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ABSTRACT:
PROVIDER: PRJNA984448 | ENA |
REPOSITORIES: ENA
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Project description:Recents studies in mammalian genomes have uncovered the extent of copy number variation (CNV) that contributes to phenotypic diversity, including health and disease status. Here we report the first glimpse of CNVs in the pig genome covering part of the chromosomes 4, 7, 14 and 17 already sequenced and assembled. We used a custom tiling oligonucleotide array with a median probe spacing of 409 bp to screen 12 unrelated Duroc boar founders of a vast-family material. After a strict CNV calling pipeline it was identified 40 copy number variable regions covering all the four chromosomes, with some overlapping segmental duplications and pig unigenes. This CNV snapshot analysis lays the groundwork for a better understanding of porcine phenotypes and genotypes for the identification of important economic traits. Keywords: comparative genome hybridization, CNV, Sus Scrofa, Nimblegen tiling array A custom 385k tiling-path array CGH was designed (Nimblegen Systems) to cover the preliminary Sus Scrofa assembly for chromosomes 4, 7, 14 and 17, from the August 2007 release (http://www.sanger.ac.uk/Projects/S_scrofa/), which was the newest version at the time of the experiment. From a pig family-material comprising 14 boar founders, 700 sows and about 12.000 offspring, 12 Duroc boar founders (A, B, C, D, E, G, H, J, K, L, M and N) were selected to function as test animals. An unrelated boar of the Hampshire breed was selected as the common reference. Each of the 12 boars were hybridized twice (technical replicates, 24 arrays) against the common reference.
2010-06-21 | E-GEOD-10753 | biostudies-arrayexpress
Project description:Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly impact on human and animal health worldwide. Mycobacterial life cycle is complex and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Eurasian wild boar (Sus scrofa) are natural reservoir hosts for MTBC and a model for mycobacterial infection and tuberculosis (TB). In the wild boar TB model, mycobacterial infection affects the expression of innate and adaptive immune response genes in mandibular lymph nodes and oropharyngeal tonsils and biomarkers have been proposed as correlates with resistance to natural infection. However, the mechanisms used by mycobacteria to manipulate host immune response are not fully characterized. Our hypothesis is that the immune system proteins under-represented in infected animals when compared to uninfected controls are used by mycobacteria to guarantee pathogen infection and transmission. To address this hypothesis, a comparative proteomics approach was used to compare host response between uninfected (TB-) and M. bovis-infected young (TB+) and adult animals with different infection status [TB lesions localized in the head (TB+) or affecting multiple organs (TB++)]. The results identified host immune system proteins that play an important role in host response to mycobacteria. Calcium binding protein A9, Heme peroxidase, Lactotransferrin, Cathelicidin and Peptidoglycan-recognition protein were under-represented in TB+ animals when compared to uninfected TB- controls but protein levels increased as infection progressed in TB++ animals when compared to TB- and/or TB+ adult wild boar. MHCI was the only protein over-represented in TB+ adult wild boar when compared to uninfected TB- controls. The results reported here suggested that M. bovis manipulates host immune response by reducing the production of immune system proteins. However, as infection progresses, wild boar immune response recover to limit pathogen multiplication and promote survival that also facilitates pathogen transmission.
2016-03-10 | PXD003251 | Pride
Project description:For gaining additional insights into the composition of the testicular proteome of the domestic pig (Sus scrofa domestica), we conducted 2DE-MS. Two-dimensional SDS PAGE was run on testicular lysates of three boars, with three gels per boar. Upon matching across gels, we arbitrarily selected protein spots for mass spectrometry analysis. Excised slices were vacuum dried and soaked with digestion buffer containing trypsin (0.01 μg/μl), followed by overnight incubation at 37°C in the same buffer without trypsin. Subsequently, peptides were extracted in solvents of increasing acetonitrile content, by sonication. Upon vacuum-centrifugation, peptides were reconstituted in 0.1% formic acid (FA). Following this, peptides were fractionated by reversed phase liquid chromatography (C18; buffer A: 0.1% FA dissolved in HPLC-H2O; buffer B: 0.1% FA, dissolved in CAN; flow-rate: 0.4 µL/min; gradient: 2-30% in 30 minutes). Eluted peptides were injected via an electrospray ionization interface into a Q-TOF mass spectrometer (one boar, Q TOF Ultima, Micromass/Waters, Manchester, UK) and an ion-trap mass spectrometer (two other boars, XCT ion-trap, Agilent Technologies, Waldbronn, Germany). We used ProteomeDiscoverer 2.4 (Thermo Fisher Scientific, San Jose, USA) for peptide and protein identification. Using Sequest HT, we searched peak lists (*.mgf) against the Sus scrofa reference proteome database (UniProt Proteome ID: UP000008227, 49,793 proteins).
2022-08-12 | PXD015649 | Pride
Project description:Sus scrofa strain:Duroc and wild boar Transcriptome or Gene expression
| PRJNA173041 | ENA
Project description:Escherichia coli STEC strains isolated from raw meat-based diets for companion animals
| PRJNA694525 | ENA
Project description:Proteins are essential for sperm function, including fertilizing capacity. Pig spermatozoa, emitted in well-defined ejaculate fractions, clearly vary in their functionality, which would be related to differences in protein composition. This study aimed firstly to update the porcine sperm proteome and secondly to identify proteins differentially expressed among mature spermatozoa from cauda epididymis and those fortuitously delivered in different ejaculate portions. Nine ejaculates from nine mature and fertile boars were manually collected in three separate ejaculate portions: the first 10 mL of sperm-rich ejaculate fraction (SRF), the rest of SRF and the post-SRF. The contents of cauda epididymides of the same boars was collected post-mortem by perfusion. All samples were centrifuged, pooling the resulting sperm pellets within the respective source-sample, which were later split to generate two technical replicates per source. The final eight sperm samples were subjected to iTRAQ-based 2D-LC-MS/MS for protein identification and quantification. A total of 1,723 proteins were identified (974 of Sus Scrofa taxonomy) and 1,602 of them were also quantified (960 of Sus Scrofa taxonomy). After an ANOVA test, 32 Sus Scrofa proteins showed quantitative differences (P < 0.01) among the sperm samples, which were particularly relevant for the functionality of spermatozoa fortuitously ejaculated in the post-SRF. The present study is the first showing quantitative differences in the protein profile of mature spermatozoa, involving proteins clearly implicated in sperm function, that prove the protein profile of boar spermatozoa is remodelled during ejaculation . These findings provide a valuable groundwork for further studies focused on identifying protein biomarkers of sperm fertility.
2018-10-02 | PXD010062 | Pride