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Summers KM. Genetic models of fibrillinopathies. Genetics 2024; 226:iyad189. [PMID: 37972149 PMCID: PMC11021029 DOI: 10.1093/genetics/iyad189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023] Open
Abstract
The fibrillinopathies represent a group of diseases in which the 10-12 nm extracellular microfibrils are disrupted by genetic variants in one of the genes encoding fibrillin molecules, large glycoproteins of the extracellular matrix. The best-known fibrillinopathy is Marfan syndrome, an autosomal dominant condition affecting the cardiovascular, ocular, skeletal, and other systems, with a prevalence of around 1 in 3,000 across all ethnic groups. It is caused by variants of the FBN1 gene, encoding fibrillin-1, which interacts with elastin to provide strength and elasticity to connective tissues. A number of mouse models have been created in an attempt to replicate the human phenotype, although all have limitations. There are also natural bovine models and engineered models in pig and rabbit. Variants in FBN2 encoding fibrillin-2 cause congenital contractural arachnodactyly and mouse models for this condition have also been produced. In most animals, including birds, reptiles, and amphibians, there is a third fibrillin, fibrillin-3 (FBN3 gene) for which the creation of models has been difficult as the gene is degenerate and nonfunctional in mice and rats. Other eukaryotes such as the nematode C. elegans and zebrafish D. rerio have a gene with some homology to fibrillins and models have been used to discover more about the function of this family of proteins. This review looks at the phenotype, inheritance, and relevance of the various animal models for the different fibrillinopathies.
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Affiliation(s)
- Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba QLD 4102, Australia
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2
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Li Z, Wang Z, Chen Z, Voegeli H, Lichtman JH, Smith P, Liu J, DeWan AT, Hoh J. Systematically identifying genetic signatures including novel SNP-clusters, nonsense variants, frame-shift INDELs, and long STR expansions that potentially link to unknown phenotypes existing in dog breeds. BMC Genomics 2023; 24:302. [PMID: 37277710 DOI: 10.1186/s12864-023-09390-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND In light of previous studies that profiled breed-specific traits or used genome-wide association studies to refine loci associated with characteristic morphological features in dogs, the field has gained tremendous genetic insights for known dog traits observed among breeds. Here we aim to address the question from a reserve perspective: whether there are breed-specific genotypes that may underlie currently unknown phenotypes. This study provides a complete set of breed-specific genetic signatures (BSGS). Several novel BSGS with significant protein-altering effects were highlighted and validated. RESULTS Using the next generation whole-genome sequencing technology coupled with unsupervised machine learning for pattern recognitions, we constructed and analyzed a high-resolution sequence map for 76 breeds of 412 dogs. Genomic structures including novel single nucleotide polymorphisms (SNPs), SNP clusters, insertions, deletions (INDELs) and short tandem repeats (STRs) were uncovered mutually exclusively among breeds. We also partially validated some novel nonsense variants by Sanger sequencing with additional dogs. Four novel nonsense BSGS were found in the Bernese Mountain Dog, Samoyed, Bull Terrier, and Basset Hound, respectively. Four INDELs resulting in either frame-shift or codon disruptions were found in the Norwich Terrier, Airedale Terrier, Chow Chow and Bernese Mountain Dog, respectively. A total of 15 genomic regions containing three types of BSGS (SNP-clusters, INDELs and STRs) were identified in the Akita, Alaskan Malamute, Chow Chow, Field Spaniel, Keeshond, Shetland Sheepdog and Sussex Spaniel, in which Keeshond and Sussex Spaniel each carried one amino-acid changing BSGS in such regions. CONCLUSION Given the strong relationship between human and dog breed-specific traits, this study might be of considerable interest to researchers and all. Novel genetic signatures that can differentiate dog breeds were uncovered. Several functional genetic signatures might indicate potentially breed-specific unknown phenotypic traits or disease predispositions. These results open the door for further investigations. Importantly, the computational tools we developed can be applied to any dog breeds as well as other species. This study will stimulate new thinking, as the results of breed-specific genetic signatures may offer an overarching relevance of the animal models to human health and disease.
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Affiliation(s)
- Zicheng Li
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA.
| | - Zuoheng Wang
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Zhiyuan Chen
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Heidi Voegeli
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Judith H Lichtman
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Peter Smith
- Department of Comparative Medicine, School of Medicine, Yale University, New Haven, CT, 06510, USA
| | - Ju Liu
- Medical Research Center, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, 16766 Jingshi Road, Jinan, Shandong, 250014, China
| | - Andrew T DeWan
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA
- Center for Perinatal Pediatric and Environmental Epidemiology, Yale University, New Haven, CT, 06510, USA
| | - Josephine Hoh
- Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT, 06510, USA.
- Department of Ophthalmology and Visual Science, School of Medicine, Yale University, New Haven, CT, 06510, USA.
- Department of Applied Mathematics, Yale University, New Haven, CT, 06510, USA.
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3
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Exploration of body weight in 115 000 young adult dogs of 72 breeds. Sci Rep 2023; 13:443. [PMID: 36624169 PMCID: PMC9829868 DOI: 10.1038/s41598-022-27055-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
High body weight (BW), due to large size or excess body fat, has been associated with developmental and metabolic alterations, and degenerative diseases in dogs. Study objectives were to determine mean BW in young adult dogs of different breeds, including changes over a 10-year period. Body weight data from the official Swedish hip dysplasia screening program were used, including data from dogs screened at 1-2.5 years of age, in breeds with ≥ 15 individual observations/year during 2007-2016. Mean BW per breed and sex was established from 114 568 dogs representing 72 breeds. Estimates of breed BW showed significant change in 33 (45%) breeds over the 10-year period. Body weight increased in five breeds (2-14% change) and decreased in 26 breeds (1-8% change). In two breeds, BW increased in male and decreased in female dogs. This observational study provides extensive breed BW data on young adult dogs. The change in breed BW, noted in almost half of the breeds, could be due to changes either in size or in body fat mass. In certain breeds, the change in BW over time might have an impact on overall health. Studies with simultaneous evaluation of BW and body condition over time are warranted.
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Sándor S, Jónás D, Tátrai K, Czeibert K, Kubinyi E. Poly(A) RNA sequencing reveals age-related differences in the prefrontal cortex of dogs. GeroScience 2022; 44:1269-1293. [PMID: 35288843 PMCID: PMC9213612 DOI: 10.1007/s11357-022-00533-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/17/2022] [Indexed: 12/02/2022] Open
Abstract
Dogs may possess a unique translational potential to investigate neural aging and dementia because they are prone to age-related cognitive decline, including an Alzheimer’s disease–like pathological condition. Yet very little is known about the molecular mechanisms underlying canine cognitive decline. The goal of the current study was to explore the transcriptomic differences between young and old dogs’ frontal cortex, which is a brain region often affected by various forms of age-related dementia in humans. RNA isolates from the frontal cortical brain area of 13 pet dogs, which represented 7 different breeds and crossbreds, were analyzed. The dogs were euthanized for medical reasons, and their bodies had been donated by their owners for scientific purposes. The poly(A) tail RNA subfraction of the total transcriptome was targeted in the sequencing analysis. Cluster analyses, differential gene expression analyses, and gene ontology analyses were carried out to assess which genes and genetic regulatory mechanisms were mostly affected by aging. Age was the most prominent factor in the clustering of the animals, indicating the presence of distinct gene expression patterns related to aging in a genetically variable population. A total of 3436 genes were found to be differentially expressed between the age groups, many of which were linked to neural function, immune system, and protein synthesis. These findings are in accordance with previous human brain aging RNA sequencing studies. Some genes were found to behave more similarly to humans than to rodents, further supporting the applicability of dogs in translational aging research.
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Affiliation(s)
- Sára Sándor
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary.
| | - Dávid Jónás
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Kitti Tátrai
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary.,Department of Genetics, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Kálmán Czeibert
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Eniko Kubinyi
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
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Genome-wide selection of discriminant SNP markers for breed assignment in indigenous sheep breeds. ANNALS OF ANIMAL SCIENCE 2021. [DOI: 10.2478/aoas-2020-0097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
The assignment of an individual to the true population of origin is one of the most important applications of genomic data for practical use in animal breeding. The aim of this study was to develop a statistical method and then, to identify the minimum number of informative SNP markers from high-throughput genotyping data that would be able to trace the true breed of unknown samples in indigenous sheep breeds. The total numbers of 217 animals were genotyped using Illumina OvineSNP50K BeadChip in Zel, Lori-Bakhtiari, Afshari, Moqani, Qezel and a wild-type Iranian sheep breed. After SNP quality check, the principal component analysis (PCA) was used to determine how the animals allocated to the groups using all genotyped markers. The results revealed that the first principal component (PC1) separated out the two domestic and wild sheep breeds, and all domestic breeds were separated from each other for PC2. The genetic distance between different breeds was calculated using FST and Reynold methods and the results showed that the breeds were well differentiated. A statistical method was developed using the stepwise discriminant analysis (SDA) and the linear discriminant analysis (LDA) to reduce the number of SNPs for discriminating 6 different Iranian sheep populations and K-fold cross-validation technique was employed to evaluate the potential of a selected subset of SNPs in assignment success rate. The procedure selected reduced pools of markers into 201 SNPs that were able to exactly discriminate all sheep populations with 100% accuracy. Moreover, a discriminate analysis of principal components (DAPC) developed using 201 linearly independent SNPs revealed that these markers were able to assign all individuals into true breed. Finally, these 201 identified SNPs were successfully used in an independent out-group breed consisting of 96 samples of Baluchi sheep breed and the results indicated that these markers are able to correctly allocate all unknown samples to true population of origin. In general, the results of this study indicated that the combined use of the SDA and LDA techniques represents an efficient strategy for selecting a reduced pool of highly discriminant markers.
