المؤلفون: Yu-dong LI, Xue BAI, Xin LIU, Wei-jia WANG, Zi-wei LI, Ning WANG, Fan XIAO, Hai-he GAO, Huai-shun GUO, Hui LI, Shou-zhi WANG

المصدر: Journal of Integrative Agriculture, Vol 21, Iss 7, Pp 2065-2075 (2022)

مصطلحات موضوعية: chicken, muscle growth and development, GWAS, selection signature, Agriculture (General), S1-972

الوصف: Improving the production of broiler chicken meat has been a goal of broiler breeding programs worldwide for many years. However, the genetic architectures of skeletal muscle production traits in chickens have not yet been fully elucidated. In the present study, a total of 519 F2 birds, derived from a cross of Arbor Acres broiler and Baier layer, were re-sequenced (26 F0 individuals were re-sequenced at a 10-fold depth; 519 F2 individuals were re-sequenced at a 3-fold depth) and the coupling of genome-wide association study (GWAS) and selection signatures (FST (fixation index) and θπ (nucleotide diversity)) was carried out to pinpoint the associated loci and genes that contribute to pectoral muscle weight (PMW) and thigh muscle weight (TMW). A total of 7 890 258 single nucleotide polymorphisms (SNPs) remained to be analyzed after quality control and imputation. The integration of GWAS and selection signature analyses revealed that genetic determinants responsible for skeletal muscle production traits were mainly localized on chromosomes 1 (168.95–172.43 Mb) and 4 (74.37–75.23 Mb). A total of 17 positional candidate genes (PCGs) (LRCH1, CDADC1, CAB39L, LOC112531568, LOC112531569, FAM124A, FOXO1, NBEA, GPALPP1, RUBCNL, ARL11, KPNA3, LHFP, GBA3, LOC112532426, KCNIP4, and SLIT2) were identified in these regions. In particular, KPNA3 and FOXO1 were the most promising candidates for meat production in chickens. These findings will help enhance our understanding of the genetic architecture of chicken muscle production traits, and the significant SNPs identified could be promising candidates for integration into practical breeding programs such as genome-wide selection (GS) to improve the meat yield of chickens.

وصف الملف: electronic resource

العلاقة: http://www.sciencedirect.com/science/article/pii/S2095311921638054Test; https://doaj.org/toc/2095-3119Test

الوصول الحر: https://doaj.org/article/968d79f4e681452fb7f1528fd61c0e0bTest

المؤلفون: Yi-Sheng Sun, Hao Sun, Han-Ping Zhu, Gao-Lei Li, Fang Xu, Hang-Jing Lu, An Tang, Bei-Bei Wu, Yu-Dong Li, Ping-Ping Yao, Jian-Min Jiang

المصدر: Frontiers in Microbiology, Vol 13 (2023)

مصطلحات موضوعية: COVID-19, RNA-seq, lncRNAs, E gene, immune response, Microbiology, QR1-502

الوصف: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that caused a global outbreak of coronavirus disease 2019 (COVID-19) pandemic. To elucidate the mechanism of SARS-CoV-2 replication and immunogenicity, we performed a comparative transcriptome profile of mRNA and long non-coding RNAs (lncRNAs) in human lung epithelial cells infected with the SARS-CoV-2 wild-type strain (8X) and the variant with a 12-bp deletion in the E gene (F8). In total, 3,966 differentially expressed genes (DEGs) and 110 differentially expressed lncRNA (DE-lncRNA) candidates were identified. Of these, 94 DEGs and 32 DE-lncRNAs were found between samples infected with F8 and 8X. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyzes revealed that pathways such as the TNF signaling pathway and viral protein interaction with cytokine and cytokine receptor were involved. Furthermore, we constructed a lncRNA-protein-coding gene co-expression interaction network. The KEGG analysis of the co-expressed genes showed that these differentially expressed lncRNAs were enriched in pathways related to the immune response, which might explain the different replication and immunogenicity properties of the 8X and F8 strains. These results provide a useful resource for studying the pathogenesis of SARS-CoV-2 variants.

