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| 5. |
- Ablondi, Michela, et al.
(författare)
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Signatures of selection in the genome of Swedish warmblood horses selected for sport performance
- 2019
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- Background A growing demand for improved physical skills and mental attitude in modern sport horses has led to strong selection for performance in many warmblood studbooks. The aim of this study was to detect genomic regions with low diversity, and therefore potentially under selection, in Swedish Warmblood horses (SWB) by analysing high-density SNP data. To investigate if such signatures could be the result of selection for equestrian sport performance, we compared our SWB SNP data with those from Exmoor ponies, a horse breed not selected for sport performance traits. Results The genomic scan for homozygous regions identified long runs of homozygosity (ROH) shared by more than 85% of the genotyped SWB individuals. Such ROH were located on ECA4, ECA6, ECA7, ECA10 and ECA17. Long ROH were instead distributed evenly across the genome of Exmoor ponies in 77% of the chromosomes. Two population differentiation tests (F-ST and XP-EHH) revealed signatures of selection on ECA1, ECA4, and ECA6 in SWB horses. Conclusions Genes related to behaviour, physical abilities and fertility, appear to be targets of selection in the SWB breed. This study provides a genome-wide map of selection signatures in SWB horses, and ground for further functional studies to unravel the biological mechanisms behind complex traits in horses.
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| 8. |
- Andersson, Lisa, et al.
(författare)
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Augendefekte bei windfarbenen Pferden
- 2012
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Ingår i: Eiðfaxi, Islandpferdemagazin. - 1023-3350. ; , s. 70-75
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Tidskriftsartikel (populärvet., debatt m.m.)
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| 9. |
- Andersson, Lisa, et al.
(författare)
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Augngallar í vindóttum hrossum
- 2012
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Ingår i: Eiðfaxi, Icelandic horse Magazine. - 1023-3342. ; , s. 42-47
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Tidskriftsartikel (populärvet., debatt m.m.)
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| 10. |
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| 11. |
- Andersson, Lisa, et al.
(författare)
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Equine multiple congenital ocular anomalies and silver coat colour result from the pleiotropic effects of mutant PMEL
- 2013
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Equine Multiple Congenital Ocular Anomalies (MCOA) syndrome is a heritable eye disorder mainly affecting silver colored horses. Clinically, the disease manifests in two distinct classes depending on the horse genotype. Horses homozygous for the mutant allele present with a wide range of ocular defects, such as iris stromal hypoplasia, abnormal pectinate ligaments, megaloglobus, iridociliary cysts and cataracts. The phenotype of heterozygous horses is less severe and predominantly includes iridociliary cysts, which occasionally extend into the temporal retina. In order to determine the genetic cause of MCOA syndrome we sequenced the entire previously characterized 208 kilobase region on chromosome 6 in ten individuals; five MCOA affected horses from three different breeds, one horse with the intermediate Cyst phenotype and four unaffected controls from two different breeds. This was performed using Illumina TruSeq technology with paired-end reads. Through the systematic exclusion of all polymorphisms barring two SNPs in PMEL, a missense mutation previously reported to be associated with the silver coat colour and a non-conserved intronic SNP, we establish that this gene is responsible for MCOA syndrome. Our finding, together with recent advances that show aberrant protein function due to the coding mutation, suggests that the missense mutation is causative and has pleiotrophic effect, causing both the horse silver coat color and MCOA syndrome.
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| 14. |
- Andersson, Lisa, et al.
(författare)
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Genetic diversity in the modern horse illustrated from genome-wide SNP data
- 2013
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.
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| 23. |
- Andersson, Lisa, et al.
