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Cui X, Chen K, Xing H, Yang Q, Krishna R, Bao Z, Wu H, Zhou W, Dong X, Han Y, Li B, Ren Q, Zaworotko MJ, Chen B. Pore chemistry and size control in hybrid porous materials for acetylene capture from ethylene. Science 2016; 353:141-4. [DOI: 10.1126/science.aaf2458] [Citation(s) in RCA: 839] [Impact Index Per Article: 93.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/05/2016] [Indexed: 01/18/2023]
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Ferretti JJ, McShan WM, Ajdic D, Savic DJ, Savic G, Lyon K, Primeaux C, Sezate S, Suvorov AN, Kenton S, Lai HS, Lin SP, Qian Y, Jia HG, Najar FZ, Ren Q, Zhu H, Song L, White J, Yuan X, Clifton SW, Roe BA, McLaughlin R. Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc Natl Acad Sci U S A 2001; 98:4658-63. [PMID: 11296296 PMCID: PMC31890 DOI: 10.1073/pnas.071559398] [Citation(s) in RCA: 661] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 1,852,442-bp sequence of an M1 strain of Streptococcus pyogenes, a Gram-positive pathogen, has been determined and contains 1,752 predicted protein-encoding genes. Approximately one-third of these genes have no identifiable function, with the remainder falling into previously characterized categories of known microbial function. Consistent with the observation that S. pyogenes is responsible for a wider variety of human disease than any other bacterial species, more than 40 putative virulence-associated genes have been identified. Additional genes have been identified that encode proteins likely associated with microbial "molecular mimicry" of host characteristics and involved in rheumatic fever or acute glomerulonephritis. The complete or partial sequence of four different bacteriophage genomes is also present, with each containing genes for one or more previously undiscovered superantigen-like proteins. These prophage-associated genes encode at least six potential virulence factors, emphasizing the importance of bacteriophages in horizontal gene transfer and a possible mechanism for generating new strains with increased pathogenic potential.
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Moran MA, Belas R, Schell MA, González JM, Sun F, Sun S, Binder BJ, Edmonds J, Ye W, Orcutt B, Howard EC, Meile C, Palefsky W, Goesmann A, Ren Q, Paulsen I, Ulrich LE, Thompson LS, Saunders E, Buchan A. Ecological genomics of marine Roseobacters. Appl Environ Microbiol 2007; 73:4559-69. [PMID: 17526795 PMCID: PMC1932822 DOI: 10.1128/aem.02580-06] [Citation(s) in RCA: 257] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode proteins involved in the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered: vir-related genes encoding a type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft Roseobacter genomes include those for carbon monoxide oxidation, dimethylsulfoniopropionate demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation.
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Research Support, U.S. Gov't, Non-P.H.S. |
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257 |
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Garver TD, Ren Q, Tuvia S, Bennett V. Tyrosine phosphorylation at a site highly conserved in the L1 family of cell adhesion molecules abolishes ankyrin binding and increases lateral mobility of neurofascin. J Cell Biol 1997; 137:703-14. [PMID: 9151675 PMCID: PMC2139872 DOI: 10.1083/jcb.137.3.703] [Citation(s) in RCA: 203] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
This paper presents evidence that a member of the L1 family of ankyrin-binding cell adhesion molecules is a substrate for protein tyrosine kinase(s) and phosphatase(s), identifies the highly conserved FIGQY tyrosine in the cytoplasmic domain as the principal site of phosphorylation, and demonstrates that phosphorylation of the FIGQY tyrosine abolishes ankyrin-binding activity. Neurofascin expressed in neuroblastoma cells is subject to tyrosine phosphorylation after activation of tyrosine kinases by NGF or bFGF or inactivation of tyrosine phosphatases with vanadate or dephostatin. Furthermore, both neurofascin and the related molecule Nr-CAM are tyrosine phosphorylated in a developmentally regulated pattern in rat brain. The FIGQY sequence is present in the cytoplasmic domains of all members of the L1 family of neural cell adhesion molecules. Phosphorylation of the FIGQY tyrosine abolishes ankyrin binding, as determined by coimmunoprecipitation of endogenous ankyrin and in vitro ankyrin-binding assays. Measurements of fluorescence recovery after photobleaching demonstrate that phosphorylation of the FIGQY tyrosine also increases lateral mobility of neurofascin expressed in neuroblastoma cells to the same extent as removal of the cytoplasmic domain. Ankyrin binding, therefore, appears to regulate the dynamic behavior of neurofascin and is the target for regulation by tyrosine phosphorylation in response to external signals. These findings suggest that tyrosine phosphorylation at the FIGQY site represents a highly conserved mechanism, used by the entire class of L1-related cell adhesion molecules, for regulation of ankyrin-dependent connections to the spectrin skeleton.