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6
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Corbee RJ, Penning LC. COMMD1 Exemplifies the Power of Inbred Dogs to Dissect Genetic Causes of Rare Copper-Related Disorders. Animals (Basel) 2021; 11:ani11030601. [PMID: 33668783 PMCID: PMC7996361 DOI: 10.3390/ani11030601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
Wilson's Disease is a rare autosomal recessive disorder in humans, often presenting with hepatic copper overload. Finding the genetic cause of a rare disease, especially if it is related to food constituents like the trace element copper, is a Herculean task. This review describes examples of how the unique population structure of in-bred dog strains led to the discovery of a novel gene and two modifier genes involved in inherited copper toxicosis. COMMD1, after the discovery in 2002, was shown to be a highly promiscuous protein involved in copper transport, protein trafficking/degradation, regulation of virus replication, and inflammation. Mutations in the ATP7A and ATP7B proteins in Labrador retrievers and Dobermann dogs resulted in a wide variation in hepatic copper levels in these breeds. To our knowledge, numerous dog breeds with inherited copper toxicosis of unknown genetic origin exist. Therefore, the possibility that men's best friend will provide new leads in rare copper storage diseases seems realistic.
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McGetrick J, Brucks D, Marshall-Pescini S, Range F. No evidence for a relationship between breed cooperativeness and inequity aversion in dogs. PLoS One 2020; 15:e0233067. [PMID: 32555709 PMCID: PMC7299310 DOI: 10.1371/journal.pone.0233067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/27/2020] [Indexed: 01/06/2023] Open
Abstract
Inequity aversion, the resistance to inequitable outcomes, has been demonstrated in a wide variety of animal species. Inequity aversion was hypothesised to have co-evolved with cooperation but only limited evidence supports this. Dogs provide a suitable model species to test this hypothesis as dogs were previously shown to be inequity averse and dog breeds vary in the extent to which they were selected for cooperativeness. Here, we compared the response of 12 individuals of "cooperative worker" breeds with that of 12 individuals of "independent worker" breeds in the "paw task" previously used to demonstrate inequity aversion in dogs. We also compared the two breed groups' subsequent social behaviours in a food tolerance test and free interaction session. Although subjects in both breed groups were inequity averse, we found no considerable difference between the groups in the extent of the negative response to inequity or in the impact of the inequity on subsequent social behaviours. However, we found differences between the breed groups in the response to reward omission with cooperative breeds tending to work for longer than independent breeds. Additionally, in the free interaction session, individuals of cooperative breeds spent more time in proximity to their partner in the baseline condition than individuals of independent breeds. Overall, our results do not provide support for the hypothesis that inequity aversion and cooperation co-evolved. However, they illuminate potential differences in selection pressures experienced by cooperative worker and independent worker dog breeds throughout their evolutionary history.
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Affiliation(s)
- Jim McGetrick
- Domestication Lab, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
- Comparative Cognition Unit, Messerli Research Institute, University of Veterinary Medicine, Medical University of Vienna & University of Vienna, Vienna, Austria
| | - Désirée Brucks
- Comparative Cognition Unit, Messerli Research Institute, University of Veterinary Medicine, Medical University of Vienna & University of Vienna, Vienna, Austria
- Institute for Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Sarah Marshall-Pescini
- Domestication Lab, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
- Comparative Cognition Unit, Messerli Research Institute, University of Veterinary Medicine, Medical University of Vienna & University of Vienna, Vienna, Austria
| | - Friederike Range
- Domestication Lab, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
- Comparative Cognition Unit, Messerli Research Institute, University of Veterinary Medicine, Medical University of Vienna & University of Vienna, Vienna, Austria
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8
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Lindblad-Toh K. What animals can teach us about evolution, the human genome, and human disease. Ups J Med Sci 2020; 125:1-9. [PMID: 32054372 PMCID: PMC7054949 DOI: 10.1080/03009734.2020.1722298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/14/2022] Open
Abstract
During the past 20 years, since I started as a postdoc, the world of genetics and genomics has changed dramatically. My main research goal throughout my career has been to understand human disease genetics, and I have developed comparative genomics and comparative genetics to generate resources and tools for understanding human disease. Through comparative genomics I have worked to sequence enough mammals to understand the functional potential of each base in the human genome as well as chosen vertebrates to study the evolutionary changes that have given many species their key traits. Through comparative genetics, I have developed the dog as a model for human disease, characterising the genome itself and determining a list of germ-line loci and somatic mutations causing complex diseases and cancer in the dog. Pulling all these findings and resources together opens new doors for understanding genome evolution, the genetics of complex traits and cancer in man and his best friend.
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Affiliation(s)
- Kerstin Lindblad-Toh
- Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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9
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10
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de Souza AF, de Ramos EC, Cury FS, Pieri NCG, Martins DS. The timeline development of female canine germ cells. Reprod Domest Anim 2019; 54:964-971. [PMID: 31006155 DOI: 10.1111/rda.13444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/13/2019] [Indexed: 11/26/2022]
Abstract
During the sex differentiation, the primordial germ cells (PGCs) pass through a differentiation, becoming spermatogonial cells in males and oocytes in females. In this phase, there is difference in gene expression and differentiation potency between males and females. Specific cell markers have been essential in the PGC meiosis beginning and become oocyte cells. However, there are few studies about germline in domestic animals. The domestic dog (Canis lupus familiaris) is an interesting animal model to be used in the investigation about the mammal development because it has several biochemical and physiological similarities to humans. In addition, some additional investigations about dogs may contribute to a better understanding of the biology and genetic components, improving clinical veterinary and zoological sciences. Here, we elucidated by immunofluorescence and quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR), the dynamics of the expression of pluripotent (POU5F1 and NANOG) and germline (DDX4, DAZL and DPPA3) markers that are very important in the development of female canine germ cells during 35-50 days post-fertilization (dpf). The female canine germ cells were positive for pluripotent markers during middle developmental period. The number of DDX4, DAZL and DPPA3 cells increased along the germ cell maturation from 45 to 50 dpf. We provided an expression analysis of the pluripotent and germline markers in paraffin sections using the middle and later periods in female canine germ cells. The results can contribute the understanding about the timeline of each marker along the maturation of female canine germ cells. These results have a great significance to demonstrate the germ cell profile changes because it may allow the development of protocols about in vitro germ cell derivation.
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Affiliation(s)
- Aline F de Souza
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Eloise C de Ramos
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Fabio S Cury
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Naira Caroline G Pieri
- Department of Reproduction, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Daniele S Martins
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil.,Department of Surgery, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
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11
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Fan TM, Selting KA. Exploring the Potential Utility of Pet Dogs With Cancer for Studying Radiation-Induced Immunogenic Cell Death Strategies. Front Oncol 2019; 8:680. [PMID: 30697532 PMCID: PMC6340932 DOI: 10.3389/fonc.2018.00680] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/27/2018] [Indexed: 01/21/2023] Open
Abstract
Radiotherapy serves as a foundational pillar for the therapeutic management of diverse solid tumors through the generation of lethal DNA damage and induction of cell death. While the direct cytotoxic effects of radiation therapy remain a cornerstone for cancer management, in the era of immunooncology there is renewed and focused interest in exploiting the indirect bystander activities of radiation, termed abscopal effects. In radioimmunobiologic terms, abscopal effects describe the radiotherapy-induced regression of cancerous lesions distant from the primary site of radiation delivery and rely upon the induction of immunogenic cell death and consequent systemic anticancer immune activation. Despite the promise of radiation therapy for awaking potent anticancer immune responses, the purposeful harnessing of abscopal effects with radiotherapy remain clinically elusive. In part, failure to fully leverage and clinically implement the promise of radiation-induced abscopal effects stems from limitations associated with existing conventional tumor models which inadequately recapitulate the complexity of malignant transformation and the dynamic nature of tumor immune surveillance. To supplement this existing gap in modeling systems, pet dogs diagnosed with solid tumors including melanoma and osteosarcoma, which are both metastatic and immunogenic in nature, could potentially serve as unique resources for exploring the fundamental underpinnings required for maximizing radiation-induced abscopal effects. Given the spontaneous course of cancer development in the context of operative immune mechanisms, pet dogs treated with radiotherapy for metastatic solid tumors might be leveraged as valuable model systems for realizing the science and best clinical practices necessary to generate potent abscopal effects with anti-metastatic immune activities.
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Affiliation(s)
- Timothy M Fan
- Comparative Oncology Research Laboratory, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign Urbana, IL, United States
| | - Kimberly A Selting
- Comparative Oncology Research Laboratory, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign Urbana, IL, United States
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12
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Tang B, Zhou Q, Dong L, Li W, Zhang X, Lan L, Zhai S, Xiao J, Zhang Z, Bao Y, Zhang YP, Wang GD, Zhao W. iDog: an integrated resource for domestic dogs and wild canids. Nucleic Acids Res 2019; 47:D793-D800. [PMID: 30371881 PMCID: PMC6323916 DOI: 10.1093/nar/gky1041] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/11/2018] [Accepted: 10/16/2018] [Indexed: 12/12/2022] Open
Abstract
The domestic dog (Canis lupus familiaris) is indisputably one of man's best friends. It is also a fundamental model for many heritable human diseases. Here, we present iDog (http://bigd.big.ac.cn/idog), the first integrated resource dedicated to domestic dogs and wild canids. It incorporates a variety of omics data, including genome sequences assemblies for dhole and wolf, genomic variations extracted from hundreds of dog/wolf whole genomes, phenotype/disease traits curated from dog research communities and public resources, gene expression profiles derived from published RNA-Seq data, gene ontology for functional annotation, homolog gene information for multiple organisms and disease-related literature. Additionally, iDog integrates sequence alignment tools for data analyses and a genome browser for data visualization. iDog will not only benefit the global dog research community, but also provide access to a user-friendly consolidation of dog information to a large number of dog enthusiasts.
