential for active retrotransposition and possibly lateral transmissions between dog and human as a result of close interactions during at least 10.000 years. The CfERV integration landscape showed a non-uniform intra-and inter-chromosomal distribution. Like in other species, different densities of ERVs were observed. Some chromosomal regions were essentially devoid of CfERVs whereas other regions had large numbers of integrations in agreement with distinct selective pressures at different loci. Most CfERVs were integrated in antisense orientation within 100 kb from annotated protein-coding genes. This integration pattern provides evidence for selection against CfERVs in sense orientation relative to chromosomal genes. In conclusion, this ERV analysis of the first carnivorous species supports the notion that different mammals interact distinctively with endogenous retroviruses and suggests that retroviral lateral transmissions between dog and human may have occurred.
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| 52. |
- Berg, Charlotte, et al.
(författare)
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48 Monitoring Animal Welfare at Slaughterhouses
- 2012. - 1500
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Ingår i: Sustainable Agriculture. - Uppsala : Baltic University Press. - 9789186189105 ; , s. 349-351
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Bokkapitel (populärvet., debatt m.m.)
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| 53. |
- Besnier, Francois, et al.
(författare)
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A genetic algorithm based method for stringent haplotyping of family data
- 2009
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Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Background: The linkage phase, or haplotype, is an extra level of information that in addition to genotype and pedigree can be useful for reconstructing the inheritance pattern of the alleles in a pedigree, and computing for example Identity By Descent probabilities. If a haplotype is provided, the precision of estimated IBD probabilities increases, as long as the haplotype is estimated without errors. It is therefore important to only use haplotypes that are strongly supported by the available data for IBD estimation, to avoid introducing new errors due to erroneous linkage phases.Results: We propose a genetic algorithm based method for haplotype estimation in family data that includes a stringency parameter. This allows the user to decide the error tolerance level when inferring parental origin of the alleles. This is a novel feature compared to existing methods for haplotype estimation. We show that using a high stringency produces haplotype data with few errors, whereas a low stringency provides haplotype estimates in most situations, but with an increased number of errors.Conclusion: By including a stringency criterion in our haplotyping method, the user is able to maintain the error rate at a suitable level for the particular study; one can select anything from haplotyped data with very small proportion of errors and a higher proportion of non-inferred haplotypes, to data with phase estimates for every marker, when haplotype errors are tolerable. Giving this choice makes the method more flexible and useful in a wide range of applications as it is able to fulfil different requirements regarding the tolerance for haplotype errors, or uncertain marker-phases.
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| 54. |
- Besnier, Francois, et al.
(författare)
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Fine mapping and replication of QTL in outbred chicken advanced intercross lines
- 2011
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Ingår i: Genetics Selection Evolution. - Paris : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 43, s. 3-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature.METHODS: We have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight.RESULTS: Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL.CONCLUSIONS: Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.
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| 55. |
- Bonnett, Brenda, et al.
(författare)
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Lifestyle risk factors for progesterone-related diabetes mellitus in elkhounds - a case-control study
- 2011
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Ingår i: Journal of Small Animal Practice. - : Wiley. - 0022-4510 .- 1748-5827. ; 52, s. 240-245
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Tidskriftsartikel (refereegranskat)abstract
- Methods: Owners of 48 diabetic elkhounds and 58 healthy elkhounds were interviewed by phone concerning lifetime diet and exercise routines. A logistic model was developed to assess the impact of diet and exercise on diabetes diagnosis. The agreement between lifetime owner-perceived body condition score (BCS) and veterinary-perceived BCS at inclusion was estimated in healthy control dogs using the Kappa statistic.Results: The model showed that diabetic dogs had increased odds for having been overweight (before diagnosis) compared with controls (OR=2 center dot 8, 95% confidence interval 1 center dot 1-7 center dot 5, P=0 center dot 034). Although feeding other food than commercial dog feed was associated with diabetes case status, the effect was not significant after BCS was entered into the model. The overall agreement between lifetime owner- and veterinary-perceived BCS at inclusion in the study was 75% and had a Kappa statistic of 0 center dot 16 (P=0 center dot 12).Clinical Significance: This study indicates that a high owner-perceived lifetime BCS is associated with progesterone-related diabetes in elkhounds.
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| 56. |
- Braga, Tiago, et al.
(författare)
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Reduction with dithiothreitol causes serglycin-specific defects in secretory granule integrity of bone marrow derived mast cells
- 2009
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Ingår i: Molecular Immunology. - : Elsevier BV. - 0161-5890 .- 1872-9142. ; 46:3, s. 422-428
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Tidskriftsartikel (refereegranskat)abstract
- Mast cell granule maturation and storage of granule components has previously been shown to be critically dependent on serglycin (SG), a proteoglycan abundantly stored in mast cell secretory granules. The N-terminal portion of serglycin contains a conserved disulfide motif that is similar to motifs found in secretory granule compounds of neuroendocrine cells. Interference with such motifs of neuroendocrine cells with dithiothreitol (DTT) has previously been shown to cause cellular missorting. To investigate the implication for serglycin, serglycin(+/+) and serglycin(-/-) bone marrow derived mast cells (BMMCs) were treated with DTT followed by assessment of proteoglycan synthesis and secretory granule integrity. Treatment of serglycin(+/+) BMMCs with DTT almost completely abolished biosynthetic incorporation of (35)S-sulfate into proteoglycans, caused a dramatic reduction of granular staining with May Grünwald/Giemsa as well as disruption of granule dense core formation as shown by transmission electron microscopy. In addition, the storage of carboxypeptidase A, a major secretory granule compound, was markedly reduced following DTT treatment. In contrast, none of these effects were seen after treatment of SG(-/-) BMMCs with DTT, indicating that they were serglycin-specific. Notably, DTT treated serglycin(+/+) BMMCs showed similar morphology as did the serglycin(-/-) BMMCs. DTT treatment affected neither the viability of the BMMCs nor the mRNA levels for serglycin or carboxypeptidase A. Together, these data indicate that DTT causes dramatic, serglycin-specific effects on mast cell granule. These findings are thus in accordance with a role for the N-terminal disulfide motif in serglycin for regulation of mast cell secretory granule integrity.
