Genetic Polymorphism of TLR4 Gene and Correlation with Mastitis in Cattle

Toll-like receptor 4 （TLR4） recognizes pathogen ligands and mediates signaling to initiate innate and adaptive immune responses. In this experiment, a 316 bp and 382 bp fragments of TLR4 gene named T4CRBR1 and T4CRBR2, of Chinese Holstein, Sanhe cattle, and Chinese Simmental was amplified by polymerase chain reaction （PCR）, respectively. The genetic polymorphisms in the three populations were detected by Single-Strand Conformational Polymorphism （SSCP） in the first locus and by digesting the fragments with restriction endonuclease Alu I in the second one. Results showed that both alleles （A and B） of two loci were found in all the three populations and the value of polymorphism information content （PIC） indicated that these were a moderate polymorphism. Statistical results of X^2 test indicated that two polymorphism sites in the three populations fitted with Hardy-Weinberg equilibrium （P 〉 0.05）. After sequencing, A-G single nucleotide polymorphism （SNP） was identified at nucleotide 4,525 in intron 1 of TLR4 gene and C-T SNP was identified at nucleotide 1,397 in exon 3 of TLR4 gene. Meanwhile, the effect of polymorphism of TLR4 gene on somatic cell score （SCS） was analyzed, the results indicated that the cattle with allele A in T4CRBR1 showed lower somatic cell score than that of allele B （P 〈 0.05）. In short, the allele A might play an important role in mastiffs resistance in bovine.

Analysis and Evaluation Indicator Selection of Chilling Tolerance of Different Cotton Genotypes

[Objectivc] This study aimed to investigate the chilling tolerance of seedlings of different cotton genotypes and screen appropriate indicators for assess- ing chilling tolerance, to establish reliable mathematical evaluation model for chilling tolerance of cotton, thus providing theoretical basis for breeding and promoting new chilling-tolerant cotton germplasms and large-scale evaluation of chilling tolerance of cotton varieties. [Method] Fifteen cotton varieties （lines） were used as experimental materials. The photosynthetic gas exchange parameters, chlorophyll fluorescence ki- netic parameters, chlorophyll content, relative soluble sugar content, malonaldehyde content, relative proiine content, relative conductivity and other 12 physiological indi- cators of seedling leaves under low temperature treatment （5 ℃, 12 h） and recovery treatment （25 ℃. 24 h） were determined; based on the chilling tolerance coefficient （CTC） of various individual indicators, the comprehensive evaluation of chilling toler- ance was conducled by using principal component analysis, hierarchical cluster anal- ysis and stepwise regression analysis. [Result] The results showed that the 12 indi- vidual physiological indicators could be classified into 7 independent comprehensive components by principal component analysis; 15 cotton varieties （lines） were clus- tered into three categories by using membership function method and hierarchical cluster analysis; the mathematical model for evaluating chilling tolerance of cotton seedlings was established： D =0.275 -0.244Fo1 ＋0.206Fv/Fm1＋0.326g,%-0.056SS ＋ 0.225MDA＋O.O38REC （FF=0.995）, and the evaluation accuracy of the equation was higher than 94.25%,0. Six identification indicators closely related to chilling tolerance were screened, including Fo,, Fv/Fm1, Seedling leaves of cotton varieties （lines） gs2, SS, MDA, and REC. [Conclusion] with high chilling tolerance are less dam- aged under low temperature stress, and are able to maintain relatively high photo- synthetic electron transport capacity and high stomatal conductance after recovery treatment, which is contributed to gas exchange and recovery of photosynthetic ca- pacity. Determination of the six indicators under the same stress condition can be adopted for rapid identification and prediction of the chilling tolerance of other cotton varieties, which provides basis for the breeding, promotion, identification and screen- ing of chilling tolerant germplasms.

