Proteomic analysis of dog plateletes and LFQ quantitation
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion
ORGANISM(S): Equus Caballus (horse)
TISSUE(S): Blood Platelet, Platelet
SUBMITTER: 
Sheng Zhang
LAB HEAD: Sheng Zhang
PROVIDER: PXD015935 | Pride | 2021-09-08
REPOSITORIES: Pride
Dataset's files
Items per page: 5 1 - 5 of 40 |
Publications
The canine activated platelet secretome (CAPS): A translational model of thrombin-evoked platelet activation response.
Cremer Signe E SE Catalfamo James L JL Goggs Robert R Seemann Stefan E SE Kristensen Annemarie T AT Szklanna Paulina B PB Maguire Patricia B PB Brooks Marjory B MB
Research and practice in thrombosis and haemostasis 20201203 1
<h4>Background</h4>Domestic dogs represent a translational animal model to study naturally occurring human disease. Proteomics has emerged as a promising tool for characterizing human platelet pathophysiology; thus a detailed characterization of the core canine activated platelet secretome (CAPS) will enhance utilization of the canine model. The objectives of this study were development of a robust, high throughput, label-free approach for proteomic identification and quantification of the canin ...[more]
Similar Datasets
Project description:The inherent diversity of canines is closely intertwined with the unique color patterns of each dog population. These variations in color patterns are believed to have originated through mutations and selective breeding practices that occurred during and after the domestication of dogs from wolves. To address the significant gaps that persist in comprehending the evolutionary processes that underlie the development of these patterns, we generated and analyzed deep-sequenced genomes of 113 Korean indigenous Jindo dogs that represent five distinct color patterns to identify the associated mutations in CBD103, ASIP, and MC1R. The degree of linkage disequilibrium and estimated allelic ages consistently indicate that the black-and-tan dogs descend from the first major founding population on Jindo island, compatible with the documented literature. We additionally demonstrate that black-and-tan dogs, in contrast to other color variations within the breed, exhibit a closer genetic affinity to ancient wolves from western Eurasia than those from eastern Eurasia. Lastly, population-specific genetic variants with moderate effects were identified, particularly in loci associated with traits underlying body size and behavioral variations, potentially explaining the observed phenotypic diversity based on coat colors. Overall, comparisons of whole genome sequences of each coat color population diverged from the same breed provided an unprecedented glimpse into the properties of evolutionary processes maintaining variation in Korean Jindo dog populations that were previously inaccessible.
2024-04-05 | E-MTAB-13939 | biostudies-arrayexpress
Project description:In this study, mass spectrometry was used to explore the canine tear proteome. Tear samples were obtained from six healthy dogs, and one-dimensional sodium dodecyl sulphate polyacrylamide gel electrophoresis (1D SDS-PAGE) was used as a first step to separate intact proteins into 17 bands. Each fraction was then trypsin digested and analysed by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF-MS/MS) to characterize the protein components in each fraction. In total, 125 tear proteins were identified, with MCA (Major Canine Allergen), Serum albumin, UPF0557 protein C10orf119 homolog, Collagen alpha-2(I) chain, Tyrosine -protein kinase Fer, Keratine type II cytoskeletal, Beta-crystallin B2, Interleukin-6 and Desmin occuring as the most confident ones with the highest scores. The results showed that the proteomic strategy used in this study was successful in the analysis of the dog tear proteome. To the best of our knowledge, this study is the first to report the comprehensive proteome profile of tears from healthy dogs by 1D SDS PAGE and MALDI-TOF.
2015-11-23 | PXD003124 | Pride
Project description:Free-breeding dogs have occupied the Galápagos islands at least since the 1830s, however, it was not until the 1900s that dog populations grew substantially, endangering wildlife and spreading disease. In 1981, authorities sanctioned the culling of free-roaming dogs. Yet there are currently large free-roaming dog populations of unknown ancestry on the islands of Isabela and Santa Cruz, whose ancestry has never been assessed on a genome-wide scale. Thus, we performed a complete genomic analysis of the current Galápagos dog population as well as historical Galápagos dogs sampled between 1969 and 2003, testing for population structure, admixture, and shared ancestry. Our dataset included samples from 187 modern and six historical Galápagos dogs, together with whole genome sequence from over 2,000 modern purebred and village dogs. Our results indicate that modern Galápagos dogs are recently admixed with purebred dogs but show no evidence of a population bottleneck related to the culling. Additionally, IBD analyses reveal evidence of shared shepherd-dog ancestry in the historical Galápagos dogs. Overall, our results demonstrate that the 1980s culling of dogs was ineffective in controlling population size and did little to reduce genetic diversity, instead producing a stable and expanding population with genomic signatures of historical dogs remaining today. The insights from this study can be used to improve population control strategies for the Galápagos Islands and other endangered endemic communities worldwide.
