21 results on '"Tao Pan"'
Search Results
2. HIV protease cleaves the antiviral m6A reader protein YTHDF3 in the viral particle
- Author
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Viviana Simon, Lubbertus C. F. Mulder, Tao Pan, Maria C. Bermúdez González, Wen Zhang, Denise Jurczyszak, Thomas Kehrer, Matthew J. Eckwahl, Sandra N. Terry, and Emma McGregor
- Subjects
RNA viruses ,CD4-Positive T-Lymphocytes ,Adenosine ,Molecular biology ,medicine.medical_treatment ,viruses ,HIV Infections ,Pathology and Laboratory Medicine ,Biochemistry ,Virions ,White Blood Cells ,Immunodeficiency Viruses ,HIV Protease ,Animal Cells ,Medicine and Health Sciences ,HIV Protease Inhibitor ,Enzyme Inhibitors ,Biology (General) ,Infectivity ,0303 health sciences ,Effector ,T Cells ,030302 biochemistry & molecular biology ,RNA-Binding Proteins ,Proteases ,3. Good health ,Enzymes ,Medical Microbiology ,Viral Pathogens ,Viruses ,Infectious diseases ,Pathogens ,Cellular Types ,Research Article ,QH301-705.5 ,Immune Cells ,Immunology ,Primary Cell Culture ,Viral diseases ,Biology ,Viral Structure ,DNA construction ,Microbiology ,Antiviral Agents ,03 medical and health sciences ,Virology ,Retroviruses ,Genetics ,medicine ,Humans ,Protease Inhibitors ,Microbial Pathogens ,030304 developmental biology ,Protease ,Blood Cells ,HEK 293 cells ,Lentivirus ,Organisms ,Virion ,Biology and Life Sciences ,HIV ,Proteins ,Cell Biology ,RC581-607 ,Reverse transcriptase ,Viral Replication ,Research and analysis methods ,Molecular biology techniques ,HEK293 Cells ,Viral replication ,Plasmid Construction ,Enzymology ,HIV-1 ,Parasitology ,Immunologic diseases. Allergy - Abstract
N6-methyladenosine (m6A) is the most abundant HIV RNA modification but the interplay between the m6A reader protein YTHDF3 and HIV replication is not well understood. We found that knockout of YTHDF3 in human CD4+ T-cells increases infection supporting the role of YTHDF3 as a restriction factor. Overexpression of the YTHDF3 protein in the producer cells reduces the infectivity of the newly produced viruses. YTHDF3 proteins are incorporated into HIV particles in a nucleocapsid-dependent manner permitting the m6A reader protein to limit infection in the new target cell at the step of reverse transcription. Importantly, HIV protease cleaves the virion-incorporated full-length YTHDF3 protein, a process which is blocked by HIV protease inhibitors used to treat HIV infected patients. Mass-spectrometry confirmed the proteolytic processing of YTHDF3 in the virion. Thus, HIV protease cleaves the virion-encapsidated host m6A effector protein in addition to the viral polyproteins to ensure optimal infectivity of the mature virion., Author summary The human transcriptome contains a large number of post-transcriptional modifications such as N6-methyladenosine (m6A). Several recent studies indicate that the HIV RNA contains numerous m6A modifications but their impact on viral replication (e.g., antiviral or proviral) remains controversial. Here we report that the m6A reader protein YTHDF3 is incorporated into HIV particles in a nucleocapsid-dependent manner and reduces viral infectivity in the next cycle of infection. Importantly, we show that HIV protease cleaves the virion-incorporated full-length YTHDF3 protein, a process which can be blocked by FDA-approved HIV protease inhibitors. Mass-spectrometry analyses confirmed the proteolytic processing of YTHDF3 in the virion and identified at least two distinct cleavage sites. These results point to virus incorporated YTHDF3 acting as a regulator of HIV biology if left unchecked by the HIV protease.