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Kondkar AA, Bray MS, Leal SM, Nagalla S, Liu DJ, Jin Y, Dong JF, Ren Q, Whiteheart SW, Shaw C, Bray PF. VAMP8/endobrevin is overexpressed in hyperreactive human platelets: suggested role for platelet microRNA. J Thromb Haemost 2010; 8:369-78. [PMID: 19943878 PMCID: PMC3312605 DOI: 10.1111/j.1538-7836.2009.03700.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Variation in platelet reactivity contributes to disorders of hemostasis and thrombosis, but the molecular mechanisms are not well understood. OBJECTIVES To discover associations between interindividual platelet variability and the responsible platelet genes, and to begin to define the molecular mechanisms altering platelet gene expression. SUBJECTS/METHODS Two hundred and eighty-eight healthy subjects were phenotyped for platelet responsiveness. Platelet RNA from subjects demonstrating hyperreactivity (n=18) and hyporeactivity (n=11) was used to screen the human transcriptome. RESULTS Distinctly different mRNA profiles were observed between subjects with differing platelet reactivity. Increased levels of mRNA for VAMP8/endobrevin, a critical v-SNARE involved in platelet granule secretion, were associated with platelet hyperreactivity (Q=0.0275). Validation studies of microarray results showed 4.8-fold higher mean VAMP8 mRNA levels in hyperreactive than hyporeactive platelets (P=0.0023). VAMP8 protein levels varied 13-fold among platelets from these normal subjects, and were 2.5-fold higher in hyperreactive platelets (P=0.05). Among our cohort of 288 subjects, a VAMP8 single-nucleotide polymorphism (rs1010) was associated with platelet reactivity in an age-dependent manner (P<0.003). MicroRNA-96 was predicted to bind to the 3'-untranslated regionof VAMP8 mRNA and was detected in platelets. Overexpression of microRNA-96 in VAMP8-expressing cell lines caused a dose-dependent decrease in VAMP8 protein and mRNA, suggesting a role in VAMP8 mRNA degradation. CONCLUSIONS These findings support a role for VAMP8/endobrevin in the heterogeneity of platelet reactivity, and suggest a role for microRNA-96 in the regulation of VAMP8 expression.
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Research Support, N.I.H., Extramural |
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149 |
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Yang B, Ren Q, Zhang JC, Chen QX, Hashimoto K. Altered expression of BDNF, BDNF pro-peptide and their precursor proBDNF in brain and liver tissues from psychiatric disorders: rethinking the brain-liver axis. Transl Psychiatry 2017; 7:e1128. [PMID: 28509900 PMCID: PMC5534963 DOI: 10.1038/tp.2017.95] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/22/2017] [Accepted: 03/28/2017] [Indexed: 12/11/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) has a role in the pathophysiology of psychiatric disorders. The precursor proBDNF is converted to mature BDNF and BDNF pro-peptide, the N-terminal fragment of proBDNF; however, the precise function of these proteins in psychiatric disorders is unknown. We sought to determine whether expression of these proteins is altered in the brain and peripheral tissues from patients with psychiatric disorders. We measured protein expression of proBDNF, mature BDNF and BDNF pro-peptide in the parietal cortex, cerebellum, liver and spleen from control, major depressive disorder (MDD), schizophrenia (SZ) and bipolar disorder (BD) groups. The levels of mature BDNF in the parietal cortex from MDD, SZ and BD groups were significantly lower than the control group, whereas the levels of BDNF pro-peptide in this area were significantly higher than controls. In contrast, the levels of proBDNF and BDNF pro-peptide in the cerebellum of MDD, SZ and BD groups were significantly lower than controls. Moreover, the levels of mature BDNF from the livers of MDD, SZ and BD groups were significantly higher than the control group. The levels of mature BDNF in the spleen did not differ among the four groups. Interestingly, there was a negative correlation between mature BDNF in the parietal cortex and mature BDNF in the liver in all the subjects. These findings suggest that abnormalities in the production of mature BDNF and BDNF pro-peptide in the brain and liver might have a role in the pathophysiology of psychiatric disorders, indicating a brain-liver axis in psychiatric disorders.
