A Novel Method for Spectral Similarity Measure by Fusing Shape and Amplitude Features

Spectral similarity measure is the basis of spectral information extraction. The description of spectral features is the key to spectral similarity measure. To express the spectral shape and amplitude features reasonably, this paper presents the definition of shape and amplitude feature vector, constructs the shape feature distance vector and amplitude feature distance vector, proposes the spectral similarity measure by fusing shape and amplitude features (SAF), and discloses the relationship of fusing SAF with Euclidean distance and spectral information divergence. Different measures were tested on the basis of United States Geological Survey (USGS) mineral_beckman_430. Generally, measures by integrating SAF achieve the highest accuracy, followed by measures based on shape features and measures based on amplitude features. In measures by integrating SAF, fusing SAF shows the highest accuracy. Fusing SAF expresses the measured results with the inner product of shape and amplitude feature distance vectors, which integrate spectral shape and amplitude features well. Fusing SAF is superior to other similarity measures that integrate SAF, such as spectral similarity scale, spectral pan-similarity measure, and normalized spectral similarity score(NS3 )

Identification of two novel single nucleotide polymorphism sites in the Myostatin (MSTN) gene and their association with carcass traits in meat-type rabbits (Oryctolagus cuniculus)

[EN] Two unknown single nucleotide polymorphism (SNP) sites in exons 1 (c.194C>T) and 2 (c.445T>A) of meat-type rabbit MSTN gene were identified in the study. Our objective was to analyse the population genetics structure of the two novel SNP sites in 230 individuals from six breeds and their associations with carcass traits of rabbits. We found that live body weight (BW), cold carcass weight (CCW), reference carcass weight (RCW), CCW percentage (PCCW) and RCW percentage (PRCW) of the rabbits with the genotype CC at the c.194C>T of exon 1 or AA at the c.445T>A of exon 2 were significantly higher than those with other genotypes. Diplotype significantly affected BW, RCW, CCW, PRCW (P<0.01) and PCCW and PCM (P<0.05). CC/AA was the advantageous diplotype for BW, RCW, CCW and PCM, and TT/AA was the advantageous diplotype for PCCW and PRCW. In contrast, TT/TT was the negative diplotype for BW, CCW, RCW, PCCW and PRCW, and TT/AA was the negative diplotype for PCM. The results sugThe studies were financially supported by Basic Science Research Fund of Sichuan Agricultural University (No.11967) and the National Modern Rabbit Production Industry Special Fund (N°. NYCYTX-44-1-3).Yang, L.; Zhang, K.; Wu, QY.; Li, J.; Lai, SJ.; Song, TZ.; Zhang, M. (2019). Identification of two novel single nucleotide polymorphism sites in the Myostatin (MSTN) gene and their association with carcass traits in meat-type rabbits (Oryctolagus cuniculus). World Rabbit Science. 27(4):249-256. https://doi.org/10.4995/wrs.2019.10610OJS249256274Abdel-Kafy E.M., Darwish S.F., Elkhishin D. 2016. Correlating single nucleotide polymorphisms in the myostatin gene with performance traits in rabbit. World Rabbit Sci., 24: 213-221. https://doi.org/10.4995/wrs.2016.4026Bellinge R.H.S., Liberles D.A., Iashi S.P.A., O'Brien P.A., Tay G.K. 2004. Myostatin and its implications on animal breeding: a review. Anim. 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Modern Journal of Animal Husbandry and Veterinary Medicine, 11: 12-13 (In Chinese).Guo R., Wan Y., Xu D., Cui L., Deng M., Zhang G., Jia R., Zhou W., Wang Z., Deng K., Huang M., Wang F., Zhang Y. 2016. Generation and evaluation of Myostatin knock-out rabbits and goats using CRISPR/Cas9 system. Sci. Rep-UK., 6: 1-10. https://doi.org/10.1038/srep29855Jiang Y.L., Li N., Wu C.X., Li L.X. 2008. Analysis on nucleotide polymorphisms of porcine myostatin gene in different breeds. J. Genet. Genomics, 28: 840-845 (In Chinese).Joulia-Ekaza D., Cabello G. 2007. The myostatin gene: physiology and pharmacological relevance. Curr. Op. Pharmacol., 7: 310-315. https://doi.org/10.1016/j.coph.2006.11.011Joulia D., Bernardi H., Garandel V., Rabenoelina F., Vernus B., Cabello G. 2003. Mechanisms involved in the inhibition of myoblast proliferation and differentiation by myostatin. Exp. Cell Res. 286, 263-275. https://doi.org/10.1016/S0014-4827(03)00074-0Jurečková J., Picek J. 2007. Shapiro-Wilk-type test of normality under nuisance regression and scale. Computational Statistics & Data Analysis, 51(10): 5184-5191. https://doi.org/10.1016/j.csda.2006.08.026Kambadur R., Sharma M., Smith T.P..L, Bass J.J. 1997. Mutation in myostatin (GDF8) in double-muscled Belgian blue and Piedmontese cattle. Gen. Res., 7: 910-915. https://doi.org/10.1101/gr.7.9.910Lin J., Arnold H.B., Della-Fera M.A, Azain M.J., Hartzell D.L., Baile CA. 2002. Myostatin knock-out in mice increases myogenesis and decreases adipogenesis. Biochem. Bioph. Res. Co., 292: 701-706. https://doi.org/10.1006/bbrc.2002.6500Li S.H., Xiong Y.Z., Zheng R., Li A.Y., Deng C.Y., Jiang S.W., Lei M.G., Weng Y.Q., Cao G.C. 2002. Polymorphism of porcine myostatin gene. J. Genet. Genomics, 29: 326-331 (In Chinese).Liu Z.Z., Li X.L., Gong Y.F., Jin X.M., Feng M.S. 2006. Relationship between polymorphism of goat MSTN gene intron 2 and body weight. Acta Vet. Zootec. Sinica, 37: 745-748.Lu J.Q., Huang W., Zhao N., Wang W.W., Hou S.S. 2008. Analysis on gene polymorphism of myostatin and carcass traits of Peking duck. China Animal Husbandry & Veterinary Medicine 35: 61-63 (In Chinese).Marchitelli C., Savarese M.C., Crisa A., Nardone A., Ajmone-Marsan P., Valentini A. 2003. Double muscling in marchigiana beef breed is caused by a stop codon in the third exon of myostatin gene. Mamm. Genome, 14: 392-395. https://doi.org/10.1007/s00335-002-2176-5McCroskery S., THomas M., Maxwell L, Sharma M., Kambadur R. 2003. Myostatin negatively regulates satellite cell activation and self-renewal. J. Cell Biol., 162: 1135-1147. https://doi.org/10.1083/jcb.200207056McPherron A.C., Lawler A.M., Lee S.J. 1997. Regulation of skeletal muscle mass in mice by a new TGF-B superfamily member. Nature, 387: 83-90. https://doi.org/10.1038/387083a0McPherron A.C, Lee S.J. 1997. Double muscling in cattle due to mutations in myostatin gene. In Proc.: National Academy of Sciences, 94: 12457-12461. https://doi.org/10.1073/pnas.94.23.12457McPherron A.C., Lee S.J. 2002. Suppression of body fat accumulation in myostatin-deficient mice. J. Clin. Invest., 109: 595-601. https://doi.org/10.1172/JCI200213562Mosher D.S., Quignon P., Bustamante C.D., Sutter N.B., Mellersh C.S., Parker H.G, Ostrander E.A. 2007. A mutation in the myostatin gene increases muscle mass and enhances racing performance in heterozygote dogs. Plos Genetics, 3: e79. https://doi.org/10.1371/journal.pgen.0030079Naveen Z., Naik B.R., Subramanyam B.V., Reddy P.M. 2016. Studies on the quality of duck meat sausages during refrigeration. Springer Plus, 5: 2061. https://doi.org/10.1186/s40064-016-3743-7Qiao X.B., Xu K.Y., Li B., Luan X., Xia T., Fan X.Z. 2014. Rabbit MSTN gene polymorphisms and genetic effect analysis. Genet. Mol. Res., 13: 2590-2597. https://doi.org/10.4238/2014.April.8.1Rios R., Carneiro I., Arce V.M., Devesa J.. 2002. 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In silico cloning and chromosomal localization of EST sequences that are related to leaf senescence using nulli-tetrasomes in wheat

