Genome-wide association study and inbreeding depression on body size traits in Qira black sheep (Ovis aries).

Qira black sheep is a famous indigenous sheep breed in China. The objectives of this study are to identify candidate genes related to body size, and to estimate the level of inbreeding depression on body size based on runs of homozygosity in Qira black sheep. Here, 188 adult Qira black sheep were genotyped with a high density (630 K) SNP chip and genome-wide association study for body weight and body size traits (including withers height, body slanting length, tail length, chest girth, chest width, and chest depth) were performed using an additive linear model. In consequence, 12 genome- and chromosome-wide significant SNPs and, accordingly, six candidate genes involved in muscle differentiation, metabolism and cell processes were identified. Of them, ZNF704 (zinc finger protein 704) was identified for body weight; AK2 (adenylate kinase 2) and PARK2 (parkin RBR E3 ubiquitin protein ligase) for tail length; MOCOS (molybdenum cofactor sulfurase) and ELP2 (elongator acetyltransferase complex subunit 2) for chest width; and MFAP1 (microfibril associated protein 1) for chest girth. Additionally, inbreeding depressions on body size were observed in the current herd. These results will provide insightful understandings into the genetic mechanisms of adult body size, and into the conservation and utilization of Qira black sheep.

Complete mitochondrial genome sequence and gene organization of Chinese indigenous chickens with phylogenetic considerations.

In this study, we sequenced the complete mitochondrial DNA of Chinese indigenous Jinhu Black-bone and Rugao chickens. The two chicken mitochondrial genomes were deposited in GenBank under accession Nos. KP742951 and KR347464, respectively. The complete mitochondrial genomes of Jinhu Black-bone and Rugao chickens were sequenced and found to span 16,785 and 16,786 bp, respectively, and consisted of 22 tRNA genes, two rRNA genes (12S rRNA and 16S rRNA), 13 protein-coding genes, and one control region (D-loop). The majority of genes were positioned on the H-strand, and the ND6 and eight tRNA genes were found to be encoded on the L-strand. The mitogenomes showed a similar gene order to that of the published Gallus gallus genome, as neither included a control region. The overall base composition of the genome of the two chickens was A = 30.22/30.28%, G = 13.57/13.49%, T = 23.74/23.76%, and C = 32.48/32.48%. Nucleotide skewness of the coding strands of the two chicken genomes (AT-skew = 0.12, GC-skew = -0.41) was biased towards T and G. Phylogenetic analysis revealed 29 subspecies, and the molecular genetic relationship among the 29 subspecies was identical to that of traditional taxonomy.

Thermally driven grain boundary migration and melting in Cu.

With molecular dynamics simulations, we systematically investigate melting of a set of Σ3〈110〉70.53° tilt grain boundaries (GB) in Cu bicrystals, including coherent twin boundaries (CTBs), 12 asymmetric tilt grain boundaries (ATGBs), and symmetric incoherent twin boundaries (SITBs), in the order of increasing length weight of SITB or GB energy. ATGBs decompose into CTBs and SITBs, which migrate and coalesce as a result of internal stress relaxation. GBs can be superheated or premelted, and GB melting temperature decreases exponentially with increasing SITB weight, owing to the systematics in GB microstructure. GB melting nucleates at disordered CTB-SITB junctions, and grows along SITBs and then into grain interiors, with the solid-liquid interfaces preferentially aligned with {111}.

Shock response of single crystal and nanocrystalline pentaerythritol tetranitrate: Implications to hotspot formation in energetic materials.

We investigate shock response of single crystal and nanocrystalline pentaerythritol tetranitrate (PETN) with a coarse-grained model and molecular dynamics simulations, as regards mechanical hotspot formation in the absence or presence of grain boundaries (GBs). Single crystals with different orientations, and columnar nanocrystalline PETN with regular hexagonal, irregular hexagonal, and random GB patterns, are subjected to shock loading at different shock strengths. In single crystals, shock-induced plasticity is consistent with resolved shear stress calculations and the steric hindrance model, and this deformation leads to local heating. For regular-shaped hexagonal columnar nanocrystalline PETN, different misorientation angles lead to activation of different/same slip systems, different deformation in individual grains and as a whole, different GB friction, different temperature distributions, and then, different hotspot characteristics. Compared to their regular-shaped hexagonal counterpart, nanocrystalline PETN with irregular hexagonal GB pattern and that with random GBs, show deformation and hotspot features specific to their GBs. Driven by stress concentration, hotspot formation is directly related to GB friction and GB-initiated crystal plasticity, and the exact deformation is dictated by grain orientations and resolved shear stresses. GB friction alone can induce hotspots, but the hotspot temperature can be enhanced if it is coupled with GB-initiated crystal plasticity, and the slip of GB atoms has components out of the GB plane. The magnitude of shearing can correlate well with temperature, but the slip direction of GB atoms relative to GBs may play a critical role. Wave propagation through varying microstructure may also induce differences in stress states (e.g., stress concentrations) and loading rates, and thus, local temperature rise. GB-related friction and plasticity induce local heating or mechanical hotspots, which could be precursors to chemical hotspot formation related to initiation in energetic materials, in the absence of other, likely more effective, means for hotspot formation such as void collapse.

Optimal Design for Marker-assisted Gene Pyramiding in Cross Population.

