Genome-wide single nucleotide polymorphism array and whole-genome sequencing reveal the inbreeding progression of Banna minipig inbred line

Inbred pigs are promising animal models for biomedical research and xenotransplantation. Established in 1980, the Banna minipig inbred (BMI) line originated from a sow and its own male offspring. It was selected from a small backcountry minority Lahu village, where records show that no other pig breed has ever been introduced. During the inbreeding process, we perfomed extreme inbreeding over 23 consecutive generations using full-sibling or parent-offspring mating. In order to investigate the inbreeding effects in BMI pigs across generations over the past 40 years, in this study we conducted a genome-wide SNP genotyping of the last 10 generations, representing generations 14-23. In total, we genotyped 57,746 SNPs, corresponding to an average decrease in heterozygosity rate of 0.0078 per generation. Furthermore, we were only able to identify 18,216 polymorphic loci with a MAF larger than 0.05, which is substantially lower than the values in previous reports on other pig breeds. In addition, we sequenced the genome of the first pig in the twenty-third generation (inbreeding coefficient 99.28%) to an average coverage of 12.4× to evaluate at the genome level the impact of advanced inbreeding. ROH analysis indicates that BMI pigs have longer ROHs than Wuzhishan and Duroc pigs. Those long ROH regions in BMI pigs are enriched for distinct functions compared with the highly polymorphic regions. Our study reveals a genome-wide allele diversity loss during the progress of inbreeding in BMI pigs and characterizes ROH and polymorphic regions as a result of inbreeding. Overall, our results indicate the successful establishment of the BMI line, which paves the way for further in-depth studies.

[Online moisture detection technology and its application prospect in drying of traditional Chinese medicine]

Drying is one of the most common unit operations in the production of traditional Chinese medicine. The drying process of traditional Chinese medicine materials is accompanied by the dynamic reduction of water content. As a key index to determine the end of the drying process, the moisture content of materials plays an important role in improving drying efficiency and saving energy. Recently, the drying process of traditional Chinese medicine is mostly monitored by offline detection, and there are few reports of online moisture detection applications. In this paper, the principle and current application of online inspection technology for the material drying process in different fields were introduced. The significance of online detection technology in drying of traditional Chinese medicine was also analyzed. Meanwhile, the application prospect of online detection technology in the field of drying of traditional Chinese medicine was predicted. In response to urgent transformation and upgrading of the traditional Chinese medicine manufacturing industry, the application of online moisture detection technology is expected to be a key breakthrough in the intelligent upgrading of traditional Chinese medicine drying technology and equipment.

The Fourier transform infrared spectra of the key organs derived from Kidney (Shen)-yang deficiency syndrome mice

OBJECTIVE

To explore an approach to rapidly and accurately identify the compounds as biomarkers of Chinese medicine (CM) syndromes.

METHOD

The Fourier transform infrared (FT-IR) spectrometry was applied to investigate the characteristic components of a mice model of Kidney (Shen)-yang deficiency syndrome (KDS), and the remedial effect of a typical CM formula Shenqi Pill (). Thirty-six females and 18 males of Balb/c mice were randomly divided into KDS, Shenqi or control group. The females and males of the same group freely were mated for 96 h, and the males were taken out and only the female mice were raised. Females of the KDS group were threatened by a ferocious cat every other day for 14 d. After delivery, the KDS, or gestational threatened, offspring were raised at standard condition for 11 weeks. Then 10 male offspring were randomly selected, anaesthetized and their representative organs, i.e. testes, kidneys, lungs and feet were collected, for the FT-IR scan. Mice of the Shenqi group were intragastric administered Shenqi Pill; while mice in the KDS and control groups were given the same volume of saline.

RESULTS

The attenuated birth outcomes of the KDS group were displayed. The remarkable FT-IR differences of all organs between KDS mice and healthy control were mainly at 1,735-1,745 cm(-1) (indicating the increased levels of lipids) and at 1,640-1,647 cm(-1) and 1,539-1,544 cm(-1) (displaying the decreased proteins). No statistic FT-IR difference between Shenqi and control mice was observed.

CONCLUSION

In accordance with major traits of KDS, prenatal stress extensively impaired the building up of proteins and resulting in the excessive lipid storage, and FT-IR could effectively identify the biomarkers of KDS.