وصف الملف: electronic resource

العلاقة: https://www.frontiersin.org/articles/10.3389/fmicb.2022.1079764/fullTest; https://doaj.org/toc/1664-302XTest

الوصول الحر: https://doaj.org/article/4e1b3f51c2be41b78872c0cf8824e97aTest

المؤلفون: Yu-dong LI, Wei-jia WANG, Zi-wei LI, Ning WANG, Fan XIAO, Hai-he GAO, Huai-shun GUO, Hui LI, Shou-zhi WANG

المصدر: Journal of Integrative Agriculture, Vol 20, Iss 10, Pp 2734-2748 (2021)

مصطلحات موضوعية: chicken, LEPR, nsSNPs, bioinformatics tools, abdominal fat content, association analysis, Agriculture (General), S1-972

الوصف: Leptin receptor (LEPR) plays a vital role in obesity in humans and animals. The objective of this study is to assess LEPR functional variants for chicken adipose deposition by integration of association and in-silico analysis using a unique chicken population, the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF). Five online bioinformatics tools were used to predict the functionality of the single nucleotide polymorphisms (SNPs) in coding region. Further, the possible structure–function relationship of high confidence SNPs was determined by bioinformatics analyses, including the conservation and stability analysis based on amino acid residues, prediction of protein ligand-binding sites, and the superposition of protein tertiary structure. Meanwhile, we analyzed the association between abdominal fat traits and 20 polymorphisms of chicken LEPR gene. The integrated results showed that rs731962924 (N867I) and rs13684622 (C1002R) could lead to striking changes in the structure and function of proteins, of which rs13684622 (C1002R) was significantly associated with abdominal fat weight (AFW, P=0.0413) and abdominal fat percentage (AFP, P=0.0260) in chickens. Therefore, we are of the opinion that rs13684622 (C1002R) may be an essential functional SNP affecting chicken abdominal fat deposition, and potentially applied to improvement of broiler abdominal fat in molecular marker-assisted selection (MAS) program. Additionally, the coupling of association with computer electronic predictive analysis provides a new avenue to identify important molecular markers for breeders.

وصف الملف: electronic resource

العلاقة: http://www.sciencedirect.com/science/article/pii/S2095311920635754Test; https://doaj.org/toc/2095-3119Test

الوصول الحر: https://doaj.org/article/74691ac8bdd64f979d7f7656020dd516Test

المؤلفون: Qi-Xiang Lu, Lu-Jie Ren, Ya-Nan Wang, Yao Xiao, Yu-Dong Li, Jia-Nan Ying, Ying Zhang, Ruihong Wang, Zhe-Chen Qi, Zheng-Ying You

المصدر: Mitochondrial DNA. Part B. Resources, Vol 6, Iss 11, Pp 3253-3254 (2021)

مصطلحات موضوعية: chloroplast genome, phylogenetic analysis, sparganium glomeratum, typhaceae, Genetics, QH426-470

الوصف: The complete chloroplast genome of Sparganium glomeratum was sequenced and assembled in this study. The circular genome is 160,391 bp in length and exhibits a typical quadripartite structure with a large single-copy (LSC, 87,660 bp) and small single-copy (SSC, 18,721 bp) regions, separated by a pair of inverted repeats (IRs, 27,005 bp). The cp genome contains 113 unique genes, including 79 protein-coding, 30 tRNA, and four rRNA genes. The phylogenetic analysis within the Poales showed that Sparganium is monophyletic and most closely related to Typha. Within Sparganium, S. glomeratum is sister to the clade of S. stoloniferum and S. euricarpum. The work reported here will provide useful information for the evolutionary studies on the genus of Sparganium.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2380-2359Test