(författare)
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Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 488:7413, s. 642-646
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Tidskriftsartikel (refereegranskat)abstract
- Locomotion in mammals relies on a central pattern-generating circuitry of spinal interneurons established during development that coordinates limb movement(1). These networks produce left-right alternation of limbs as well as coordinated activation of flexor and extensor muscles(2). Here we show that a premature stop codon in the DMRT3 gene has a major effect on the pattern of locomotion in horses. The mutation is permissive for the ability to perform alternate gaits and has a favourable effect on harness racing performance. Examination of wild-type and Dmrt3-null mice demonstrates that Dmrt3 is expressed in the dI6 subdivision of spinal cord neurons, takes part in neuronal specification within this subdivision, and is critical for the normal development of a coordinated locomotor network controlling limb movements. Our discovery positions Dmrt3 in a pivotal role for configuring the spinal circuits controlling stride in vertebrates. The DMRT3 mutation has had a major effect on the diversification of the domestic horse, as the altered gait characteristics of a number of breeds apparently require this mutation.
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| 24. |
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| 26. |
- Andersson, Lisa, et al.
(författare)
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Targeted analysis of four breeds narrows equine Multiple Congenital Ocular Anomalies locus to 208 kilobases
- 2011
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Ingår i: Mammalian Genome. - : Springer Science and Business Media LLC. - 0938-8990 .- 1432-1777. ; 22, s. 353-360
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Tidskriftsartikel (refereegranskat)abstract
- The syndrome Multiple Congenital Ocular Anomalies (MCOA) is the collective name ascribed to heritable congenital eye defects in horses. Individuals homozygous for the disease allele (MCOA phenotype) have a wide range of eye anomalies, while heterozygous horses (Cyst phenotype) predominantly have cysts that originate from the temporal ciliary body, iris, and/or peripheral retina. MCOA syndrome is highly prevalent in the Rocky Mountain Horse but the disease is not limited to this breed. Affected horses most often have a Silver coat color; however, a pleiotropic link between these phenotypes is yet to be proven. Locating and possibly isolating these traits would provide invaluable knowledge to scientists and breeders. This would favor maintenance of a desirable coat color while addressing the health concerns of the affected breeds, and would also provide insight into the genetic basis of the disease. Identical-by-descent mapping was used to narrow the previous 4.6-Mb region to a 264-kb interval for the MCOA locus. One haplotype common to four breeds showed complete association to the disease (Cyst phenotype, = 246; MCOA phenotype, n = 83). Candidate genes from the interval, SMARCC2 and IKZF4, were screened for polymorphisms and genotyped, and segregation analysis allowed the MCOA syndrome region to be shortened to 208 kb. This interval also harbors PMEL17, the gene causative for Silver coat color. However, by shortening the MCOA locus by a factor of 20, 176 other genes have been unlinked from the disease and only 15 genes remain.
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| 27. |
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| 29. |
- Andersson, Lisa, et al.
(författare)
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The same ELA class II risk factors confer equine insect bite hypersensitivity in two distinct populations
- 2012
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Ingår i: Immunogenetics. - : Springer Science and Business Media LLC. - 0093-7711 .- 1432-1211. ; 64:3, s. 201-208
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Tidskriftsartikel (refereegranskat)abstract
- Insect bite hypersensitivity (IBH) is a chronic allergic dermatitis common in horses. Affected horses mainly react against antigens present in the saliva from the biting midges, Culicoides ssp, and occasionally black flies, Simulium ssp. Because of this insect dependency, the disease is clearly seasonal and prevalence varies between geographical locations. For two distinct horse breeds, we genotyped four microsatellite markers positioned within the MHC class II region and sequenced the highly polymorphic exons two from DRA and DRB3, respectively. Initially, 94 IBH-affected and 93 unaffected Swedish born Icelandic horses were tested for genetic association. These horses had previously been genotyped on the Illumina Equine SNP50 BeadChip, which made it possible to ensure that our study did not suffer from the effects of stratification. The second population consisted of 106 unaffected and 80 IBH-affected Exmoor ponies. We show that variants in the MHC class II region are associated with disease susceptibility (p(raw)=2.34x10(-5)), with the same allele (COR112:274) associated in two separate populations. In addition, we combined microsatellite and sequencing data in order to investigate the pattern of homozygosity and show that homozygosity across the entire MHC class II region is associated with a higher risk of developing IBH (p=0.0013). To our knowledge this is the first time in any atopic dermatitis suffering species, including man, where the same risk allele has been identified in two distinct populations.