- Published
- 2020
3. RNA modifications and structures cooperate to guide RNA–protein interactions
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Auinash Kalsotra, Cole J.T. Lewis, and Tao Pan
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0301 basic medicine ,Riboswitch ,RNA-induced transcriptional silencing ,RNA Stability ,Computational biology ,Article ,03 medical and health sciences ,0302 clinical medicine ,Protein Splicing ,RNA, Messenger ,Molecular Biology ,Genetics ,Chemistry ,Intron ,Proteins ,RNA ,Cell Biology ,Non-coding RNA ,RNA silencing ,030104 developmental biology ,RNA editing ,Protein Biosynthesis ,Nucleic Acid Conformation ,030217 neurology & neurosurgery ,Small nuclear RNA ,RNA, Guide, Kinetoplastida - Abstract
An emerging body of evidence indicates that post-transcriptional gene regulation not only relies on the linear sequence of messenger RNAs but also on their folding into intricate secondary structures and on chemical modification of the RNA bases. These features, which are highly dynamic and interdependent, exert direct control over the transcriptome thereby influencing many aspects of cell function. Here, we consider that coupling of RNA modifications and structure actively shapes RNA-protein interactions through individual steps of gene expression.
- Published
- 2017
4. Stress Response and Adaptation Mediated by Amino Acid Misincorporation during Protein Synthesis
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Xiaoyun Wang and Tao Pan
- Subjects
0301 basic medicine ,Adaptation, Biological ,Medicine (miscellaneous) ,Aminoacylation ,Computational biology ,Ribosome ,03 medical and health sciences ,RNA, Transfer ,Stress, Physiological ,Protein biosynthesis ,Animals ,Humans ,Supplement—Frontiers in Amino Acid Research ,TRNA aminoacylation ,Amino Acids ,chemistry.chemical_classification ,Nutrition and Dietetics ,Chemistry ,Proteins ,Translation (biology) ,Genetic code ,Amino acid ,030104 developmental biology ,Biochemistry ,Genetic Code ,Protein Biosynthesis ,Mutation ,Transfer RNA ,Transfer RNA Aminoacylation ,Food Science - Abstract
Translation of genetic information into functional proteins is critical for all cellular life. Accurate protein synthesis relies on proper aminoacylation of transfer RNAs (tRNAs) and decoding of mRNAs by the ribosome with the use of aminoacyl-tRNAs. Mistranslation can lead to pathologic consequences. All cells contain elaborate quality control mechanisms in translation, although translational fidelity may be regulated by various factors such as nutrient limitation or reactive oxygen species. Translation fidelity is maintained via the accuracy of tRNA aminoacylation by the aminoacyl-tRNA synthetases and matching of the mRNA codon with the tRNA anticodon by the ribosome. Stringent substrate discrimination and proofreading are critical in aminoacylating tRNAs with their cognate amino acid to maintain high accuracy of translation. Although the composition of the cellular proteome generally adheres to the genetic code, accumulating evidence indicates that cells can also deliberately mistranslate; they synthesize mutant proteins that deviate from the genetic code in response to stress or environmental changes. Mistranslation with tRNA charged with noncognate amino acids can expand the proteome to enhance stress response and help adaptation. Here, we review current knowledge on mistranslation through tRNA misacylation and describe advances in our understanding of translational control in the regulation of stress response and human diseases.
- Published
- 2016
5. The mitochondrial genome of the Kentish Plover Charadrius alexandrinus (Charadriiformes: Charadriidae) and phylogenetic analysis of Charadrii
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Kexin Li, Qing Chang, Tao Pan, Chaochao Hu, Wan Chen, Chenling Zhang, and Wei Liu
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0301 basic medicine ,Mitochondrial DNA ,Charadriiformes ,Codon, Initiator ,Biochemistry ,Polymerase Chain Reaction ,Birds ,Evolution, Molecular ,03 medical and health sciences ,Monophyly ,RNA, Transfer ,Species Specificity ,Phylogenetics ,Genetics ,Animals ,Molecular Biology ,Phylogeny ,Base Composition ,biology ,Phylogenetic tree ,Kentish plover ,Nucleotides ,Genetic Variation ,Proteins ,biology.organism_classification ,Charadrius ,030104 developmental biology ,Evolutionary biology ,RNA, Ribosomal ,Genome, Mitochondrial ,Codon, Terminator ,Taxonomy (biology) - Abstract
The suborder Charadrii (Aves: Charadriiformes), one of the most species-rich radiations within shorebirds, which contains good source for studies of ecology, behaviour and evolution. The resources of mitogenome have rapidly accumulated in recent years due to the advanced genomic sequencing, while suborder Charadrii’s mitogenome has not been well studied. The primary objective of this study was to determine the complete mitogenome sequence of Charadrius alexandrinus, and investigated the evolutionary relationship within Charadrii. The mitogenome of C. alexandrinus were generated by amplification of overlapping Polymerase Chain Reaction (PCR) fragments. In this study, we determined the complete mitogenome sequence of the Kentish Plover Charadrius alexandrinus, and comparative analysed 11 species to illustrate mitogenomes structure and investigated their evolutionary relationship within Charadrii. The Charadrii mitogenomes displayed moderate size variation, the mean size was 16,944 bp (SD = 182, n = 11), and most of the size variation due to mutations in the control region (CR). Nucleotide composition was consistently biased towards AT rich, and the A+T content also varies for each protein-coding genes. The variation in ATP8 and COIII was the highest and lowest respectively. The GC skew was always negative, with the ATP8 had higher value than other regions. The average uncorrected pairwise distances revealed heterogeneity of evolutionary rate for each gene, the COIII, COI and COII have slow evolutionary rate, whereas the gene of ATP8 has the relative fast rate. The highest value of Ks and Ka were ND1 and ATP8, and the ratios of Ka/Ks are lower than 0.27, indicating that they were under purifying selection. Phylogenomic analysis based on the complete mitochondrial genomes strongly supported the monophyly of the suborder Charadrii. This study improves our understanding of mitogenome structure and evolution, and providing further insights into phylogeny and taxonomy in Charadrii. In future, sequencing more mitogenomes from various taxonomic levels will significantly improve our understanding of phylogenetic relationships within Charadrii.