الوصول الحر: https://doaj.org/article/0b8b9cd02f6a43f39118044c65caf684Test

المؤلفون: Zheng-Ying You, Lu-Jie Ren, Yu-Dong Li, Jia-Nan Ying, Ying Zhang, Yin-Jiao Yu, Xin-Wei Xu, Rui-Hong Wang, Zhe-Chen Qi, Qi-Xiang Lu

المصدر: Mitochondrial DNA. Part B. Resources, Vol 6, Iss 1, Pp 48-49 (2021)

مصطلحات موضوعية: chloroplast genome, hippuris vulgaris, plantaginaceae, phylogenetic analysis, Genetics, QH426-470

الوصف: Two complete chloroplast genomes of Hippuris vulgaris (H. vulgaris_A and H. vulgaris_B), representing two distinct clades in China, were sequenced and assembled in this study. The circular genomes were 152,763 and 152,713 bp in length and exhibit a typical quadripartite structure of the large single-copy (LSC, 82,983/82,949 bp) and small single-copy (SSC, 18,294/18,278 bp) regions, separated by a pair of inverted repeats (IRs, both 25,743 bp). Both two cp genomes identically contain 133 genes, including 88 protein-coding genes, 37 tRNA, and eight rRNA genes. The phylogenetic analysis within Plantaginaceae demonstrated Hippuris an independent clade included in the expanded Plantaginaceae.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2380-2359Test

الوصول الحر: https://doaj.org/article/923185e841c74544a5c4316403a47114Test

المؤلفون: Yu-Dong Li, Zhuo-Chao Tang, Zhuo-Jia Fu

المصدر: Mathematics, Vol 8, Iss 11, p 1940 (2020)

مصطلحات موضوعية: meshless method, functionally graded material, first-order shear deformation theory, bending of plates, numerical simulation, Mathematics, QA1-939

الوصف: In this paper, an easy-to-implement domain-type meshless method—the generalized finite difference method (GFDM)—is applied to simulate the bending behavior of functionally graded (FG) plates. Based on the first-order shear deformation theory (FSDT) and Hamilton’s principle, the governing equations and constrained boundary conditions of functionally graded plates are derived. Based on the multivariate Taylor series and the weighted moving least-squares technique, the partial derivative of the underdetermined displacement at a certain node can be represented by a linear combination of the displacements at its adjacent nodes in the GFDM implementation. A certain node of the local support domain is formed according to the rule of “the shortest distance”. The proposed GFDM provides the sparse resultant matrix, which overcomes the highly ill-conditioned resultant matrix issue encountered in most of the meshless collocation methods. In addition, the studies show that irregular distribution of structural nodes has hardly any impact on the numerical performance of the generalized finite difference method for FG plate bending behavior. The method is a truly meshless approach. The numerical accuracy and efficiency of the GFDM are firstly verified through some benchmark examples, with different shapes and constrained boundary conditions. Then, the effects of material parameters and thickness on FG plate bending behavior are numerically investigated.

وصف الملف: electronic resource

العلاقة: https://www.mdpi.com/2227-7390/8/11/1940Test; https://doaj.org/toc/2227-7390Test

الوصول الحر: https://doaj.org/article/3a7fccdcfd224e75b467e29f6417ec6bTest

المؤلفون: Xue Li, Jin-Zhong Xu, Wen-Jie Wang, Yi-Wang Chen, Dao-Qiong Zheng, Ya-Nan Di, Ping Li, Pin-Mei Wang, Yu-Dong Li

المصدر: Evolutionary Bioinformatics, Vol 2016, Iss Suppl. 1, Pp 1-4 (2016)

مصطلحات موضوعية: Evolution, QH359-425

وصف الملف: electronic resource

العلاقة: http://www.la-press.com/genome-sequencing-and-evolutionary-analysis-of-marine-gut-fungus-asper-article-a5500Test; https://doaj.org/toc/1176-9343Test