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| 30. |
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| 31. |
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| 32. |
- Andreeva, M. A., et al.
(författare)
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Depth selective investigations of magnetic multilayers by X-ray resonant magnetic reflectivity
- 2006
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Ingår i: Journal of Magnetism and Magnetic Materials. - : Elsevier BV. - 0304-8853 .- 1873-4766. ; 300:1, s. e371-e374
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Tidskriftsartikel (refereegranskat)abstract
- We have measured and analyzed the X-ray resonant Bragg reflectivity spectra from BCC [Fe/Co]n superstructure near the L2,3 absorption edges of iron. The developed general computer code for the reflectivity calculations from arbitrary anisotropic multilayers allows us to test the different approaches to the treatment of the Bragg reflectivity spectra. We have proved that the observed asymmetry of the spectrum shape at the first-order Bragg peak for the right and left circular polarizations is predominantly caused by the magnetization of the central part of iron layers. The influence of interfaces is almost negligible. The fit of the energy dependence of the integral intensity of the Bragg reflection for the [Fe6/Co6]50 sample gives the value of the magnetic moment of Fe atoms in the central parts of Fe layers ∼2.6 μB, that is larger than the volume value.
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| 33. |
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| 34. |
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| 35. |
- Axling, Johanna, et al.
(författare)
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Use of diagnostic reports to estimate prevalence and distribution of skeletal lesions in young Thoroughbreds
- 2016
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Ingår i: Veterinary Journal. - : Elsevier BV. - 1090-0233 .- 1532-2971. ; 214, s. 72-76
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Tidskriftsartikel (refereegranskat)abstract
- Diagnostic reports written to assist stud managers in the sale of young Thoroughbreds have not previously been used as a data source for the study of skeletal lesions. However, analyses of these reports may provide efficient and cost-effective insights into the prevalence and distribution of skeletal lesions within a population. Diagnostic reports written by veterinarians were acquired from Thoroughbred stud managers in Australia and New Zealand. The reports were based on approximately 1300 sets of weanling and yearling radiographs taken between 2002 and 2007. The prevalence and anatomical distribution of skeletal lesions in weanlings (299 horses) and yearlings (1004 horses) were determined from these reports. Overall, 69.9% of weanlings and 64.5% of yearlings were reported as having one or more skeletal lesions. Diagnostic reports in weanlings were a strong indication of what was likely to be seen in subsequent yearling reports. These diagnostic reports are typically used by stud managers in the sales process and the potential drawback is that some categories of skeletal lesions may be under-reported. However, there was substantial agreement between the prevalence and distribution of several skeletal lesions reported in this study and those previously reported from direct evaluation of radiographs for Australian and New Zealand Thoroughbred yearlings. Strong agreement was found for osteophytes, enthesiophytes and other modelling in the hocks, and for lesions in the hind fetlocks and stifles. This indicates that written diagnostic reports are a useful and a reliable source of data for the study of some skeletal lesions in young Thoroughbred horses. (C) 2016 Elsevier Ltd. All rights reserved.
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| 36. |
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| 37. |
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| 38. |
- Björck, Matts, et al.