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Affiliation(s)
- Bixia Tang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Zhou
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lili Dong
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wulue Li
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiangquan Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li Lan
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang Zhai
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingfa Xiao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhang Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiming Bao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ya-Ping Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Guo-Dong Wang
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Wenming Zhao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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Abstract
Dogs are second only to humans in medical surveillance and preventative health care, leading to a recent perception of increased cancer incidence. Scientific priorities in veterinary oncology have thus shifted, with a demand for cancer genetic screens, better diagnostics, and more effective therapies. Most dog breeds came into existence within the last 300 years, and many are derived from small numbers of founders. Each has undergone strong artificial selection, in which dog fanciers selected for many traits, including body size, fur type, color, skull shape, and behavior, to create novel breeds. The adoption of the breed barrier rule-no dog may become a registered member of a breed unless both its dam and its sire are registered members-ensures a relatively closed genetic pool within each breed. As a result, there is strong phenotypic homogeneity within breeds but extraordinary phenotypic variation between breeds. One consequence of this is the high level of breed-associated genetic disease. We and others have taken advantage of this to identify genes for a large number of canine maladies for which mouse models do not exist, particularly with regard to cancer.
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Affiliation(s)
- Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Dayna L Dreger
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA; .,Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jacquelyn M Evans
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
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14
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Wilding C. The genetic basis of size in pet dogs: The study of quantitative genetic variation in an undergraduate laboratory practical. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 46:623-629. [PMID: 30394677 DOI: 10.1002/bmb.21180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/13/2018] [Accepted: 09/22/2018] [Indexed: 06/08/2023]
Abstract
The teaching of quantitative genetic variation in the undergraduate laboratory practical environment can be difficult as, for quantitative phenotypes that are under the control of multiple loci, detection of phenotypic differences caused by individual variants is problematical without large samples, impractical in such classes. Pet dogs provide a clear example of quantitative genetic variation with individual breeds ranging in size from 1 to 70 kg weight yet with little intrabreed variability. In contrast to humans where there are few identified genetic variants known to be involved in the genetically controlled size phenotype, in dogs, seven single nucleotide polymorphisms (SNPs) in six genes have been demonstrated to explain half of the phenotypic variance. In the practical described here, a single G-A SNP (within intron 2 of the insulin-like growth factor 1 gene) is studied through PCR, sequencing, and bioinformatics. Average breed weight of dogs of different genotypes at this SNP show significant differences in size (median [IQR] of AA = 10 kg [6-15 kg], AG = 23.75 kg [14-30 kg], GG = 30 kg [24.5-37 kg] from our class data) with an estimate of just ≈N = 16 dogs needing to be genotyped to demonstrate a significant difference in size between dogs harboring the two homozygous genotypes. In the practical described herein, from a single laboratory and a single computer session, students are able to see the clear effect of genotype on a quantitative trait. Examination of the variant in the Ensembl browser (www.ensembl.org) allows students to understand the genomic basis of this variant and appreciate the wealth of data and information publicly available in genome browsers. © 2018 International Union of Biochemistry and Molecular Biology, 46(6):623-629, 2018.
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Affiliation(s)
- Craig Wilding
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, L3 3AF, United Kingdom
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Gunter LM, Barber RT, Wynne CDL. A canine identity crisis: Genetic breed heritage testing of shelter dogs. PLoS One 2018; 13:e0202633. [PMID: 30138476 PMCID: PMC6107223 DOI: 10.1371/journal.pone.0202633] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 08/07/2018] [Indexed: 11/19/2022] Open
Abstract
Previous research in animal shelters has determined the breeds of dogs living in shelters by their visual appearance; however the genetic breed testing of such dogs is seldom conducted, and few studies have compared the breed labels assigned by shelter staff to the results of this testing. In the largest sampling of shelter dogs’ breed identities to-date, 459 dogs at Arizona Animal Welfare League & SPCA (AAWL) in Phoenix, Arizona, and 460 dogs at San Diego Humane Society & SPCA (SDHS) in San Diego, California, were genetically tested using a commercially available product to determine their breed heritage. In our sample, genetic analyses identified 125 distinct breeds with 91 breeds present at both shelters, and 4.9% of the dogs identified as purebreds. The three most common breed signatures, in order of prevalence, American Staffordshire Terrier, Chihuahua, and Poodle, accounted for 42.5% or all breed identifications at the great grandparent level. During their stay at the shelter, dogs with pit bull-type ancestries waited longer to be adopted than other dogs. When we compared shelter breed assignment as determined by visual appearance to that of genetic testing, staff at SDHS was able to successfully match at least one breed in the genetic heritage of 67.7% of dogs tested; however their agreement fell to 10.4% when asked to identify more than one breed. Lastly, we found that as the number of pit bull-type relatives in a dog’s heritage increased, so did the shelter’s ability to match the results of DNA analysis. In total when we consider the complexity of shelter dog breed heritage and the failure to identify multiple breeds based on visual identification coupled with our inability to predict how these breeds then interact within an individual dog, we believe that focusing resources on communicating the physical and behavioral characteristics of shelter dogs would best support adoption efforts.
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Affiliation(s)
- Lisa M. Gunter
- Department of Psychology, Arizona State University, Tempe, Arizona, United States of America
- * E-mail:
| | - Rebecca T. Barber
- Mary Lou Fulton Teachers College, Arizona State University, Tempe, Arizona, United States of America
| | - Clive D. L. Wynne
- Department of Psychology, Arizona State University, Tempe, Arizona, United States of America
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Höglund K, Häggström J, Hanås S, Merveille AC, Gouni V, Wiberg M, Lundgren Willesen J, Entee KM, Mejer Sørensen L, Tiret L, Seppälä EH, Lohi H, Chetboul V, Fredholm M, Lequarré AS, Ljungvall I. Interbreed variation in serum serotonin (5-hydroxytryptamine) concentration in healthy dogs. J Vet Cardiol 2018; 20:244-253. [PMID: 29921518 DOI: 10.1016/j.jvc.2018.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 05/04/2018] [Accepted: 05/14/2018] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Serotonin (5-hydroxytryptamine [5-HT]) has several biological functions. In different species, excessive 5-HT has been linked to valvular lesions, similar to those seen in dogs with myxomatous mitral valve disease. Previous studies suggest higher 5-HT in healthy Cavalier King Charles Spaniels (CKCSs), a breed highly affected by myxomatous mitral valve disease, compared to other breeds. OBJECTIVE To investigate potential interbreed variation in serum 5-HT in healthy dogs. ANIMALS 483 healthy dogs of nine breeds aged 1-7 years. METHODS Dogs were examined at five European centers. Absence of cardiovascular, organ-related, or systemic diseases was ensured by thorough clinical investigations including echocardiography. Serum was frozen and later analyzed by enzyme-linked immunosorbent assay (ELISA). RESULTS Median 5-HT concentration was 252.5 (interquartile range = 145.5-390.6) ng/mL. Overall breed difference was found (p<0.0001), and 42% of pairwise breed comparisons were significant. Univariate regression analysis showed association between serum 5-HT concentration and breed, center of examination, storage time, and sex, with higher 5-HT in females. In multiple regression analysis, the final model had an adjusted R2 of 0.27 with breed (p<0.0001), center (p<0.0001), and storage time (p=0.014) remaining significant. Within centers, overall breed differences were found at 3/5 centers (p≤0.028), and pairwise comparisons within those centers showed breed differences in 42% of comparisons. Among the included breeds, Newfoundlands, Belgian Shepherds and CKCSs had highest 5-HT concentrations. CONCLUSIONS Interbreed variation in serum 5-HT concentration was found in healthy dogs aged 1-7 years. These differences should be taken into account when designing clinical studies.
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Affiliation(s)
- K Höglund
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Science, Uppsala, Sweden.