Leaf senescence is a notably important trait that limits the yield and biomass accumulation of agronomic crops. Therefore, determining the chromosomal position of the expression sequence tags (ESTs) that are associated with leaf senescence is notably interesting in the manipulation of leaf senescence for crop improvement. A total of 32 ESTs that were previously identified during the delaying leaf senescence stage in the stay-green wheat cultivar CN17 were mapped to 42 chromosomes, a chloroplast, a mitochondrion, and a ribosome using in silico mapping. Then, we developed 19 pairs of primers based on these sequences and used them to determine the polymorphisms between the stay-green cultivars (CN12, CN17, and CN18) and the control cultivar MY11. Among the 19 pairs of primers, 5 pairs produced polymorphisms between the stay-green cultivar and the non-stay-green control. Further studies of Chinese Spring nullisomic-tetrasomics show that JK738991 is mapped to 3B, JK738983 is mapped to 5D, and JK738989 is mapped to 2A, 4A, and 3D. The other two ESTs, JK738994 and JK739003, were not assigned to a chromosome using the Chinese Spring nullisomic-tetrasomics, which indicates that these ESTs may be derived from rye DNA in the wide cross. In particular, the ESTs that produce polymorphisms are notably useful in identifying the stay-green cultivar using molecular marker-assisted selection. The results also suggest that the in silico mapping data, even from a comparison genomic analysis based on the homogeneous comparison, are useful at some points, but the data were not always reliable, which requires further investigation using experimental methods

