Genome-wide scans for selection signatures in indigenous pigs revealed candidate genes relating to heat tolerance

Heat stress is a major problem that constrains pig productivity. Understanding and identifying adaptation to heat stress has been the focus of recent studies, and the identification of genome-wide selection signatures can provide insights into the mechanisms of environmental adaptation. Here, we generated whole-genome re-sequencing data from six Chinese indigenous pig populations to identify genomic regions with selection signatures related to heat tolerance using multiple methods: three methods for intra-population analyses (Integrated Haplotype Score, Runs of Homozygosity and Nucleotide diversity Analysis) and three methods for inter-population analyses (Fixation index (F_ST), Cross-population Composite Likelihood Ratio and Cross-population Extended Haplotype Homozygosity). In total, 1 966 796 single nucleotide polymorphisms were identified in this study. Genetic structure analyses and F_ST indicated differentiation among these breeds. Based on information on the location environment, the six breeds were divided into heat and cold groups. By combining two or more approaches for selection signatures, outlier signals in overlapping regions were identified as candidate selection regions. A total of 163 candidate genes were identified, of which, 29 were associated with heat stress injury and anti-inflammatory effects. These candidate genes were further associated with 78 Gene Ontology functional terms and 30 Kyoto Encyclopedia of Genes and Genomes pathways in enrichment analysis (P < 0.05). Some of these have clear relevance to heat resistance, such as the AMPK signalling pathway and the mTOR signalling pathway. The results improve our understanding of the selection mechanisms responsible for heat resistance in pigs and provide new insights of introgression in heat adaptation.

Peripheral CD4 +CD8 + double positive T cells: A potential marker to evaluate renal impairment susceptibility during systemic lupus erythematosus

Lupus nephritis (LN) has a high incidence in systemic lupus erythematosus (SLE) patients, but there is a lack of sensitive predictive markers. The purpose of the study was to investigate the association between the CD4 +CD8 + double positive T (DPT) lymphocytes and LN. The study included patients with SLE without renal impairment (SLE-NRI), LN, nephritic syndrome (NS), or nephritis. Peripheral blood lymphocyte subsets were analyzed by flow cytometry. Biochemical measurements were performed with peripheral blood in accordance with the recommendations proposed by the National Center for Clinical Laboratories. The proportions of DPT cells in the LN group were significantly higher than that in the SLE-NRI group ( t=4.012, P<0.001), NS group ( t=3.240, P=0.001), and nephritis group ( t=2.57, P=0.011). In the LN group, the risk of renal impairment increased significantly in a DPT cells proportion-dependent manner. The risk of LN was 5.136 times (95% confidence interval, 2.115-12.473) higher in cases with a high proportion of DPT cells than those whose proportion of DPT cells within the normal range. These findings indicated that the proportion of DPT cells could be a potential marker to evaluate LN susceptibility, and the interference of NS and nephritis could be effectively excluded when assessing the risk of renal impairment during SLE with DPT cell proportion.

The retinoblastoma 1 gene (RB1) modulates the proliferation of chicken preadipocytes

1. The objective of this study was to reveal the role of chicken RB1 (Gallus gallus RB1, gRB1) in the proliferation of preadipocytes. 2. To measure gene expression of gRB1 in the proliferation of chicken preadipocyte, quantitative real-time PCR was used. The expression levels of gRB1 transiently increased during this process. 3. To detect the effect of gRB1 on the proliferation of chicken preadipocyte, MTT assay and cell-cycle analysis were performed. MTT assay showed that overexpression of gRB1 significantly suppressed (P < 0.05) the proliferation of chicken preadipocytes, and knockdown of gRB1 promoted the proliferation of chicken preadipocytes. Cell-cycle analysis showed that the proportion of preadipocytes in the G1 and G2 phases significantly increased (P < 0.05), and the proportion of preadipocytes in the S phase significantly decreased (P < .05) after up-regulation of the expression of gRB1. The proportion of preadipocytes in the S phase significantly increased (P < 0.05) after down-regulation of gRB1. 4. Quantitative real-time PCR was used to detect the effect of gRB1 on the expression of genes related to proliferation of chicken preadipocytes. Gene expression analysis showed that gRB1 knockdown promoted markers indicating proliferation of Ki-67 (MKi67) expression at 96 h (P < 0.05), and overexpression of gRB1 reduced MKi67 expression at 72 h (P < 0.05). 5. This study demonstrated that gRB1 inhibited preadipocyte proliferation at least in part by inhibiting the G1 to S phase transition.

