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Search Results: 1 - 10 of 52054 matches for " Feng-Jie Lai "
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Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses
Feng-Jie Sun,Gustavo Caetano-Anollés
PLOS Computational Biology , 2008, DOI: 10.1371/journal.pcbi.1000018
Abstract: Transfer RNAs (tRNAs) are ancient molecules that are central to translation. Since they probably carry evolutionary signatures that were left behind when the living world diversified, we reconstructed phylogenies directly from the sequence and structure of tRNA using well-established phylogenetic methods. The trees placed tRNAs with long variable arms charging Sec, Tyr, Ser, and Leu consistently at the base of the rooted phylogenies, but failed to reveal groupings that would indicate clear evolutionary links to organismal origin or molecular functions. In order to uncover evolutionary patterns in the trees, we forced tRNAs into monophyletic groups using constraint analyses to generate timelines of organismal diversification and test competing evolutionary hypotheses. Remarkably, organismal timelines showed Archaea was the most ancestral superkingdom, followed by viruses, then superkingdoms Eukarya and Bacteria, in that order, supporting conclusions from recent phylogenomic studies of protein architecture. Strikingly, constraint analyses showed that the origin of viruses was not only ancient, but was linked to Archaea. Our findings have important implications. They support the notion that the archaeal lineage was very ancient, resulted in the first organismal divide, and predated diversification of tRNA function and specificity. Results are also consistent with the concept that viruses contributed to the development of the DNA replication machinery during the early diversification of the living world.
Evolutionary Patterns in the Sequence and Structure of Transfer RNA: A Window into Early Translation and the Genetic Code
Feng-Jie Sun, Gustavo Caetano-Anollés
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002799
Abstract: Transfer RNA (tRNA) molecules play vital roles during protein synthesis. Their acceptor arms are aminoacylated with specific amino acid residues while their anticodons delimit codon specificity. The history of these two functions has been generally linked in evolutionary studies of the genetic code. However, these functions could have been differentially recruited as evolutionary signatures were left embedded in tRNA molecules. Here we built phylogenies derived from the sequence and structure of tRNA, we forced taxa into monophyletic groups using constraint analyses, tested competing evolutionary hypotheses, and generated timelines of amino acid charging and codon discovery. Charging of Sec, Tyr, Ser and Leu appeared ancient, while specificities related to Asn, Met, and Arg were derived. The timelines also uncovered an early role of the second and then first codon bases, identified codons for Ala and Pro as the most ancient, and revealed important evolutionary take-overs related to the loss of the long variable arm in tRNA. The lack of correlation between ancestries of amino acid charging and encoding indicated that the separate discoveries of these functions reflected independent histories of recruitment. These histories were probably curbed by co-options and important take-overs during early diversification of the living world.
The ancient history of the structure of ribonuclease P and the early origins of Archaea
Feng-Jie Sun, Gustavo Caetano-Anollés
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-153
Abstract: To study the evolution of this complex, we constructed rooted phylogenetic trees of RPR molecules and substructures and estimated RPP age using a cladistic method that embeds structure directly into phylogenetic analysis. The general approach was used previously to study the evolution of tRNA, SINE RNA and 5S rRNA, the origins of metabolism, and the evolution and complexity of the protein world, and revealed here remarkable evolutionary patterns. Trees of molecules uncovered the tripartite nature of life and the early origin of archaeal RPRs. Trees of substructures showed molecules originated in stem P12 and were accessorized with a