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Comparative Study |
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Ferreira MEDS, Colombo AL, Paulsen I, Ren Q, Wortman J, Huang J, Goldman MHS, Goldman GH. The ergosterol biosynthesis pathway, transporter genes, and azole resistance in Aspergillus fumigatus. Med Mycol 2005; 43 Suppl 1:S313-9. [PMID: 16110826 DOI: 10.1080/13693780400029114] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The continuous use of triazoles can result in the development of drug resistance. Azole-resistant clinical isolates, spontaneous and induced mutants of Aspergillus fumigatus have been documented. The azoles block the ergosterol biosynthesis pathway by inhibiting the enzyme 14-alpha-demethylase, product of the CYP51. Fungal azole resistance involves both amino acid changes in the target site that alter drug-target interactions and those that decrease net azole accumulation. The reduced intracellular accumulation has also been correlated with overexpression of multidrug resistance (MDR) efflux transporter genes of the ATP-binding cassette (ABC) and the major facilitator superfamily (MFS) classes. About 20 genes are involved in the A. fumigatus ergosterol biosynthesis pathway. There are several duplicated genes in this pathway. Interestingly, erg3 and erg11 showed two copies in A. fumigatus. In general, Aspergillus spp. have proportionally more MFS transporter encoding genes than Saccharomyces cerevisiae, S. pombe, and Neurospora crassa. The drug H+ (12 and 14 spanners) sub-families are also proportionally greater than in the other species. Although the numbers of ABC transporter encoding genes are comparable, again the Aspergillus spp. have more ABC transporters related to multidrug permease than the other fungal species.
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Review |
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115 |
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Abstract
Histone H2A.Z is structurally and functionally distinct from the major H2As. To understand the function of H2A.Z acetylation, we performed a mutagenic analysis of the six acetylated lysines in the N-terminal tail of Tetrahymena H2A.Z. Tetrahymena cannot survive with arginines at all six sites. Retention of one acetylatable lysine is sufficient to provide the essential function of H2A.Z acetylation. This essential function can be mimicked by deleting the region encompassing all six sites, or by mutations that reduce the positive charge of the N terminus at the acetylation sites themselves, or at other sites in the tail. These properties argue that the essential function of H2A.Z acetylation is to modify a "charge patch" by reducing the charge of the tail.
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Palenik B, Ren Q, Tai V, Paulsen IT. Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity. Environ Microbiol 2009; 11:349-59. [PMID: 19196269 DOI: 10.1111/j.1462-2920.2008.01772.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The extent to which cultured strains represent the genetic diversity of a population of microorganisms is poorly understood. Because they do not require culturing, metagenomic approaches have the potential to reveal the genetic diversity of the microbes actually present in an environment. From coastal California seawater, a complex and diverse environment, the marine cyanobacteria of the genus Synechococcus were enriched by flow cytometry-based sorting and the population metagenome was analysed with 454 sequencing technology. The sequence data were compared with model Synechococcus genomes, including those of two coastal strains, one isolated from the same and one from a very similar environment. The natural population metagenome had high sequence identity to most genes from the coastal model strains but diverged greatly from these genomes in multiple regions of atypical trinucleotide content that encoded diverse functions. These results can be explained by extensive horizontal gene transfer presumably with large differences in horizontally transferred genetic material between different strains. Some assembled contigs showed the presence of novel open reading frames not found in the model genomes, but these could not yet be unambiguously assigned to a Synechococcus clade. At least three distinct mobile DNA elements (plasmids) not found in model strain genomes were detected in the assembled contigs, suggesting for the first time their likely importance in marine cyanobacterial populations and possible role in horizontal gene transfer.