Single nucleotide polymorphism analysis of exons 3 and 4 of IGF-1 gene in pigs

The IGF-1 gene has been implicated as a candidate gene for the regulation of pig growth traits. We analyzed exons 3 and 4 of IGF-1 gene polymorphisms of the Banna mini-pig (28), the Tibetan mini-pig (30), the Junmu pig (55), and L. Yorkshire species (50) using PCR-SSCP. Three genotypes in exon 3 and 6 genotypes in exon 4 were observed, among which, one single nucleotide polymorphism, G201A, on exon 3 and two single nucleotide polymorphisms, A440G and T455C, on exon 4 were found. Statistical analysis of genotype frequencies revealed that the A allele was dominant in the large pig at the G201A locus (PIC = 0.20-0.34), and the AT alleles were dominant in the large pig at the A440G and T455C loci (PIC = 0.30-0.60). The genotype distribution between the various groups was significantly different (P< 0.01), with the highest heterozygosity seen in Junmu pigs at 0.223 and the lowest seen in L. Yorkshire at 0.098. The genetic distance of the Junmu pig from the L. Yorkshire is the smallest, the distance from the Tibetan miniature pigs is larger, and the distance from the Banna mini-pig is the largest. The IGF-1 gene polymorphism and heterozygosity results from various pig breeds indicate that IGF-1 is substantially polymorphic with significant difference of the polymorphic distribution and expression levels among various pig breeds. This information provides a theoretical basis for the genetic background of miniature pigs but also provides means to breed improved pig varieties.

Immunogenicity and immune modulation of osteogenic differentiated mesenchymal stem cells from Banna minipig inbred line

Mesenchymal stem cells (MSCs) represent a good choice for cell transplantation due to their multilineage differentiation ability and low immunogenicity. Our previous in vitro studies indicated that undifferentiated swine MSCs show low immunogenicity suppressing the proliferative responses of human peripheral blood lymphocyte to several antigens. In this study, we investigated the immunogenicity and immune modulation ability of osteogenic differentiated MSCs. SLA class I (P1, P14) was detectable by reverse-transcriptase polymerase chain reaction on both differentiated and undifferentiated MSCs. SLA class II (SLA-DRA, SLA-DQA) was only detectable on differentiated MSCs mixed lymphocyte reaction assays demonstrated that both differentiated and undifferentiated MSCs failed to stimulate proliferative responses by human peripheral blood lymphocytes (hPBLs). Furthermore, as undifferentiated MSCs, osteogenic differentiated MSCs also suppressed hPBL proliferation to phytohemaglutinin.

Suppression of human peripheral blood lymphocyte proliferation by immortalized mesenchymal stem cells derived from bone marrow of Banna Minipig inbred-line

This study sought to investigate whether mesenchymal stem cells (MSC) derived from Banna Minipig Inbred-line (BMI-MSC) suppressed human peripheral blood lymphocyte (hPBLs) proliferation in a one-way mixed lymphocyte reaction system. BMI-MSC failed to stimulate proliferative responses by hPBLs, which were activated by allogenic endothelial cells, BMI-PBLs and non-specific mitogenic stimuli. Furthermore, BMI-MSC also suppressed proliferation of hPBLs stimulated by mismatched allogenic, as well as xenogenic PBLs, and the mitogenic stimulus ConA. The suppression occurred in dose-dependent fashion when the ratio of hPBLs to BMI-MSC varied from 1 to 5 fold; fewer, BMI-MSC (0.001 to 0.01 times) showed no obvious suppression. When BMI-MSC were added to hPBLs stimulated for 72 hours, the proliferative suppression was still evident. Addition of anti-FasL or anti-TGF-beta1 antibody attenuated the proliferative suppression, while antibody against IL-10 had no effect on it. Further immunofluorescence analysis demonstrated that FasL and TGF-beta1 constitutively expressed BMI-MSC. These findings suggest that BMI-MSC suppress hPBLs proliferation relying on FasL and TGF-beta1 mediated pathways.

