Genomic Reconstruction of the History of Native Sheep Reveals the Peopling Patterns of Nomads and the Expansion of Early Pastoralism in East Asia.

China has a rich resource of native sheep (Ovis aries) breeds associated with historical movements of several nomadic societies. However, the history of sheep and the associated nomadic societies in ancient China remains poorly understood. Here, we studied the genomic diversity of Chinese sheep using genome-wide SNPs, mitochondrial and Y-chromosomal variations in > 1,000 modern samples. Population genomic analyses combined with archeological records and historical ethnic demographics data revealed genetic signatures of the origins, secondary expansions and admixtures, of Chinese sheep thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia. Originating from the Mongolian Plateau ∼5,000‒5,700 years ago, Chinese sheep were inferred to spread in the upper and middle reaches of the Yellow River ∼3,000‒5,000 years ago following the expansions of the Di-Qiang people. Afterwards, sheep were then inferred to reach the Qinghai-Tibetan and Yunnan-Kweichow plateaus ∼2,000‒2,600 years ago by following the north-to-southwest routes of the Di-Qiang migration. We also unveiled two subsequent waves of migrations of fat-tailed sheep into northern China, which were largely commensurate with the migrations of ancestors of Hui Muslims eastward and Mongols southward during the 12th‒13th centuries. Furthermore, we revealed signs of argali introgression into domestic sheep, extensive historical mixtures among domestic populations and strong artificial selection for tail type and other traits, reflecting various breeding strategies by nomadic societies in ancient China.

Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments.

Global climate change has a significant effect on extreme environments and a profound influence on species survival. However, little is known of the genome-wide pattern of livestock adaptations to extreme environments over a short time frame following domestication. Sheep (Ovis aries) have become well adapted to a diverse range of agroecological zones, including certain extreme environments (e.g., plateaus and deserts), during their post-domestication (approximately 8-9 kya) migration and differentiation. Here, we generated whole-genome sequences from 77 native sheep, with an average effective sequencing depth of ∼5× for 75 samples and ∼42× for 2 samples. Comparative genomic analyses among sheep in contrasting environments, that is, plateau (>4,000 m above sea level) versus lowland (<100 m), high-altitude region (>1500 m) versus low-altitude region (<1300 m), desert (<10 mm average annual precipitation) versus highly humid region (>600 mm), and arid zone (<400 mm) versus humid zone (>400 mm), detected a novel set of candidate genes as well as pathways and GO categories that are putatively associated with hypoxia responses at high altitudes and water reabsorption in arid environments. In addition, candidate genes and GO terms functionally related to energy metabolism and body size variations were identified. This study offers novel insights into rapid genomic adaptations to extreme environments in sheep and other animals, and provides a valuable resource for future research on livestock breeding in response to climate change.

Research advances on the origin, evolution and genetic diversity of Chinese native sheep breeds.

China has a rich resource of native sheep breeds, some of which possess specific traits such as prolificacy, excellent lamb pelts, multiple horns, fat tails and strong stress resistance. All these have been the focus of research. However, there is still a controversy about the origin of sheep breeds and a lack of comprehensive and systematic studies on genetic diversity of Chinese native sheep. In this review, we summarize recent research advances on the origin, evolution and genetic diversity of Chinese native sheep breeds based on paternal, maternal, and autosomal markers. This review will provide useful information for the conservation and utilization of sheep genetic resources, breeding of new sheep breeds and the sustainable development of Chinese sheep industry.

Mitogenomic Meta-Analysis Identifies Two Phases of Migration in the History of Eastern Eurasian Sheep.

Despite much attention, history of sheep (Ovis aries) evolution, including its dating, demographic trajectory and geographic spread, remains controversial. To address these questions, we generated 45 complete and 875 partial mitogenomic sequences, and performed a meta-analysis of these and published ovine mitochondrial DNA sequences (n = 3,229) across Eurasia. We inferred that O. orientalis and O. musimon share the most recent female ancestor with O. aries at approximately 0.790 Ma (95% CI: 0.637-0.934 Ma) during the Middle Pleistocene, substantially predating the domestication event (∼8-11 ka). By reconstructing historical variations in effective population size, we found evidence of a rapid population increase approximately 20-60 ka, immediately before the Last Glacial Maximum. Analyses of lineage expansions showed two sheep migratory waves at approximately 4.5-6.8 ka (lineages A and B: ∼6.4-6.8 ka; C: ∼4.5 ka) across eastern Eurasia, which could have been influenced by prehistoric West-East commercial trade and deliberate mating of domestic and wild sheep, respectively. A continent-scale examination of lineage diversity and approximate Bayesian computation analyses indicated that the Mongolian Plateau region was a secondary center of dispersal, acting as a "transportation hub" in eastern Eurasia: Sheep from the Middle Eastern domestication center were inferred to have migrated through the Caucasus and Central Asia, and arrived in North and Southwest China (lineages A, B, and C) and the Indian subcontinent (lineages B and C) through this region. Our results provide new insights into sheep domestication, particularly with respect to origins and migrations to and from eastern Eurasia.