- Published
- 2017
6. Function and origin of mistranslation in distinct cellular contexts
- Author
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Tao Pan and Michael H. Schwartz
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0301 basic medicine ,Genetics ,Cellular process ,Proteins ,Context (language use) ,Computational biology ,Biology ,Genetic code ,Biochemistry ,Article ,Translational fidelity ,Fight-or-flight response ,03 medical and health sciences ,030104 developmental biology ,RNA, Transfer ,Genetic Code ,Stress, Physiological ,Three-domain system ,Protein Biosynthesis ,Animals ,Humans ,Adaptation ,Molecular Biology ,Ribosomes ,Function (biology) - Abstract
Mistranslation describes errors during protein synthesis that prevent the amino acid sequences specified in the genetic code from being reflected within proteins. For a long time, mistranslation has largely been considered an aberrant cellular process that cells actively avoid at all times. However, recent evidence has demonstrated that cells from all three domains of life not only tolerate certain levels and forms of mistranslation, but actively induce mistranslation under certain circumstances. To this end, dedicated biological mechanisms have recently been found to reduce translational fidelity, which indicates that mistranslation is not exclusively an erroneous process and can even benefit cells in particular cellular contexts. There currently exists a spectrum of mistranslational processes that differ not only in their origins, but also in their molecular and cellular effects. These findings suggest that the optimal degree of translational fidelity largely depends on a specific cellular context. This review aims to conceptualize the basis and functional consequence of the diverse types of mistranslation that have been described so far.
- Published
- 2017
7. An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation
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Sivan Navon, Yuval Dorfan, Tamir Tuller, Orna Dahan, Asaf Carmi, Tao Pan, Yitzhak Pilpel, John M. Zaborske, Itay Furman, and Kalin Vestsigian
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Genetics ,0303 health sciences ,Biochemistry, Genetics and Molecular Biology(all) ,PROTEINS ,RNA ,Translation (biology) ,Computational biology ,Biology ,Ribosomal RNA ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Eukaryotic translation ,Transfer RNA ,Protein biosynthesis ,Coding region ,Gene ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
Recent years have seen intensive progress in measuring protein translation. However, the contributions of coding sequences to the efficiency of the process remain unclear. Here, we identify a universally conserved profile of translation efficiency along mRNAs computed based on adaptation between coding sequences and the tRNA pool. In this profile, the first approximately 30-50 codons are, on average, translated with a low efficiency. Additionally, in eukaryotes, the last approximately 50 codons show the highest efficiency over the full coding sequence. The profile accurately predicts position-dependent ribosomal density along yeast genes. These data suggest that translation speed and, as a consequence, ribosomal density are encoded by coding sequences and the tRNA pool. We suggest that the slow "ramp" at the beginning of mRNAs serves as a late stage of translation initiation, forming an optimal and robust means to reduce ribosomal traffic jams, thus minimizing the cost of protein expression.