2024-10-01 | GSE276576 | GEO
Project description:Diverse dataset of 1247 dogs from many breeds and wolves used to investigate the origins of dog domestication
2014-11-20 | GSE63439 | GEO
Project description:Dogs are commonly used models of human inherited retinal disorders. Because the dog retina contains a macula-like region, dogs are susceptible to maculopathies with many shared genetic etiologies with humans. Human macular gene expression has been characterized and provides insight into the underlying basis of macular disease. We sought to compare macular gene expression profiles in dogs and humans and interrogate macular disease-associated genes for differential expression between macula and periphery. RNA sequencing was performed on 8mm samples of the dog macular region and superior peripheral region, sampling retina and retinal pigmented epithelium/choroid separately. Read sequences were mapped to CanFam3.1 and raw read counts were analyzed to determine significantly differentially expressed genes between macula and periphery within each tissue. A similar analytic pipeline was used with a published dataset of human samples to allow direct dog/human comparisons. Pathways and processes involved in significantly DEGs were identified using the Database for Annotation, Visualization and Integrated Discovery. Dogs and humans shared the extent and direction of macular retinal differential gene expression, with multiple shared biological pathways implicated in differential expression. There were fewer similarities between dog and human in the supporting tissues of the retina (the RPE, choroid, sclera). Many genes implicated in heritable retinal and macular disorders in both dogs and humans were differentially expressed between macula and periphery. Approximately 2/3 of genes associated with human age-related macular degeneration were differentially expressed in at least one human tissue, whereas approximately half were differentially expressed in at least one dog tissue. This work underpins the dog macular retinal region as analogous to the human macula in terms of differential gene expression. Whilst age-related maculopathy has not been described in dogs, evidence supports the study of aging of the macula and susceptibility to age-associated pathology in dogs.
2024-07-25 | GSE227619 | GEO
Project description:The complexity and low accessibility of the human brain make it challenging to understand its development, function, and disorders. Brain diseases including neurodegenerative disease and psychiatric diseases incur huge medical and social burdens without effective treatments. While mouse has substantially contributed to our current understanding of brain, the translational value of mouse models may limit to certain aspects of a disease due to the apparent differences in brain structure (gyrencephalic versus lissencephalic) and behavior between mice and humans. Nonhuman primates are, in theory, the best animals to understand human brains. However, monkeys are extremely expensive and inefficient to reproduce (5 years to reach sexual maturity and only one progeny per pregnancy). Dogs have similar gyrencephalic brain structure as humans. Due to the human selection and domestication, dogs have developed exquisite and complex dog-human heterospecific social capabilities. For example, dogs can learn by observing human social and communicative behaviors such as a pointing gesture to find hidden food. Indeed, psychologists have learned that average dogs can count, reason and recognize words and gestures on par with a human 2-year-old. Compared with nonhuman primates, dogs have relatively lower costs of husbandry and shorter breeding times, with multiple offspring per pregnancy. Given that gene editing and animal cloning by somatic nuclear transfer have been available in dogs in recent years and other advantages described above, dogs are thus a potential model for studying human brain development and disease. However, to what extent the dog brain is conserved with the human brain at the molecular level remains unclear.
2022-08-12 | PXD034449 | Pride
Project description:The complexity and low accessibility of the human brain make it challenging to understand its development, function, and disorders. Brain diseases including neurodegenerative disease and psychiatric diseases incur huge medical and social burdens without effective treatments. While mouse has substantially contributed to our current understanding of brain, the translational value of mouse models may limit to certain aspects of a disease due to the apparent differences in brain structure (gyrencephalic versus lissencephalic) and behavior between mice and humans. Nonhuman primates are, in theory, the best animals to understand human brains. However, monkeys are extremely expensive and inefficient to reproduce (5 years to reach sexual maturity and only one progeny per pregnancy). Dogs have similar gyrencephalic brain structure as humans. Due to the human selection and domestication, dogs have developed exquisite and complex dog-human heterospecific social capabilities. For example, dogs can learn by observing human social and communicative behaviors such as a pointing gesture to find hidden food. Indeed, psychologists have learned that average dogs can count, reason and recognize words and gestures on par with a human 2-year-old. Compared with nonhuman primates, dogs have relatively lower costs of husbandry and shorter breeding times, with multiple offspring per pregnancy. Given that gene editing and animal cloning by somatic nuclear transfer have been available in dogs in recent years and other advantages described above, dogs are thus a potential model for studying human brain development and disease. However, to what extent the dog brain is conserved with the human brain at the molecular level remains unclear.