Improved extracellular endo-1,4-β-mannosidase activity of recombinant Pichia pastoris by optimizing signal peptide

In order to improve the extracellular endo-1,4-β-mannosidase(MAN) activity of recombinant Pichia pastoris, optimization of signal peptides was investigated. At first, five potential signal peptides(W1, MF4 I, INU1 A, αpre, HFBI) were chosen to be analyzed by Signal P 4.0, among which W1 was designed. Then, the widely used signal peptide α-factor in expression vector p GAPZαA was replaced by those five signal peptides to reconstruct five new expression vectors. MAN activity was assayed after expression vectors were transformed into Pichia pastoris. The data show that the relative efficiencies of W1, MF4 I, INU1 A, αpre, and HFBI signal peptides are 23.5%, 203.5%, 0, 79.7%, and 120.3% compared with α-factor, respectively. The further gene copy number determination by the quantitative real-time PCR reveals that the MAN activities mediated by α-factor from 1 to 6 gene copy number levels are 12.95, 43.33, 126.63, 173.53, 103.23 and 88.63 U/m L, while those mediated by MF4 I are 79.22, 133.89, 260.14, 347.5, 206.15 and 181.89 U/m L, respectively. The maximum MAN activity reached 347.5 U/m L with 4 gene copies mediated by MF4 I. These results indicate that replacing the signal peptide α-factor with MF4 I and increasing MAN gene copies to a proper number can greatly improve the secretory expression of MAN.

Development of Three Multiplex PCR Primer Sets for Ark Shell(Scapharca broughtonii)and Their Validation in Parentage Assignment

Scapharca broughtonii is a commercially important and over-exploited species.In order to investigate its genetic diversity and population structure,43 novel polymorphic microsatellites were isolated and characterized.The number of alleles per locus ranged from 3 to 22 with an average of 6.93,and the observed and expected heterozygosities varied between 0.233 and 1.000,and 0.250 and 0.953,with an average of 0.614 and 0.707,respectively.Three highly informative multiplex PCRs were developed from nine of those microsatellites for S.broughtonii.We evaluated and validated these multiplex PCRs in 8 full-sib families.The average polymorphism information content(PIC) was 0.539.The frequency of null alleles was estimated as 3.13% of all the alleles segregation based on a within-family analysis of Mendelian segregation patterns.Parentage analysis of real offspring demonstrated that 100% of all offspring were unambiguously allocated to a pair of parents based on 3 multiplex sets.Those 43 microsatellite loci with high variability will be helpful for the analysis of population genetics and conservation of wild stock of S.broughtonii.The 3 sets of multiplex PCRs could be an important tool of pedigree reconstruction,population genetic analysis and brood stock management.

Melanocortin-1 receptor gene variants in four Chinese ethnic populations

There is strong relationship between melanocortin-1 receptor (MCIR) gene variants and human hair color and skin type. Based on a sequencing study of MC1R gene in 50 individuals from the Uygur, Tibetan, Wa and Dai ethnic populations, we discuss the occurrence of 7 mc1r variants consisting of 5 nonsynonymous sites (Val60Leu, Arg67Gln, Val92Met, Arg163Gln and Ala299Val) and 2 synonymous sites (C414T and A942G), among which C414T and Ala299Val were reported for the first time. Confirmation and analysis were the made of 122 individuals at three common point mutations (Val92Met, Arg163Gln, A942G) using PCR-SSCP. The frequency of Arg163Gln variant varies in the four ethnic populations, with percentage of 40%, 85.0%, 66. 2% and 72.7%, respectively, while those of Val92Met and A942G are roughly similar in these four populations. The different environments, migration and admixture of various ethnic groups in China might have impact on the observed frequency of Arg163Gln.

Construction of a Normalized Full-Length cDNA Library of Cephalopod Amphioctopus fangsiao and Development of Microsatellite Markers

Amphioctopus fangsiao is one of the most economically important species and has been considered to be a candidate for aquaculture. In order to facilitate its fine-scale genetic analyses, we constructed a normalized full-length library successfully and developed a set of microsatellite markers in this study. The normalized full-length library had a storage capacity of 6.9×105 independent clones. The recombination efficiency was 95% and the average size of inserted fragments was longer than 1000 bp. A total of 3440 high quality ESTs were obtained, which were assembled into 1803 unigenes. Of these unigenes, 450(25%) were assigned into 33 Gene Ontology terms, 576(31.9%) into 153 Kyoto Encyclopedia of Genes and Genomes pathways, and 275(15.3%) into 22 Clusters of Orthologous Groups. Seventy-six polymorphic microsatellite markers were identified. The number of alleles per locus ranged from 4 to 17, and the observed and expected heterozygosities varied between 0.167 and 0.967 and between 0.326 and 0.944, respectively. Twelve loci were significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction and no linkage disequilibrium was found between different loci. This study provided not only a useful resource for the isolation of the functional genes, but also a set of informative microsatellites for the assessment of population structure and conservation genetics of A. fangsiao.