catalytic P1-P4 core structure before the first substructure was lost in Archaea. This core currently interacts with RPPs and ancient segments of the tRNA molecule. Finally, a census of protein domain structure in hundreds of genomes established RPPs appeared after the rise of metabolic enzymes at the onset of the protein world.The study provides a detailed account of the history and early diversification of a fundamental ribonucleoprotein and offers further evidence in support of the existence of a tripartite organismal world that originated by the segregation of archaeal lineages from an ancient community of primordial organisms.With few exceptions [1], ribonuclease P (RNase P) is one of two universal ribozymes (the other is the ribosome) that are present in all living organisms. This ribonucleoprotein is generally composed of an RNA subunit, the RNase P RNA (RPR), and one or more protein subunits, the RNase P proteins (RPPs) [2]. RNase P functions as a phosphodiesterase carrying out the 5' endonucleolytic cleavage of transfer RNA (tRNA) precursor transcripts (pre-tRNA) to form mature functional tRNAs [3-5]. Regions of the RPR that contribute to the recognition of the substrate cleavage sites [the tRNA pseudouridine (TΨC) loop and CCA tail] are well studied. Remarkably, the catalytic function can be conducted by the RNA subunit indepen
Dramatic Co-Activation of WWOX/WOX1 with CREB and NF-κB in Delayed Loss of Small Dorsal Root Ganglion Neurons upon Sciatic Nerve Transection in Rats
Meng-Yen Li,Feng-Jie Lai,Li-Jin Hsu,Chen-Peng Lo,Ching-Li Cheng,Sing-Ru Lin,Ming-Hui Lee,Jean-Yun Chang,Dudekula Subhan,Ming-Shu Tsai,Chun-I Sze,Subbiah Pugazhenthi,Nan-Shan Chang,Shur-Tzu Chen
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0007820
Abstract: Tumor suppressor WOX1 (also named WWOX or FOR) is known to participate in neuronal apoptosis in vivo. Here, we investigated the functional role of WOX1 and transcription factors in the delayed loss of axotomized neurons in dorsal root ganglia (DRG) in rats.
Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event?
Nicolas Martin, Elizabeth A Ruedi, Richard LeDuc, Feng-Jie Sun, Gustavo Caetano-Anollés
Biology Direct , 2007, DOI: 10.1186/1745-6150-2-23
Abstract: We focus on (1) pairwise comparison of gene arrangement sequences in A. gossypii and S. cerevisiae, (2) reconstruction of gene arrangements ancestral to A. gossypii, S. cerevisiae, and K. waltii, (3) synteny patterns arising within and between lineages, and (4) expected gene orientation of duplicate gene sets. The existence of syntenic patterns between ancestral gene sets and A. gossypii, S. cerevisiae, and K. waltii, and other evidence, suggests that gene-interleaving relationships are the natural consequence of topological rearrangements in chromosomes and that a more gradual scenario of genome evolution involving segmental duplication and recombination constitutes a more parsimonious explanation. Furthermore, phylogenetic trees reconstructed under alternative hypotheses placed the putative whole-genome duplication event after the divergence of the S. cerevisiae and K. waltii lineages, but in the lineage leading to K. waltii. This is clearly incompatible with an ancient genome duplication event in S. cerevisiae.Because the presence of syntenic patterns appears to be a condition that is necessary, but not sufficient, to support the existence of the whole-genome duplication event, our results prompt careful re-evaluation of paleopolyploidization in the yeast lineage and the evolutionary meaning of syntenic patterns.This article was reviewed by Kenneth H. Wolfe (nominated by Nicolas Galtier), Austin L. Hughes (nominated by Eugene Koonin), Mikhail S. Gelfand, and Mark Gerstein.The existence of an ancient whole-genome duplication (WGD) event in Saccharomyces cerevisiae [1] has been debated over the past several years. WGD followed by massive gene loss could explain duplicated genes that are interspersed throughout the genome and syntenic relationships with other hemiascomycete yeasts [2-4]. An alternative view is that evolution proceeded gradually through segmental chromosomal duplications that occurred independently, sometimes massively, and were extensively shuffled
Biological Synthesis of L-ascorbyl Palmitate