| | - J Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Science, Uppsala, Sweden
| | - S Hanås
- Department of Clinical Sciences, Swedish University of Agricultural Science, Uppsala, Sweden; Evidensia Animal Clinic, 723 41 Västerås, Sweden
| | - A-C Merveille
- Department of Clinical Sciences, University of Liège, Belgium
| | - V Gouni
- Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, Unité de Cardiologie d'Alfort, Maisons-Alfort Cedex, France; Inserm, U955, Equipe 3, Créteil Cedex, France
| | - M Wiberg
- Department of Equine and Small Animal Medicine, University of Helsinki, Finland
| | - J Lundgren Willesen
- Department of Veterinary Clinical Sciences, University of Copenhagen, Denmark
| | - K Mc Entee
- Department of Clinical Sciences, University of Liège, Belgium; Laboratory of Physiology and Pharmacology, Université Libre de Bruxelles, Belgium
| | - L Mejer Sørensen
- Department of Veterinary Clinical Sciences, University of Copenhagen, Denmark
| | - L Tiret
- U955 IMRB, Team 10, Inserm, Ecole nationale vétérinaire d'Alfort, UPEC, Maisons-Alfort, France
| | - E H Seppälä
- Research Programs Unit, Molecular Neurology, University of Helsinki and Folkhälsan Institute of Genetics, Finland
| | - H Lohi
- Research Programs Unit, Molecular Neurology, University of Helsinki and Folkhälsan Institute of Genetics, Finland
| | - V Chetboul
- Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, Unité de Cardiologie d'Alfort, Maisons-Alfort Cedex, France; Inserm, U955, Equipe 3, Créteil Cedex, France
| | - M Fredholm
- Department of Veterinary Clinical Sciences, University of Copenhagen, Denmark
| | - A-S Lequarré
- Department of Clinical Sciences, University of Liège, Belgium
| | - I Ljungvall
- Department of Clinical Sciences, Swedish University of Agricultural Science, Uppsala, Sweden
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de Souza AF, Pieri NCG, Roballo KCS, Bressan FF, Casals JB, Ambrósio CE, Perecin F, Martins DS. Dynamics of male canine germ cell development. PLoS One 2018; 13:e0193026. [PMID: 29489867 PMCID: PMC5831030 DOI: 10.1371/journal.pone.0193026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 02/02/2018] [Indexed: 12/18/2022] Open
Abstract
Primordial germ cells (PGCs) are precursors of gametes that can generate new individuals throughout life in both males and females. Additionally, PGCs have been shown to differentiate into embryonic germ cells (EGCs) after in vitro culture. Most studies investigating germinative cells have been performed in rodents and humans but not dogs (Canis lupus familiaris). Here, we elucidated the dynamics of the expression of pluripotent (POU5F1 and NANOG), germline (DDX4, DAZL and DPPA3), and epigenetic (5mC, 5hmC, H3K27me3 and H3K9me2) markers that are important for the development of male canine germ cells during the early (22-30 days post-fertilization (dpf)), middle (35-40 dpf) and late (45-50 dpf) gestational periods. We performed sex genotype characterization, immunofluorescence, immunohistochemistry, and quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) analyses. Furthermore, in a preliminary study, we evaluated the capacity of canine embryo PGCs (30 dpf) to differentiate into EGCs. To confirm the canine EGCs phenotype, we performed alkaline phosphatase detection, immunohistochemistry, electron and transmission scanning microscopy and RT-qPCR analyses. The PGCs were positive for POU5F1 and H3K27me3 during all assessed developmental periods, including all periods between the gonadal tissue stage and foetal testes development. The number of NANOG, DDX4, DAZL, DPPA3 and 5mC-positive cells increased along with the developing cords from 35-50 dpf. Moreover, our results demonstrate the feasibility of inducing canine PGCs into putative EGCs that present pluripotent markers, such as POU5F1 and the NANOG gene, and exhibit reduced expression of germinative genes and increased expression of H3K27me3. This study provides new insight into male germ cell development mechanisms in dogs.
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Affiliation(s)
- Aline F. de Souza
- Department of Surgery, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Naira C. Godoy Pieri
- Department of Reproduction, Faculty of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Kelly C. S. Roballo
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Fabiana F. Bressan
- Department of Surgery, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Juliana B. Casals
- Department of Surgery, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Carlos E. Ambrósio
- Department of Surgery, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Felipe Perecin
- Department of Surgery, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Daniele S. Martins
- Department of Surgery, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
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Van den Bossche L, Schoonenberg VAC, Burgener IA, Penning LC, Schrall IM, Kruitwagen HS, van Wolferen ME, Grinwis GCM, Kummeling A, Rothuizen J, van Velzen JF, Stathonikos N, Molenaar MR, Helms BJ, Brouwers JFHM, Spee B, van Steenbeek FG. Aberrant hepatic lipid storage and metabolism in canine portosystemic shunts. PLoS One 2017; 12:e0186491. [PMID: 29049355 PMCID: PMC5648188 DOI: 10.1371/journal.pone.0186491] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/02/2017] [Indexed: 02/06/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a poorly understood multifactorial pandemic disorder. One of the hallmarks of NAFLD, hepatic steatosis, is a common feature in canine congenital portosystemic shunts. The aim of this study was to gain detailed insight into the pathogenesis of steatosis in this large animal model. Hepatic lipid accumulation, gene-expression analysis and HPLC-MS of neutral lipids and phospholipids in extrahepatic (EHPSS) and intrahepatic portosystemic shunts (IHPSS) was compared to healthy control dogs. Liver organoids of diseased dogs and healthy control dogs were incubated with palmitic- and oleic-acid, and lipid accumulation was quantified using LD540. In histological slides of shunt livers, a 12-fold increase of lipid content was detected compared to the control dogs (EHPSS P<0.01; IHPSS P = 0.042). Involvement of lipid-related genes to steatosis in portosystemic shunting was corroborated using gene-expression profiling. Lipid analysis demonstrated different triglyceride composition and a shift towards short chain and omega-3 fatty acids in shunt versus healthy dogs, with no difference in lipid species composition between shunt types. All organoids showed a similar increase in triacylglycerols after free fatty acids enrichment. This study demonstrates that steatosis is probably secondary to canine portosystemic shunts. Unravelling the pathogenesis of this hepatic steatosis might contribute to a better understanding of steatosis in NAFLD.
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Affiliation(s)
- Lindsay Van den Bossche
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Vivien A. C. Schoonenberg
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Iwan A. Burgener
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Louis C. Penning
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ingrid M. Schrall
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Hedwig S. Kruitwagen
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Monique E. van Wolferen
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Guy C. M. Grinwis
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Anne Kummeling
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jan Rothuizen
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jeroen F. van Velzen
- Laboratory for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nikolas Stathonikos
- Department of Pathology, University Medical Center, Utrecht, The Netherlands
| | - Martijn R. Molenaar
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine & Institute of Biomembranes, Utrecht, The Netherlands
| | - Bernd J. Helms
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine & Institute of Biomembranes, Utrecht, The Netherlands
| | - Jos F. H. M. Brouwers
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine & Institute of Biomembranes, Utrecht, The Netherlands
| | - Bart Spee
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frank G. van Steenbeek
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- * E-mail:
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Mazzatenta A, Carluccio A, Robbe D, Giulio CD, Cellerino A. The companion dog as a unique translational model for aging. Semin Cell Dev Biol 2017; 70:141-153. [DOI: 10.1016/j.semcdb.2017.08.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/06/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
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Söder J, Wernersson S, Hagman R, Karlsson I, Malmlöf K, Höglund K. Metabolic and Hormonal Response to a Feed-challenge Test in Lean and Overweight Dogs. J Vet Intern Med 2016; 30:574-82. [PMID: 26822126 PMCID: PMC4913616 DOI: 10.1111/jvim.13830] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 10/23/2015] [Accepted: 12/21/2015] [Indexed: 11/30/2022] Open
Abstract
Background Obese dogs risk poor life quality, creating a need for increased knowledge of metabolism in overweight dogs. Objectives Investigate postprandial metabolic and hormonal responses to a high‐fat mixed‐meal in dogs and responses of lean versus overweight dogs. Animals Twenty‐eight healthy intact male Labrador Retrievers were included. Methods Prospective observational study. Twelve dogs were grouped as lean (body condition score (BCS 4–5), 10 as slightly overweight (BCS 6), and 6 as overweight (BCS 6.5–8) on a 9‐point scale. After an overnight fast, urine and blood samples were collected. Dogs were then fed a high‐fat mixed‐meal, and blood was collected hourly for 4 hours and urine after 3 hours. Results Postprandial concentrations of insulin and glucagon were increased at 1 hour (both P < 0.0001), triglycerides at 2 hours (P < 0.0001), and glucose at 3 hours (P = 0.004); and all remained increased throughout the feed‐challenge in all dogs. Postprandial urine cortisol/creatinine ratio was higher than fasting values (P = 0.001). Comparing between groups, there was an overall higher triglyceride response in overweight compared to lean (P = 0.001) and slightly overweight (P = 0.015) dogs. Overweight dogs also had higher fasting cortisol/creatinine ratio compared to lean dogs (P = 0.024). Conclusions and Clinical Importance Postprandial responses of dogs to a high‐fat mixed‐meal were similar to those previously reported in people. The higher postprandial triglyceride response and fasting cortisol/creatinine ratio in the overweight dogs could be early signs of metabolic imbalance. Thus, although overweight dogs often appear healthy, metabolic alterations might be present.
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Affiliation(s)
- J Söder
- Department of Anatomy, Physiology and Biochemistry, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - S Wernersson
- Department of Anatomy, Physiology and Biochemistry, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - R Hagman
- Department of Clinical Sciences, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - I Karlsson
- Department of Anatomy, Physiology and Biochemistry, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - K Malmlöf
- Department of Anatomy, Physiology and Biochemistry, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - K Höglund
- Department of Anatomy, Physiology and Biochemistry, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Yu L, Sawle AD, Wynn J, Aspelund G, Stolar CJ, Arkovitz MS, Potoka D, Azarow KS, Mychaliska GB, Shen Y, Chung WK. Increased burden of de novo predicted deleterious variants in complex congenital diaphragmatic hernia. Hum Mol Genet 2015; 24:4764-73. [PMID: 26034137 DOI: 10.1093/hmg/ddv196] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/22/2015] [Indexed: 01/10/2023] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a serious birth defect that accounts for 8% of all major birth anomalies. Approximately 40% of cases occur in association with other anomalies. As sporadic complex CDH likely has a significant impact on reproductive fitness, we hypothesized that de novo variants would account for the etiology in a significant fraction of cases. We performed exome sequencing in 39 CDH trios and compared the frequency of de novo variants with 787 unaffected controls from the Simons Simplex Collection. We found no significant difference in overall frequency of de novo variants between cases and controls. However, among genes that are highly expressed during diaphragm development, there was a significant burden of likely gene disrupting (LGD) and predicted deleterious missense variants in cases (fold enrichment = 3.2, P-value = 0.003), and these genes are more likely to be haploinsufficient (P-value = 0.01) than the ones with benign missense or synonymous de novo variants in cases. After accounting for the frequency of de novo variants in the control population, we estimate that 15% of sporadic complex CDH patients are attributable to de novo LGD or deleterious missense variants. We identified several genes with predicted deleterious de novo variants that fall into common categories of genes related to transcription factors and cell migration that we believe are related to the pathogenesis of CDH. These data provide supportive evidence for novel genes in the pathogenesis of CDH associated with other anomalies and suggest that de novo variants play a significant role in complex CDH cases.