Mast cell density and the context of clinicopathological parameters and expression of p185,estrogen receptor,and proliferating cell nuclear antigen in gastric carcinoma

AIM:To investigate the relationship between the mast cell density(MCD)and the context of clinicopathological parameters and expression of p185,estrogen receptor(ER), and proliferating cell nuclear antigen(PCNA)in gastric carcinoma. METHODS:Mast cell,p185,ER,and PCNA were detected using immunohistochemical S-P labeling method.Mast cell was counted in tissue of gastric carcinoma and regional lymph nodes respectively,and involved lymph nodes(ILN)were examined as usual. RESULTS:MCD was significantly related to both age and depth of penetration(x^2=4.688,P<0.05 for age and x^2=9.350, P<0.01 for depth of penetration)between MCD>21/0.03 mm^2 and MCD≤21/0.03 mm^2 in 100 patients;MCD in 1-6 ILN group patients was significantly higher than that in 7-15 ILN or>15 ILN group patients(u=6.881,8.055,P<0.01); There were significant differences intergroup in positive expression rate of p185,ER and PCNA between MCD>21/ 0.03 mm^2 and MCD≤21/0.03 mm^2 in 100 patients. CONCLUSION:Mast cell may have effect on inhibiting invasive growth of tumor,especially in the aged patients; The number of mast cells,in certain degree,may predicate the number of involved lymph nodes,which is valuable for assessment of prognosis;MCD was related to the expression of p185,ER,and PCNA in gastric carcinoma.It suggests that mast cell accumulation may inhibit the proliferation and the dissemination of the gastric carcinoma. INTRODUCTION Recently,many studies have reported on the association of mast cell with various tumorst.In several malignancies,mast cell has been found to correlate with growth,penetration and prognosis of tumor.Therefore,our study was undertaken to investigate the relationship between the mast cell density (MCD)and the context of clinicopathological parameters and expression of p 185,estrogen receptor(ER),and proliferating cell nuclear antigen(PCNA)in gastric carcinoma.

QTL Analysis of Chalkiness in Rice

A population of 150 recombination inbred lines （RILs） derived from the cross between rice varieties V20B and CPSLO17, was applied to locate the QTLs related to chalkiness traits and evaluate their genetic effects. A genetic linkage map was constructed based on 8 602 SLAF （specific-locus amplified fragment） markers, combine with the chatkiness traits of the tested lines. Four QTLs that related to chalkiness were detected using MapQTL 5 software, named qC-5a, qC-5b, qC-5c and qC-5d. The LOD threshold values of qC-5a, qC-5b, qC-5c and qC-5d were 4.02, 4.09, 3.94 and 4.1, respectively, explaining 11.6%, 11.8%, 11.2% and 11.8% of the observed phenotypic variance. All the four detected QTL alleles came from Iow-chalkiness parent V20B.

Genetic Biodiversity in Buffalo Population of Iraq Using Microsatellites Markers

Genetic structure of Iraqi buffalo population, in the South, Middle and North area of the country was characterized, using six microsatellite markers （ETHI52, ETH02, ETH225, CSSM060, BM1706 and INRA005）. Seventy alleles were detected across the six loci. Total number of alleles per locus （TNA） varied from 3 （INRA005 locus） to 16 （ETH 152 locus）. The mean number of allele （MNA） across the six loci in Iraqi indigenous buffalo was 11.4. The locus ETHI52 was the most polymorphic marker according to its number of allele （16）, the expected heterozygosity （0.86） and polymorphism information content （0.80） number of alleles （3）, expected Heterozygosity （0.1-0.2） and polymorphism information content （0.1-0.2）. Results showed that these markers were suitable in population genetics researches. It was concluded that a high degree of genetic diversity exist in the Iraqi buffalo populations.