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Research Support, U.S. Gov't, Non-P.H.S. |
16 |
76 |
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Ren Q, Sierro N, Witholt B, Kessler B. FabG, an NADPH-dependent 3-ketoacyl reductase of Pseudomonas aeruginosa, provides precursors for medium-chain-length poly-3-hydroxyalkanoate biosynthesis in Escherichia coli. J Bacteriol 2000; 182:2978-81. [PMID: 10781572 PMCID: PMC102012 DOI: 10.1128/jb.182.10.2978-2981.2000] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli hosts expressing fabG of Pseudomonas aeruginosa showed 3-ketoacyl coenzyme A (CoA) reductase activity toward R-3-hydroxyoctanoyl-CoA. Furthermore, E. coli recombinants carrying the poly-3-hydroxyalkanoate (PHA) polymerase-encoding gene phaC in addition to fabG accumulated medium-chain-length PHAs (mcl-PHAs) from alkanoates. When E. coli fadB or fadA mutants, which are deficient in steps downstream or upstream of the 3-ketoacyl-CoA formation step during beta-oxidation, respectively, were transformed with fabG, higher levels of PHA were synthesized in E. coli fadA, whereas similar levels of PHA were found in E. coli fadB, compared with those of the corresponding mutants carrying phaC alone. These results strongly suggest that FabG of P. aeruginosa is able to reduce mcl-3-ketoacyl-CoAs generated by the beta-oxidation to 3-hydroxyacyl-CoAs to provide precursors for the PHA polymerase.
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Joós B, Ren Q, Duesbery MS. Peierls-Nabarro model of dislocations in silicon with generalized stacking-fault restoring forces. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 50:5890-5898. [PMID: 9976957 DOI: 10.1103/physrevb.50.5890] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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69 |
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Sun ZB, Li SD, Ren Q, Xu JL, Lu X, Sun MH. Biology and applications of Clonostachys rosea. J Appl Microbiol 2020; 129:486-495. [PMID: 32115828 DOI: 10.1111/jam.14625] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 01/07/2023]
Abstract
Clonostachys rosea is a promising saprophytic filamentous fungus that belongs to phylum Ascomycota. Clonostachys rosea is widespread around the world and exists in many kinds of habitats, with the highest frequency in soil. As an excellent mycoparasite, C. rosea exhibits strong biological control ability against numerous fungal plant pathogens, nematodes and insects. These behaviours are based on the activation of multiple mechanisms such as secreted cell-wall-degrading enzymes, production of antifungal secondary metabolites and induction of plant defence systems. Besides having significant biocontrol activity, C. rosea also functions in the biodegradation of plastic waste, biotransformation of bioactive compounds, as a bioenergy sources and in fermentation. This mini review summarizes information about the biology and various applications of C. rosea and expands on its possible uses.
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Review |
5 |
67 |
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Klinke S, Ren Q, Witholt B, Kessler B. Production of medium-chain-length poly(3-hydroxyalkanoates) from gluconate by recombinant Escherichia coli. Appl Environ Microbiol 1999; 65:540-8. [PMID: 9925580 PMCID: PMC91059 DOI: 10.1128/aem.65.2.540-548.1999] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It was shown recently that recombinant Escherichia coli, defective in the beta-oxidation cycle and harboring a medium-chain-length (MCL) poly(3-hydroxyalkanoate) (PHA) polymerase-encoding gene of Pseudomonas, is able to produce MCL PHA from fatty acids but not from sugars or gluconate (S. Langenbach, B. H. A. Rehm, and A. Steinbüchel, FEMS Microbiol. Lett. 150:303-309, 1997; Q. Ren, Ph.D. thesis, ETH Zürich, Zürich, Switzerland, 1997). In this study, we report the formation of MCL PHA from gluconate by recombinant E. coli. By introduction of genes coding for an MCL PHA polymerase and the cytosolic thioesterase I ('thioesterase I) into E. coli JMU193, we were able to engineer a pathway for the synthesis of MCL PHA from gluconate. We used two expression systems, i.e., the bad promoter and alk promoter, for the 'thioesterase I- and PHA polymerase-encoding genes, respectively, which enabled us to modulate their expression independently over a range of inducer concentrations, which resulted in a maximum MCL PHA accumulation of 2.3% of cell dry weight from gluconate. We found that the amount of PHA and the 'thioesterase I activity are directly correlated. Moreover, the polymer accumulated in the recombinant E. coli consisted mainly of 3-hydroxyoctanoate monomers. On the basis of our data, we propose an MCL PHA biosynthesis pathway scheme for recombinant E. coli JMU193, harboring PHA polymerase and 'thioesterase I, when grown on gluconate, which involves both de novo fatty acid synthesis and beta-oxidation.
