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  • 1
    Publication Date: 2013-06-11
    Description: Background: Comparative genomics is a powerful tool to transfer genomic information from model species to related non-model species. Channel catfish (Ictalurus punctatus) is the primary aquaculture species in the United States. Its existing genome resources such as genomic sequences generated from next generation sequencing, BAC end sequences (BES), physical maps, linkage maps, and integrated linkage and physical maps using BES-associated markers provide a platform for comparative genomic analysis between catfish and other model teleost fish species. This study aimed to gain understanding of genome organizations and similarities among catfish and several sequenced teleost genomes using linkage group 8 (LG8) as a pilot study. Results: With existing genome resources, 287 unique genes were identified in LG8. Comparative genome analysis indicated that most of these 287 genes on catfish LG8 are located on two homologous chromosomes of zebrafish, medaka, stickleback, and three chromosomes of green-spotted pufferfish. Large numbers of conserved syntenies were identified. Detailed analysis of the conserved syntenies in relation to chromosome level similarities revealed extensive inter-chromosomal and intra-chromosomal rearrangements during evolution. Of the 287 genes, 35 genes were found to be duplicated in the catfish genome, with the vast majority of the duplications being interchromosomal. Conclusions: Comparative genome analysis is a powerful tool even in the absence of a well-assembled whole genome sequence. In spite of sequence stacking due to low resolution of the linkage and physical maps, conserved syntenies can be identified although the exact gene order and orientation are unknown at present. Through chromosome-level comparative analysis, homologous chromosomes among teleosts can be identified. Syntenic analysis should facilitate annotation of the catfish genome, which in turn, should facilitate functional inference of genes based on their orthology.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 2
    Publication Date: 2013-05-22
    Description: Delivery of therapeutic agents by nanoparticles made of grapefruit-derived lipids Nature Communications 4, (2013). doi:10.1038/ncomms2886 Authors: Qilong Wang, Xiaoying Zhuang, Jingyao Mu, Zhong-Bin Deng, Hong Jiang, Xiaoyu Xiang, Baomei Wang, Jun Yan, Donald Miller & Huang-Ge Zhang
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2022-01-31
    Description: Transgenerational effects of multiple stressors on marine organisms are emerging environmental themes. We thus experimentally tested for transgenerational effects of seawater acidification and hypoxia on the early development traits of the mussel Mytilus edulis. Fertilization rate, embryo deformity rate, and larval shell length were negatively impacted by acidification, while hypoxia had little effect except for increasing deformity rates under control pH conditions. Offspring from low pH/O2 parents were less negatively affected by low pH/O2 conditions than offspring from control parents; however, low pH/O2 conditions still negatively affected developmental traits in offspring from acclimated parents compared to control seawater conditions. Our results demonstrate that experimental seawater acidification and hypoxia can adversely affect early developmental traits of M. edulis and that parental exposure can only partially alleviate these impacts. If experimental observations hold true in nature, it is unlikely that parental exposure will confer larval tolerance to ocean acidification for M. edulis.
    Type: Article , PeerReviewed
    Format: text
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  • 4
    Publication Date: 2014-12-09
    Description: The ―NH 2 , ―NO 2 , ―NHNO 2 , ―C(NO 2 ) 3 and ―CF(NO 2 ) 2 substitution derivatives of 4,4′,5,5′-tetranitro-2,2′-1H,1′H-2,2′-biimidazole were studied at B3LYP/aug-cc-pVDZ level of density functional theory. The crystal structures were obtained by molecular mechanics (MM) methods. Detonation properties were evaluated using Kamlet–Jacobs equations based on the calculated density and heat of formation. The thermal stability of the title compounds was investigated via the energy gaps ( ∆E LUMO − HOMO ) predicted. Results show that molecules T5 ( D  = 10.85 km·s −1 , P  = 57.94 GPa) and T6 ( D  = 9.22 km·s −1 , P  = 39.21 GPa) with zero or positive oxygen balance are excellent candidates for high energy density oxidizers (HEDOs). All of them appear to be potential explosives compared with the famous ones, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetraazocane (HMX, D  = 8.96 km·s −1 , P  = 35.96 GPa) and hexanitrohexaazaisowurtzitane (CL-20, D  = 9.38 km·s −1 , P  = 42.00 GPa). In addition, bond dissociation energy calculation indicates that T5 and T6 are also the most thermally stable ones among the title compounds. Copyright © 2014 John Wiley & Sons, Ltd. The ―NH 2 , ―NO 2 , ―NHNO 2 , ―C(NO 2 ) 3 and ―CF(NO 2 ) 2 substitution derivatives of 4,4',5,5'-tetranitro-2,2'-1H,1'H- 2,2'-biimidazole were studied at B3LYP/aug-cc- pVDZ level of density functional theory. The crystal structures were obtained by molecular mechanics methods. The thermal stability of the title compounds was investigated via the energy gaps (ΔELUMO-HOMO) predicted. Results show that 4,4',5,5'-tetranitro-2,2'- 1H,1'H- 2,2'-biimidazole-1,1'-ditrinitromethyl amino (T5), (D = 10.85 km s –1 , P = 57.94 GPa) and 4,4',5,5'-tetranitro-2,2'-1H,1'H-2,2'- biimidazole-1,1'-difluorodinitromethylamino (T6) (D = 9.22 km s –1 , P = 39.21 GPa) with zero or positive oxygen balance, are excellent candidates for high energy density oxidizers.