(författare)
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Element-specific magnetic moment profile in BCC Fe/Co superlattices
- 2004
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Ingår i: Journal of Magnetism and Magnetic Materials. - : Elsevier BV. - 0304-8853 .- 1873-4766. ; 284, s. 273-280
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Tidskriftsartikel (refereegranskat)abstract
- BCC Fe/Co superlattices with individual layer thicknesses in the range of 2–9 monolayers have been investigated byX-ray magnetic circular dichroism in combination with SQUID magnetometry in order to study the magnetic momentdistribution in the superlattices. The magnetic moment for Co was found to remain constant, within 0:1 mB=atom, at1:6 mB=atom for all the superlattices. The Fe atoms at the interface have an enhanced moment of about 3:0 mB=atom. Inaddition, a complex dependence of the size of the moments on the thickness of the Fe layer was found and attributed tointerface roughness effects. Element-specific hysteresis curves were also recorded. These measurements show that themagnetic moments of Fe and Co were, as expected, coupled during reversal of the magnetic moment direction.
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| 39. |
- Björnsdóttir, Sigridur, et al.
(författare)
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The effect of the ‘Gait keeper’ mutation in the DMRT3 gene on gaiting ability in Icelandic horses
- 2014
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Ingår i: Journal of Animal Breeding and Genetics. - : Wiley. - 0931-2668 .- 1439-0388. ; 131, s. 415-425
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Tidskriftsartikel (refereegranskat)abstract
- A nonsense mutation in DMRT3 (‘Gait keeper' mutation) has a predominant effect on gaiting ability in horses, being permissive for the ability to perform lateral gaits and having a favourable effect on speed capacity in trot. The DMRT3 mutant allele (A) has been found in high frequency in gaited breeds and breeds bred for harness racing, while other horse breeds were homozygous for the wild-type allele (C). The aim of this study was to evaluate further the effect of the DMRT3 nonsense mutation on the gait quality and speed capacity in the multigaited Icelandic horse and demonstrate how the frequencies of the A- and C- alleles have changed in the Icelandic horse population in recent decades. It was confirmed that homozygosity for the DMRT3 nonsense mutation relates to the ability to pace. It further had a favourable effect on scores in breeding field tests for the lateral gait t€olt, demonstrated by better beat quality, speed capacity and suppleness. Horses with the CA genotype had on the other hand significantly higher scores for walk, trot, canter and gallop, and they performed better beat and suspension in trot and gallop. These results indicate that the AA genotype reinforces the coordination of ipsilateral legs, with the subsequent negative effect on the synchronized movement of diagonal legs compared with the CA genotype. The frequency of the A-allele has increased in recent decades with a corresponding decrease in the frequency of the C-allele. The estimated frequency of the A-allele in the Icelandic horse population in 2012 was 0.94. Selective breeding for lateral gaits in the Icelandic horse population has apparently altered the frequency of DMRT3 genotypes with a predicted loss of the C-allele in relatively few years. The results have practical implications for breeding and training of Icelandic horses and other gaited horse breeds.
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| 40. |
- Braganca, F. M. Serra, et al.
(författare)
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Improving gait classification in horses by using inertial measurement unit (IMU) generated data and machine learning
- 2020
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- For centuries humans have been fascinated by the natural beauty of horses in motion and their different gaits. Gait classification (GC) is commonly performed through visual assessment and reliable, automated methods for real-time objective GC in horses are warranted. In this study, we used a full body network of wireless, high sampling-rate sensors combined with machine learning to fully automatically classify gait. Using data from 120 horses of four different domestic breeds, equipped with seven motion sensors, we included 7576 strides from eight different gaits. GC was trained using several machine-learning approaches, both from feature-extracted data and from raw sensor data. Our best GC model achieved 97% accuracy. Our technique facilitated accurate, GC that enables in-depth biomechanical studies and allows for highly accurate phenotyping of gait for genetic research and breeding. Our approach lends itself for potential use in other quadrupedal species without the need for developing gait/animal specific algorithms.
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| 41. |
- Brandariz-Fontes, Claudia, et al.