- Published
- 2010
8. Affinity Monolith-Integrated Poly(methyl methacrylate) Microchips for On-Line Protein Extraction and Capillary Electrophoresis
- Author
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Tao Pan, Xiuhua Sun, Adam T. Woolley, and Weichun Yang
- Subjects
Glycidyl methacrylate ,Ethylene glycol dimethacrylate ,Green Fluorescent Proteins ,Article ,Antibodies ,Analytical Chemistry ,chemistry.chemical_compound ,Capillary electrophoresis ,Polymethyl Methacrylate ,Monolith ,Methyl methacrylate ,Serum Albumin ,Fluorescent Dyes ,geography ,geography.geographical_feature_category ,Chromatography ,Elution ,Electrophoresis, Capillary ,Proteins ,Fluoresceins ,Microarray Analysis ,Poly(methyl methacrylate) ,chemistry ,Immunoglobulin G ,visual_art ,visual_art.visual_art_medium ,Ethylene glycol ,Fluorescein-5-isothiocyanate - Abstract
Immunoaffinity monolith pretreatment columns have been coupled with capillary electrophoresis separation in poly(methyl methacrylate) (PMMA) microchips. Microdevices were designed with eight reservoirs to enable the electrically controlled transport of selected analytes and solutions to carry out integrated immunoaffinity extraction and electrophoretic separation. The PMMA microdevices were fabricated reproducibly and with high fidelity by solvent imprinting and thermal bonding methods. Monoliths with epoxy groups for antibody immobilization were prepared by direct in situ photopolymerization of glycidyl methacrylate and ethylene glycol dimethacrylate in a porogenic solvent consisting of 70% 1-dodecanol and 30% cyclohexanol. Antifluorescein isothiocyanate was utilized as a model affinity group in the monoliths, and the immobilization process was optimized. A mean elution efficiency of 92% was achieved for the monolith-based extraction of fluorescein isothiocyanate (FITC)-tagged human serum albumin. FITC-tagged proteins were purified from a contaminant protein and then separated electrophoretically using these devices. The developed immunoaffinity column/capillary electrophoresis microdevices show great promise for combining sample pretreatment and separation in biomolecular analysis.
- Published
- 2008
9. Mitochondrial genome of the Anhui musk deer (Moschus anhuiensis)
- Author
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Xiaoxue Zhu, Wenbo Shi, Lizhi Zhou, Baowei Zhang, Hui Wang, and Tao Pan
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Genetics ,Mitochondrial DNA ,biology ,Deer ,Moschus anhuiensis ,Ribosomal rna gene ,Proteins ,Mitochondrion ,biology.organism_classification ,DNA, Mitochondrial ,Genome ,Intergenic region ,RNA, Transfer ,RNA, Ribosomal ,Genome, Mitochondrial ,Transfer RNA ,Animals ,Molecular Biology ,Gene - Abstract
The Anhui musk deer (Moschus anhuiensis) is an endangered species which is endemic to a narrow region in two National Nature Reserves in Dabie Mountains, Anhui Province, China. In this study, we determined the complete mitochondrial genome of M. anhuiensis. The results showed that the total length of the mitogenome was 16,351 bp as a circular DNA and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. Overall base composition of the complete mitochondrial DNA was 34.0% A, 28.1% T, 25.0% C, and 12.9% G. The M. anhuiensis mitochondrial genome had 21 tRNA genes folded in the typical cloverleaf structure, with a unique exception of tRNA(Ser). The mitochondrial genes from M. anhuiensis were overlapped in a total of 72 bp at seven locations, as well as interleaved with a total of 62 bp intergenic spacers.
- Published
- 2012
10. N6-Methyladenosine in Nuclear RNA is a Major Substrate of the Obesity-Associated FTO
- Author
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Xu Zhao, Guanqun Zheng, Ye Fu, Yun-Gui Yang, Guifang Jia, Tomas Lindahl, Chuan He, Qing Dai, Ying Yang, Tao Pan, and Chengqi Yi
- Subjects
Adenosine ,endocrine system diseases ,Alpha-Ketoglutarate-Dependent Dioxygenase FTO ,Biology ,Methylation ,Article ,Substrate Specificity ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Humans ,Obesity ,RNA, Messenger ,Molecular Biology ,030304 developmental biology ,Cell Nucleus ,0303 health sciences ,Gene knockdown ,Messenger RNA ,Methyltransferase complex ,MRNA modification ,RNA ,nutritional and metabolic diseases ,Proteins ,Cell Biology ,pathological conditions, signs and symptoms ,Molecular biology ,chemistry ,030220 oncology & carcinogenesis ,MRNA methylation ,N6-Methyladenosine ,Oxidation-Reduction ,HeLa Cells - Abstract
We report here that fat mass and obesity-associated protein (FTO) has efficient oxidative demethylation activity targeting the abundant N6-methyladenosine (m(6)A) residues in RNA in vitro. FTO knockdown with siRNA led to increased amounts of m(6)A in mRNA, whereas overexpression of FTO resulted in decreased amounts of m(6)A in human cells. We further show the partial colocalization of FTO with nuclear speckles, which supports the notion that m(6)A in nuclear RNA is a major physiological substrate of FTO.