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| 57. |
- Branth, Stefan, et al.
(författare)
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Metabolic stress-like condition can be induced by prolonged strenuous exercise in athletes
- 2009
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Ingår i: Upsala Journal of Medical Sciences. - : Taylor & Francis. - 0300-9734 .- 2000-1967. ; 114:1, s. 12-25
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Tidskriftsartikel (refereegranskat)abstract
- Few studies have examined energy metabolism during prolonged, strenuous exercise. We wanted therefore to investigate energy metabolic consequences of a prolonged period of continuous strenuous work with very high energy expenditure. Twelve endurance-trained athletes (6 males and 6 females) were recruited. They performed a 7-h bike race on high work-load intensity. Physiological, biochemical, endocrinological, and anthropometric muscular compartment variables were monitored before, during, and after the race. The energy expenditure was high, being 5557 kcal. Work-load intensity (% of VO2 peak) was higher in females (77.7%) than in men (69.9%). Muscular glycogen utilization was pronounced, especially in type I fibres (>90%). Additionally, muscular triglyceride lipolysis was considerably accelerated. Plasma glucose levels were increased concomitantly with an unchanged serum insulin concentration which might reflect an insulin resistance state in addition to proteolytic glyconeogenesis. Increased reactive oxygen species (malondialdehyde (MDA)) were additional signs of metabolic stress. MDA levels correlated with glycogen utilization rate. A relative deficiency of energy substrate on a cellular level was indicated by increased intracellular water of the leg muscle concomitantly with increased extracellular levels of the osmoregulatory amino acid taurine. A kindred nature of a presumed insulin-resistant state with less intracellular availability of glucose for erythrocytes was also indicated by the findings of decreased MCV together with increased MCHC (haemoconcentration) after the race. This strenuous energy-demanding work created a metabolic stress-like condition including signs of insulin resistance and deteriorated intracellular glucose availability leading to compromised fuelling of ion pumps, culminating in a disturbed cellular osmoregulation indicated by taurine efflux and cellular swelling. © 2009 Informa UK Ltd All rights reserved.
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| 58. |
- Brunberg, Emma, et al.
(författare)
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Feather pecking behavior in laying hens : Hypothalamic gene expression in birds performing and receiving pecks
- 2011
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Ingår i: Poultry Science. - : Elsevier BV. - 0032-5791 .- 1525-3171. ; 90:6, s. 1145-1152
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Tidskriftsartikel (refereegranskat)abstract
- Feather pecking (FP) is a welfare and economic problem in the egg production sector. Beak trimming, the current method used to reduce FP, is also criticized. The present study used gene expression to explore the biological mechanisms underlying this behavior, which could lead to a greater understanding of the cause and a tool to mitigate the problem. White Leghorn hens performing and receiving FP, as well as neutral control birds, were identified on a commercial farm. Hypothalamic RNA from 11 peckers, 10 victims, and 10 controls was hybridized onto GeneChip Chicken Genome Arrays (Affymetrix Inc., Santa Clara, CA) to compare gene expression profiles in the different groups. Eleven transcripts corresponding to 10 genes differed significantly between the 3 groups (adjusted P < 0.05). Eight of these transcripts differed in the peckers compared with the controls, 1 was upregulated in the victims compared with the controls, and 6 differed significantly in the peckers compared with the victims. Additionally, 5 transcripts showed a trend (adjusted P < 0.1) to differ in the pecker-victim comparison. Some of the products of the differently expressed genes are involved in disorders, such as intestinal inflammation and insulin resistance, which fit well with the previously proposed hypothesis that FP is an abnormal foraging behavior. Other findings may also support the proposal that FP is linked to immune mechanisms and may serve as an animal model for obsessive compulsive disorder in humans. In conclusion, this study provides a gene list that may be useful in further research on the mechanisms behind FP.
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| 59. |
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| 60. |
- Crooks, Lucy, et al.
(författare)
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An Improved Method for Estimating Chromosomal Line Origin in QTL Analysis of Crosses Between Outbred Lines
- 2011
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Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 1, s. 57-64
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Tidskriftsartikel (refereegranskat)abstract
- Estimating the line origin of chromosomal sections from marker genotypes is a vital step in quantitative trait loci analyses of outbred line crosses. The original, and most commonly used, algorithm can only handle moderate numbers of partially informative markers. The advent of high-density genotyping with SNP chips motivates a new method because the generic sets of markers on SNP chips typically result in long stretches of partially informative markers. We validated a new method for inferring line origin, triM (tracing inheritance with Markov models), with simulated data. A realistic pattern of marker information was achieved by replicating the linkage disequilibrium from an existing chicken intercross. There were approximately 1500 SNP markers and 800 F-2 individuals. The performance of triM was compared to GridQTL, which uses a variant of the original algorithm but modified for larger datasets. triM estimated the line origin with an average error of 2%, was 10% more accurate than GridQTL, considerably faster, and better at inferring positions of recombination. GridQTL could not analyze all simulated replicates and did not estimate line origin for around a third of individuals at many positions. The study shows that triM has computational benefits and improved estimation over available algorithms and is valuable for analyzing the large datasets that will be standard in future.
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