الوصول الحر: https://doaj.org/article/166f52d3fdf54463939bdfe279d6fab1Test

المؤلفون: Ying Zhu, Hong-Yi Liu, Hai-Qiong Yang, Yu-Dong Li, He-Min Zhang

المصدر: PeerJ, Vol 5, p e3358 (2017)

مصطلحات موضوعية: Giant panda, Microsatellite fragment length, Long-term fecal DNA storage, Microsatellite base pair repeat unit, Storage time, Storage type, Medicine, Biology (General), QH301-705.5

الوصف: Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH −20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs) and frozen at −20 °C), storage time (one, three and six months), fragment length, and repeat motif of microsatellite loci) on the success rate of microsatellite amplification, allelic dropout (ADO) and false allele (FA) rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates (P

وصف الملف: electronic resource

العلاقة: https://peerj.com/articles/3358.pdfTest; https://peerj.com/articles/3358Test/; https://doaj.org/toc/2167-8359Test

الوصول الحر: https://doaj.org/article/8574692410634047814b51c4e3e3e09aTest

المؤلفون: Xue Li, Jin-Zhong Xu, Wen-Jie Wang, Yi-Wang Chen, Dao-Qiong Zheng, Ya-Nan Di, Ping Li, Pin-Mei Wang, Yu-Dong Li

المصدر: Evolutionary Bioinformatics, Vol 12s1 (2016)

مصطلحات موضوعية: Evolution, QH359-425

الوصف: Aspergillus sp. Z5, isolated from the gut of marine isopods, produces prolific secondary metabolites with new structure and bioactivity. Here, we report the draft sequence of the approximately 33.8-Mbp genome of this strain. To the best of our knowledge, this is the first genome sequence of Aspergillus strain isolated from marine isopod Ligia oceanica. The phylogenetic analysis supported that this strain was closely related to A. versicolor , and genomic analysis revealed that Aspergillus sp. Z5 shared a high degree of colinearity with the genome of A. sydowii. Our results may facilitate studies on discovering the biosynthetic pathways of secondary metabolites and elucidating their evolution in this species.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1176-9343Test

الوصول الحر: https://doaj.org/article/2fcc2b078a944a90b671c703264c6a63Test

المؤلفون: Yue-Yue Wang, Yu-Dong Li, Jian-Bo Liu, Xin-Xin Ran, Yuan-Yang Guo, Ni-Ni Ren, Xin Chen, Hui Jiang, Yong-Quan Li

المصدر: PLoS ONE, Vol 9, Iss 7, p e103031 (2014)

مصطلحات موضوعية: Medicine, Science

الوصف: Phosphopantetheinyl transferases (PPTases), which play an essential role in both primary and secondary metabolism, are magnesium binding enzymes. In this study, we characterized the magnesium binding residues of all known group II PPTases by biochemical and evolutionary analysis. Our results suggested that group II PPTases could be classified into two subgroups, two-magnesium-binding-residue-PPTases containing the triad Asp-Xxx-Glu and three-magnesium-binding-residue-PPTases containing the triad Asp-Glu-Glu. Mutations of two three-magnesium-binding-residue-PPTases and one two-magnesium-binding-residue-PPTase indicate that the first and the third residues in the triads are essential to activities; the second residues in the triads are non-essential. Although variations of the second residues in the triad Asp-Xxx-Glu exist throughout the whole phylogenetic tree, the second residues are conserved in animals, plants, algae, and most prokaryotes, respectively. Evolutionary analysis suggests that: the animal group II PPTases may originate from one common ancestor; the plant two-magnesium-binding-residue-PPTases may originate from one common ancestor; the plant three-magnesium-binding-residue-PPTases may derive from horizontal gene transfer from prokaryotes.

وصف الملف: electronic resource

العلاقة: http://europepmc.org/articles/PMC4103896?pdf=renderTest; https://doaj.org/toc/1932-6203Test

الوصول الحر: https://doaj.org/article/67bc11f5573c47ef91b5bccc5729365bTest