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Ren Q, Thony-Meyer L. Physical interaction of CcmC with heme and the heme chaperone CcmE during cytochrome c maturation. J Biol Chem 2001; 276:32591-6. [PMID: 11384983 DOI: 10.1074/jbc.m103058200] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Biogenesis of c-type cytochromes requires the covalent attachment of heme to the apoprotein. In Escherichia coli, this process involves eight membrane proteins encoded by the ccmABCDEFGH operon. CcmE binds heme covalently and transfers it to apocytochromes c in the presence of other Ccm proteins. CcmC is necessary and sufficient to incorporate heme into CcmE. Here, we report that the CcmC protein directly interacts with heme. We further show that CcmC co-immunoprecipitates with CcmE. CcmC contains two conserved histidines and a signature sequence, the so-called tryptophan-rich motif, which is the only element common to cytochrome c maturation proteins of bacteria, archae, plant mitochondria, and chloroplasts. We report that mutational changes of these motifs affecting the function of CcmC in cytochrome c maturation do not influence heme binding of CcmC. However, the mutants are defective in the CcmC-CcmE interaction, suggesting that these motifs are involved in the formation of a CcmC-CcmE complex. We propose that CcmC, CcmE, and heme interact directly with each other, establishing a periplasmic heme delivery pathway for cytochrome c maturation.
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Ren Q, Bennett V. Palmitoylation of neurofascin at a site in the membrane-spanning domain highly conserved among the L1 family of cell adhesion molecules. J Neurochem 1998; 70:1839-49. [PMID: 9572267 DOI: 10.1046/j.1471-4159.1998.70051839.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This report presents the first evidence that a member of the L1 family of nervous system cell-adhesion molecules is covalently modified by thioesterification with palmitate, and identifies a highly conserved cysteine in the predicted membrane-spanning domain as the site of modification. Neurofascin is constitutively palmitoylated at cysteine-1213 at close to a 1:1 molar stoichiometry. Kinetics of palmitate incorporation into neurofascin expressed in resting neuroblastoma cells indicate that the palmitate modification has the same turnover rate as the polypeptide chain and does not affect the protein stability of neurofascin. Palmitoylation of neurofascin expressed in dorsal root ganglion neurons is not required for delivery of neurofascin to the plasma membrane or targeting to axons. Palmitoylation also has no effect on ankyrin-binding activity of neurofascin, on the oligomeric state of neurofascin in solution, or on cell-adhesion activity of neurofascin expressed in neuroblastoma cells. A significant difference between native and C1213L neurofascin is that these proteins were localized in distinct fractions within a low-density membrane population enriched in signaling molecules. These results indicate a palmitate-dependent targeting of neurofascin to a specialized membrane microdomain.
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Ren Q, Joós B, Duesbery MS. Test of the Peierls-Nabarro model for dislocations in silicon. PHYSICAL REVIEW. B, CONDENSED MATTER 1995; 52:13223-13228. [PMID: 9980511 DOI: 10.1103/physrevb.52.13223] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Yin H, Liu Z, Guan G, Liu A, Ma M, Ren Q, Luo J. Detection and differentiation of Theileria luwenshuni and T. uilenbergi infection in small ruminants by PCR. Transbound Emerg Dis 2008; 55:233-7. [PMID: 18666967 DOI: 10.1111/j.1865-1682.2008.01031.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Theileria luwenshuni and T. uilenbergi are newly identified Theileria species highly pathogenic for sheep and goats in China. As they are morphologically indistinguishable and poorly characterized, there is no easily applicable method available to differentiate between these species. In the present study, PCR assays are described for the differentiation and detection of T. luwenshuni and T. uilenbergi using species-specific primers, which were designed based on the hypervariable region of the small subunit ribosomal RNA gene sequences. By testing 100 field blood samples of sheep collected from five geographically different regions where the Theileria species were described to be prevalent, the PCR assays not only detected infected samples but also identified mixed infection. This suggests that these PCR assays are useful tools for the detection of and differentiation between T. luwenshuni and T. uilenbergi.