XU Feng-Jie,TAN Tian-Wei,

生物工程学报 , 2005,
Abstract: Biological synthesis of L-Ascorbyl Palmitate in organic system were studied in this text. The contradiction between conversion of vitamin C and concentration of L-Ascorbyl Palmitate were resolved. High conversion of vitamin C and concentration of L-Ascorbyl Palmitate were obtained by Novo435. A series of solvents(log P from -0.24 to 3.5 )were investigated for the reaction,and acetone was found to be the most suitable from the standpoint of the enzyme activity and solubility of L-ascorbic. And the equilibrium of the reaction was affected by the addition of the molecular sieves and temperature. Reaction carried out at 60 degrees C and with 20% 0.4nm molecular sieves is good for the enzyme to keep its activity and for making the equilibrium go to the product. With 1.094 g palmitic acid, 0.107 g vitamin C and 0.020 g Novo435, rotate rate of 200 r/min, the conversion of ascorbic reached 80% and the concentration of L-ascorbyl palmitate is 20 g/L after 48 h. Furthermore, reaction batch of Novo435 and substrates recycle were observed, the result indicated that Novo435 may used 4-5 times continuously with high conversion. And 6-O-unsaturated acyl L-ascorbates were synthesized through Novo435 condensation of ascorbic acid and various unsaturated fatty acids with high conversion in this text.

LI Feng-jie,WANG Duo-yun,

天然气地球科学 , 2006,
Abstract: On the basis of a comprehensive study of core, log well and outcrop profile, taking the the high resolution sequence stratigraphic theory as a direction, the detailed analysis on the subdivision of different orders of the base-level cycles in Yanchang formation has been performed and a corresponding high resolution sequence framework has been established in Xifeng oilfield, Ordos basin. Yanchang formation can be divided one super-long, 5 long, 13 middle and 36 short base-level cycles. The short base-level may be divided two types of cycles that consist of six subtypes. The middle and long base-level cycles are usually of symmetric structures. The authors analyse the relationship between the stacking pattern of different orders of the base-level cycles and the distribution and evolution law of sediment facies.
Underlying Mechanism of Impulsive Consumption Behavior: The Influence of Promotion Focus on Impulsive Consumption Behavior
冲动性消费行为内在机制研究述评 ———提升调节点在冲动性消费行为中所起作用

JING Feng-Jie,XIONG Su-Hong,

心理科学进展 , 2008,
Abstract: 有关冲动性消费行为研究的文献众多,但难以从内在联系上进行统一。最近,利用提升调节点对冲动性消费行为内在机制的揭示是该领域的一个突破,从而有望把一些相关文献统一起来。作者介绍了冲动性消费行为内在过程;综述了用于冲动性消费行为内在机制研究的相关理论;从内在机制这个角度对有关冲动性消费行为文献进行评述。文章的最后提出了冲动性消费行为内在机制的进一步研究方向:利用调节点等相关理论,特别是调节适应理论对冲动性消费行为内在机制做进一步探讨。
From Web directories to lightweight ontology: natural language processing and formalization

JU Qi,YANG Feng-jie,

计算机应用研究 , 2010,
Abstract: 为了解决以自然语言表示节点标签的分类树很难通过自动软件agents来进行自动推理的问题,通过词性标志、词义辨析、连接词辨析和受约束的自然语言定义及转换等步骤,将分类树中每一个节点对应的自然语言标签转换成了机器能够识别的逻辑表达式,从而使整个分类树转换成了一个轻量级本体,它适合应用在数据整合的语义匹配、文档分类和语义搜索等方面的自动推理,从而促进了本体知识的自动化推理,为以后文本自动检索奠定基础。
Feng-Jie Cheng,Yi-Sen Wang,Yan-Cheng Liu
Acta Crystallographica Section E , 2011, DOI: 10.1107/s1600536810053687
Abstract: In the title compound, [Ni(C7H3NO4)(C12H9N5)(H2O)2], the NiII atom is coordinated in a distorted octahedral geometry by one N and two O atoms from a pyridine-2,6-dicarboxylate ligand, one N atom from a 3,5-bis(4-pyridyl)-1H-1,2,4-triazole ligand in equatorial positions and two water molecules in axial positions. The crystal packing is consolidated by intermolecular O—H...O, O—H...N and N—H...O hydrogen bonds.
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