(författare)
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Y-Chromosome Analysis in Retuertas Horses
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:5, s. e64985-
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Tidskriftsartikel (refereegranskat)abstract
- Several studies based on a variety of genetic markers have attempted to establish the origins of horse domestication. Thus far a discrepancy between the results of mitochondrial DNA analysis, which show high levels of diversity, and results from the Y-chromosome, with almost no genetic variability, has been identified. Most previous work on the horse Y-chromosome has focused on widespread, popular breeds or local Asian breeds. It is possible that these breeds represent a reduced set of the genetic variation present in the species. Additional genetic variation may be present in local breeds and ancient feral populations, such as the Retuertas horse in Spain. In this study we analyzed the Y-chromosome of the Retuertas horse, a feral horse population on the Iberian Peninsula that is at least several hundred years old, and whose genetic diversity and morphology suggests that it has been reproductively isolated for a long time. Data from the Retuertas horse was compared to another 11 breeds from the region (Portugal, Spain and France) or likely of Iberian origin, and then to data from 15 more breeds from around the globe. We sequenced 31 introns, Zinc finger Y-chromosomal protein (ZFY) and anonymous Y-linked fragments and genotyped 6 microsatellite loci found on the Y-chromosome. We found no sequence variation among all individuals and all breeds studied. However, fifteen differences were discovered between our data set and reference sequences in GenBank. We show that these likely represent errors within the deposited sequences, and suggest that they should not be used as comparative data for future projects.
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| 42. |
- Brunberg, Emma, et al.
(författare)
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A missense mutation in PMEL17 is associated with the Silver coat color in the horse
- 2006
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Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 7, s. 46-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The Silver coat color, also called Silver dapple, in the horse is characterized by dilution of the black pigment in the hair. This phenotype shows an autosomal dominant inheritance. The effect of the mutation is most visible in the long hairs of the mane and tail, which are diluted to a mixture of white and gray hairs. Herein we describe the identification of the responsible gene and a missense mutation associated with the Silver phenotype. Results: Segregation data on the Silver locus (Z) were obtained within one half-sib family that consisted of a heterozygous Silver colored stallion with 34 offspring and their 29 non-Silver dams. We typed 41 genetic markers well spread over the horse genome, including one single microsatellite marker (TKY284) close to the candidate gene PMEL17 on horse chromosome 6 (ECA6q23). Significant linkage was found between the Silver phenotype and TKY284 (theta = 0, z = 9.0). DNA sequencing of PMEL17 in Silver and non-Silver horses revealed a missense mutation in exon 11 changing the second amino acid in the cytoplasmic region from arginine to cysteine (Arg618Cys). This mutation showed complete association with the Silver phenotype across multiple horse breeds, and was not found among non-Silver horses with one clear exception; a chestnut colored individual that had several Silver offspring when mated to different non-Silver stallions also carried the exon 11 mutation. In total, 64 Silver horses from six breeds and 85 non-Silver horses from 14 breeds were tested for the exon 11 mutation. One additional mutation located in intron 9, only 759 bases from the missense mutation, also showed complete association with the Silver phenotype. However, as one could expect to find several non-causative mutations completely associated with the Silver mutation, we argue that the missense mutation is more likely to be causative. Conclusion: The present study shows that PMEL17 causes the Silver coat color in the horse and enable genetic testing for this trait.
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| 43. |
- Brunberg, Emma, et al.