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Research Support, Non-U.S. Gov't |
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50 |
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Ren Q, Han XY, Wang F, Zhang XY, Han LC, Luo YY, Zhou XH, Ji LN. Exon sequencing and association analysis of polymorphisms in TCF7L2 with type 2 diabetes in a Chinese population. Diabetologia 2008; 51:1146-1152. [PMID: 18493736 DOI: 10.1007/s00125-008-1039-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Accepted: 04/08/2008] [Indexed: 01/18/2023]
Abstract
AIMS/HYPOTHESIS Recently, variants in the transcription factor 7-like 2 (TCF7L2) gene have been found to be consistently associated with type 2 diabetes in different populations. In this study, we hypothesized that TCF7L2 also contributed to genetic susceptibility for type 2 diabetes in a Chinese population. METHODS We looked for new variants by direct sequencing of all exons and intron-exon junctions of TCF7L2 in 100 Chinese type 2 diabetic patients, and then we genotyped five single nucleotide polymorphisms (SNPs) by Snapshot technology in 1,000 Chinese individuals. RESULTS By sequencing, we identified six SNPs (c.1,637C>A; c.1,674C>G; c.1,709G>A; c.1,846C>G; c.1,888C>T; and c.1,876T>G), and three of them led to non-synonymous polymorphisms (c.1,637C>A, His-->Gln or Pro-->Thr; c.1,674C>G, Pro-->Arg; and c.1,709G>A, Ala-->Thr). All of them are rare except c.1,637C>A, which had a frequency of 0.23 for the minor A allele in 98 sequenced individuals. In a case-control study, one of the newly discovered SNPs (c.1,637C>A), together with four reported ones (rs7903146, rs12255372, rs290487 and rs3814573) were genotyped. Comparison between allele and genotype frequencies of these SNPs in patients and controls showed marginal association for rs7903146 and rs290487 with type 2 diabetes (p = 0.063, OR 1.982, 95% CI 1.128-3.485; p = 0.071, OR 1.237, 95% CI 0.983-1.557, respectively). No association was found for rs12255372, rs3814573, c.1,637C>A and type 2 diabetes (p = 0.278-1.000). CONCLUSIONS/INTERPRETATION With the current sample size, we did not find any mutation in the coding sequence of TCF7L2 that confers a genetic risk for type 2 diabetes in a Chinese population, and did not replicate some of the major positive results obtained in other populations.
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Ren Q, Sierro N, Kellerhals M, Kessler B, Witholt B. Properties of engineered poly-3-hydroxyalkanoates produced in recombinant Escherichia coli strains. Appl Environ Microbiol 2000; 66:1311-20. [PMID: 10742205 PMCID: PMC91986 DOI: 10.1128/aem.66.4.1311-1320.2000] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To prepare medium-chain-length poly-3-hydroxyalkanoates (PHAs) with altered physical properties, we generated recombinant Escherichia coli strains that synthesized PHAs with altered monomer compositions. Experiments with different substrates (fatty acids with different chain lengths) or different E. coli hosts failed to produce PHAs with altered physical properties. Therefore, we engineered a new potential PHA synthetic pathway, in which ketoacyl-coenzyme A (CoA) intermediates derived from the beta-oxidation cycle are accumulated and led to the PHA polymerase precursor R-3-hydroxyalkanoates in E. coli hosts. By introducing the poly-3-hydroxybutyrate acetoacetyl-CoA reductase (PhbB) from Ralstonia eutropha and blocking the ketoacyl-CoA degradation step of the beta-oxidation, the ketoacyl-CoA intermediate was accumulated and reduced to the PHA precursor. Introduction of the phbB gene not only caused significant changes in the monomer composition but also caused changes of the physical properties of the PHA, such as increase of polymer size and loss of the melting point. The present study demonstrates that pathway engineering can be a useful approach for producing PHAs with engineered physical properties.
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Ren Q, Venugopalan V, Schomacker K, Deutsch TF, Flotte TJ, Puliafito CA, Birngruber R. Mid-infrared laser ablation of the cornea: a comparative study. Lasers Surg Med 1992; 12:274-81. [PMID: 1508021 DOI: 10.1002/lsm.1900120306] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The ablation thresholds and patterns of collateral damage in cornea produced by Er:YAG (2.94 microns) and Er:YSGG (2.79 microns) lasers were measured. Two different pulse durations, 200 microseconds (normal spiking mode) and 100 ns (Q-switched mode), were used at both wavelengths. In the normal spiking mode, damage zones of 16 +/- 2 microns and 39 +/- 7 microns and ablation thresholds of 250 +/- 20 mJ/cm2 and 420 +/- 35 mJ/cm2 were measured at 2.94 microns and 2.79 microns, respectively. In the Q-switched mode, damage zones of 4 +/- 2 microns and ablation thresholds of 150 +/- 10 mJ/cm2 were found irrespective of the laser used. The similarity between the results using the Er:YAG and Er:YSGG lasers in the Q-switched mode suggest that either laser can be used with equal effectiveness for corneal trephination.