Prediction of apatite lattice constants from their constituent elemental radii and artificial intelligence methods

Lattice constants (LCs) of all possible 96 apatite compounds, A(5)(BO(4))(3)C, constituted by A[double bond]Ba(2+), Ca(2+), Cd(2+), Pb(2+), Sr(2+), Mn(2+); B[double bond]As(5+), Cr(5+), P(5+), V(5+); and C[double bond]F(1-), Cl(1-), Br(1-), OH(1-), are predicted from their elemental ionic radii, using pattern recognition (PR) and artificial neural networks (ANN) techniques. In particular, by a PR study it is demonstrated that ionic radii predominantly govern the LCs of apatites. Furthermore, by using ANN techniques, prediction models of LCs a and c are developed, which reproduce well the measured LCs (R(2)=0.98). All the literature reported on 30 pure and 22 mixed apatite compounds are collected and used in the present work. LCs of all possible 66 new apatites (assuming they exist) are estimated by the developed ANN models. These proposed new apatites may be of interest to biomedical research especially in the design of new apatite biomaterials for bone remodeling. Similarly these techniques may also be applied in the study of interface growth behaviors involving other biomaterials.

[The RAPD analysis of haploid strain of thermotolearnt yeast]

The haploid strains HZ line from the thermololeant strain HU-TY-1 of Saccharomyces cerevisiae have been obtained by sporulation, and the analysis of growth and fermentation test was performed. The strains HZ-21 and HZ-84 were used as the analysis of random amplified polymerphic DNA (RAPD). The result showed that there were some polymorphic DNA fragments of genomic DNA among haploid, the diploid parent strain HU-TY-1 and the original strain LK, some of them may be correlation with thermotolerant property.

[Genetic analysis of 35 microsatellite loci in 5 lineages of xishuangbanna miniature pig inbred line]

The polymorphism of 35 microsatellites in 5 lineages of Xishuangbanna small-ear miniature pig inbred line (XMI) was analysed. Nmuber of alleles of each lineage was counted, and rates of homozygote for 35 microsatellite loci in 5 lineages were calculated. According to gene frequencies of 35 microsatellites polymorphism information content (PIC) and mean heterozygosity were calculated for each lineage, and genetic distances between these lineage were estimated. The dendrograms were obtained based on genetic distances. The results suggest that rates of homozygote in these lineage are all high, and that is the highest in lineage 151. The results also suggest that polymorphism information content and mean heterozygosity in all the lineages are low. Composition of alleles of each lineage was quite different and the genetic relationship between lineages accorded with the process of inbred line. So it is suggested that the inbreeding degree of 5 lineages of XMI are all high, and the richness of genetic diversity is lower than general commercial pig breeds. It also shows each lineage has been different groups with individual genes.

Functional consequences of the Ser334-->Pro mutation in a human factor X variant (factor XMarseille)

A factor X molecular variant was identified in a 55-year-old woman at a routine preoperative coagulation screening. Plasma factor X antigen was normal, whereas factor X activity was decreased when factor X was activated by either the extrinsic pathway (21%), the intrinsic pathway (21%) or the factor X activator from Russell viper venom, RVV-X (26%). Factor XMarseille was isolated from plasma by immunoaffinity chromatography and compared with normal factor X purified by the same method. Activation of factor XMarseille by factor IXa or by RVV-X in a purified system showed that the rate of cleavage was decreased, whereas once produced, factor XaMarseille had a normal catalytic efficiency for either the peptide substrate S-2765 (D-Arg-Gly-Arg-NH-Np) or prothrombin. The rate of inhibition of factor XaMarseille by antithrombin III was also normal. Defective proteolysis of factor XMarseille by factor IXa or by RVV-X was the consequence of a threefold decrease in the kcat for the activation of factor XMarseille while the Km of RVV-X or factor IXa for factor X was normal. We have determined the molecular basis of the defect in the factor XMarseille gene by amplification of all eight exons, single-strand conformational polymorphism analysis of the amplified exons and subsequent sequence analysis. The patient was homozygous for a T-->C mutation in exon VIII, resulting in the substitution of Ser334 by proline. From comparison of three-dimensional models of various serine proteases, it appears that Ser334 is located within a surface-exposed variable region of factor X. This observation suggests that the Ser334-->Pro mutation either is responsible for a misalignment of the active sites of specific factor X activators in close proximity to the cleavage site, or that the Ser-->Pro mutation alters the spatial orientation of the cleavage site by nonlocal modifications of factor X structure.