- Published
- 2011
11. Protein fingerprint of colorectal cancer, adenomatous polyps, and normal mucosa using ProteinChip analysis on laser capture microdissected cells
- Author
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Wenhong, Xu, Yiding, Chen, Wenqian, He, Zhixuan, Fu, Tao, Pan, Hong, He, Jiekai, Yu, Qichun, Wei, Shu, Zheng, and Suzhan, Zhang
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Male ,Proteomics ,Gene Expression Profiling ,Protein Array Analysis ,Computational Biology ,Proteins ,Reproducibility of Results ,Laser Capture Microdissection ,Middle Aged ,Peptide Mapping ,Sensitivity and Specificity ,Tight Junctions ,Adenomatous Polyps ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Humans ,Female ,Colorectal Neoplasms ,Aged - Abstract
To find new biomarkers and establish histopathology protein fingerprint models for early detection of colorectal cancer (CRC), laser capture microdissection (LCM) was utilized to obtain 3 groups of cells of interest--CRC tissues, their adjacent normal colorectal tissues, and their adjacent adenomatous polyps tissues--from the same 12 CRC patients. Each sample was then detected by surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS) technology and CM10 protein chip as well as bioinformatics tools. Model 1 formed by 15 protein peaks could be used to distinguish CRC tissues from normal tissues. The diagnostic pattern constructed using support vector machine (SVM) including the 15 proteins showed maximum Youden index (YI). Model 2 formed by 14 protein peaks could be used to distinguish CRC tissues from adenomatous polyps tissues. The two patterns were validated and the results showed that the sensitivity and specificity were both 100.0%. Model 3 formed by 15 protein peaks could distinguish adenomatous polyps tissues from normal tissues with a sensitivity of 92.3% and specificity of 100.0%. The protein peaks m/z 3570 and 5224 were identified in screening for changes during cancer progression. Peak 5224 was significantly upregulated in CRC. However, peak 3570 was significantly downregulated in CRC. LCM technology coupled with SELDI protein chip and bioinformatics approaches could effectively screen the differentially expressed protein profiles and establish molecular diagnosis models with high sensitivity and specificity for CRC.
- Published
- 2014
12. Increased levels of oxidative stress markers detected in the brains of mice devoid of prion protein
- Author
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David R. Brown, Jean Manson, Ruliang Li, Robert B. Petersen, Boon Seng Wong, Pierluigi Gambetti, George Perry, Tao Pan, Mark A. Smith, Tong Liu, and Man Sun Sy
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Proteasome Endopeptidase Complex ,Macromolecular Substances ,animal diseases ,Oxidative phosphorylation ,Biology ,Protein oxidation ,medicine.disease_cause ,Biochemistry ,Lipid peroxidation ,Mice ,Cellular and Molecular Neuroscience ,chemistry.chemical_compound ,Ubiquitin ,Multienzyme Complexes ,Malondialdehyde ,medicine ,Animals ,PrPC Proteins ,Brain Chemistry ,Mice, Knockout ,Aldehydes ,Brain ,Proteins ,Ketones ,Lipids ,nervous system diseases ,Cell biology ,Cysteine Endopeptidases ,Oxidative Stress ,Proteasome ,chemistry ,biology.protein ,Lipid Peroxidation ,Oxidation-Reduction ,Biomarkers ,Oxidative stress ,Homeostasis - Abstract
Although minor abnormalities have been reported in prion protein (PrP) knock-out (Prnp-/-) mice, the normal physiological function of PrP, the causative agent implicated in transmissible spongiform encephalopathies (TSE), remains unresolved. Since there are increasing correlations between oxidative stress and amyloidoses, we decided to investigate whether PrP plays a role in oxidative modulation. We found higher levels of oxidative damage to proteins and lipids in the brain lysates of Prnp-/- as compared to wild-type (WT) mice of the same genetic background. These two indicators, protein oxidation and lipid peroxidation, are hallmarks of cellular oxidative damage. Elevated levels of ubiquitin-protein conjugates were also observed in Prnp-/- mice, a probable consequence of cellular attempts to remove the damaged proteins as indicated by increased proteasome activity. Taken together, these findings are indicative of a role for PrP in oxidative homeostasis in vivo.