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Lazarus P, Sheikh SN, Ren Q, Schantz SP, Stern JC, Richie JP, Park JY. p53, but not p16 mutations in oral squamous cell carcinomas are associated with specific CYP1A1 and GSTM1 polymorphic genotypes and patient tobacco use. Carcinogenesis 1998; 19:509-14. [PMID: 9525287 DOI: 10.1093/carcin/19.3.509] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Inactivation of tumor suppressor genes like p53 and p16 play a key role in tumor progression, with a high incidence of mutations existing for both genes in oral squamous cell carcinomas. Previous studies have demonstrated, (i) a correlation between the prevalence of p53 mutations and tobacco use [Brennan et al. (1995) New Engl. J. Med., 332, 712-717; Lazarus et al. (1996) Carcinogenesis, 17, 733-739], and (ii) a link between genotypes in specific xenobiotic metabolizing enzymes and oral cancer susceptibility [Park et al. (1997) Cancer Epid. Biomarkers Prev., 6, 791-797). In this paper, we present results of our examination of a series of 80 oral squamous cell carcinomas for p53 exons 5-9 and p16 exons 1-2 mutations, and the potential association of these mutations with specific genotyping patterns. p53 mutation prevalence in oral tumors was linked with increased patient tobacco use using several stratification criteria. There was a significantly higher prevalence of p53 mutations in OCSCCs from patients who smoked > 30 pack-years as compared to tumors from patients who smoked < or = 30 pack-years (OR = 2.8; CI = 1.1-7.2). No significant association was observed with patient alcohol consumption. There was a significant association between the prevalence of p53 mutations in oral tumors and CYP1A1 genotyping patterns in these oral cancer patients, with the highest p53 mutation prevalence observed in subjects with the CYP1A1 [val]/GSTM1 [+] genotype (OR = 6.0; CI = 1.2-29.7). A significant association was not observed between the prevalence of p16 mutations in oral tumors and tobacco use, or CYP1A1 [val] or GSTM1 (0/0) genotypes. These data suggest that the induction of mutations in specific tumor suppressor genes or oncogenes in oral tumors may be associated with specific carcinogen exposures, and that this association may be linked to specific polymorphic genotypes in xenobiotic-metabolizing enzyme genes.
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Wang JX, Zhao XF, Liang YL, Li L, Zhang W, Ren Q, Wang LC, Wang LY. Molecular characterization and expression of the antimicrobial peptide defensin from the housefly (Musca domestica). Cell Mol Life Sci 2006; 63:3072-82. [PMID: 17131057 PMCID: PMC11136183 DOI: 10.1007/s00018-006-6284-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A 430-bp cDNA encoding the insect antimicrobial peptide defensin was cloned from the housefly, and designated Musca domestica defensin (Mdde). The open reading frame of the cDNA encoded a 92-amino acid peptide with an N-terminal signal sequence followed by a propeptide that is processed by cleavage to a 40-amino acid mature peptide. Northern analysis and in situ hybridization identified the corresponding mRNA in the fat body of bacterially challenged houseflies and in the epidermis of the body wall of naive and challenged houseflies. The Gram-negative bacterium (Escherichia coli) is a strong inducer of the gene. By RT-PCR, Mdde mRNA was also detected in naive and challenged insects. These findings suggest that the defensin gene is constitutively expressed in the epidermis of the housefly body wall. The predicted mature form of Mdde was expressed as a recombinant peptide in E. coli and Pichia pastoris. The recombinant Mdde expressed in Pichia was active against Gram-positive and some Gram-negative bacteria.