Development and Application of the Diffusive Gradients in Thin-Films Technique for Measuring Psychiatric Pharmaceuticals in Natural Waters

Psychiatric pharmaceuticals are widely distributed in the aquatic environment and have attracted recent attention due to their potential for environmental effects. A robust and reliable in situ passive sampling approach, the diffusive gradients in thin-films (DGT) technique, is developed here to measure 14 psychiatric pharmaceuticals. A new binding material, mixed-mode cation exchange resin (Poly-Sery MCX, 40 μm, CNW, Germany), was used for the first time in DGT and compared to XAD and HLB. Reliable elution efficiencies of the pharmaceuticals from the binding gels were obtained in methanol/ammonia, and diffusion coefficients for all the compounds were determined. The influence of diffusive layer thickness (0.515–2.015 mm), deployment time (3–168 h), and important environmental conditions—pH (3.02–9.45), ionic strength (0.0001–0.5 M), and dissolved organic matter (0–20 mg L–1)—were evaluated. The capacity of XAD, HLB, and MCX gels for binding all the test pharmaceuticals was ∼335 μg per disc, meaning that DGT could theoretically be deployed for over 30 months if there are no competitive effects or confounding factors. The uptake kinetics of psychiatric pharmaceuticals onto MCX gel were much faster than those onto XAD and HLB gels in the first hour. DGT measured concentrations of test pharmaceuticals at two sample points in a river (over 6 days) were comparable to those obtained by grab sampling. This study demonstrates the accuracy and reliability of DGT for measuring psychiatric pharmaceuticals across a wide range of freshwater conditions found in the natural environment

Cytogenetic and molecular identification of a new wheat-Thinopyrum intermedium addition line with resistance to powdery mildew

Thinopyrum intermedium, which has many useful traits, is valuable for wheat breeding. A new wheat-Thinopyrum addition line, SN100109, was developed from the progeny of common wheat cultivar Yannong 15 and Th. intermedium. It was resistant to most races of Blumeria graminis f. sp tritici (Bgt), which caused powdery mildew in wheat, and its reactions were different from the reactions of gene Pm40 and Pm43. Genomic in situ hybridization (GISH) and molecular marker analysis were used to identify the genomic composition of SN100109. GISH results showed that SN100109 was a wheat-Th. intermedium disomic addition line containing one pair of J chromosomes, and the resistance gene was located on the alien additional chromosomes of SN100109. And four molecular markers BE425942, BF482714, Xgdm93 and BV679214 which were assigned to homologous group 2, were specific molecular markers of the additional chromosomes. All the results indicated that SN100109 contained one pair of 2J chromosomes. SN100109 can be used as a novel germplasm source for introducing powdery mildew resistance genes to wheat in breeding programs

Molecular characterization of seven novel Glu-A1^mx alleles from Triticum monococcum ssp. monococcum

Seven Glu-A1m allelic variants of the Glu-A1mx genes in Triticum monococcum ssp. monococcum, designated as 1Ax2.1a, 1Ax2.1b, 1Ax2.1c, 1Ax2.1d, 1Ax2.1e, 1Ax2.1f, and 1Ax2.1g were characterized. Their authenticity was confirmed by successful expression of the coding regions in E. coli, and except for the 1Ax2.1a with the presence of internal stop codons at position of 313 aa, all correspond to the subunit in seeds. However, all the active six genes had a same DNA size although their encoding subunits showed different molecular weight. Our study indicated that amino acid residue substitutions rather than previously frequently reported insertions/deletions played an important role on the subunit evolution of these Glu-A1mx alleles. Since variation in the Glu-A1x locus in common wheat is rare, these novel genes at the Glu-A1mx can be used as candidate genes for further wheat quality improvement

Molecular characterization of different Triticum monococcum ssp. monococcum Glu-A1^mx alleles

High-molecular-weight glutenin subunits (HMW-GSs) are important seed storage proteins associated with bread-making quality in common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD). Variation in the Glu-A1x locus in common wheat is scare. Diploid Triticum monococcum ssp. monococcum (2n = 2x = 14, AmAm) is the first cultivated wheat. In the present study, allelic variations at the Glu-A1mx locus were systematically investigated in 197 T. monococcum ssp. monococcum accessions. Out of the 8 detected Glu-A1mx alleles, 5 were novel, including Glu-A1m-b, Glu-A1m-c, Glu-A1m-d, Glu-A1m-g, and Glu-A1m-h. This diversity is higher than that of common wheat. Compared with 1Ax1 and 1Ax2*, which are present in common wheat, these alleles contained three deletions/insertions as well as some single nucleotide polymorphism variations that might affect the elastic properties of wheat flour. New variations in T. monococcum probably occurred after the divergence between A and Am and are excluded in common wheat populations. These allelic variations could be used as novel resources to further improve wheat quality

Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists tree of life based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution