Copy number variants in locally raised Chinese chicken genomes determined using array comparative genomic hybridization

BACKGROUND: Copy number variants contribute to genetic variation in birds. Analyses of copy number variants in chicken breeds had focused primarily on those from commercial varieties with nothing known about the occurrence and diversity of copy number variants in locally raised Chinese chicken breeds. To address this deficiency, we characterized copy number variants in 11 chicken breeds and compared the variation among these breeds. RESULTS: We presented a detailed analysis of the copy number variants in locally raised Chinese chicken breeds identified using a customized comparative genomic hybridization array. We identified 833 copy number variants contained within 308 copy number variant regions. The median and mean sizes of the copy number variant regions were 14.6 kb and 35.1 kb, respectively. Of the copy number variant regions, 138 (45%) involved gain of DNA, 159 (52%) involved loss of DNA, and 11 (3%) involved both gain and loss of DNA. Principal component analysis and agglomerative hierarchical clustering revealed the close relatedness of the four locally raised chicken breeds, Shek-Ki, Langshan, Qingyuan partridge, and Wenchang. Biological process enrichment analysis of the copy number variant regions confirmed the greater variation among the four aforementioned varieties than among the seven other breeds studied. CONCLUSION: Our description of the distribution of the copy number variants and comparison of the differences among the copy number variant regions of the 11 chicken breeds supplemented the information available concerning the copy number variants of other Chinese chicken breeds. In addition to its relevance for functional analysis, our results provided the first insight into how chicken breeds can be clustered on the basis of their genomic copy number variation

The Airlines’ Recent Experience Under the Railway Labor Act

Silky-feather has been selected and fixed in some breeds due to its unique appearance. This phenotype is caused by a single recessive gene (hookless, h). Here we map the silky-feather locus to chromosome 3 by linkage analysis and subsequently fine-map it to an 18.9 kb interval using the identical by descent (IBD) method. Further analysis reveals that a C to G transversion located upstream of the prenyl (decaprenyl) diphosphate synthase, subunit 2 (PDSS2) gene is causing silky-feather. All silky-feather birds are homozygous for the G allele. The silky-feather mutation significantly decreases the expression of PDSS2 during feather development in vivo. Consistent with the regulatory effect, the C to G transversion is shown to remarkably reduce PDSS2 promoter activity in vitro. We report a new example of feather structure variation associated with a spontaneous mutation and provide new insight into the PDSS2 function

The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility

Rose-comb, a classical monogenic trait of chickens, is characterized by a drastically altered comb morphology compared to the single-combed wild-type. Here we show that Rose-comb is caused by a 7.4 Mb inversion on chromosome 7 and that a second Rose-comb allele arose by unequal crossing over between a Rose-comb and wild-type chromosome. The comb phenotype is caused by the relocalization of the MNR2 homeodomain protein gene leading to transient ectopic expression of MNR2 during comb development. We also provide a molecular explanation for the first example of epistatic interaction reported by Bateson and Punnett 104 years ago, namely that walnut-comb is caused by the combined effects of the Rose-comb and Pea-comb alleles. Transient ectopic expression of MNR2 and SOX5 (causing the Pea-comb phenotype) occurs in the same population of mesenchymal cells and with at least partially overlapping expression in individual cells in the comb primordium. Rose-comb has pleiotropic effects, as homozygosity in males has been associated with poor sperm motility. We postulate that this is caused by the disruption of the CCDC108 gene located at one of the inversion breakpoints. CCDC108 is a poorly characterized protein, but it contains a MSP (major sperm protein) domain and is expressed in testis. The study illustrates several characteristic features of the genetic diversity present in domestic animals, including the evolution of alleles by two or more consecutive mutations and the fact that structural changes have contributed to fast phenotypic evolution

The Crest Phenotype in Chicken Is Associated with Ectopic Expression of HOXC8 in Cranial Skin

The Crest phenotype is characterised by a tuft of elongated feathers atop the head. A similar phenotype is also seen in several wild bird species. Crest shows an autosomal incompletely dominant mode of inheritance and is associated with cerebral hernia. Here we show, using linkage analysis and genome-wide association, that Crest is located on the E22C19W28 linkage group and that it shows complete association to the HOXC-cluster on this chromosome. Expression analysis of tissues from Crested and non-crested chickens, representing 26 different breeds, revealed that HOXC8, but not HOXC12 or HOXC13, showed ectopic expression in cranial skin during embryonic development. We propose that Crest is caused by a cis-acting regulatory mutation underlying the ectopic expression of HOXC8. However, the identification of the causative mutation(s) has to await until a method becomes available for assembling this chromosomal region. Crest is unfortunately located in a genomic region that has so far defied all attempts to establish a contiguous sequence

The Effect of Manufacturing Errors on the Performance of a Gas-Dynamic Bearing Gyroscope

The purpose of this paper is to investigate the effect of manufacturing errors on the performance of a gas-dynamic bearing gyroscope. Five kinds of manufacturing errors including bearing taper error, oval error, trigone error, eccentricity of the axis, and angular deviation of the axis are studied. A mathematic model of these errors is established to describe the variation of gas film thickness. The Reynolds equation is solved, and the perturbation method is applied to analyze the performance of the gas-dynamic bearing with the manufacturing errors. Based on the analysis, the interference torque and overload limit are investigated to assess the effects of manufacturing errors. Results show that taper error will cause interference torque. Oval error or trigone error will cause interference torque with a radial specific force. The eccentricity or angular deviation of the axis will cause interference torque with any specific force. In general, the interference torque is small, which is 10–1000 times smaller than that under the condition of both radial and axial specific forces. The manufacturing errors also reduce the ultimate overload significantly. The taper error has the greatest influence on the gas-dynamic bearing gyroscope among the manufacturing errors studied in this paper

The Effect of Manufacturing Errors on the Performance of a Gas-Dynamic Bearing Gyroscope

The purpose of this paper is to investigate the effect of manufacturing errors on the performance of a gas-dynamic bearing gyroscope. Five kinds of manufacturing errors including bearing taper error, oval error, trigone error, eccentricity of the axis, and angular deviation of the axis are studied. A mathematic model of these errors is established to describe the variation of gas film thickness. The Reynolds equation is solved, and the perturbation method is applied to analyze the performance of the gas-dynamic bearing with the manufacturing errors. Based on the analysis, the interference torque and overload limit are investigated to assess the effects of manufacturing errors. Results show that taper error will cause interference torque. Oval error or trigone error will cause interference torque with a radial specific force. The eccentricity or angular deviation of the axis will cause interference torque with any specific force. In general, the interference torque is small, which is 10–1000 times smaller than that under the condition of both radial and axial specific forces. The manufacturing errors also reduce the ultimate overload significantly. The taper error has the greatest influence on the gas-dynamic bearing gyroscope among the manufacturing errors studied in this paper

Sulfonyl as a Traceless Activation Group for Enantioselective Mannich Reaction Catalyzed by Thiourea to Access Chiral β-Aminophosphonates

An efficient enantioselective Mannich reaction of N-protected α-sulfones with β-benzenesulfonyl phosphonates was developed by using a chiral cinchona alkaloid-derived thiourea as a catalyst. This method was used to obtain a series of chiral α-sulfonyl-β-aminophosphonates in yields of up to 96% with 89:11 dr and 88% ee. These compounds were further transformed into β-aminophosphonates or chiral azetidines with various functional groups by a Horner–Wadsworth–Emmons/aza-Michael addition reaction sequence.</jats:p

Imaging Characteristics of Disturbance Flow Field Surrounding a Hypersonic Target

The disturbance flow field arises naturally with hypersonic target flying in near space. In situations where traditional infrared and radar systems lose effectiveness, space-based optical detection of this surrounding flow can serve as an alternative method for detecting high-speed targets. This paper presents a remote sensing imaging analysis of the disturbance flow field surrounding a hypersnoic target at different flight altitudes and Mach numbers. Utilizing Fourier Optics and Background-Oriented Schlieren, in conjunction with the fourth-order Runge-Kutta ray tracing algorithm, the imaging blurring and imaging deviation of three typical backgrounds under the influence of the disturbance flow field are obtained. Additionally, the study analyzes the influence of flight conditions and parameters of the imaging system on the imaging characteristics, and provides optical design recommendations. The results indicate that the presence of disturbance flow fields leads to varying degrees of visually apparent blurring effects and indiscernible deviation effects on the background images. Furthermore, the profiles of the disturbance flow field are extracted, in agreement with current experimental research. This study verifies the feasibility of space-based optical detection of hypersonic targets through disturbance flow field remote sensing imaging and contributes to the advancement of imaging research in this field

Organocatalytic Enantioselective 1,3-Dipolar Cycloadditions between Seyferth–Gilbert Reagent and Isatylidene Malononitriles: Synthesis of Chiral Spiro-phosphonylpyrazoline-oxindoles

A new method has been developed for the catalytic enantioselective 1,3-dipolar cycloaddition of the Seyferth–Gilbert reagent (SGR) to isatylidene malononitriles using a cinchona alkaloid derivative as a catalyst. This method allowed for the synthesis of a series of chiral spiro-phosphonylpyrazoline-oxindoles in good yields with excellent enantioselectivities. The synthetic utility of this method was further demonstrated by its use in a three-component domino reaction involving isatin, malononitrile, and SGR based on sequential Knoevenagel condensation and 1,3-dipolar cycloaddition reactions