- Published
- 2001
13. Mitochondrial genome of the Emberiza rustica (Emberizidae: Emberiza)
- Author
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Jinyun Chen, Tao Pan, Longfei Hu, Liqian Ren, Lei Yu, and Baowei Zhang
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RNA, Transfer ,RNA, Ribosomal ,Genome, Mitochondrial ,Molecular Sequence Data ,Genetics ,Animals ,Proteins ,Passeriformes ,Molecular Biology - Abstract
Emberiza rustica, least concern species (IUCN), is a passerine bird in the bunting family with wide geographical range. The complete mitochondrial genome of E. rustica (16,798 bp in length) had been analyzed for building the database. Similar to the typical mtDNA of vertebrates, it contained 37 genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and a non-coding region (D-loop). All the protein-coding genes in E. rustica were distributed on the H-strand, except for the ND6 subunit gene and 10 tRNA genes which were encoded on the L-strand.
- Published
- 2013
14. N6-methyl-Adenosine modification in messenger and long non-coding RNA
- Author
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Tao Pan
- Subjects
Adenosine ,RNA Splicing ,RNA transport ,Alpha-Ketoglutarate-Dependent Dioxygenase FTO ,Biochemistry ,Methylation ,Deep sequencing ,Article ,RNA Transport ,Protein biosynthesis ,Animals ,Humans ,RNA, Messenger ,RNA Processing, Post-Transcriptional ,Molecular Biology ,Cell Nucleus ,Messenger RNA ,biology ,Gene Expression Profiling ,RNA ,Proteins ,Long non-coding RNA ,Protein Biosynthesis ,RNA splicing ,biology.protein ,Demethylase ,RNA, Long Noncoding - Abstract
N6-methyl-adenosine (m(6)A) is the most abundant modification in mammalian mRNA and long non-coding RNA. First discovered in the 1970s, m(6)A modification has been proposed to function in mRNA splicing, export, stability, and immune tolerance. Interest and excitement in m(6)A modification has recently been revived based on the discovery of a mammalian enzyme that removes m(6)A and the application of deep sequencing to localize modification sites. The m(6)A demethylase fat mass and obesity associated protein (FTO) controls cellular energy homeostasis and is the first enzyme discovered that reverses an RNA modification. m(6)A Sequencing demonstrates cell-type- and cell-state-dependent m(6)A patterns, indicating that m(6)A modifications are highly regulated. This review describes the current knowledge of mammalian m(6)A modifications and future perspectives on how to push the field forward.
- Published
- 2013
15. Mitochondrial genome of Protobothrops jerdonii (Squamata: Viperidae: Crotalinae)
- Author
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Xin Huang, Hui Wang, Baowei Zhang, Xiaoxue Zhu, Liang Zhang, and Tao Pan
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Genetics ,Mitochondrial DNA ,Squamata ,biology ,Proteins ,biology.organism_classification ,DNA, Mitochondrial ,RNA, Transfer ,Viperidae ,RNA, Ribosomal ,biology.animal ,Genome, Mitochondrial ,Animals ,Crotalinae ,Bothrops ,Molecular Biology - Abstract
Protobothrops jerdonii is a common venomous snake that is widely distributed in southwestern China and other adjacent countries of Asia. In this study, the complete mitochondrial genome of P. jerdonii was determined. The circle genome with the 17,239 bp total length contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 control regions. Overall base composition of the complete mtDNA was 33.13% A, 25.07% T, 29.31% C, and 12.50% G. All the genes in P. jerdonii were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.
