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Search Results: 1 - 10 of 72746 matches for " Feng-Jie Sun "
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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
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
Colorectal carcinoma-associated antigen Ca-Hb3 detected by one-dimensional SDS-polyacrylamide gel electrophoresis and liquid chromatography-tandem mass spectrometry
Shuo Sun, Feng-Jie Guo, Yong-Qing Tong, Jian-Gao Zhu, Guan-Cheng Li
World Journal of Gastroenterology , 2008,
Abstract: AIM: To comprehensively identify the proteins of tumor relative antigen Ca-Hb3 recognized by colorectal carcinoma monoclonal antibody Hb3.METHODS: Ca-Hb3 was isolated by SDS-polyacrylamide gel electrophoresis (PAGE) followed by digestion with trypsin. Trypsin peptides were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The proteins identified by mass spectrometry were analyzed using bioinformatics.RESULTS: Ca-Hb3 was identified as a CKAP4-like protein by Nano HPLC tandem mass spectrometry analysis. The molecular weight of CKAP4-like protein was 62.02 kDa, including one hydrophobic region, one transmembrane domain, five coiled coils, four glycosylation sites and forty-nine phosphorylation sites. CKAP4-like protein had a high homogeneity with DeltaNp63α. The characteristic expression of DeltaNp63α that is considered a potential oncogene in the isoforms of p63 was similar to that of Ca-Hb3.CONCLUSION: Ca-Hb3 is probably a CKAP4-like protein, belonging to DeltaNp63α isoform of p63 family.
A novel bacteriophage KSL-1 of 2-Keto-gluconic acid producer Pseudomonas fluorescens K1005: isolation, characterization and its remedial action
Wen-Jing Sun, Chang-Feng Liu, Lin Yu, Feng-jie Cui, Qiang Zhou, Si-lian Yu, Lei Sun
BMC Microbiology , 2012, DOI: 10.1186/1471-2180-12-127
Abstract: The phage KSL-1 of Pseudomonas fluorescens K1005 was isolated from abnormal 2KGA fermentation broth. It belonged to the Siphoviridae family with a hexagonal head diameter of about 99?nm and a non-contractile tail of about 103?nm?×?39?nm. The genome size of phage KSL-1 was estimated to be approximately 53 kbp. Its optimal MOI to infect P. fluorescens K1005 was about 0.001. One-step growth curve gave its latent and burst periods of 90?min and 75?min with a burst size of 52 phage particles per infected cell. This phage was stable with a pH range of 7.0–10.0, and sensitive to thermal treatment. Finally, a simple remedial action was proposed by feeding fresh seed culture. Compared with the infected 2KGA fermentation, the remedial experiments restored 2KGA fermentation performance by increasing the produced 2KGA concentration to 159.89?g/L and shortening the total fermentation time of 80?h with the productivity and yield of 2.0?g/L.h and 0.89?g/g. The obtained data proved that this method was effective to combat the phage infections problems during the 2KGA fermentation.The phage KSL-1 was a novel bacteriophage specifically infecting Pseudomonas fluorescens K1005. The remedial action of feeding fresh seed culture to the infected broth was an easily-operating and effective method to maintain a high 2KGA yield and avoid the draft of infected broth.
Simultaneous Identification and Quantification of Canrenone and 11-α-Hydroxy-Canrenone by LC-MS and HPLC-UVD
Da-Ming Huang,Tian-Zhen Zhang,Feng-Jie Cui,Wen-Jing Sun,Li-Ming Zhao,Meng-Yi Yang,Ya-Juan Wang
Journal of Biomedicine and Biotechnology , 2011, DOI: 10.1155/2011/917232
Abstract: A procedure for simultaneous identification and quantification of canrenone and its biotransformed product 11-α-hydroxy-canrenone by high-performance liquid chromatography with ultraviolet detector (HPLC-UVD) and mass spectrometry (LC-MS) methods was proposed. The optimal determination variables on the HPLC-UVD or LC-MS coupled with a ZORBAX Eclipse XDB-C18 column (150 mm × 4.6 mm, 5 μm) were set as follows: detection wavelength of 280 nm, mobile phase of water and methanol gradient elution, temperature for the chromatographic column of 30°C, flow rate of mobile phase of 0.8 mL/min, sample injection volume of 5 μL, and elution time of 40 min. The MS conditions were set as follows: the flow rate of sheath gas, aux gas, and sweep gas were kept at 35 arb, 5 arb, and 0 arb, respectively. The temperature of capillary was held at 300°C, and capillary voltage was set at 30.00 V. Tube lens were performed at 100.00 V. The proposed method was validated by linearity (2 ≥ 0.9910), average recovery (94.93%, RSD1.21%), precision (RSD ≤ 1.31%), limit of detection, and limit of quantification (LOD 0.1~0.12 mg/L, LOQ 0.5~0.67 mg/L), which proved to be affordable for simultaneously determining canrenone and its bio-transformed product 11-α-hydroxy-canrenone.