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Gailitis RP, Patterson SW, Samuels MA, Hagen K, Ren Q, Waring GO. Comparison of laser phacovaporization using the Er-YAG and the Er-YSGG laser. ARCHIVES OF OPHTHALMOLOGY (CHICAGO, ILL. : 1960) 1993; 111:697-700. [PMID: 8489455 DOI: 10.1001/archopht.1993.01090050131042] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
OBJECTIVE To study the interaction of the erbium (Er)-YAG (2.94 microns) and the Er-YSGG (2.79 microns) lasers with the human crystalline lens tissue. METHODS Fresh human crystalline lens sections were used to measure the photovaporization threshold, rate, and damage zone of the two lasers. RESULTS We found the photovaporization threshold for the Er-YAG and the Er-YSGG lasers to be 1.4 J/cm2 and 5.5 J/cm2, respectively. At 10 J/cm2, the photovaporization rate is 67.9 microns per pulse for the Er-YAG laser and 18.4 microns per pulse for the Er-YSGG laser. The increased rate of photovaporization as a function of radiant energy for the Er-YAG laser is almost twice that for the Er-YSGG. Damage zones for the Er-YAG laser ranged from 4 to 9 microns compared with 10 to 22 microns for the Er-YSGG. CONCLUSIONS It is apparent that both lasers can adequately photovaporize human crystalline lens tissue and should be further studied for this purpose.
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Comparative Study |
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Khalil-Manesh F, Gonick HC, Weiler EW, Prins B, Weber MA, Purdy R, Ren Q. Effect of chelation treatment with dimercaptosuccinic acid (DMSA) on lead-related blood pressure changes. ENVIRONMENTAL RESEARCH 1994; 65:86-99. [PMID: 8162887 DOI: 10.1006/enrs.1994.1023] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
An elevation in mean blood pressure was found in rats treated with low lead (0.01%) for 6 months and then only water for an additional 6 months (discontinuous low lead). No change in blood pressure was found in rats similarly treated with high lead (0.5%) (discontinuous high lead). Administration of DMSA (0.5% in drinking water), for 5 days every 2 months following cessation of lead administration, resulted in a significant lowering of blood pressure in both groups of animals. In the low-lead but not the high-lead group, this was associated with an increase in plasma cyclic GMP (acting as a second messenger for endothelium-derived relaxing factor, EDRF) and a decrease in the plasma concentration of a 12-kDa hypertension-associated protein. Plasma endothelin-3 (ET-3) levels were decreased in discontinuous high-lead rats, increased in discontinuous low-lead rats, but were unaltered by DMSA treatment. We infer that the elevated blood pressure in the discontinuous low-lead rats is related to an increase in the putative vasoconstrictors, ET-3 and the hypertension-associated protein, without a change in the vasodilator, EDRF. With DMSA treatment, plasma cyclic GMP in low-lead rats increased above normal, and the hypertension-associated protein decreased, resulting in lowered blood pressure. DMSA was shown to act as an antioxidant in vitro. Thus the DMSA effect on plasma cGMP (EDRF) may occur via a scavenging effect on EDRF-inactivating reactive oxygen species.
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Ren Q, Simon G, Parel JM. Ultraviolet solid-state laser (213-nm) photorefractive keratectomy. In vitro study. Ophthalmology 1993; 100:1828-34. [PMID: 8259282 DOI: 10.1016/s0161-6420(93)31390-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Replacing the gas argon fluoride (193 nm) excimer laser with a solid-state laser source in the far-ultraviolet spectrum region would eliminate the hazards of a gas laser and would reduce its size, which is desirable for photorefractive keratectomy. The authors investigated corneal reshaping using a frequency-quintupled (213 nm) pulsed (10 ns) neodymium:YAG laser coupled to a computer-controlled optical scanning delivery system. METHODS A 250 +/- 15-mJ/cm2 radiant exposure was used to ablate a 5-mm optical zone in human cadaver eyes and rabbit eyes. The 213-nm laser pulses were delivered through and shaped by a computer-controlled optical scanning delivery system, producing a 0.5-mm spot with a quasi-Guassian energy distribution on the cornea. Corneal surface changes were documented by computer-assisted corneal topography. Light microscopy, scanning electron microscopy, and transmission electron microscopy were performed to examine the effects on corneal surface quality and cellular components. RESULTS Corneal topographic measurements showed myopic corrections ranging from 2.3 to 6.1 diopters. Results of postoperative examination with the slit lamp and operating microscope demonstrated a smoothly ablated surface without corneal haze. Histologic results showed a smoothly sloping surface without recognizable steps. The surface quality and cellular effects were similar to that of previously described excimer photorefractive keratectomy. CONCLUSION The authors demonstrated that an ultraviolet (213-nm) solid-state laser coupled to an optical scanning delivery system is capable of reshaping the corneal surface with smooth transition. The scanning beam delivery system may offer the advantage of producing spatially resolved, customized, aspheric corrections to optimize the quality of vision after photorefractive keratectomy.
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