Abstract:
:We evaluated differences in gene expression in pigs from the Porcine Reproductive and Respiratory Syndrome (PRRS) Host Genetics Consortium initiative showing a range of responses to PRRS virus infection. Pigs were allocated into four phenotypic groups according to their serum viral level and weight gain. RNA obtained from blood at 0, 4, 7, 11, 14, 28, and 42 days post-infection (DPI) was hybridized to the 70-mer 20K Pigoligoarray. We used a blocked reference design for the microarray experiment. This allowed us to account for individual biological variation in gene expression, and to assess baseline effects before infection (0 DPI). Additionally, this design has the flexibility of incorporating future data for differential expression analysis. We focused on evaluating transcripts showing significant interaction of weight gain and serum viral level. We identified 491 significant comparisons [false discovery rate (FDR) = 10%] across all DPI and phenotypic groups. We corroborated the overall trend in direction and level of expression (measured as fold change) at 4 DPI using qPCR (r = 0.91, p ≤ 0.0007). At 4 and 7 DPI, network and functional analyses were performed to assess if immune related gene sets were enriched for genes differentially expressed (DE) across four phenotypic groups. We identified cell death function as being significantly associated (FDR ≤ 5%) with several networks enriched for DE transcripts. We found the genes interferon-alpha 1(IFNA1), major histocompatibility complex, class II, DQ alpha 1 (SLA-DQA1), and major histocompatibility complex, class II, DR alpha (SLA-DRA) to be DE (p ≤ 0.05) between phenotypic groups. Finally, we performed a power analysis to estimate sample size and sampling time-points for future experiments. We concluded the best scenario for investigation of early response to PRRSV infection consists of sampling at 0, 4, and 7 DPI using about 30 pigs per phenotypic group.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Arceo ME,Ernst CW,Lunney JK,Choi I,Raney NE,Huang T,Tuggle CK,Rowland RR,Steibel JPdoi
10.3389/fgene.2012.00321subject
Has Abstractpub_date
2013-01-16 00:00:00pages
321issn
1664-8021journal_volume
3pub_type
杂志文章abstract::This study tests in a genetically informative design whether exercise behavior causally influences subjective wellbeing (SWB) and internalizing problems (INT). If exercise causally influences SWB and INT, genetic and environmental factors influencing exercise behavior will also influence SWB and INT. Furthermore, with...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00004
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pub_type: 杂志文章
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pub_type: 杂志文章,评审
doi:10.3389/fgene.2020.572045
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doi:10.3389/fgene.2019.00394
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2014.00402
更新日期:2014-11-21 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00514
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journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2014.00085
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abstract::Mosquitoes are one of the deadliest animals on earth because of their ability to transmit a wide range of human pathogens. Traditional mosquito control methods use chemical insecticides, but with dwindling long-term effectiveness and negative effects on the environment, microbial forms of control have become common al...
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pub_type: 杂志文章,评审
doi:10.3389/fgene.2020.504354
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abstract::Filamentous pathogens, such as phytopathogenic oomycetes and fungi, secrete a remarkable diversity of apoplastic effector proteins to facilitate infection, many of which are able to induce cell death in plants. Over the past decades, over 177 apoplastic cell death-inducing proteins (CDIPs) have been identified in fila...
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00310
更新日期:2014-01-17 00:00:00
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pub_type: 杂志文章
doi:10.3389/fgene.2020.575776
更新日期:2020-10-14 00:00:00
abstract::Apomixis, an asexual mode of reproduction through seeds, has immense scope for crop improvement due to its ability to fix hybrid vigor. In C. ciliaris, a predominantly apomictically reproducing range grass, apomixis is genetically controlled by an apospory-specific-genomic-region (ASGR) which is enriched with retrotra...
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pub_type: 杂志文章
doi:10.3389/fgene.2020.00795
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abstract::At the end of introns, the polypyrimidine tract (Py) is often close to the 3' AG in a consensus (Y)20NCAGgt in humans. Interestingly, we have found that they could also be separated by purine-rich elements including G tracts in thousands of human genes. These regulatory elements between the Py and 3' AG (REPA) mainly ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00741
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abstract::In genome wide association studies (GWAS), family-based studies tend to have less power to detect genetic associations than population-based studies, such as case-control studies. This can be an issue when testing if genes in a family-based GWAS have a direct effect on the phenotype of interest over and above their po...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00243
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journal_title:Frontiers in genetics
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doi:10.3389/fgene.2015.00259
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doi:10.3389/fgene.2019.00125
更新日期:2019-02-20 00:00:00
abstract::[This corrects the article on p. 23 in vol. 9, PMID: 29456554.]. ...
journal_title:Frontiers in genetics
pub_type: 杂志文章,已发布勘误
doi:10.3389/fgene.2018.00109
更新日期:2018-04-04 00:00:00
abstract::The arrangement of chromatin within interphase nuclei seems to be caused by topological constraints and related to gene expression depending on tissue and developmental stage. In yeast and animals it was found that homologous and heterologous chromatin association are required to realize faithful expression and DNA re...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2014.00389
更新日期:2014-11-13 00:00:00
abstract::The Galway sheep population is the only native Irish sheep breed and this livestock genetic resource is currently categorised as 'at-risk'. In the present study, comparative population genomics analyses of Galway sheep and other sheep populations of European origin were used to investigate the microevolution and recen...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00927
更新日期:2019-10-08 00:00:00
abstract::The phenotype of carcass traits in beef cattle are affected by random genetic and non-genetic effects, which both can be modulated by an environmental variable such as Temperature-Humidity Index (THI), a key environmental factor in cattle production. In this study, a multivariate reaction norm model (MRNM) was used to...
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pub_type: 杂志文章
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更新日期:2020-12-23 00:00:00
abstract::Accurate inference of causal gene regulatory networks from gene expression data is an open bioinformatics challenge. Gene interactions are dynamical processes and consequently we can expect that the effect of any regulation action occurs after a certain temporal lag. However such lag is unknown a priori and temporal a...
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pub_type: 杂志文章
doi:10.3389/fgene.2013.00303
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doi:10.3389/fgene.2019.00547
更新日期:2019-06-06 00:00:00
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pub_type: 杂志文章
doi:10.3389/fgene.2013.00097
更新日期:2013-05-31 00:00:00
abstract::The direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for direct measurement of RNA molecules without the need of conversion to complementary DNA, fragmentation or amplification. As such, it is virtually capable of detecting any given RNA modification present in the molecule that is being s...
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pub_type: 杂志文章
doi:10.3389/fgene.2020.00211
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