Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection

Citation: Koltes, J. E., Fritz-Waters, E., Eisley, C. J., Choi, I., Bao, H., Kommadath, A., . . . Reecy, J. M. (2015). Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection. Bmc Genomics, 16, 13. doi:10.1186/s12864-015-1635-9Background: Previously, we identified a major quantitative trait locus (QTL) for host response to Porcine Respiratory and Reproductive Syndrome virus (PRRSV) infection in high linkage disequilibrium (LD) with SNP rs80800372 on Sus scrofa chromosome 4 (SSC4). Results: Within this QTL, guanylate binding protein 5 (GBP5) was differentially expressed (DE) (p < 0.05) in blood from AA versus AB rs80800372 genotyped pigs at 7,11, and 14 days post PRRSV infection. All variants within the GBP5 transcript in LD with rs80800372 exhibited allele specific expression (ASE) in AB individuals (p < 0.0001). A transcript re-assembly revealed three alternatively spliced transcripts for GBP5. An intronic SNP in GBP5, rs340943904, introduces a splice acceptor site that inserts five nucleotides into the transcript. Individuals homozygous for the unfavorable AA genotype predominantly produced this transcript, with a shifted reading frame and early stop codon that truncates the 88 C-terminal amino acids of the protein. RNA-seq analysis confirmed this SNP was associated with differential splicing by QTL genotype (p < 0.0001) and this was validated by quantitative capillary electrophoresis (p < 0.0001). The wild-type transcript was expressed at a higher level in AB versus AA individuals, whereas the five-nucleotide insertion transcript was the dominant form in AA individuals. Splicing and ASE results are consistent with the observed dominant nature of the favorable QTL allele. The rs340943904 SNP was also 100 % concordant with rs80800372 in a validation population that possessed an alternate form of the favorable B QTL haplotype. Conclusions: GBP5 is known to play a role in inflammasome assembly during immune response. However, the role of GBP5 host genetic variation in viral immunity is novel. These findings demonstrate that rs340943904 is a strong candidate causal mutation for the SSC4 QTL that controls variation in host response to PRRSV.Additional Authors: Lunney, J. K.;Liu, P.;Carpenter, S.;Rowland, R. R. R.;Dekkers, J. C. M.;Reecy, J. M

Exploring genetic control of swine responses to viral diseases.

Our goal is to understand genomic control of viral disease responses focusing on the economically most important disease of pigs, porcine reproductive and respiratory syndrome

Investigating Preceding Determinants Affecting Primary School Students Online Learning Experience Utilizing Deep Learning Neural Network

The pandemic has caused all of the programs that are offered in primary schools to be interrupted. Evaluating the student’s learning at this level is essential because education development throughout the epidemic is critical, as there was no other educational alternative available during the pandemic. This study examines the use of deep learning neural network (DLNN) to evaluate the parameters influencing primary school students’ online learning experiences during the COVID-19 pandemic. The researchers considered this issue since primary students’ online learning experiences needed more attention. To carefully analyze the relationships between the parameters of primary students’ learning experience, an online questionnaire was utilized, subject to parents’ participation. A total of 385 Filipino elementary school students were selected and surveyed using a purposive sampling method. Participants in this research ranged in age from seven to thirteen and were supervised by their parents or legal guardians. The result of the study showed that open communication, social presence, design and organization, and facilitation had the most impact on predicting students’ experiences with online education, having a high accuracy from DLNN of 96.12%. This demonstrates the significance of open communication, draws attention to the importance of helping students feel welcomed and appreciated, and demonstrates the influence that instructors have on the overall positive learning experiences of their students. Finally, the findings of this study gave a strong framework and clear conclusions that both schools and the government’s education department could use to improve the way primary education is taught online across the country. Finally, the results and findings of this study could be applied and extended to other related education studies worldwide