Crizotinib： From Chemical Entity to Anticancer Agent

Crizotinib is a mesenchymal-epithelial transition/anaplastic largecell kinase （MET/ALK） multi-targeted receptor tyrosine kinase inhibitor and has been rapidly and successfully developed as an inhibitor in ALK-rearranged NSCLC （non-small cell lung cancer）. Lung cancer is the major cause of cancer-related mortality, accounting for over one quarter of cancer deaths. Lung cancers are generally divided into two main categories： SCLC （small cell lung cancer） and NSCLC. NSCLC accounts for approximately 85% of all lung cancers. ALK gene rearrangements are identified and targeted resulting in promising response rates for NSCLC in early studies. Considering the significance of Crizotinib in the treatment of NSCLC, the synthesis, pharmacodynamics, pharmacokinetics, therapeutic trials and adverse events are briefly overviewed in order to make more scholars, medical workers and patients have a more clear and comprehensive recognition on Crizotinib.

JAMIP:an artificial-intelligence aided data-driven infrastructure for computational materials informatics

Materials informatics has emerged as a promisingly new paradigm for accelerating materials discovery and design.It exploits the intelligent power of machine learning methods in massive materials data from experiments or simulations to seek new materials,functionality,and principles,etc.Developing specialized facilities to generate,collect,manage,learn,and mine large-scale materials data is crucial to materials informatics.We herein developed an artificial-intelligence-aided data-driven infrastructure named Jilin Artificial-intelligence aided Materials-design Integrated Package(JAMIP),which is an open-source Python framework to meet the research requirements of computational materials informatics.It is integrated by materials production factory,high-throughput first-principles calculations engine,automatic tasks submission and monitoring progress,data extraction,management and storage system,and artificial intelligence machine learning based data mining functions.We have integrated specific features such as an inorganic crystal structure prototype database to facilitate high-throughput calculations and essential modules associated with machine learning studies of functional materials.We demonstrated how our developed code is useful in exploring materials informatics of optoelectronic semiconductors by taking halide perovskites as typical case.By obeying the principles of automation,extensibility,reliability,and intelligence,the JAMIP code is a promisingly powerful tool contributing to the fast-growing field of computational materials informatics.

Hybridization and genome evolution I： The role of contingency during hybrid speciation

Homoploid hybrid speciation （HHS） involves the recombination of two differentiated genomes into a novel, func- tional one without a change in chromosome number. Theoretically, there are numerous ways for two parental genomes to recom- bine. Hence, chance may play a large role in the formation of a hybrid species. If these genome combinations can evolve rapidly following hybridization and sympatric situations are numerous, recurrent homoploid hybrid speciation is a possibility. We argue that three different, but not mutually exclusive, types of contingencies could influence this process. First, many of these ＂hopeful monsters＂ of recombinant parent genotypes would likely have low fitness. Only specific combinations of parental genomic con- tributions may produce viable, intra-fertile hybrid species able to accommodate potential constraints arising from intragenomic conflict. Second, ecological conditions （competition, geography of the contact zones or the initial frequency of both parent spe- cies） might favor different outcomes ranging from sympatric coexistence to the formation of hybrid swarms and ultimately hybrid speciation. Finally, history may also play an important role in promoting or constraining recurrent HHS if multiple hybridization events occur sequentially and parental divergence or isolation differs along this continuum. We discuss under which conditions HHS may occur multiple times in parallel and to what extent recombination and selection may fuse the parent genomes in the same or different ways. We conclude by examining different approaches that might help to solve this intriguing evolutionary puz- zle [Current Zoology 59 （5）： 667-674, 2013].

Development and characterization of synthetic amphiploids of Oryza sativa and Oryza latifolia

Oryza sativa and Oryza latifolia belong to the AA and CCDD genomes of Oryza, respectively. In this study, amphiploids were obtained from the tube seedlings of O. sativa × O. latifolia F1 hybrids by treatment with colchicine, an agent for chromosome doubling. Subse- quently, amphiploids were investigated using the methods of morphology, genomic in situ hybridization, and molec- ular markers. Amphiploids were characterized by a shorter plant height, larger diameter of stem, longer and wider leaves, darker leaf color, decreased spikelets per panicle and panicle length, and larger spikelets and anthers than the original F1 hybrid. Based on the mitotic metaphase chro- mosome number of the investigated root tips, the somatic chromosome number of the amphiploid is 2n = 72. Additionally, the amphiploid is an allohexaploid, and its genomic constitution is AACCDD by genomic in situ hybridization analysis. Finally, the amphiploids were identified to be true using 37 polymorphic markers at the DNA level.