Cost-effective imprinting combining macromolecular crowding and a dummy template for the fast purification of punicalagin from pomegranate husk extract.

The combination of molecular crowding and virtual imprinting was employed to develop a cost-effective method to prepare molecularly imprinted polymers. By using linear polymer polystyrene as a macromolecular crowding agent, an imprinted polymer recognizable to punicalagin had been successfully synthesized with punicalin as the dummy template. The resulting punicalin-imprinted polymer presented a remarkable selectivity to punicalagin with an imprinting factor of 3.17 even at extremely low consumption of the template (template/monomer ratio of 1:782). In contrast, the imprinted polymer synthesized without crowding agent, did not show any imprinting effect at so low template amount. The imprinted polymers made by combination of molecular crowding and virtual imprinting can be utilized for the fast separation of punicalagin from pomegranate husk extract after optimizing the protocol of solid-phase extraction with the recovery of 85.3 ± 1.2%.

Bioassay-guided preparation of antioxidant, anti-inflammatory active fraction from crabapples (Malus prunifolia (Willd.) Borkh.).

The aim of current study was to optimize the extraction process and purification of main components (MC) to obtain high antioxidant, anti-inflammatory effective fractions from crabapple (Malus prunifolia (Willd.) Borkh.). The effects of three variables including ethanol concentration A1, solid-liquid ratio A2, extraction temperature A3 were investigated and optimized by response surface methodology (RSM) coupled with Box-Behnken design (BBD). The adsorption/desorption characteristics of MC on the five types of macroporous resins were investigated. According to batch adsorption test, HPD-300 resins were selected for kinetics. The adsorption mechanism showed that the process was appropriate by pseudo-second-order kinetics model, and purification parameters of MC were optimized through adsorption/desorption experiments with the column packed by HPD-300 resin. The effective fractions were obviously superior to other fractions according to DPPH, ABTS, COX-2 and 15-LOX radical scavenging. This work implies that the purified active fraction with high contents of antioxidants and anti-inflammatory compounds from crabapple might be potential source for natural products and food industries.

[Survey and analysis of ethyl carbamate in commercial fermented foods in Hangzhou in 2010].

OBJECTIVE: To observe the ethyl carbamate concentrations in different commercial fermented foods in Hangzhou in 2010. METHODS: In 2010, 237 commercial fermented food samples of eight categories, including yellow wine, white spirit, wine, beer, cooking wine, sauce, vinegar and fermented bean curd, were purchased from 3 different size markets respectively in Hangzhou. The ethyl carbamate was measured by gas chromatography-mass spectrometry in selection ion mode, after the samples were coupled with D5-ethyl carbamate, and purified by diatomite solid phase extraction column. RESULTS: The results showed that ethyl carbamate was detected in all samples analyzed (100%) with the range from 2.0 µg/kg to 515.0 µg/kg. The ethyl carbamate average (median) levels in 8 food categories were descending with fermented red bean curd (182.2 µg/kg (161.2 µg/kg)), yellow wine (159.6 µg/kg (121.0 µg/kg)), cooking wine (86.8 µg/kg (95.6 µg/kg)), white spirit (72.0 µg/kg (60.5 µg/kg)), soy sauce (47.2 µg/kg (40.7µg/kg)), vinegar (26.7 µg/kg (31.8 µg/kg)), wine (15.7 µg/kg (16.8 µg/kg)) and beer (2.2 µg/kg (2.3 µg/kg)). CONCLUSION: The ethyl carbamate was detected in all fermented foods in Hangzhou in 2010, and the levels of ethyl carbamate in red bean curd and yellow wine were higher than others.

Global genomic diversity and conservation priorities for domestic animals are associated with the economies of their regions of origin.

Domestic animals play a key role in human survival and the development of civilization. However, the genetic resources of domestic animals are facing an alarming rate of erosion due to socioeconomic changes, economic globalization and financial constraints. In this study, through genome-wide SNP analysis, we estimated the heterozygosity, inbreeding coefficient, effective population size, and runs of homozygosity to identify the breeds facing the risk of extinction for sheep and cattle across the world. In particular, we quantified the contribution of 97 sheep breeds and 53 cattle breeds to genomic diversity (within-breed, between-breed and total) and prioritized the breeds for conservation. Additionally, we compared the average values of genomic diversity between breeds from regions (or countries) in different economic categories (underdeveloped, developing and developed), and found that breeds in developed regions exhibit significantly higher levels of total genomic diversity than those in underdeveloped and developing regions. Altogether, our results suggested that conservation priority should be given to breeds in developed regions to secure the future genomic diversity hotspots of domestic animal resources.