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Affiliation(s)
- Lan Yu
- Division of Molecular Genetics, Department of Pediatrics
| | | | - Julia Wynn
- Division of Molecular Genetics, Department of Pediatrics
| | | | - Charles J Stolar
- California Pediatric Surgery Group, Santa Barbara, CA 93105, USA
| | - Marc S Arkovitz
- Division of Pediatric Surgery, Tel Hashomer Medical Center, Tel Hashomer, Israel
| | - Douglas Potoka
- Department of Pediatric Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Kenneth S Azarow
- Pediatric Surgery Division, Department of Surgery, Oregon Health Science University, Portland, OR 97239, USA and
| | - George B Mychaliska
- Section of Pediatric Surgery, Department of Surgery, University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Yufeng Shen
- Departments of System Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY 10032, USA,
| | - Wendy K Chung
- Division of Molecular Genetics, Department of Pediatrics,
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Seifi Moroudi R, Masoudi AA, Vaez Torshizi R, Zandi M. Identification of learning and memory genes in canine; promoter investigation and determining the selective pressure. Mol Biol Rep 2014; 41:8019-30. [PMID: 25192892 DOI: 10.1007/s11033-014-3699-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/23/2014] [Indexed: 11/26/2022]
Abstract
One of the important behaviors of dogs is trainability which is affected by learning and memory genes. These kinds of the genes have not yet been identified in dogs. In the current research, these genes were found in animal models by mining the biological data and scientific literatures. The proteins of these genes were obtained from the UniProt database in dogs and humans. Not all homologous proteins perform similar functions, thus comparison of these proteins was studied in terms of protein families, domains, biological processes, molecular functions, and cellular location of metabolic pathways in Interpro, KEGG, Quick Go and Psort databases. The results showed that some of these proteins have the same performance in the rat or mouse, dog, and human. It is anticipated that the protein of these genes may be effective in learning and memory in dogs. Then, the expression pattern of the recognized genes was investigated in the dog hippocampus using the existing information in the GEO profile. The results showed that BDNF, TAC1 and CCK genes are expressed in the dog hippocampus, therefore, these genes could be strong candidates associated with learning and memory in dogs. Subsequently, due to the importance of the promoter regions in gene function, this region was investigated in the above genes. Analysis of the promoter indicated that the HNF-4 site of BDNF gene and the transcription start site of CCK gene is exposed to methylation. Phylogenetic analysis of protein sequences of these genes showed high similarity in each of these three genes among the studied species. The dN/dS ratio for BDNF, TAC1 and CCK genes indicates a purifying selection during the evolution of the genes.
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Affiliation(s)
- Reihane Seifi Moroudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, P.O. Box 14115-336, Tehran, Iran
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Arata S, Takeuchi Y, Inoue M, Mori Y. "Reactivity to stimuli" is a temperamental factor contributing to canine aggression. PLoS One 2014; 9:e100767. [PMID: 24972077 PMCID: PMC4074066 DOI: 10.1371/journal.pone.0100767] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 05/30/2014] [Indexed: 11/27/2022] Open
Abstract
Canine aggression is one of the most frequent problems in veterinary behavioral medicine, which in severe cases may result in relinquishment or euthanasia. As it is important to reveal underlying factors of aggression for both treatment and prevention, we recently developed a questionnaire on aggression and temperamental traits and found that “reactivity to stimuli” was associated with aggression toward owners, children, strangers, and other dogs of the Shiba Inu breed. In order to examine whether these associations were consistent in other breeds, we asked the owners of insured dogs of Anicom Insurance Inc. to complete our questionnaire. The top 17 contracted breeds were included. The questionnaire consisted of dogs' general information, four items related to aggression toward owners, children, strangers, and other dogs, and 20 other behavioral items. Aggression-related and behavioral items were rated on a five-point frequency scale. Valid responses (n = 5610) from owners of dogs aged 1 through 10 years were collected. Factor analyses on 18 behavioral items (response rate over 95%) extracted five largely consistent factors in 14 breeds: “sociability with humans,” “fear of sounds,” “chase proneness,” “reactivity to stimuli,” and “avoidance of aversive events.” By stepwise multiple regression analyses, using the Schwartz's Bayesian information criterion (BIC) method with aggression points as objective variables and general information and temperamental factor points as explanatory variables, “reactivity to stimuli,” i.e., physical reactivity to sudden movement or sound at home, was shown to be significantly associated with owner-directed aggression in 13 breeds, child-directed aggression in eight breeds, stranger-directed aggression in nine breeds, and dog-directed aggression in five breeds. These results suggest that “reactivity to stimuli” is simultaneously involved in several types of aggression. Therefore, it would be worth taking “reactivity to stimuli” into account in the treatment and prevention of canine aggression.
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Affiliation(s)
- Sayaka Arata
- Department of Animal Resource Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukari Takeuchi
- Department of Animal Resource Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
| | - Mai Inoue
- Claims Service Department, Anicom Insurance Inc., Tokyo, Japan
| | - Yuji Mori
- Department of Animal Resource Sciences, The University of Tokyo, Tokyo, Japan
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Kranenburg HJC, Hazewinkel HAW, Meij BP. Naturally Occurring Spinal Hyperostosis in Dogs as a Model for Human Spinal Disorders. ILAR J 2014; 55:150-63. [DOI: 10.1093/ilar/ilu012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Mehrkam LR, Wynne CD. Behavioral differences among breeds of domestic dogs (Canis lupus familiaris): Current status of the science. Appl Anim Behav Sci 2014. [DOI: 10.1016/j.applanim.2014.03.005] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Stock KF, Reents R. Genomic selection: Status in different species and challenges for breeding. Reprod Domest Anim 2014; 48 Suppl 1:2-10. [PMID: 23962210 DOI: 10.1111/rda.12201] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Technical advances and development in the market for genomic tools have facilitated access to whole-genome data across species. Building-up on the acquired knowledge of the genome sequences, large-scale genotyping has been optimized for broad use, so genotype information can be routinely used to predict genetic merit. Genomic selection (GS) refers to the use of aggregates of estimated marker effects as predictors which allow improved individual differentiation at young age. Realizable benefits of GS are influenced by several factors and vary in quantity and quality between species. General characteristics and challenges of GS in implementation and routine application are described, followed by an overview over the current status of its use, prospects and challenges in important animal species. Genetic gain for a particular trait can be enhanced by shortening of the generation interval, increased selection accuracy and increased selection intensity, with species- and breed-specific relevance of the determinants. Reliable predictions based on genetic marker effects require assembly of a reference for linking of phenotype and genotype data to allow estimation and regular re-estimation. Experiences from dairy breeding have shown that international collaboration can set the course for fast and successful implementation of innovative selection tools, so genomics may significantly impact the structures of future breeding and breeding programmes. Traits of great and increasing importance, which were difficult to improve in the conventional systems, could be emphasized, if continuous availability of high-quality phenotype data can be assured. Equally elaborate strategies for genotyping and phenotyping will allow tailored approaches to balance efficient animal production, sustainability, animal health and welfare in future.
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Affiliation(s)
- K F Stock
- Vereinigte Informationssysteme Tierhaltung w.V. (vit), Verden, Germany.
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Sjöstrand K, Wess G, Ljungvall I, Häggström J, Merveille AC, Wiberg M, Gouni V, Lundgren Willesen J, Hanås S, Lequarré AS, Mejer Sørensen L, Wolf J, Tiret L, Kierczak M, Forsberg S, McEntee K, Battaille G, Seppälä E, Lindblad-Toh K, Georges M, Lohi H, Chetboul V, Fredholm M, Höglund K. Breed differences in natriuretic peptides in healthy dogs. J Vet Intern Med 2014; 28:451-7. [PMID: 24495256 PMCID: PMC4857989 DOI: 10.1111/jvim.12310] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 11/26/2013] [Accepted: 12/18/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Measurement of plasma concentration of natriuretic peptides (NPs) is suggested to be of value in diagnosis of cardiac disease in dogs, but many factors other than cardiac status may influence their concentrations. Dog breed potentially is 1 such factor. OBJECTIVE To investigate breed variation in plasma concentrations of pro-atrial natriuretic peptide 31-67 (proANP 31-67) and N-terminal B-type natriuretic peptide (NT-proBNP) in healthy dogs. ANIMALS 535 healthy, privately owned dogs of 9 breeds were examined at 5 centers as part of the European Union (EU) LUPA project. METHODS Absence of cardiovascular disease or other clinically relevant organ-related or systemic disease was ensured by thorough clinical investigation. Plasma concentrations of proANP 31-67 and NT-proBNP were measured by commercially available ELISA assays. RESULTS Overall significant breed differences were found in proANP 31-67 (P < .0001) and NT-proBNP (P < .0001) concentrations. Pair-wise comparisons between breeds differed in approximately 50% of comparisons for proANP 31-67 as well as NT-proBNP concentrations, both when including all centers and within each center. Interquartile range was large for many breeds, especially for NT-proBNP. Among included breeds, Labrador Retrievers and Newfoundlands had highest median NT-proBNP concentrations with concentrations 3 times as high as those of Dachshunds. German Shepherds and Cavalier King Charles Spaniels had the highest median proANP 31-67 concentrations, twice the median concentration in Doberman Pinschers. CONCLUSIONS AND CLINICAL IMPORTANCE Considerable interbreed variation in plasma NP concentrations was found in healthy dogs. Intrabreed variation was large in several breeds, especially for NT-proBNP. Additional studies are needed to establish breed-specific reference ranges.