Experimental infection of clade 1.1.2 (H5N1), clade 2.3.2.1c (H5N1) and clade 2.3.4.4 (H5N6) highly pathogenic avian influenza viruses in dogs

Since the emergence of highly pathogenic avian influenza (HPAI) H5N1 in Asia, the haemagglutinin (HA) gene of this virus lineage has continued to evolve in avian populations, and H5N1 lineage viruses now circulate concurrently worldwide. Dogs may act as an intermediate host, increasing the potential for zoonotic transmission of influenza viruses. Virus transmission and pathologic changes in HPAI clade 1.1.2 (H5N1)-, 2.3.2.1c (H5N1)- and 2.3.4.4 (H5N6)-infected dogs were investigated. Mild respiratory signs and antibody response were shown in dogs intranasally infected with the viruses. Lung histopathology showed lesions that were associated with moderate interstitial pneumonia in the infected dogs. In this study, HPAI H5N6 virus replication in dogs was demonstrated for the first time. Dogs have been suspected as a "mixing vessel" for reassortments between avian and human influenza viruses to occur. The replication of these three subtypes of the H5 lineage of HPAI viruses in dogs suggests that dogs could serve as intermediate hosts for avian-human influenza virus reassortment if they are also co-infected with human influenza viruses.

Detection of Severe Acute Respiratory Syndrome-Like, Middle East Respiratory Syndrome-Like Bat Coronaviruses and Group H Rotavirus in Faeces of Korean Bats

Bat species around the world have recently been recognized as major reservoirs of several zoonotic viruses, such as severe acute respiratory syndrome coronavirus (SARS‐CoV), Middle East respiratory syndrome coronavirus (MERS‐CoV), Nipah virus and Hendra virus. In this study, consensus primer‐based reverse transcriptase polymerase chain reactions (RT‐PCRs) and high‐throughput sequencing were performed to investigate viruses in bat faecal samples collected at 11 natural bat habitat sites from July to December 2015 in Korea. Diverse coronaviruses were first detected in Korean bat faeces, including alphacoronaviruses, SARS‐CoV‐like and MERS‐CoV‐like betacoronaviruses. In addition, we identified a novel bat rotavirus belonging to group H rotavirus which has only been described in human and pigs until now. Therefore, our results suggest the need for continuing surveillance and additional virological studies in domestic bat.

Pandemic influenza virus, pH1N1, induces asthmatic symptoms via activation of innate lymphoid cells

BACKGROUND

The pandemic strain of the influenza A virus (pH1N1) in 2009 caused many complications in patients. In this study, we introduce asthmatic symptoms as a complication of pH1N1 infection in children, not having a relationship with asthma history. The aim of this study was to quantify asthmatic symptoms in pH1N1-infected children and elucidate the underlying mechanisms of airway hyper-responsiveness (AHR) induced in a murine model of pH1N1 infection.

METHODS

As a retrospective study, pH1N1-infected children who were hospitalized with moderate to severe acute asthmatic symptoms were enrolled and administered a methacholine challenge test (MCT) at 3 months post-discharge. Additionally, the induction of AHR by pH1N1 infection was measured by MCT in wild-type and Rag1(-/-) mice. The effect of the innate immune response on the development of AHR following pH1N1 infection was investigated.

RESULTS

More than 70% of the pH1N1-infected children without a pre-infection diagnosis of asthma had a negative response on the MCT. None of these children had recurrent wheezing or asthma during the 3 years following pH1N1 infection. The development of AHR in pH1N1-infected mice was associated with an elevation in IL-33 and innate lymphoid cells 2 (ILC2).

CONCLUSIONS

This study demonstrates that pH1N1 infection directly induces transient asthmatic symptoms in patients regardless of their medical history. pH1N1 infection was shown to stimulate the rapid development of AHR and Th2-type cytokine secretion in mice via the activation of ILC2; it may be activated independently of adaptive immunity.