Emergence and mechanism of carbapenem-resistant Escherichia coli in Henan, China, 2014.

The emergence and dissemination of carbapenem-resistant Escherichia coli (E. coli) strains is a main risk for global public health, but little is known of carbapenemase producing E. coli in Henan, China. The study was undertaken to investigate the prevalence and mechanism of carbapenem-resistant E. coli strains in a hospital in Xinxiang, Henan, China, 2014. A total of 5 carbapenemase-producing E. coli strains were screened from 1014 isolates. We found that they were all resistant to meropenem and imipenem. Amikacin showed the best sensitivity, with gentamicin coming up next. The positive rate of blaNDM was 80% (4/5). The sequencing results showed that two isolates belonged to blaNDM-1 whereas other 2 isolates carried the blaNDM-5. Other carbapenemase genes including blaIMP,blaVIM, blaKPC and blaOXA-48 were not detected. The blaCTX-M-15,blaTEM-1,sul2, aad, and aac(6")-Ib-cr were also detected. MLST analysis showed that NDM-producing E. coli were sporadic. Conjugation test indicated blaNDM could be transferred. In conclusion, the blaNDM was the principal resistance mechanism of carbapenem-resistant E. coli in the hospital, Henan, China.

A strategy of improving the imprinting effect of molecularly imprinted polymer: Effect of heterogeneous macromolecule crowding.

The topic in the present work is to prepare molecularly imprinted polymer (MIP) in heterogeneous crowding surrounding for improving imprinting effect. For the first time, heterogeneous crowding surrounding was made up of a tetrahydrofuran (THF) solution of low molecular weight polyethene glycol (PEG) and high molecular weight polystyrene (PS). The MIP prepared in heterogeneous crowding surrounding against procyanidin B2 can display apparent imprinting effect (imprinting factor of 5.13) in the situation of difficult imprinting at single crowding surrounding or non-crowding surrounding. The necessity of simultaneous use of low and high molecular weight crowding agents for enhanced imprinting effect was further proved. NMR peak shifts of active hydrogen of procyanidin B2 strongly suggested that the interaction between functional monomer and template can be enhanced due to the effect of heterogeneous crowding in the self-assembly process. The influence of molecular weight and amount of PEG, molecular weight of PS, as well as the ratio of procyanidin B2 to functional monomer on the imprinting factor was investigated. The MIP was then used to extract purify procyanidin B2 from extract of grape seed. The recovery of procyanidin B2 obtained was 87% with relative standard deviation of less than 5%.

Preparation of ionic liquid-mediated imprinted monolith for selective capture and purification of corilagin.

A method for solid-phase extraction (SPE) of corilagin from natural plant extracts based on molecularly imprinted polymers (MIPs) was developed. For the preparation of corilagin-MIP monoliths, 4-vinylpyridine was used as functional monomer, and ethylene glycol dimethacrylate was used as cross-linking monomer, using a mixture of 1-butyl-3-methylimidazoliumtetrafluoroborate (ionic liquid)-N,N-dimethylformamide-dimethyl sulfoxide as a porogen. A morphological characteristic of the corilagin imprinted monolith was further studied by scanning electron microscopy and nitrogen sorption method. The greatest imprinting factor of COR was up to 9. The MIPs were used as solid-phase extraction (SPE) sorbents for purification of COR and the mean recoveries of corilagin was 78.0% with COR purity of 98.0% from the crude extract of phyllanthus urinaria L. The resulting COR-imprinted polymer also displayed the good performance of fragment imprinting polymer for gallic acid with the mean recoveries of 94.0% and purity of 99.7%.

[Clinical observation on effects of leflunomid and total glucosides of paeony on rheumatoid arthritis].

OBJECTIVE: The observe the clinical effect of leflunomide (LEF) and total glucosides of Paeony (TGP) on rheumatoid arthritis (RA) and their influences on laboratory findings. METHODS: Eighty patients with RA were randomly divided into 2 groups, 40 in each group: the treated group treated with TGP and leflunomide, and the control group treated with LEF alone, the therapeutic course for both groups was 12 weeks. Clinical effect after treatment, changes of symptoms and physical signs before and after treatment were observed and the relative laboratory indexes were detected as well. RESULTS: The total effective rate in the treated group was higher than that in the control group (97.5% vs 85.0%, P < 0.05). The clinical and laboratory indexes in the treated group were improved significantly after treatment (P < 0.05, P < 0.01), with the improvement superior to those in the control group (P < 0.05, P < 0.01) respectively. There was no significant difference in adverse reaction between the two groups. CONCLUSION: Combined application of TGP and LEF is superior to using of LEF alone in treating RA, owing to its quicker initiating action and less adverse reaction.