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Affiliation(s)
- K Sjöstrand
- Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Kis A, Bence M, Lakatos G, Pergel E, Turcsán B, Pluijmakers J, Vas J, Elek Z, Brúder I, Földi L, Sasvári-Székely M, Miklósi Á, Rónai Z, Kubinyi E. Oxytocin receptor gene polymorphisms are associated with human directed social behavior in dogs (Canis familiaris). PLoS One 2014; 9:e83993. [PMID: 24454713 PMCID: PMC3893090 DOI: 10.1371/journal.pone.0083993] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/11/2013] [Indexed: 01/01/2023] Open
Abstract
The oxytocin system has a crucial role in human sociality; several results prove that polymorphisms of the oxytocin receptor gene are related to complex social behaviors in humans. Dogs' parallel evolution with humans and their adaptation to the human environment has made them a useful species to model human social interactions. Previous research indicates that dogs are eligible models for behavioral genetic research, as well. Based on these previous findings, our research investigated associations between human directed social behaviors and two newly described (-212AG, 19131AG) and one known (rs8679684) single nucleotide polymorphisms (SNPs) in the regulatory regions (5' and 3' UTR) of the oxytocin receptor gene in German Shepherd (N = 104) and Border Collie (N = 103) dogs. Dogs' behavior traits have been estimated in a newly developed test series consisting of five episodes: Greeting by a stranger, Separation from the owner, Problem solving, Threatening approach, Hiding of the owner. Buccal samples were collected and DNA was isolated using standard protocols. SNPs in the 3' and 5' UTR regions were analyzed by polymerase chain reaction based techniques followed by subsequent electrophoresis analysis. The gene-behavior association analysis suggests that oxytocin receptor gene polymorphisms have an impact in both breeds on (i) proximity seeking towards an unfamiliar person, as well as their owner, and on (ii) how friendly dogs behave towards strangers, although the mediating molecular regulatory mechanisms are yet unknown. Based on these results, we conclude that similarly to humans, the social behavior of dogs towards humans is influenced by the oxytocin system.
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Affiliation(s)
- Anna Kis
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
- Research Centre for Natural Sciences, Institute of Cognitive Neuroscience and Psychology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Melinda Bence
- Comparative Ethology Research Group, MTA-ELTE, Budapest, Hungary
| | | | - Enikő Pergel
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Borbála Turcsán
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
- Research Centre for Natural Sciences, Institute of Cognitive Neuroscience and Psychology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Jolanda Pluijmakers
- Department of Ethology and Animal Welfare, Catholic University College Ghent, Brugge, Belgium
| | - Judit Vas
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Zsuzsanna Elek
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Ildikó Brúder
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
| | - Levente Földi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
| | - Mária Sasvári-Székely
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Ádám Miklósi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
- Comparative Ethology Research Group, MTA-ELTE, Budapest, Hungary
| | - Zsolt Rónai
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Enikő Kubinyi
- Comparative Ethology Research Group, MTA-ELTE, Budapest, Hungary
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Bellumori TP, Famula TR, Bannasch DL, Belanger JM, Oberbauer AM. Prevalence of inherited disorders among mixed-breed and purebred dogs: 27,254 cases (1995-2010). J Am Vet Med Assoc 2013; 242:1549-55. [PMID: 23683021 DOI: 10.2460/javma.242.11.1549] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine the proportion of mixed-breed and purebred dogs with common genetic disorders. DESIGN Case-control study. ANIMALS 27,254 dogs with an inherited disorder. PROCEDURES Electronic medical records were reviewed for 24 genetic disorders: hemangiosarcoma, lymphoma, mast cell tumor, osteosarcoma, aortic stenosis, dilated cardiomyopathy, hypertrophic cardiomyopathy, mitral valve dysplasia, patent ductus arteriosus, ventricular septal defect, hyperadrenocorticism, hypoadrenocorticism, hypothyroidism, elbow dysplasia, hip dysplasia, intervertebral disk disease, patellar luxation, ruptured cranial cruciate ligament, atopy or allergic dermatitis, bloat, cataracts, epilepsy, lens luxation, and portosystemic shunt. For each disorder, healthy controls matched for age, body weight, and sex to each affected dog were identified. RESULTS Genetic disorders differed in expression. No differences in expression of 13 genetic disorders were detected between purebred dogs and mixed-breed dogs (ie, hip dysplasia, hypo- and hyperadrenocorticism, cancers, lens luxation, and patellar luxation). Purebred dogs were more likely to have 10 genetic disorders, including dilated cardiomyopathy, elbow dysplasia, cataracts, and hypothyroidism. Mixed-breed dogs had a greater probability of ruptured cranial cruciate ligament. CONCLUSIONS AND CLINICAL RELEVANCE Prevalence of genetic disorders in both populations was related to the specific disorder. Recently derived breeds or those from similar lineages appeared to be more susceptible to certain disorders that affect all closely related purebred dogs, whereas disorders with equal prevalence in the 2 populations suggested that those disorders represented more ancient mutations that are widely spread through the dog population. Results provided insight on how breeding practices may reduce prevalence of a disorder.
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Affiliation(s)
- Thomas P Bellumori
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California-Davis, Davis, CA 95616, USA
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Evidence of coat color variation sheds new light on ancient canids. PLoS One 2013; 8:e75110. [PMID: 24098367 PMCID: PMC3788791 DOI: 10.1371/journal.pone.0075110] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/09/2013] [Indexed: 01/25/2023] Open
Abstract
We have used a paleogenetics approach to investigate the genetic landscape of coat color variation in ancient Eurasian dog and wolf populations. We amplified DNA fragments of two genes controlling coat color, Mc1r (Melanocortin 1 Receptor) and CBD103 (canine-β-defensin), in respectively 15 and 19 ancient canids (dogs and wolf morphotypes) from 14 different archeological sites, throughout Asia and Europe spanning from ca. 12 000 B.P. (end of Upper Palaeolithic) to ca. 4000 B.P. (Bronze Age). We provide evidence of a new variant (R301C) of the Melanocortin 1 receptor (Mc1r) and highlight the presence of the beta-defensin melanistic mutation (CDB103-K locus) on ancient DNA from dog-and wolf-morphotype specimens. We show that the dominant KB allele (CBD103), which causes melanism, and R301C (Mc1r), the variant that may cause light hair color, are present as early as the beginning of the Holocene, over 10 000 years ago. These results underline the genetic diversity of prehistoric dogs. This diversity may have partly stemmed not only from the wolf gene pool captured by domestication but also from mutations very likely linked to the relaxation of natural selection pressure occurring in-line with this process.
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Miklósi A, Topál J. What does it take to become 'best friends'? Evolutionary changes in canine social competence. Trends Cogn Sci 2013; 17:287-94. [PMID: 23643552 DOI: 10.1016/j.tics.2013.04.005] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 04/08/2013] [Indexed: 11/17/2022]
Abstract
The traditional and relatively narrow-focused research on ape-human comparisons has recently been significantly extended by investigations of different clades of animals, including the domestic dog (Canis familiaris). Here, we provide a short overview of how the comparative investigation of canine social behaviour advances our understanding of the evolution of social skills and argue that a system-level approach to dog social cognition provides a broader view on the 'human-likeness' of canine social competence. We introduce the concept of evolutionary social competence as a collateral notion of developmental social competence. We argue that such an extended perspective on social competence provides a useful tool for conceptualising wolf-dog differences in socio-cognitive functioning, as well as for considering specific social skills not in isolation, but as a part of a system.
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Affiliation(s)
- Adám Miklósi
- Department of Ethology, Eötvös University, Budapest, Hungary.
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The 2013 Genetics Society of America Medal. Genetics 2013; 194:5-7. [DOI: 10.1534/genetics.113.150672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Kranenburg HC, Hazewinkel HA, Meij BP. Spinal hyperostosis in humans and companion animals. Vet Q 2013; 33:30-42. [DOI: 10.1080/01652176.2013.770181] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Bensky MK, Gosling SD, Sinn DL. The World from a Dog’s Point of View. ADVANCES IN THE STUDY OF BEHAVIOR 2013. [DOI: 10.1016/b978-0-12-407186-5.00005-7] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Yu L, Wynn J, Cheung YH, Shen Y, Mychaliska GB, Crombleholme TM, Azarow KS, Lim FY, Chung DH, Potoka D, Warner BW, Bucher B, Stolar C, Aspelund G, Arkovitz MS, Chung WK. Variants in GATA4 are a rare cause of familial and sporadic congenital diaphragmatic hernia. Hum Genet 2012; 132:285-92. [PMID: 23138528 DOI: 10.1007/s00439-012-1249-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 10/30/2012] [Indexed: 01/16/2023]
Abstract
Congenital diaphragmatic hernia (CDH) is characterized by incomplete formation of the diaphragm occurring as either an isolated defect or in association with other anomalies. Genetic factors including aneuploidies and copy number variants are important in the pathogenesis of many cases of CDH, but few single genes have been definitively implicated in human CDH. In this study, we used whole exome sequencing (WES) to identify a paternally inherited novel missense GATA4 variant (c.754C>T; p.R252W) in a familial case of CDH with incomplete penetrance. Phenotypic characterization of the family included magnetic resonance imaging of the chest and abdomen demonstrating asymptomatic defects in the diaphragm in the two "unaffected" missense variant carriers. Screening 96 additional CDH patients identified a de novo heterozygous GATA4 variant (c.848G>A; p.R283H) in a non-isolated CDH patient. In summary, GATA4 is implicated in both familial and sporadic CDH, and our data suggests that WES may be a powerful tool to discover rare variants for CDH.