    Print ISSN: 0894-3230
    Electronic ISSN: 1099-1395
    Topics: Chemistry and Pharmacology , Physics
    Published by Wiley-Blackwell
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  • 5
    Publication Date: 2014-10-02
    Description: Background: Intronless genes are a feature of prokaryotes; however, they are widespread and unequally distributed among eukaryotes and represent an important resource to study the evolution of gene architecture. Although many databases on exons and introns exist, there is currently no cohesive database that collects intronless genes in plants into a single database.Description: In this study, we present the Poaceae Intronless Genes Database (PIGD), a user-friendly web interface to explore information on intronless genes from different plants. Five Poaceae species, Sorghum bicolor, Zea mays, Setaria italica, Panicum virgatum and Brachypodium distachyon, are included in the current release of PIGD. Gene annotations and sequence data were collected and integrated from different databases. The primary focus of this study was to provide gene descriptions and gene product records. In addition, functional annotations, subcellular localization prediction and taxonomic distribution are reported. PIGD allows users to readily browse, search and download data. BLAST and comparative analyses are also provided through this online database, which is available at http://pigd.ahau.edu.cn/. Conclusion: PIGD provides a solid platform for the collection, integration and analysis of intronless genes in the Poaceae. As such, this database will be useful for subsequent bio-computational analysis in comparative genomics and evolutionary studies.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 6
    Publication Date: 2013-11-13
    Description: In order to meet the energy saving requirement of the excavator, hybrid excavators are becoming the hot spot for researchers. The initial problem is to match the parameter of each component, because the system is tending to be more complicated due to the introduction of the accumulator. In this paper, firstly, a new architecture is presented which is hydraulic hybrid excavator based on common pressure rail combined switched function (HHES). Secondly, the general principle of dynamic programming algorithm (DPA) is explained. Then, the method by using DPA for parameter matching of HHES is described in detail. Furthermore, the DPA is translated into the M language for simulation. Finally, the calculation results are analyzed, and the optimal matching group is obtained.
    Print ISSN: 1110-757X
    Electronic ISSN: 1687-0042
    Topics: Mathematics
    Published by Hindawi
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  • 7
    Publication Date: 2013-11-12
    Description: Background: Comparative mapping is a powerful tool to study evolution of genomes. It allows transfer of genome information from the well-studied model species to non-model species. Catfish is an economically important aquaculture species in United States. A large amount of genome resources have been developed from catfish including genetic linkage maps, physical maps, BAC end sequences (BES), integrated linkage and physical maps using BES-derived markers, physical map contig-specific sequences, and draft genome sequences. Application of such genome resources should allow comparative analysis at the genome scale with several other model fish species. Results: In this study, we conducted whole genome comparative analysis between channel catfish and four model fish species with fully sequenced genomes, zebrafish, medaka, stickleback and Tetraodon. A total of 517 Mb draft genome sequences of catfish were anchored to its genetic linkage map, which accounted for 62% of the total draft genome sequences. Based on the location of homologous genes, homologous chromosomes were determined among catfish and the four model fish species. A large number of conserved syntenic blocks were identified. Analysis of the syntenic relationships between catfish and the four model fishes supported that the catfish genome is most similar to the genome of zebrafish. Conclusion: The organization of the catfish genome is similar to that of the four teleost species, zebrafish, medaka, stickleback, and Tetraodon such that homologous chromosomes can be identified. Within each chromosome, extended syntenic blocks were evident, but the conserved syntenies at the chromosome level involve extensive inter-chromosomal and intra-chromosomal rearrangements. This whole genome comparative map should facilitate the whole genome assembly and annotation in catfish, and will be useful for genomic studies of various other fish species.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 8
    Publication Date: 2013-12-13
    Description: The hydraulic transformer is used in the hydraulic system to enhance the efficiency. However, how to control the angle displacement of the port plate is becoming a critical issue because of the new structure of the hydraulic transformer. This paper presents a new method for the angle displacement control system. Firstly, the basic principle of the system is presented. Then, the disturbance which is mainly the friction torque between the port plate and the cylinder block is calculated to estimate the range. Furthermore, the guaranteed cost control (GCC) is analyzed and combined with the disturbance and the characteristics of parameter uncertainties. Finally, the proposed control method is compared with the traditional PI control and the simulation result shows the effectiveness of the proposed design method.
    Print ISSN: 1024-123X
    Electronic ISSN: 1563-5147
    Topics: Mathematics , Technology
    Published by Hindawi
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  • 9
    Publication Date: 2018-01-03
    Description: Chemical Reviews DOI: 10.1021/acs.chemrev.6b00750
    Print ISSN: 0009-2665
    Electronic ISSN: 1520-6890
    Topics: Chemistry and Pharmacology
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  • 10
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