(författare)
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Icelandic horses with the Silver coat colour show altered behaviour in a fear reaction test
- 2013
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Ingår i: Applied Animal Behaviour Science. - : Elsevier BV. - 0168-1591 .- 1872-9045. ; 146, s. 72-78
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Tidskriftsartikel (refereegranskat)abstract
- The colour of a horse's coat has long been discussed to reflect its temperament. One opinion is that Silver coloured horses are nervous, difficult to handle and react more strongly to different fear stimuli. The objective with the present study was to investigate if mutations associated with the Silver coat colour affect fear reactions in Icelandic horses. The hypothesis was that horses with the Silver mutation Arg618Cys in PMEL show stronger fear reactions than horses without the mutation (e.g. Black/Brown or Chestnut horses). Twenty-seven Icelandic horses (nine Silver, nine Chestnuts and nine Black/Brown) matched for sire, were exposed to the fear stimulus (a suddenly moving plastic bag) while feeding from a container. The test was repeated five times and behavioural responses and latency to return to the feed container were recorded. All horses were genotyped for the Silver mutation. The proportion of Silver horses that were hesitant to approach the test set-up before each trial was significantly higher (P < 0.05) than the proportion of non-Silver horses and this difference was most pronounced before the first two trials. No differences in reaction vigour or latency to resume feeding were found between the differently coloured horses. The results suggest that Silver horses are more cautious in novel situations rather than more reactive in fearful situations. One likely explanation for this difference is that the Silver mutation is associated with multiple congenital ocular anomalies (MCOA) syndrome and visual impairment. Furthermore, offspring (regardless of coat colour) from sires with a Best Linear Unbiased Prediction (BLUP, an index indicating which traits a horse will pass on to its offspring) value above 100 for the temperament trait 'Spirit', showed a greater fear reaction (P < 0.01) and reacted for a longer time (P < 0.01) than horses from sires with a lower (<100) index. These results indicate that horses with a high BLUP value for 'Spirit' seem to express stronger fear reactions. Breeding for Silver coat colour and the 'Spirit' trait, as it is currently defined, may need to be reconsidered if these results are confirmed in a larger cohort. (c) 2013 Elsevier B.V. All rights reserved.
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| 44. |
- Chalkias, Helena, et al.
(författare)
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Identification of novel candidate genes for the inverted teat defect in sows using a genome-wide marker panel
- 2017
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Ingår i: Journal of Applied Genetics. - : Springer Science and Business Media LLC. - 1234-1983 .- 2190-3883. ; 58, s. 249-259
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Tidskriftsartikel (refereegranskat)abstract
- The number of functional teats is an important selection criterion in pig breeding. Inherited defects of the udder, such as the inverted teat, do have a considerable negative impact on the nursing ability of the sow. To investigate the genetic background of this defect and the number of functional teats in Swedish maternal lines, samples from 230 Yorkshire pigs were selected for genotyping using the PorcineSNP60K BeadChip (Illumina Inc.), each pig with at least one inverted teat was matched with one non-affected pig (fullsib or pairs with matching herd and gender). A genome-wide association study on these 230 pigs was performed using the two-step approach implemented in GenABEL using 46,652 single nucleotide polymorphisms across all autosomes and the X chromosome. A number of significant regions were identified for the inverted teat defect on chromosomes 2, 10, and 18. Many of the regions associated with the number of functional teats were located in the same or close regions, except two associated markers on the X chromosome and one on chromosome 3. We identified some of the regions on chromosomes previously reported in one linkage and one gene expression study. We conclude, despite being able to suggest new candidate genes, that further studies are needed to better understand the biologic background of the teat development. Despite the in-depth comparison of identified regions for the inverted teat defect done here, more studies are required to allow a clear identification of genetic regions relevant for this defect across many pig populations.
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| 45. |
- Ciuciulkaite, Agne, MSc, 1991-, et al.
(författare)
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Magnetic and all-optical switching properties of amorphous TbxCo100-x alloys
- 2020
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Ingår i: Physical Review Materials. - : American Physical Society (APS). - 2475-9953. ; 4:10
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Tidskriftsartikel (refereegranskat)abstract
- Amorphous TbxCo100-x magnetic alloys exhibit a list of intriguing properties, such as perpendicular magnetic anisotropy, high magneto-optical activity, and magnetization switching using ultrashort optical pulses. Varying the Tb:Co ratio in these alloys allows for tuning properties such as the saturation magnetic moment, coercive field, and the performance of light-induced magnetization switching. In this paper, we investigate the magnetic, optical, and magneto-optical properties of various TbxCo100-x thin-film alloy compositions. We report on the effect the choice of different seeding layers has on the structural and magnetic properties of TbxCo100-x layers. We also demonstrate that for a range of alloys, deposited on fused silica substrates, with Tb content of 24-30 at. %, helicity-dependent all-optical switching of magnetization can be achieved, albeit in a multishot framework. We explain this property to arise from the helicity-dependent laser-induced magnetization on the Co sublattice due to the inverse Faraday effect. Our paper provides an insight into material aspects for future potential hybrid magnetoplasmonic TbCo-based architectures.
