Global transcriptional response of pig brain and lung to natural infection by Pseudorabies virus.

BACKGROUND: Pseudorabies virus (PRV) is an alphaherpesviruses whose native host is pig. PRV infection mainly causes signs of central nervous system disorder in young pigs, and respiratory system diseases in the adult. RESULTS: In this report, we have analyzed native host (piglets) gene expression changes in response to acute pseudorabies virus infection of the brain and lung using a printed human oligonucleotide gene set from Illumina. A total of 210 and 1130 out of 23,000 transcript probes displayed differential expression respectively in the brain and lung in piglets after PRV infection (p-value < 0.01), with most genes displaying up-regulation. Biological process and pathways analysis showed that most of the up-regulated genes are involved in cell differentiation, neurodegenerative disorders, the nervous system and immune responses in the infected brain whereas apoptosis, cell cycle control, and the mTOR signaling pathway genes were prevalent in the infected lung. Additionally, a number of differentially expressed genes were found to map in or close to quantitative trait loci for resistance/susceptibility to pseudorabies virus in piglets. CONCLUSION: This is the first comprehensive analysis of the global transcriptional response of the native host to acute alphaherpesvirus infection. The differentially regulated genes reported here are likely to be of interest for the further study and understanding of host viral gene interactions.

Corrigendum to "Incidence and detection of Beak and Feather disease virus in psittacine birds in the UAE" [Biomol. Detect. Quantif. 6 (January) (2016) 27-32].

[This corrects the article DOI: 10.1016/j.bdq.2015.10.001.].

Incidence and detection of beak and feather disease virus in psittacine birds in the UAE.

Beak and feather disease is caused by Circovirus, which affects actively growing beak and feather cells of avian species. The disease affects mainly young birds while older birds may overcome the disease with few lasting effects. Due to lack of treatment, the only way to control the disease is through hygiene and early diagnosis. As a diagnostic tool, we have established a Taqman probe based real-time PCR assay to detect the presence of the viral genome in psittacine birds in UAE and reported the incidence of circovirus in different species of psittacine birds. The sensitivity of our assay was found to be very high with detection limit of up to 3.5 fg of DNA in the sample. The mean prevalence of circovirus was found to be 58.33% in African Grey Parrots, 34.42% in Cockatoos, 31.8% in amazon parrots and 25.53% in Macaws. The Taqman assay is a quick, reliable and sensitive detection method that has been instrumental in identifying this disease that was not previously reported in the region.

Expression profile of genes from 12p in testicular germ cell tumors of adolescents and adults associated with i(12p) and amplification at 12p11.2-p12.1.

Gain of 12p material is invariably associated with testicular germ cell tumors (TGCTs) of adolescents and adults, most usually as an isochromosome 12p. We analyzed TGCTs with i(12p) using a global approach to expression profiling targeting chromosomes (comparative expressed sequence hybridization, CESH). This indicated overexpression of genes from 12p11.2-p12.1 relative to testis tissue and fibroblasts. The nonseminoma subtype showed higher levels of expression than seminomas. Notably, 12p11.2-p12.1 is amplified in about 10% of TGCTs and CESH analysis of such amplicon cases showed high levels of overexpression from this region. Microarray analysis, including cDNA clones representing most UniGene clusters from 12p11.2-p12.1, was applied to DNA and RNA from 5 TGCTs with amplification of 12p11.2-p12.1 and seven TGCTs with gain of the entire short arm of chromosome 12. Expression profiles were consistent with the CESH data and overexpression of EST595078, MRPS35 and LDHB at 12p11.2-p12.1 was detected in most TGCTs. High-level overexpression of BCAT1 was specific to nonseminomas and overexpression of genes such as CMAS, EKI1, KRAS2, SURB7 and various ESTs correlated with their amplification. Genes such as CCND2, GLU3, LRP6 and HPH1 at 12p13 were also overexpressed. The overexpressed sequences identified, particularly those in the region amplified, represent candidate genes for involvement in TGCT development.

Definition of chromosome aberrations in testicular germ cell tumor cell lines by 24-color karyotyping and complementary molecular cytogenetic analyses.

Many of the reported karyotypes for adult testicular germ cell tumors (GCTs) are complex and incomplete, although the presence of an isochromosome 12p, i(12p), and gain of 12p material have consistently been found. Here, an accurate definition of the chromosome aberrations associated with four cell lines derived from GCTs (GCT27, H12.1, Tera1, and Tera2) has been produced using 24-color karyotyping by mulifluor in situ hybridization, comparative genomic hybridization analysis, and further fluorescence in situ hybridization analysis to confirm some chromosomal assignments and refine involvement of specific regions of 12p. There was karyotypic heterogeneity. Isochromosomes in addition to i(12p) were found, as were other rearrangements with breakpoints at or near centromeric regions. The most frequent non-centromeric breakpoints were at 1p31 approximately p32, 1p21 approximately p22, 11q13, and Xq22, although consistent partner chromosomes were not involved. One cell line (Tera1) showed a subtle dosage increase in the copy number of a 12p probe known to be within the smallest overlapping region of amplification that has been defined in a number of testicular GCTs with amplicons at 12p11 approximately p12. The chromosome rearrangements and associated imbalances may be significant in GCT progression and the characterized cell lines can be used to investigate these further.

