Detecting selection signatures on the X chromosome of the Chinese Debao pony.

The X chromosome shows a special interaction between demographic factors and genetic variation, and the analysis of X-linked genomic variation can therefore provide insights into the unique effects of demography and selection on the horse genome that cannot be readily detected by autosomal markers. Debao (DB) ponies have experienced intense selective pressure for the development of their small stature (<106 cm at adult height). To identify selective sweeps on the X chromosome of the DB pony, we performed a genome-wide scan of three Chinese horse breeds using an Equine SNP70 BeadChip. Using Yili and Mongolian horses (>134 cm at adult height) as reference groups, both FST and XP-EHH revealed that five regions on the X chromosome were under strong selection, resulting in 95 overlapping genes. Seven of these genes, SMS, PHEX, ACSL4, CHRDL1, CACNA1F, DKC1 and CDKL5, are involved in bone development, growth hormone secretion and fat deposition. The region showing the strongest selection pressure was located at the position of 86.6-87.5 Mb. The subsequent genome-wide association analysis of the adult height of three Chinese horse breeds detected the two most significant SNPs in the same region, and these two SNPs overlapped with the gene CHRDL1. As a member of the bone morphogenetic protein (BMP) superfamily, CHRDL1 antagonizes the function of BMP4 and plays an important role in embryonic bone formation and cartilage generation. Our results provide new insights into the X-linked selection in Chinese Debao pony.

New insights into mitogenomic phylogeny and copy number in eight indigenous sheep populations based on the ATP synthase and cytochrome c oxidase genes.

The origins and phylogeny of different sheep breeds has been widely studied using polymorphisms within the mitochondrial hypervariable region. However, little is known about the mitochondrial DNA (mtDNA) content and phylogeny based on mtDNA protein-coding genes. In this study, we assessed the phylogeny and copy number of the mtDNA in eight indigenous (population size, n=184) and three introduced (n=66) sheep breeds in China based on five mitochondrial coding genes (COX1, COX2, ATP8, ATP6 and COX3). The mean haplotype and nucleotide diversities were 0.944 and 0.00322, respectively. We identified a correlation between the lineages distribution and the genetic distance, whereby Valley-type Tibetan sheep had a closer genetic relationship with introduced breeds (Dorper, Poll Dorset and Suffolk) than with other indigenous breeds. Similarly, the Median-joining profile of haplotypes revealed the distribution of clusters according to genetic differences. Moreover, copy number analysis based on the five mitochondrial coding genes was affected by the genetic distance combining with genetic phylogeny; we also identified obvious non-synonymous mutations in ATP6 between the different levels of copy number expressions. These results imply that differences in mitogenomic compositions resulting from geographical separation lead to differences in mitochondrial function.

[Health economic evaluation of bivalent human papilloma virus vaccine in China: based on the dynamic model].

Objective: This study aims to evaluate the prevention effect and cost-effectiveness of a prophylactic bivalent human papilloma virus (HPV) vaccine. Methods: A multiple health status dynamic model was developed, including natural history of diseases and prevention strategies. We built 19 prevention strategies including visual inspection with acetic acid/lugol's iodine (VIA/VILI) and/or 3 does prophylactic bivalent HPV vaccine administered to adolescent girls at the age of 15 years old every year under the assumption that vaccine coverage and screening coverage were 70%. The incremental cost-effectiveness ratio (ICER), optimal price of 3 does vaccine and cost-effectiveness frontier of these strategies were analyzed compared with no-intervention. The ICER threshold is 152 087 CNY. Results: Compared with no-intervention, Routine vaccination reduced the incidence of cervical cancer by 69.5%, superior to 5 strategies including VIA/VILI screening only. The range of effect was between 9.0% and 69.2%, and the effect of strategy increased significantly with the increase of screening frequency. Combination vaccination with screening at ages of 35 reduced the incidence of cervical cancer by 72.0%, and the effect increased with the increase of screening frequency. Combination vaccination with screening every 3 years between (35-64) years old reduced the incidence by 89.4%. Compared with no-intervention, the ICER of combination vaccination with screening twice between 35 years and 64 years was 121 292 CNY/life-year, which was cost-effective. The price of vaccine had a significant impact on the ICER of the strategy; when the vaccine price was less than 600 CNY, only routine vaccination or supplementary vaccination between 16-39 years old after routine vaccination was cost-effective; when the vaccine price was less than 1 200 CNY, supplementary vaccination between 16-19 years old plus VIA/VILI was cost-effective. Conclusion: Ther prevention strategy was cost-effective, which could effectively reduce the incidence of cervical cancer by implementation of HPV vaccination combined with VIA/VILI in suitable aging females.