- Published
- 2013
16. In-channel atom-transfer radical polymerization of thermoset polyester microfluidic devices for bioanalytical applications
- Author
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Daniel T. Chiu, Adam T. Woolley, Tao Pan, and Gina S. Fiorini
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Materials science ,Polyesters ,Clinical Biochemistry ,Radical polymerization ,macromolecular substances ,Biochemistry ,Article ,Analytical Chemistry ,Polyethylene Glycols ,Electrophoresis, Microchip ,chemistry.chemical_compound ,Capillary electrophoresis ,Polymer chemistry ,Amino Acids ,Fluorescent Dyes ,chemistry.chemical_classification ,Atom-transfer radical-polymerization ,technology, industry, and agriculture ,Proteins ,Polymer ,Microfluidic Analytical Techniques ,Polyester ,chemistry ,Chemical engineering ,Surface modification ,Adsorption ,Peptides ,Ethylene glycol ,Fluorescein-5-isothiocyanate ,Protein adsorption - Abstract
A new technique for polymer microchannel surface modification, called in-channel atom-transfer radical polymerization, has been developed and applied in the surface derivatization of thermoset polyester (TPE) microdevices with poly(ethylene glycol) (PEG). X-ray photoelectron spectroscopy, electroosmotic flow (EOF), and contact angle measurements indicate that PEG has been grafted on the TPE surface. Moreover, PEG-modified microchannels have much lower and more pH-stable EOF, more hydrophilic surfaces and reduced nonspecific protein adsorption. Capillary electrophoresis separation of amino acid and peptide mixtures in these PEG-modified TPE microchips had good reproducibility. Phosducin-like protein and phosphorylated phosducin-like protein were also separated to measure the phosphorylation efficiency. Our results indicate that PEG-grafted TPE microchips have broad potential application in biomolecular analysis.
- Published
- 2007
17. Circularly permuted DNA, RNA and proteins--a review
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Olke C. Uhlenbeck and Tao Pan
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Protein Folding ,Base Sequence ,Stereochemistry ,Molecular Sequence Data ,RNA ,Proteins ,General Medicine ,Saccharomyces cerevisiae ,Circular permutation in proteins ,Biology ,Folding (chemistry) ,chemistry.chemical_compound ,RNA, Transfer, Phe ,Biochemistry ,chemistry ,Transfer RNA ,Genetics ,Animals ,Protein folding ,Binding site ,DNA, Circular ,DNA ,Macromolecule - Abstract
Circular permutation represents a form of macromolecular isomerization when the normal termini are covalently linked and new termini introduced by breaking the backbone elsewhere. Here, we describe implications of circular permutation on the folding and function of biologically relevant macromolecules. A method permitting the analysis of the folding of all circularly permuted isomers of RNA is presented that has been successfully applied for a tRNA and the binding site of the coliphage R17 coat protein.
- Published
- 1993
18. Extractive fermentation in cloud point system for lipase production by Serratia marcescens ECU1010.
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Tao Pan, Zhilong Wang, Jian-He Xu, Zhenqiang Wu, and Hanshi Qi
- Subjects
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FERMENTATION , *SERRATIA marcescens , *LIPASES , *SURFACE active agents , *PROTEINS , *CELLS , *SALTWATER solutions , *LEAVENING agents , *HYDROLASES - Abstract
Extractive microbial fermentation for production of lipase by Serratia marcescens ECU1010 has been carried out in cloud point system. The cloud point system is composed of mixture nonionic surfactants with a ratio of Triton X-114 to Triton X-45 4:1 in aqueous solution. The lipase prefers to partition into the surfactant rich phase (coacervate phase) whereas the cells and other hydrophilic proteins retain in the dilute phase of cloud point system. Thus, a concentration factor 4.2-fold and a purification factor 1.3-fold of the lipase have been achieved in the extractive fermentation process. This is the first report about extractive fermentation of proteins in cloud point system. [ABSTRACT FROM AUTHOR]
- Published
- 2010
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19. Normal cellular prion protein is a ligand of selectins: binding requires LeX but is inhibited by sLeX.
- Author
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Chaoyang Li, Poki Wong, Tao Pan, Fan Xiao, Shaoman Yin, Binggong Chang, Shin-Chung Kang, James Ironside, and Man-Sun Sy
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PROTEINS ,SELECTINS ,SIALIC acids ,PROTEIN binding ,BIOCHEMISTRY - Abstract
The normal PrPC (cellular prion protein) contains sLeX [sialyl-LeX (Lewis X)] and LeX. sLeX is a ligand of selectins. To examine whether PrPC is a ligand of selectins, we generated three human PrPC–Ig fusion proteins: one with LeX, one with sLeX, and the other with neither LeX nor sLeX. Only LeX-PrPC–Ig binds E-, L- and P-selectins. Binding is Ca2+-dependent and occurs with nanomolar affinity. Removal of sialic acid on sLeX-PrPC–Ig enables the fusion protein to bind all selectins. These findings were confirmed with brain-derived PrPC. The selectins precipitated PrPC in human brain in a Ca2+-dependent manner. Treatment of brain homogenates with neuraminidase increased the amounts of PrPC precipitated. Therefore the presence of sialic acid prevents the binding of PrPC in human brain to selectins. Hence, human brain PrPC interacts with selectins in a manner that is distinct from interactions in peripheral tissues. Alternations in these interactions may have pathological consequences. [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