2022-08-12 | PXD033420 | Pride
Project description:Diverse dataset of 1247 dogs from many breeds and wolves used to investigate the origins of dog domestication DNA for 1228 dogs from 35 breeds and 19 wolves was extracted from whole blood samples and genotyped on the Affymetrix Canine v2 Arrays. Genotypes were called using Affymetrix's snp5-probeset-genotype software and the BRLMM-P calling algorithm. The included breed designations are owner reported.
2014-11-20 | E-GEOD-63439 | biostudies-arrayexpress
Project description:Gastrointestinal (GI) mucus is continuously secreted and lines the entire length of the GI tract. Essential for health, it keeps the noxious luminal content away from the epithelium and propels forward the digesta. The aim of our study was to characterize the composition and structures of mucus throughout the various GI segments in dog. Mucus from the stomach, small intestine (duodenum, jejunum, ileum), and large intestine (cecum, proximal and distal colon) was collected from 5 dogs. pH and water content of GI mucus and digesta were analyzed. Composition of all GI-tract segments from a domestic and a laboratory dog was determined by label-free global proteomics. A colonic-focussed composition analysis with TMT-labelled proteomics was used on jenunal and proximal and distal colonic mucus samples from 3 laboratory and 1 domestic dog. Finally, the composition of jejunal and colonic mucus samples of 3 laboratory and 1 domestic dog was evaluated with lipidomics and metabolomics. Structural properties were investigated using cryoSEM and rheology. The proteome was similar across the different GI segments. The highest abundant secreted gel-forming mucin in the gastric mucus was mucin 5AC, whether mucin 2 had highest abundance in the intestinal mucus. Lipid and metabolite abundance was generally higher in the jejunal mucus than the colonic mucus. In conclusion, the mucus is a highly viscous and hydrated material. The proteins, lipids and metabolites were similar throughout the GI tract, although abundances depended on location. These data provide an important baseline for future studies on human and canine intestinal diseases and the dog model in drug absorption.
2022-03-07 | PXD029356 | Pride
Project description:Phosphorylation is the most commonly studied protein post-translational modification (PTM) in biological systems due to its importance in controlling cell division, survival, growth, etc. Despite the thorough research in phosphoproteomics of cells and tissues there is little information on circulating phosphoproteins. We compared serum from 10 healthy dogs and 10 dogs affected by B. canis-caused babesiosis with no organ dysfunctions by employing gel-free LC-MS/MS analysis of individual samples and tandem mass tag (TMT) label-based quantitative analyses of pools, both supported by phosphopeptide enrichment. Results showed a moderate number of phosphorylated proteins (50-55), with 89 phosphorylation sites not previously published for dogs although a number of them matched phosphorylation sites found in mammalian orthologs. Three phosphopeptides showed significant variation in babesiosis-affected dog sera compared to controls: Serum amyloid A (SAA) phosphorylated at serine 101 (up-regulation), kininogen 1 phosphorylated at threonine 326, and fibrinogen α phosphorylated at both threonine 20 and serine 22 (down-regulation). 71.9 % of the detected phosphorylated sites were phosphoserine, 16.8 % phosphothreonine and only 11.2 % phosphotyrosine residues. TMT label-based quantitative analysis showed α-2-HS-glycoprotein / Fetuin A to be the most abundant phosphoprotein (50-70% of all phosphoproteins) followed by kininogen-1 (10-20%). The alterations of phosphorylated proteins observed in canine babesiosis caused by Babesia canis suggest new insights into the largely neglected role of extracellular protein phosphorylation in health and disease, encouraging urgent further research on this area. To the best of our knowledge the present study represents the first attempt to characterize canine serum phosphoproteome.
2018-11-13 | PXD010894 | Pride