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Affiliation(s)
- Lan Yu
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY 10032, USA.
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Hall NJ, Wynne CDL. The canid genome: behavioral geneticists' best friend? GENES BRAIN AND BEHAVIOR 2012; 11:889-902. [DOI: 10.1111/j.1601-183x.2012.00851.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 06/12/2012] [Accepted: 09/04/2012] [Indexed: 12/27/2022]
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Abstract
For nearly 350 years, veterinary medicine and human medicine have been separate entities, with one geared toward the diagnosis and treatment in animals and the other toward parallel goals in the owners. However, that model no longer fits, since research on diseases of humans and companion animals has coalesced.– The catalyst for this union has been the completion of the human genome sequence, coupled with draft sequence assemblies of genomes for companion animals., Here, we summarize the critical events in canine genetics and genomics that have led to this development, review major applications in canine health that will be of interest to human caregivers, and discuss expectations for the future.
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Affiliation(s)
- Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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39
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Altered cell cycle gene expression and apoptosis in post-implantation dog parthenotes. PLoS One 2012; 7:e41256. [PMID: 22905100 PMCID: PMC3419697 DOI: 10.1371/journal.pone.0041256] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 06/22/2012] [Indexed: 11/19/2022] Open
Abstract
Mature oocytes can be parthenogenetically activated by a variety of methods and the resulting embryos are valuable for studies of the respective roles of paternal and maternal genomes in early mammalian development. In the present study, we report the first successful development of parthenogenetic canine embryos to the post-implantation stage. Nine out of ten embryo transfer recipients became pregnant and successful in utero development of canine parthenotes was confirmed. For further evaluation of these parthenotes, their fetal development was compared with artificially inseminated controls and differentially expressed genes (DEGs) were compared using ACP RT-PCR, histological analysis and immunohistochemistry. We found formation of the limb-bud and no obvious differences in histological appearance of the canine parthenote recovered before degeneration occurred; however canine parthenotes were developmentally delayed with different cell cycle regulating-, mitochondria-related and apoptosis-related gene expression patterns compared with controls. In conclusion, our protocols were suitable for activating canine oocytes artificially and supported early fetal development. We demonstrated that the developmental abnormalities in canine parthenotes may result from defective regulation of apoptosis and aberrant gene expression patterns, and provided evidence that canine parthenotes can be a useful tool for screening and for comparative studies of imprinted genes.
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Fernandes RA, Wenceslau CV, Reginato AL, Kerkis I, Miglino MA. Derivation and characterization of progenitor stem cells from canine allantois and amniotic fluids at the third trimester of gestation. Placenta 2012; 33:640-4. [PMID: 22560723 DOI: 10.1016/j.placenta.2012.03.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 03/28/2012] [Accepted: 03/31/2012] [Indexed: 12/14/2022]
Abstract
Fetal tissues are frequently discarded before (amniocentesis) or after birth, which both facilitates stem cell access and helps to overcome ethical concerns. In the present study, we aimed to isolate and characterize stem cells from the allantoic and amniotic fluids (ALF; AMF) of third trimester canine fetuses. This gestation age has not been previously explored for stem cells isolation. The gestational age, cell culture conditions and method of isolation used in this study allowed for the establishment and efficient expansion of ALF and AMF cells. We showed that the majority of ALF and ALF cells express the stem cell markers, such as vimentin, nestin and cytokeratin 18 (CK18). Under appropriate culture conditions AMF derived cells can undergo differentiation into osteogenic, adipogenic, chondrogenic and neuron-like lineages. ALF derived cells showed adipogenic, and chondrogenic potential. Therefore, ALF and AMF cells derived at the third gestation trimester can be qualified as progenitor stem cells, accordingly referred as (alantoic fluid progenitor/stem) ALF PS cells and (amniotic fluid progenitor/stem) AMF PS cells.
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Affiliation(s)
- R A Fernandes
- University of São Paulo, Faculty of Veterinary Medicine, Department of Surgery and Department of Pathology, São Paulo, Brazil
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41
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Evolutionary genomics of dog domestication. Mamm Genome 2012; 23:3-18. [DOI: 10.1007/s00335-011-9386-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 11/29/2011] [Indexed: 01/07/2023]
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42
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Streitberger K, Schweizer M, Kropatsch R, Dekomien G, Distl O, Fischer MS, Epplen JT, Hertwig ST. Rapid genetic diversification within dog breeds as evidenced by a case study on Schnauzers. Anim Genet 2011; 43:577-86. [DOI: 10.1111/j.1365-2052.2011.02300.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2011] [Indexed: 11/28/2022]
Affiliation(s)
| | - M. Schweizer
- Naturhistorisches Museum der Burgergemeinde Bern; Bernastrasse 15; CH 3005; Bern; Switzerland
| | - R. Kropatsch
- Humangenetik; Ruhr-Universität; Universitätsstr. 150; 44801; Bochum; Germany
| | - G. Dekomien
- Humangenetik; Ruhr-Universität; Universitätsstr. 150; 44801; Bochum; Germany
| | - O. Distl
- Institut für Tierzucht und Vererbungsforschung; Stiftug Tierärztliche Hochschule Hannover; Bünteweg 17p; 30559; Hannover; Germany
| | - M. S. Fischer
- Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum; Friedrich-Schiller-Universität; Erbertstr. 1; 07743; Jena; Germany
| | - J. T. Epplen
- Humangenetik; Ruhr-Universität; Universitätsstr. 150; 44801; Bochum; Germany
| | - S. T. Hertwig
- Naturhistorisches Museum der Burgergemeinde Bern; Bernastrasse 15; CH 3005; Bern; Switzerland
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Ding L, Wiener H, Abebe T, Altaye M, Go RCP, Kercsmar C, Grabowski G, Martin LJ, Khurana Hershey GK, Chakorborty R, Baye TM. Comparison of measures of marker informativeness for ancestry and admixture mapping. BMC Genomics 2011; 12:622. [PMID: 22185208 PMCID: PMC3276602 DOI: 10.1186/1471-2164-12-622] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 12/20/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Admixture mapping is a powerful gene mapping approach for an admixed population formed from ancestral populations with different allele frequencies. The power of this method relies on the ability of ancestry informative markers (AIMs) to infer ancestry along the chromosomes of admixed individuals. In this study, more than one million SNPs from HapMap databases and simulated data have been interrogated in admixed populations using various measures of ancestry informativeness: Fisher Information Content (FIC), Shannon Information Content (SIC), F statistics (FST), Informativeness for Assignment Measure (In), and the Absolute Allele Frequency Differences (delta, δ). The objectives are to compare these measures of informativeness to select SNP markers for ancestry inference, and to determine the accuracy of AIM panels selected by each measure in estimating the contributions of the ancestors to the admixed population. RESULTS FST and In had the highest Spearman correlation and the best agreement as measured by Kappa statistics based on deciles. Although the different measures of marker informativeness performed comparably well, analyses based on the top 1 to 10% ranked informative markers of simulated data showed that In was better in estimating ancestry for an admixed population. CONCLUSIONS Although millions of SNPs have been identified, only a small subset needs to be genotyped in order to accurately predict ancestry with a minimal error rate in a cost-effective manner. In this article, we compared various methods for selecting ancestry informative SNPs using simulations as well as SNP genotype data from samples of admixed populations and showed that the In measure estimates ancestry proportion (in an admixed population) with lower bias and mean square error.
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Affiliation(s)
- Lili Ding
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Howard Wiener
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tilahun Abebe
- Department of Biology, University of Northern Iowa, Cedar Falls, IA, USA
| | - Mekbib Altaye
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Rodney CP Go
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Carolyn Kercsmar
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Greg Grabowski
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Lisa J Martin
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Gurjit K Khurana Hershey
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Ranajit Chakorborty
- Center for Computational Genomics, Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Tesfaye M Baye
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
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Wenceslau CV, Miglino MA, Martins DS, Ambrósio CE, Lizier NF, Pignatari GC, Kerkis I. Mesenchymal Progenitor Cells from Canine Fetal Tissues: Yolk Sac, Liver, and Bone Marrow. Tissue Eng Part A 2011; 17:2165-76. [DOI: 10.1089/ten.tea.2010.0678] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Cristiane Valverde Wenceslau
- Departments of Surgery and Pathology, University of São Paulo, São Paulo, Brazil
- National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC), Ribeirão Preto, Brazil
| | - Maria Angélica Miglino
- Departments of Surgery and Pathology, University of São Paulo, São Paulo, Brazil
- National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC), Ribeirão Preto, Brazil
| | - Daniele Santos Martins
- Faculty of Animal Sciences and Food Engineering, University of São Paulo, São Paulo, Brazil
| | - Carlos Eduardo Ambrósio
- National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC), Ribeirão Preto, Brazil
- Faculty of Animal Sciences and Food Engineering, University of São Paulo, São Paulo, Brazil
| | | | | | - Irina Kerkis
- Faculty of Animal Sciences and Food Engineering, University of São Paulo, São Paulo, Brazil
- Laboratory of Genetics, Butantan Institute, São Paulo, Brazil
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Lequarré AS, Andersson L, André C, Fredholm M, Hitte C, Leeb T, Lohi H, Lindblad-Toh K, Georges M. LUPA: a European initiative taking advantage of the canine genome architecture for unravelling complex disorders in both human and dogs. Vet J 2011; 189:155-9. [PMID: 21752675 DOI: 10.1016/j.tvjl.2011.06.013] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The domestic dog offers a unique opportunity to explore the genetic basis of disease, morphology and behaviour. Humans share many diseases with our canine companions, making dogs an ideal model organism for comparative disease genetics. Using newly developed resources, genome-wide association studies in dog breeds are proving to be exceptionally powerful. Towards this aim, veterinarians and geneticists from 12 European countries are collaborating to collect and analyse the DNA from large cohorts of dogs suffering from a range of carefully defined diseases of relevance to human health. This project, named LUPA, has already delivered considerable results. The consortium has collaborated to develop a new high density single nucleotide polymorphism (SNP) array. Mutations for four monogenic diseases have been identified and the information has been utilised to find mutations in human patients. Several complex diseases have been mapped and fine mapping is underway. These findings should ultimately lead to a better understanding of the molecular mechanisms underlying complex diseases in both humans and their best friend.