[Effect of PM2.5 on the level of nuclear factor erythroid-2 related factor 2 in chronic obstructive pulmonary disease mice and its relationship with oxidative stress].

OBJECTIVE: To explore the effects of fine particulate matter on the level of nuclear factor erythroid-2 related factor 2 (Nrf2) in pulmonary tissues of chronic obstructive pulmonary disease (COPD) mouse models and its relationship with oxidative stress. METHODS: Totally 40 BALB/c mice were randomly divided into normal control group, normal PM2.5 group, COPD control group and COPD PM2.5 group.COPD mice were established using exposure of cigarette smoking.PM2.5 (20 mg/kg) was intratracheally instilled in PM2.5 group mice.Mice pulmonary function was measured by mice noninvasive body plethysmograph and lung histopathology was observed in normal control group and normal PM2.5 group mice.The mRNA and protein expression of Nrf2 was measured with real-time polymerase chain reaction (PCR) and Western blot methods.Total antioxidative capacity (TAC) was measured by O-phenanthroline colorimetry.Glutathione peroxidase (GSH-PX) was measured by improved Hafeman colorimetry and malondialdehyde (MDA) by thiobarbiturieacid colorimetry. RESULTS: Nrf2 mRNA and protein in normal control group, normal PM2.5 group, COPD control group and COPD PM2.5 group were 1.00, 4.46±0.42, 4.93±0.63, 6.41±0.35 and 0.92±0.08, 1.23±0.07, 1.20±0.09, 1.43±0.10.Nrf2 mRNA and protein in COPD control group were increased than those in normal control group while those in normal PM2.5 group and COPD PM2.5 group were respectively higher than each control group.Comparing to normal PM2.5 group, the Nrf2 mRNA and protein in COPD PM2.5 group were increased (all P<0.01). TAC and GSH-PX in each group were (5.1±0.4), (2.9±0.4), (3.3±0.3), (1.8±0.3) and (13.4±0.5), (9.9±0.7), (9.8±0.7), (7.0±0.6) U/mgpro.TAC and GSH-PX in COPD control group were decreased than those in normal control group while those in normal PM2.5 group and COPD PM2.5 group were respectively lower than each control group.Comparing to normal PM2.5 group, the Nrf2 mRNA and protein in COPD PM2.5 group were decreased (all P<0.01). MDA in each group were (2.9±0.4), (4.8±0.5), (4.5±0.3), and (6.2±0.4) nmol/mgpro.MDA in COPD control group were increased than those in normal control group while those in normal PM2.5 group and COPD PM2.5 group were respectively higher than each control group.Comparing to normal PM2.5 group, the MDA in COPD PM2.5 group were increased (all P<0.01). Positive correlations were observed between Nrf2 mRNA, protein and MDA, while negative correlations were observed between Nrf2 mRNA, protein and TAC, GSH-PX in all groups (all P<0.05). CONCLUSIONS: PM2.5 can induce Nrf2 expression and aggravate oxidative stress in COPD mice.The increased expression of Nrf2 is closely associated with oxidative stress.

Relationship between serum interleukin-17 level and inflammatory bowel disease.