Marker-assisted gene pyramiding aims to produce individuals with superior economic traits according to the optimal breeding scheme which involves selecting a series of favorite target alleles after cross of base populations and pyramiding them into a single genotype. Inspired by the science of evolutionary computation, we used the metaphor of hill-climbing to model the dynamic behavior of gene pyramiding. In consideration of the traditional cross program of animals along with the features of animal segregating populations, four types of cross programs and two types of selection strategies for gene pyramiding are performed from a practical perspective. Two population cross for pyramiding two genes (denoted II), three population cascading cross for pyramiding three genes(denoted III), four population symmetry (denoted IIII-S) and cascading cross for pyramiding four genes (denoted IIII-C), and various schemes (denoted cross program-A-E) are designed for each cross program given different levels of initial favorite allele frequencies, base population sizes and trait heritabilities. The process of gene pyramiding breeding for various schemes are simulated and compared based on the population hamming distance, average superior genotype frequencies and average phenotypic values. By simulation, the results show that the larger base population size and the higher the initial favorite allele frequency the higher the efficiency of gene pyramiding. Parents cross order is shown to be the most important factor in a cascading cross, but has no significant influence on the symmetric cross. The results also show that genotypic selection strategy is superior to phenotypic selection in accelerating gene pyramiding. Moreover, the method and corresponding software was used to compare different cross schemes and selection strategies.

[Expression of C-fos in nasopharyngeal carcinoma and the relationship with chemosensitivity and prognosis].

Objective:To investigate the expression of C-fos in patients with nasopharyngeal carcinoma(NPC), and analyze the relationship between the expression of C-fos and the clinical characteristics, chemosensitivity and prognosis. Method:Clinical and follow-up data of 75 NPC patients was analyzed retrospectively. The expression of C-fos was detected by immunohistochemical assay, and chemosensitivity was detected by ATP bioluminescent anticancer drug sensitivity detection technology. The relationship between them was studied.Result:The expression of C-fos in NPC was statistically higher than that in the control nasopharyngeal mucosa(P<0.001). It was found that C-fos had no statistical relationship with the gender, age, pathologic type, clinical stage of tumor classification, lymph node status, metastasis status and overall stage of NPC patients(P>0.05). NPC had different chemosensitivity with 8 anticancer drugs(P<0.001).There was a significant difference in chemosensitivity of paclitaxel between the high expression of C-fos group and the low expression of C-fos group(P=0.036). The rate of tumor progression was significantly higher in NPC patients with high expression of C-fos than in the low expression group(P=0.014).There was no significant difference in overall survival between the two groups(P=0.076). Conclusion:C-fos is highly expressed in NPC tissues, and the high expression of C-fos in NPC tissues may be related to tumor progression and resistance to paclitaxel.

Estrogen/ERR-α signaling axis is associated with fiber-type conversion of upper airway muscles in patients with obstructive sleep apnea hypopnea syndrome.

Estrogen is related with the low morbidity associated with obstructive sleep apnea hypopnea syndrome (OSAS) in women, but the underlying mechanisms remain largely unknown. In this study, we examined the relationship between OSAS and estrogen related receptor-α (ERR-α). We found that the expression levels of ERR-α and Myh7 were both downregulated in palatopharyngeal tissues from OSAS patients. In addition, we report that ERR-α is dynamically expressed during differentiation of C2C12 myoblasts. Knockdown of ERR-α via instant siRNA resulted in reduced expression of Myh7, but not Myh4. Furthermore, differentiation of C2C12 cells under 3% chronic intermittent hypoxia, a model resembling human OSAS, was impaired and accompanied by a obvious reduction in Myh7 expression levels. Moreover, activation of ERR-α with 17ß-estradiol (E2) increased the expression of Myh7, whereas pretreatment with the ERR-α antagonist XCT790 reversed the E2-induced slow fiber-type switch. A rat ovariectomy model also demonstrated the switch to fast fiber type. Collectively, our findings suggest that ERR-α is involved in estrogen-mediated OSAS by regulating Myhc-slow expression. The present study illustrates an important role of the estrogen/ERR-α axis in the pathogenesis of OSAS, and may represent an attractive therapeutic target, especially in postmenopausal women.

Design and comparison of gene-pyramiding schemes in animals.

Marker-assisted gene pyramiding provides a promising way to develop new animal breeds or lines, in which genes responsible for certain favorable characters identified in different breeds or lines are incorporated. In consideration of features of animal populations, we proposed five schemes for pyramiding three genes, denoted Scheme A-E, and five schemes for pyramiding four genes, denoted Scheme F-J. These schemes are representative of the possible alternatives. We also provided an algorithm to compute the population sizes needed in each generation. We compared these schemes with respect to the total population size and the number of generations required under different situations. The results show that there is no scheme that is optimal in all cases. Among the schemes for pyramiding three genes from three lines (L1, L2 and L3), Scheme D (a three-way cross between the three lines are first performed, followed by a backcross to L1 and a subsequent intercross to obtain the desired genotype) has a significant advantage over the other schemes when the recombination rate between adjacent genes ranges from 0.1 to 0.4, while Scheme A (a two-way cross between L1 and L2 and a subsequent intercross are performed, followed by a cross with L3 and a subsequent intercross to obtain the desired genotype) is optimal when recombination rate is 0.5. Among schemes for pyramiding four genes from four lines (L1, L2, L3 and L4), Scheme I (seperately, a two-way cross between L1 and L2 (L3 and L4) followed by a backcross to L1 (L3) and a subsequent intercross are performed, then the offspring from the two sides are crossed and followed by a backcross to L1 and a subsequent intercross to obtain the desired genotype) is optimal when the recombination rate ranges from 0.1 to 0.4, while Scheme F (cross and subsequent intercross between the four lines are performed successively) is the optimal when the recombination rate is 0.5. We also disscuss how the animals' reproductive capacity, the probabilities of obtaining the desired genotypes and genetic distance between adjacent genes would affect the design of an optimal scheme.