Preparation of phenylboronate affinity rigid monolith with macromolecular porogen.

Boronate-affinity monolithic column was first prepared via polystyrene (PS) as porogen in this work. The monolithic polymer was synthetized using 4-vinylphenylboronic acid (4-VPBA) as functional monomer, ethylene glycol dimethacrylate (EDMA) as crosslinker monomer, and a mixture of PS solution in tetrahydrofuran, the linear macromolecular porogen, and toluene as porogen. Isoquercitrin (ISO) and hyperoside (HYP), isomer diol flavonoid glycosides, can be baseline separated on the poly(VPBA-co-EDMA) monolith. The effect of polymerization variables on the selectivity factor, e.g., the ratio of monomer to crosslinker (M/C), the amount of PS and the molecular weight of macromolecular porogen was investigated. The surface properties of the monolithic polymer were characterized by scanning electron microscopy and nitrogen adsorption. The best polymerization condition was the M/C ratio of 7:3, and the PS concentration of 40 mg/ml. The poly(VPBA-co-EDMA) polymer was also applied to extract cis-diol flavonoid glycosides from the crude extraction of cotton flower. After treated by poly(VPBA-co-EDMA) for solid phase extraction, high purity ISO and HYP (>99.96%) can be obtained with recovery of 83.7% and 78.6%, respectively.

A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries).

Horns are a cranial appendage found exclusively in Bovidae, and play important roles in accessing resources and mates. In sheep (Ovies aries), horns vary from polled to six-horned, and human have been selecting polled animals in farming and breeding. Here, we conducted a genome-wide association study on 24 two-horned versus 22 four-horned phenotypes in a native Chinese breed of Sishui Fur sheep. Together with linkage disequilibrium (LD) analyses and haplotype-based association tests, we identified a genomic region comprising 132.0-133.1 Mb on chromosome 2 that contained the top 10 SNPs (including 4 significant SNPs) and 5 most significant haplotypes associated with the polycerate phenotype. In humans and mice, this genomic region contains the HOXD gene cluster and adjacent functional genes EVX2 and KIAA1715, which have a close association with the formation of limbs and genital buds. Our results provide new insights into the genetic basis underlying variable numbers of horns and represent a new resource for use in sheep genetics and breeding.

[The changes of serum interferon-inducible protein-10 levels in children with type 1 diabetes mellitus].

OBJECTIVE: Type 1 diabetes mellitus (T1DM) has been recognized as a T-cell mediated autoimmune disease, the migration of immune effector cells from the bloodstream into the pancreatic islet may be a crucial step in the pathogenesis of T1DM. However, a clinically applicable method for measuring pancreatic beta-cell specific T-cell function in cases of T1DM has not been established. Interferon-inducible protein-10 (IP-10) is a chemokine that promotes the migration of activated T cells. The aim of this study was to investigate the role of IP-10 in the pathogenesis of childhood T1DM. METHODS: Serum IP-10 levels were measured by ELISA in 50 children with T1DM and 30 healthy children, and the levels of autoantibodies [glutamic acid decarboxylase (GAD), isle tcell antibody (ICA), insulin autoantibody (IAA) and tyrosine phosphatase (IA-2)] in diabetic children were measured as well. Comparisons were made among groups divided by autoantibody condition and disease period. RESULTS: The serum levels of IP-10 in patients with T1DM [(367 +/- 130) ng/L] were significantly higher than those in controls [(133 +/- 43) ng/L] (t = 9.49, P < 0.01). IP-10 levels in autoantibody positive [(385 +/- 147) ng/L] and negative diabetic children [(311 +/- 101) ng/L] were both higher than those in controls, but the difference was not significant. The serum levels of IP-10 among diabetic children who were positive for 1, 2 or 3 kinds of autoantibody did not show significant difference (F = 1.46, P > 0.05). IP-10 levels in newly diagnosed patients were much higher than those with disease period longer than 2 years (t = 4.30, P < 0.01), although both of them were higher than those in controls. CONCLUSION: The serum levels of IP-10 in children with T1DM were higher than those in controls, but they were not affected by either the presence of autoantibody or the number of positive autoantibodies. IP-10 levels decreased gradually with disease period prolonged.