Microarray analysis of differentially expressed genes in the liver between Bai'er layers and broilers

In this study, we profiled gene expression in chicken liver and screened differentially expressed genes in the Bai'er layers and fat line broilers. Birds were derived from the 14th generation of Northeast Agricultural University fat broiler lines and Bai'er layers. Chicken genome arrays were used to screen differentially expressed genes in liver tissue from the Bai'er layers and fat line broilers. We screened 671 differentially expressed genes between broilers and layers at the ages of 2 and 4 weeks. We observed enrichment of a series of significant pathways, including the mitogen-activated protein kinase signaling pathway, cell cycle, mammalian target of rapamycin signaling pathway, and p53 signaling pathway. At 2 and 4 weeks, 94 shared differentially expressed genes were observed. We speculated that these genes regulate chicken lipid metabolism.

Differentially expressed genes in the liver of lean and fat chickens

This study aimed to investigate gene expression in the chicken liver for lean and fat broiler lines. Birds used in this study were 2 and 4 weeks of age; they were derived from the 14th generation of Northeast Agricultural University broiler lines, which were divergently selected based on abdominal fat content. Chicken Genome Arrays were used to screen differentially expressed genes in the liver tissue from lean and fat birds. At 2 and 4 weeks of age, 770 and 452 genes were differentially expressed between the 2 lines, respectively. The differentially expressed genes were involved in Wnt, insulin signaling, and cell cycle pathways. At 2 and 4 weeks, 42 shared, differentially expressed genes were revealed by the analysis. We speculate that these genes might regulate chicken lipid metabolism.

Polymorphisms of XRCC1 gene and risk of gastric cardiac adenocarcinoma

X-ray repair cross complementing 1 (XRCC1) protein plays an important role in base excision repair. Single nucleotide polymorphisms (SNPs) in XRCC1 gene may affect DNA repairing ability and genetic susceptibility to cancer. This study was designed to investigate the correlation of XRCC1 Arg194Trp Arg280His and Arg399Gln SNPs with the risk of gastric cardiac adenocarcinoma (GCA). Genotypes were analyzed by polymerase chain reaction-restriction fragment length polymorphism assay in 455 patients with GCA and 650 age and sex-matched controls. We did not find any significant difference in allele and genotype distributions of Arg194Trp Arg399Gln between the groups (P > 0.05). However, a significant increase in GCA risk was seen among smokers if they carried at least one XRCC1 280His (Arg280His + His280His) genotype (odds ratio = 1.59, 95%confidence interval = 1.01-2.51) compared with smokers not carrying these genotype. Our results indicated that XRCC1 Arg194Trp and Arg399Gln SNPs might not be associated with the risk of GCA. However, smokers with His allele at codon 280 had a significantly increased risk of GCA.

Dumbbell shaped exophytic and endobronchial lipomatous hamartoma

A 63-year-old man presented with a dumbbell-shaped mass obstructing his left upper lobe. He underwent a left upper lobectomy for suspected malignancy. An unexpected pathological diagnosis of endobronchial lipomatous hamartoma was made. Only 6 other cases have been reported in the English literature and only two cases were both endobronchial and exophytic.

p16(CDKN2) gene polymorphism: association with histologic subtypes of epithelial ovarian cancer in China

p16 is an important tumor suppressor gene, which is inactivated in many kinds of tumors. The common variants of p16 may be associated with the risk of certain tumors development. We analyzed the frequency of two adjacent polymorphisms in p16 exon 3 (540C-->G and 580C-->T) and their haplotype in blood samples from epithelial ovarian cancer (EOC) patients and healthy controls using polymerase chain reaction-restriction fragment length polymorphism. The results showed that the genotype frequency of p16 580C-->T polymorphism was significantly different among histologic subtypes of EOC (P= 0.02). T allele carriers significantly reduced the risk of serous EOC; the adjusted odds ratio was 0.40 (95% CI = 0.19-0.84). There are neither association between p16 540C-->G polymorphism and EOC development, progression, nor association between the haplotypes of two single nucleotide polymorphisms and the tumor development. Our results suggested that the p16 580C-->T polymorphism might affect the individual susceptibility to specific subtypes of EOC. Different types of ovarian cancer might adopt distinct carcinogenetic pathways. However, this result may be further validated in a larger sample of patients.