By detecting expression of interleukin (IL)-17A, IL-10 and interferon-γ (IFN-γ) in serum of inflammatory bowel disease (IBD) patients, this study aims to analyze the effects of these factors on the pathogenesis of IBD. According to illness status, selected patients were divided into Crohn’s disease (CD) group (28 patients), ulcerative colitis (UC) group (74 patients) and normal control group (36 patients); enzymelinked immunosorbent assay (ELISA) was used to detect IL-17A, IL-10 and IFN-γ levels in serum; immunohistochemical assay was used to detect local IL-17A expression in the colonic mucosa of each group. Clinical results showed that IL-17A content of the UC group and CD group was significantly higher than that of the normal control group (p less than 0.05); IL-17A content of the CD group was higher than that of the UC group (p>0.05). The UC group had the highest IL-10 content, and the difference between the UC group and other two groups had statistical significance (p less than 0.05); the difference of IL-10 content between UC group and normal control group had no statistical significance (p>0.05). There was no significant difference of IFN-γ level between the CD group and the UC group and normal control group (p>0.05), and no significant difference of IFN-γ level was shown between the CD group and the UC group (p>0.05). Both the CD and UC groups showed IL-17A positive staining in cytoplasm of lymphocyte, however no positive staining was found in any layer of intestinal mucosa of the normal control group. IL-17A was locally expressed in the colon of IBD patients in remission; furthermore, it also had high expression in serum; thus, there still existed high expression of pro-inflammatory factor, which might be related to relapse of IBD. Therefore, prevention of IL-17A may become a feasible therapy for IBD in the future.

Codon optimization enhances the expression of porcine ß-defensin-2 in Escherichia coli.

Porcine ß-defensin-2 (pBD2) is a cationic antimicrobial peptide that has therapeutic potential. The amount of pBD2 in nature is limited, and the expression of pBD2 in Escherichia coli is low, probably because a different gene codon is used by prokaryotic organisms to that used by eukaryotes. Codon preference optimization is one of the ways to increase heterologous expression of pBD2. To achieve high expression of pBD2, the pBD2 gene was redesigned according to the preferred codon in E. coli without altering the amino acid sequence. The optimized gene was inserted into expression vector pET-30a and transformed into E. coli BL21 (DE3) plysS. Our results showed that pBD2 was expressed as His-Tag fusion protein at a level that was approximately 4-6 times greater than from the native gene, based on total protein expression. Expressed fusion pBD2 showed antimicrobial activity against both E. coli and Staphylococcus aureus. Moreover, pBD2 showed weak hemolytic activity and strong heat resistance. These results indicate that fusion pBD2 is functional and has similar properties to those of pBD2 from the native gene. Our current study demonstrated that codon optimization could enhance pBD2 expression in E. coli without altering its function. Therefore, the expression of pBD2 after codon optimization in heterologous host cells might be useful and is worthy of further research.

Study on characteristics of chemokine CXCL10 gene cloned from cDNA expression library of Ujumqin sheep.

Chemokines were a major regulator of body's inflammatory and immune responses. In this study, the cDNA fragment of chemokine CXC ligand 10 (CXCL10) was cloned from the Ujumqin sheep ear marginal tissue cDNA expression library; the CXCL10 gene had 103 amino acids and a molecular weight of 11.47 kDa, and it shared a high homology among cattle, sheep, and goat, while a low homology compared with mouse. The CXCL10 protein had 4 conservative cysteine residues, located in 28, 30, 55, and 72 sites. The expression pattern and intracellular distribution of recombinant CXCL10 proteins in Ujumqin sheep fibroblast cells showed that there were green fluorescence signals both in cytoplasm and nucleolus after 24 h of transfection, the number of positive cells was increased with time, the peak level of fluorescence signal was reached after 48 h of transfection and the transfection efficiency was 33.3%; there was a significant decrease in fluorescence intensity after 72 h of transfection. Expression of recombinant CXCL10 gene in Escherichia coli had a time- and temperature-dependency on the amount of protein expression, and a small quantity of inducer was needed.

Tracing genetic differentiation of Chinese Mongolian sheep using microsatellites.

The genetic consequences of population differentiation and isolation have been the subject of conservation biology. In this study, we analysed the genetic diversity and structure of Mongolian sheep in China. These animals belong to a traditional local breed with high production, extensive adaption, early maturity and roughage resistance. For this purpose, 26 microsatellites were genotyped for five Mongolian sheep populations. The Bayesian clustering indicated five clusters as the most probable genetic structure of the populations investigated. In addition, a clear genetic structure was revealed in three populations distributed at large geographical scales, while the other cluster encompassed UQ and HLBR sheep that displayed no clear differentiation, probably due to their close and small geographical distributions. Overall, our results are helpful in understanding the interplay of population dynamics in these close genetic lineages of Mongolian sheep.