- View/download PDF
20. Surface-Modified Poly(methyl methacrylate) Capillary Electrophoresis Microchips for Protein and Peptide Analysis.
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Jikun Liu, Tao Pan, Woolley, Adam T., and Milton L. Lee
- Subjects
- *
ELECTROPHORESIS , *INTEGRATED circuits , *PROTEINS , *PEPTIDES , *SERUM albumin , *OXYGEN - Abstract
Polymeric materials have emerged as appealing alternatives to conventional inorganic substrates for the fabrication of microscale analytical systems; however, native polymeric surfaces typically require covalent modification to ensure optimum biocompatibility. 2-Bromoisobutyryl bromide was immobilized on poly(methyl methaciylate) (PMMA) substrates activated using an oxygen plasma. Atom-transfer radical polymerization was then performed to graft poly(ethylene glycol) (PEG) on the PMMA surface. PMMA microcapillary electrophoresis (μCE) devices made with the covalently modified surfaces exhibited substantially reduced electroosmotic flow and nonspecific adsorption of proteins on microchannel surfaces. Experiments using fluorescein isothiocyanate-conjugated bovine serum albumin indicated that both column efficiency and migration time reproducibility were I order of magnitude better with derivatized compared to untreated PMMA FACE chips. Fast, reproducible, and efficient separations of proteins and peptides were demonstrated using the PEG-grafted PMMA μCE chips. All analyses were completed in less than 60 s, and separation efficiencies as high as 5.2 × 104 plates for a 3.5-cm-long separation channel were obtained. These results demonstrate the general applicability of surface-grafted PMMA microdevices for a broad range of protein analyses. [ABSTRACT FROM AUTHOR]
- Published
- 2004
- Full Text
- View/download PDF
21. A 32 kDa protein—whose phosphorylation correlates with oncogenic Ras‐induced cell cycle arrest in activated Xenopus egg extracts—is identified as ribosomal protein S6.
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Jerry Pinghwa Pian, Tun‐Lan Huang, Pei‐Chi Tsai, Jian‐Peng Shi, Hong Cu, and Bin‐Tao Pan
- Subjects
PROTEINS ,RIBOSOMES ,PHOSPHORYLATION ,CANCER - Abstract
Oncogenic Ras induces cell‐cycle arrest in mammalian cells and in fertilized Xenopus eggs. How oncogenic Ras induces cell‐cycle arrest remains unclear. We previously showed that oncogenic Ras induces cell‐cycle arrest in activated Xenopus egg extracts (cycling extracts) and that the induced cell‐cycle arrest correlates with hyperphosphorylation of a 32 kDa protein. However, the identity of the 32 kDa protein was not known. By using a sucrose density‐gradient centrifugation, Triton X‐100–acetic acid–urea (TAU)‐gel electrophoresis, composite agarose‐polyacrylamide gel electrophoresis (CAPAGE), SDS–PAGE, and partial tryptic peptide sequence analysis, the 32 kDa protein has now been identified as S6, a 40S subunit ribosomal protein. Hence, our results indicate that the oncogenic Ras‐induced cell‐cycle arrest is correlated with hyperphosphorylation of S6, suggesting that phosphorylation of S6 plays an important role in the induced cell‐cycle arrest. It has been shown that conditional deletion of gene encoding S6 in mammalian cells prevents proliferation, demonstrating the importance of S6 in cell proliferation. The exact role S6 plays in cell proliferation is unclear. However, phosphorylation of S6 has been implicated in the regulation of protein synthesis. Thus, our results are consistent with the concept that oncogenic Ras induces S6 phosphorylation to influence protein synthesis, thereby contributing to the cell‐cycle arrest. In addition, our results also demonstrate that composite agarose‐polyacrylamide gel electrophoresis is suitable for the separation of large molecular complexes. © 2004 Wiley‐Liss, Inc. [ABSTRACT FROM AUTHOR]
- Published
- 2004
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