Optimization of Pressurized Liquid Extraction of Three Major Acetophenones from Cynanchum bungei Using a Box-Behnken Design
Wei Li,Li-Chun Zhao,Yin-Shi Sun,Feng-Jie Lei,Zi Wang,Xiong-Bin Gui,Hui Wang
International Journal of Molecular Sciences , 2012, DOI: 10.3390/ijms131114533
Abstract: In this work, pressurized liquid extraction (PLE) of three acetophenones (4-hydroxyacetophenone, baishouwubenzophenone, and 2,4-dihydroxyacetophenone) from Cynanchum bungei (ACB) were investigated. The optimal conditions for extraction of ACB were obtained using a Box-Behnken design, consisting of 17 experimental points, as follows: Ethanol (100%) as the extraction solvent at a temperature of 120 °C and an extraction pressure of 1500 psi, using one extraction cycle with a static extraction time of 17 min. The extracted samples were analyzed by high-performance liquid chromatography using an UV detector. Under this optimal condition, the experimental values agreed with the predicted values by analysis of variance. The ACB extraction yield with optimal PLE was higher than that obtained by soxhlet extraction and heat-reflux extraction methods. The results suggest that the PLE method provides a good alternative for acetophenone extraction.
Gamma-aminobutyric acid promotes human hepatocellular carcinoma growth through overexpressed gamma-aminobutyric acid A receptor 3 subunit
Yan Liu, Yue-Hui Li, Feng-Jie Guo, Jia-Jia Wang, Rui-Li Sun, Jin-Yue Hu, Guan-Cheng Li
World Journal of Gastroenterology , 2008,
Abstract: AIM: To investigate the expression pattern of gamma-aminobutyric acid A (GABAA) receptors in hepatocellular carcinoma (HCC) and indicate the relationship among gamma-aminobutyric acid (GABA), gamma-aminobutyric acid A receptor α3 subunit (GABRA3) and HCC.METHODS: HCC cell line Chang, HepG2, normal liver cell line L-02 and 8 samples of HCC tissues and paired non-cancerous tissues were analyzed with semiquantitative polymerase chain reaction (PCR) for the expression of GABAA receptors. HepG2 cells were treated with gamma-aminobutyric acid (GABA) at serial concentrations (0, 1, 10, 20, 40 and 60 μmol/L), and their proliferating abilities were analyzed with the 3-(4, 5-methylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay, cell doubling time test, colon formation assay, cell cycle analysis and tumor planted in nude mice. Small interfering RNA was used for knocking down the endogenous GABRA3 in HepG2. Proliferating abilities of these cells treated with or without GABA were analyzed.RESULTS: We identified the overexpression of GABRA3 in HCC cells. Knockdown of endogenous GABRA3 expression in HepG2 attenuated HCC cell growth, suggesting its role in HCC cell viability. We determined the in vitro and in vivo effect of GABA in the proliferation of GABRA3-positive cell lines, and found that GABA increased HCC growth in a dose-dependent manner. Notably, the addition of GABA into the cell culture medium promoted the proliferation of GABRA3-expressing HepG2 cells, but not GABRA3-knockdown HepG2 cells. This means that GABA stimulates HepG2 cell growth through GABRA3.CONCLUSION: GABA and GABRA3 play important roles in HCC development and progression and can be a promising molecular target for the development of new diagnostic and therapeutic strategies for HCC.
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.
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