Microsatellite analysis revealed genetic diversity and population structure among Chinese cashmere goats.

Most cashmere goats are found in northern China and Mongolia. They are regarded as precious resources for their production of high quality natural fibre for the textile industry. It was the first time that the genetic diversity and population structure of nine Chinese cashmere populations has been assessed using 14 ISAG/FAO microsatellite markers. In addition, two Iranian populations and one West African goat population were genotyped for comparison. Results indicated that the genetic diversity of Chinese cashmere goats was rich, but less than those of the Iranian goat populations. All pairwise F(ST) values between the Chinese cashmere goat populations reached a highly significant level (P < 0.001), suggesting that they should all be considered as separate breeds. Finally, clustering analysis divided Chinese cashmere goats into at least two clusters, with the Tibetan Hegu goats alone in one cluster. An extensive admixture was detected among the Chinese goat breeds (except the Hegu), which have important implications for breeding management.

Evaluation of the genetic diversity and population structure of Chinese indigenous horse breeds using 27 microsatellite markers.

We determined the genetic diversity and evolutionary relationships among 26 Chinese indigenous horse breeds and two introduced horse breeds by genotyping these animals for 27 microsatellite loci. The 26 Chinese horse breeds come from 12 different provinces. Two introduced horse breeds were the Mongolia B Horse from Mongolia and the Thoroughbred Horse from the UK. A total of 330 alleles were detected, and the expected heterozygosity ranged from 0.719 (Elenchuns) to 0.780 (Dali). The mean number of alleles among the horse breeds ranged from 6.74 (Hequ) to 8.81 (Debao). Although there were abundant genetic variations found, the genetic differentiation was low between the Chinese horses, which displayed only 2.4% of the total genetic variance among the different breeds. However, genetic differentiation (pairwise FST) among Chinese horses, although moderate, was still apparent and varied from 0.001 for the Guizou-Luoping pair to 0.064 for the Jingjiang-Elenchuns pair. The genetic differentiation patterns and genetic relationships among Chinese horse breeds were also consistent with their geographical distribution. The Thoroughbred and Mongolia B breeds could be discerned as two distinct breeds, but the Mongolia B horse in particular suffered genetic admixture with Chinese horses. The Chinese breeds could be divided into five major groups, i.e. the south or along the Yangtze river group (Bose, Debao, Wenshan, Lichuan, Jianchang, Guizhou, Luoping, Jinjiang and Dali), the Qinghai-Tibet Plateau group (Chaidamu, Hequ, Datong, Yushu, Tibet Grassland and Tibet Valley), the Northeast of China group (Elenchuns, Jilin and Heihe), the Northwest of China group (Kazakh, Yili and Yanqi) and the Inner Mongolia group (Mongolia A, Sanhe, Xinihe,Wuzhumuqin and Sengeng). This grouping pattern was further supported by principal component analysis and structure analysis.

A novel maternal lineage revealed in sheep (Ovis aries).

It is generally believed that domestic sheep have two maternal lineages (haplotypes A and B), based on mitochondrial DNA analysis. In the present study, we provide evidence that a novel maternal lineage (haplotype C) is exhibited in Chinese native sheep. To verify this finding, 231 samples were collected from six Chinese local breeds, which cover the vast geographical region of sheep inhabitation in China. For comparison, 50 samples were collected from two Western breeds collected in China. Mitochondrial DNA was screened by PCR single-strand conformational polymorphism (SSCP), leading to the identification of novel band patterns in ND2 and ND4 genes in the Chinese breeds. Interestingly, mutations at the two loci were in strong linkage disequilibrium. Direct sequencing of the DNA fragments revealed a non-synonymous substitution in ND2. Furthermore, two synonymous mutations were identified by comparisons of the novel type (haplotype C) and the established types (haplotypes A and B). The entire mitochondrial control region for 55 samples was then sequenced to construct a phylogenetic tree and median joining network. Both the tree and network demonstrated a topology of three groups, which is in consistent with the SSCP analysis. Unlike Western breeds, Chinese breeds are composed mainly of haplotypes A and B, but with a small fraction of haplotype C. According to Fu's test and mismatch distribution, haplotype C has not been subject to a recent population expansion. Based on these results, we propose a novel origin for Chinese sheep.