Association analysis between pseudorabies antibody and five single-nucleotide polymorphisms in pigs.

Pseudorabies has become endemic and represents a widespread problem for pig production in the world, causing great economic losses associated with reproductive failure and neonatal mortality in the pig industry. Most diseases are the results of mutations of functional genes. Single-nucleotide polymorphisms (SNPs) from the coding regions of the mediators of pro-inflammatory responses or other candidate genes in pigs could indicate their potential involvement in susceptibility or resistance to PrV (pseudorabies virus) infection. There have been no previous association studies with candidate host genes that may influence PrV phenotypic traits. In order to perform association studies to identify genes contributing to PrV phenotypes, the genotypes of five SNPs from four genes (IL10, CXCL12, BAT2 and EHMT2) were determined for 178 sow samples using a high throughput microarray-based methodology. PrV antibodies were tested by enzyme-linked immunosorbent assay (ELISA) to determine whether there was an association between antibody levels and particular genotypes. The association between SNP genotypes and the PrV antibody levels were analysed using the Duncan method of one-way ANOVA procedure using the SAS (Statistical Analysis Systems) software package. The results showed that the glycoprotein E-ELISA antibody level of pigs with genotypes 11(AA) and 12(AG) was significantly higher than in pigs with genotype 22(GG) (P < 0.05) of SNP in the gene EHMT2-SNP2. The SNP of EHMT2 may be an effective potential tool to identify susceptible and resistant animals when used in conjunction with traditional selection methods.

Association of four new single-nucleotide polymorphisms in follicle-stimulating hormone receptor and zona pellucida glycoprotein with reproductive traits in pigs.

Two new single-nucleotide polymorphisms (SNPs) (C1166T and G1190A) were discovered in the follicle-stimulating hormone receptor (FSHR) gene and two (G261A and T302C) in the zona pellucida glycoprotein (ZP3) gene. These SNPs were genotyped in three Chinese domestic purebred sow lines (42 Small Meishan, 46 Qingping and 41 Jinhua sows) and three European purebred sow lines (225 Duroc, 195 Large White and 65 Landrace sows) by using SNP chips. Phenotypic data including the functional teat number (i.e. milk-producing teats, TN) and number of piglets born alive per litter (NBA). These traits were tested for association with the genotypes of four SNPs. The association analysis revealed genotype of G261A in the ZP3 gene was significantly (P < 0.01) associated with overall NBA and NBA at later parities (NBA2+) but not with NBA at first parity (NBA1). There was a significant (P < 0.05) difference between sows with genotype GG (14.83 ± 0.18) and AA (14.26 ± 0.09) in TN at position 261 in the ZP3 gene. No significant associations were observed for the SNPs in the FSHR gene with NBA or TN in our populations. The results showed that the new SNPs in the ZP3 gene may be an effective potential marker to be used in conjunction with traditional selection methods.

Identification of mutations of zona pellucida glycoprotein (ZP3) and its association with pig reproductive traits.

Reproduction is a complex trait, controlled by genetic and environmental factors. Genetic improvement of this trait is important for animal breeders to improve the animal's production efficiency. Apart from genetic factors, animal production can be affected by environmental factors, i.e. the nursing ability of the sow, which is in turn affected directly by effective teat number (teats producing milk normally, TN) and number of piglets born alive (NBA). The objective of this study was to find new mutations, such as single nucleotide polymorphisms (SNPs) from the Zona Pellucida glycoprotein gene (ZP3) using Single Strand Chain Polymorphism (SSCP) and nucleotide sequencing and to investigate association between genetic variations and sow reproductive traits. We identified 13 new SNPs from exon 1, two new SNPs from intron 2, one SNP from intron 6 and a 18 bp (GCACGTGGTCCTCCTGG)-deletion/insertion from intron 2 of the ZP3 gene. Five out of these mutations were selected to genotype in five different breeds (Small Meishan, Qingping, Duroc, Landrace and Large White) and association with reproductive traits in European breeds (Duroc, Landrace and Large White). The sows with genotype AA had more 1.11 piglets NBA than of the sows with genotype AB (p < 0.05) in the 18 bp deletion/insertion of intron 2, while non-significant associations between the other mutations and reproductive traits (NBA and TN) were found.