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| 46. |
- Da Silva, Vinicius, et al.
(författare)
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Copy number variations associated with insect bite hypersensitivity in Friesian horses
- 2016
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Ingår i: Annual meeting of the European Association for Animal Production. - 1382-6077. ; , s. 286-286
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Copy number variations (CNVs) are the largest source of genetic variation that has been identified in the equine genome so far. CNV-based GWAS could therefore facilitate detection of genetic variation for traits of interest. The aim of our study was to identify, characterize and associate CNVs in Friesian horses with insect bite hypersensitivity (IBH), a common equine allergy to insects that causes intense itch and seriously reduces welfare. After pre-processing of raw intensity signals from 670,796 SNPs for 138 cases and 131 controls, CNVs were identified using PennCNV and merged into CNV regions (CNVRs) using CNVRuler. A SNP-based GWAS performed beforehand (chi squared test with 1df) showed a clear association between the ELA region on ECA20 and IBH in Friesian horses. Regions identified on ECA9, 11 and 20 have rather consistently been associated with IBH across equine breeds investigated so far. Currently, the CNV analysis is at an early stage and different strategies to improve the SNP array overall signal quality are being tested. The preliminary CNV-based GWAS, which analysed gains and losses separately by logistic regression, indicated a loss in the ELA region significantly more frequent in affected horses. CNVRs significantly associated with IBH could point to genes involved in this complex polygenic disease. Our study will increase the knowledge on CNVs in horses and will highlight which genes and pathways are affected by CNVs. Moreover, it will facilitate in our attempt to improve selection against IBH.
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| 47. |
- Da Silva, Vinicius, et al.
(författare)
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Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity
- 2018
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Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- Background: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide.Results: Genotypes were obtained using the Axiom (R) Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH.Conclusions: CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity in Friesian horses. Although subsequent analyses are needed for verification, nucleotide differences, as well as more complex structural variations like CNVs, seem to contribute to IBH sensitivity. IBH should be considered as a common disease with a complex genomic architecture.
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- Darin, Niklas, 1964, et al.
(författare)
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γ-glutamyl transpeptidase deficiency caused by a large homozygous intragenic deletion in GGT1.
- 2018
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Ingår i: European journal of human genetics : EJHG. - : Springer Science and Business Media LLC. - 1476-5438 .- 1018-4813. ; 26, s. 808-817
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Tidskriftsartikel (refereegranskat)abstract
- γ-Glutamyl transpeptidase deficiency (glutathionuria, OMIM 231950) is a rare disease, with only six patients reported in the literature, although this condition has probably been underdiagnosed due the difficulty to routinely analyze glutathione in clinical samples and to the fact that no genetic defect has been coupled to the disease so far. We report two siblings with mild psychomotor developmental delay and mild neurological symptoms, who presented a markedly increased excretion of glutathione in urine and a very low γ-glutamyl transpeptidase activity in serum. Whole-genome sequencing revealed the presence of a 16.9kb homozygous deletion in GGT1, one of the genes encoding enzymes with γ-glutamyl transpeptidase activity in the human genome. Close analysis revealed the presence of a 13bp insertion at the deletion junction. This is the first report of a genetic variant as the cause of glutathionuria. In addition, genetic characterization of the patients' parents and a healthy sibling has provided direct genetic evidence regarding the autosomal recessive nature of this disease.
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