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Affiliation(s)
- Anne-Sophie Lequarré
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000 Liège, Belgium.
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The function of dog models in developing gene therapy strategies for human health. Mamm Genome 2011; 22:476-85. [PMID: 21732191 DOI: 10.1007/s00335-011-9348-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 06/18/2011] [Indexed: 10/18/2022]
Abstract
The domestic dog is of great benefit to humankind, not only through companionship and working activities cultivated through domestication and selective breeding, but also as a model for biomedical research. Many single-gene traits have been well-characterized at the genomic level, and recent advances in whole-genome association studies will allow for better understanding of complex, multigenic hereditary diseases. Additionally, the dog serves as an invaluable large animal model for assessment of novel therapeutic agents. Thus, the dog has filled a crucial step in the translation of basic research to new treatment regimens for various human diseases. Four well-characterized diseases in canine models are discussed as they relate to other animal model availability, novel therapeutic approach, and extrapolation to human gene therapy trials.
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Abstract
BACKGROUND Our understanding of disease is increasingly informed by changes in gene expression between normal and abnormal tissues. The release of the canine genome sequence in 2005 provided an opportunity to better understand human health and disease using the dog as clinically relevant model. Accordingly, we now present the first genome-wide, canine normal tissue gene expression compendium with corresponding human cross-species analysis. METHODOLOGY/PRINCIPAL FINDINGS The Affymetrix platform was utilized to catalogue gene expression signatures of 10 normal canine tissues including: liver, kidney, heart, lung, cerebrum, lymph node, spleen, jejunum, pancreas and skeletal muscle. The quality of the database was assessed in several ways. Organ defining gene sets were identified for each tissue and functional enrichment analysis revealed themes consistent with known physio-anatomic functions for each organ. In addition, a comparison of orthologous gene expression between matched canine and human normal tissues uncovered remarkable similarity. To demonstrate the utility of this dataset, novel canine gene annotations were established based on comparative analysis of dog and human tissue selective gene expression and manual curation of canine probeset mapping. Public access, using infrastructure identical to that currently in use for human normal tissues, has been established and allows for additional comparisons across species. CONCLUSIONS/SIGNIFICANCE These data advance our understanding of the canine genome through a comprehensive analysis of gene expression in a diverse set of tissues, contributing to improved functional annotation that has been lacking. Importantly, it will be used to inform future studies of disease in the dog as a model for human translational research and provides a novel resource to the community at large.
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Wilkinson S, Wiener P, Archibald AL, Law A, Schnabel RD, McKay SD, Taylor JF, Ogden R. Evaluation of approaches for identifying population informative markers from high density SNP chips. BMC Genet 2011; 12:45. [PMID: 21569514 PMCID: PMC3118130 DOI: 10.1186/1471-2156-12-45] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 05/13/2011] [Indexed: 12/31/2022] Open
Abstract
Background Genetic markers can be used to identify and verify the origin of individuals. Motivation for the inference of ancestry ranges from conservation genetics to forensic analysis. High density assays featuring Single Nucleotide Polymorphism (SNP) markers can be exploited to create a reduced panel containing the most informative markers for these purposes. The objectives of this study were to evaluate methods of marker selection and determine the minimum number of markers from the BovineSNP50 BeadChip required to verify the origin of individuals in European cattle breeds. Delta, Wright's FST, Weir & Cockerham's FST and PCA methods for population differentiation were compared. The level of informativeness of each SNP was estimated from the breed specific allele frequencies. Individual assignment analysis was performed using the ranked informative markers. Stringency levels were applied by log-likelihood ratio to assess the confidence of the assignment test. Results A 95% assignment success rate for the 384 individually genotyped animals was achieved with < 80, < 100, < 140 and < 200 SNP markers (with increasing stringency threshold levels) across all the examined methods for marker selection. No further gain in power of assignment was achieved by sampling in excess of 200 SNP markers. The marker selection method that required the lowest number of SNP markers to verify the animal's breed origin was Wright's FST (60 to 140 SNPs depending on the chosen degree of confidence). Certain breeds required fewer markers (< 100) to achieve 100% assignment success. In contrast, closely related breeds require more markers (~200) to achieve > 95% assignment success. The power of assignment success, and therefore the number of SNP markers required, is dependent on the levels of genetic heterogeneity and pool of samples considered. Conclusions While all SNP selection methods produced marker panels capable of breed identification, the power of assignment varied markedly among analysis methods. Thus, with effective exploration of available high density genetic markers, a diagnostic panel of highly informative markers can be produced.
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Affiliation(s)
- Samantha Wilkinson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK.
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Overall KL. That dog is smarter than you know: advances in understanding canine learning, memory, and cognition. Top Companion Anim Med 2011; 26:2-9. [PMID: 21435620 DOI: 10.1053/j.tcam.2011.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 01/07/2011] [Indexed: 11/11/2022]
Abstract
Tests of canine cognition are now receiving much deserved attention. Not only are dogs excellent models for human anxiety-related conditions and those involving brain aging, but how dogs learn and problem solve are interesting stand-alone topics. A number of factors can affect learning at the molecular level including stress or distress, factors that affect olfaction, effects of breed and nutritional factors including that may affect available brain energy. This review provides an overview of how these factors may affect baseline learning and brain aging.
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Affiliation(s)
- Karen L Overall
- Center for Neurobiology and Behavior, Psychiatry Department, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
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Guo G, Zhou Z, Wang Y, Zhao K, Zhu L, Lust G, Hunter L, Friedenberg S, Li J, Zhang Y, Harris S, Jones P, Sandler J, Krotscheck U, Todhunter R, Zhang Z. Canine hip dysplasia is predictable by genotyping. Osteoarthritis Cartilage 2011; 19:420-9. [PMID: 21215318 PMCID: PMC3065507 DOI: 10.1016/j.joca.2010.12.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 12/14/2010] [Accepted: 12/21/2010] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To establish a predictive method using whole genome genotyping for early intervention in canine hip dysplasia (CHD) risk management, for the prevention of the progression of secondary osteoarthritis (OA), and for selective breeding. DESIGN Two sets of dogs (six breeds) were genotyped with dense SNPs covering the entire canine genome. The first set contained 359 dogs upon which a predictive formula for genomic breeding value (GBV) was derived by using their estimated breeding value (EBV) of the Norberg angle (a measure of CHD) and their genotypes. To investigate how well the formula would work for an individual dog with genotype only (without using EBV), a cross validation was performed by masking the EBV of one dog at a time. The genomic data and the EBV of the remaining dogs were used to predict the GBV for the single dog that was left out. The second set of dogs included 38 new Labrador retriever dogs, which had no pedigree relationship to the dogs in the first set. RESULTS The cross validation showed a strong correlation (R>0.7) between the EBV and the GBV. The independent validation showed a moderate correlation (R=0.5) between GBV for the Norberg angle and the observed Norberg angle (no EBV was available for the new 38 dogs). Sensitivity, specificity, positive and negative predictive values of the genomic data were all above 70%. CONCLUSIONS Prediction of CHD from genomic data is feasible, and can be applied for risk management of CHD and early selection for genetic improvement to reduce the prevalence of CHD in breeding programs. The prediction can be implemented before maturity, at which age current radiographic screening programs are traditionally applied, and as soon as DNA is available.
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Affiliation(s)
- Gang Guo
- Department of Animal Science, China Agricultural University, Beijing, China
| | - Zhengkui Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
,Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
,Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Yachun Wang
- Department of Animal Science, China Agricultural University, Beijing, China
| | - Keyan Zhao
- Department of Computational Biology and Statistics, Cornell University, Ithaca, New York, United States of America
| | - Lan Zhu
- Department of Statistics, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - George Lust
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, United States of America
| | - Linda Hunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Steven Friedenberg
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Zhang
- Department of Animal Science, China Agricultural University, Beijing, China
| | - Stephen Harris
- The WALTHAM Centre for Pet Nutrition, Waltham on the Wolds, Leicestershire, UK
| | - Paul Jones
- The WALTHAM Centre for Pet Nutrition, Waltham on the Wolds, Leicestershire, UK
| | - Jody Sandler
- Guiding Eyes for the Blind, Yorktown Hts, New York, United States of America
| | - Ursula Krotscheck
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Rory Todhunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Zhiwu Zhang
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
,Address for correspondence: Zhiwu Zhang, Institute for Genomic Diversity, Biotechnology, Cornell University, Ithaca NY 14853, Phone: 607 255 3270, Fax: 607 255 6465,
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