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Gu Z, Jiang Q, Zhang G. Extracellular signal-regulated kinase and c-Jun N-terminal protein kinase in ischemic tolerance. Neuroreport 2001; 12:3487-91. [PMID: 11733697 DOI: 10.1097/00001756-200111160-00023] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The alterations and involvement of extracellular signal-regulated kinase (ERK) and c-Jun N-terminal protein kinase (JNK) activation were examined in the hippocampal CA1 region in a rat model of global brain ischemic tolerance. Western blotting study showed that ERK activation (diphosphorylation) level was decreased (3.75-, 0.56-, and 0.23-fold vs sham control) and JNK activation level was increased (3.82-, 4.63-, and 5.30-fold vs sham control) 3 days after more severe ischemic insults (6 min, 8 min, and 10 min of ischemia, respectively). These alterations were significantly prevented by pretreatment with preconditioning ischemia, which also provided neuronal protection against ischemic injury. Inhibition of ERK activation after preconditioning ischemia by PD98059, a specific ERK kinase inhibitor, significantly prevented the inhibitory effects of preconditioning ischemia on both JNK activation and ischemic injury. The results suggest that ERK activation after preconditioning ischemia may result in the prevention of JNK activation and thus be involved in the protective responses in ischemic tolerance in hippocampal CA1 region.
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Okazaki T, Suenaga K, Lian Y, Gu Z, Shinohara H. Intrafullerene electron transfers in Sm-containing metallofullerenes: Sm@C2n (74 < or = 2n < or = 84). J Mol Graph Model 2001; 19:244-51. [PMID: 11391876 DOI: 10.1016/s1093-3263(00)00093-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The electronic properties of Sm-containing metallofullerenes, Sm@C74, Sm@C76 (I, II), Sm@C78, Sm@C80, Sm@C82 (I, II, III) and Sm@C84 (I, II, III), are characterized by UV-Vis-NIR absorption spectroscopy and electron energy-loss spectroscopy (EELS). The UV-Vis-NIR absorption spectra of Sm@C74, Sm@C80, Sm@C82 (I, II, III) and Sm@C84 (I, II) are quite similar to those of the corresponding Ca, Sr, Ba, Eu, Tm, Yb-based metallofullerenes. In contrast, the absorption spectra of Sm@C76 (I, II), Sm@C78 and Sm@C84(III) show a novel feature: the onset for Sm@C78 is observed approximately 2600 nm, which corresponds to a small band gap (approximately 0.5 eV). Furthermore, the oxidation states of Sm atom in the various fullerene cages are investigated by EELS, which reveals that the Sm atom takes +2 oxidation state in the fullerene cages. A probable rationale for the tendency to have the Sm2+ state is presented based on a simple thermochemical cycle model.
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Han J, Flemington C, Houghton AB, Gu Z, Zambetti GP, Lutz RJ, Zhu L, Chittenden T. Expression of bbc3, a pro-apoptotic BH3-only gene, is regulated by diverse cell death and survival signals. Proc Natl Acad Sci U S A 2001; 98:11318-23. [PMID: 11572983 PMCID: PMC58727 DOI: 10.1073/pnas.201208798] [Citation(s) in RCA: 324] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BH3-only proteins function at a proximal point in a conserved cell death pathway by binding, through their BH3 domains, to other Bcl-2 family members and triggering mitochondrial events associated with apoptosis. Here, we describe a strongly pro-apoptotic BH3-only protein, designated Bbc3, whose expression increases in response to diverse apoptotic stimuli. bbc3 mRNA levels were induced by exposure to DNA-damaging agents and by wild-type p53, which mediates DNA damage-induced apoptosis. p53 transactivated bbc3 through consensus p53 binding sites within the bbc3 promoter region, indicating that bbc3 is a direct target of p53. Additionally, bbc3 mRNA was induced by p53-independent apoptotic stimuli, including dexamethasone treatment of thymocytes, and serum deprivation of tumor cells. Insulin-like growth factor-1 and epidermal growth factor, growth factors with broad anti-apoptotic activity, were each sufficient to suppress Bbc3 expression in serum-starved tumor cells. These results suggest that the transcriptional regulation of bbc3 contributes to the transduction of diverse cell death and survival signals.
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104
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Jiang Q, Gu Z, Zhang G. Nuclear translocation of extracellular signal-regulated kinases in neuronal excitotoxicity. Neuroreport 2001; 12:2417-21. [PMID: 11496121 DOI: 10.1097/00001756-200108080-00026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Subcellular distributions of extracellular signal-kinases (ERK1/2), including their activated form (p-ERK1/2), were investigated in glutamate-induced apoptotic-like death in cultured rat cortical neurons by Western immunoblot and immunocytochemistry. During 15 min glutamate exposure, p-ERK1/2 was increased in both cytosol and nuclear extracts, but prominently so in nuclear extracts. Simultaneously, ERK1/2 were mildly decreased in cytosol (to 0.7-fold vs sham control), largely increased in nuclear extracts (to 6.2-fold vs sham control), but not changed in total cell extracts. Immunocytochemistry studies also showed a large increase in nuclear and a mild decrease in cytosol extracts of ERK1/2 at 15 min of exposure. After glutamate exposure, all the above changes reverted simultaneously. The nuclear increase of ERK1/2 was largely prevented by inhibition of ERK1/2 activation, but prolonged by elongation of ERK1/2 activation. These observations suggest that stimulation of glutamate receptors in cortical neurons may incur an activation-dependent transient nuclear translocation of ERK1/2, which might be involved in excitotoxicity through a simultaneous strong elevation of p-ERK1/2 in nucleus.
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105
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Fang Y, Gu Z, Chen W. [X-ray and clinical characteristics in sagittal fracture of the mandibular condyle]. ZHONGHUA KOU QIANG YI XUE ZA ZHI = ZHONGHUA KOUQIANG YIXUE ZAZHI = CHINESE JOURNAL OF STOMATOLOGY 2001; 36:250-2. [PMID: 11718002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
OBJECTIVE To study the X-ray and clinical characteristics in sagittal fracture of the mandibular condyle (SFMC). METHODS 14 cases (15 sides) of SFMC in 48 cases who had condylar fractures were studied in the research, every patient was examined by the conventional x-ray, 2D-CT and 3D-CT, and followed up for 3-39 months. RESULTS The fracture line mainly passed through lateral 1/3 and middle 1/3 of anterior condyle and the middle 1/3 of posterior condyle. Following-up (3-39 months) showed that the patients' occlusions were normal in all cases. CONCLUSIONS The fracture line mainly located in the lateral pterygoid muscle fossa. Good results can be gotten by effective treatment. The 2D-CT and 3D-CT are valuable to the diagnosis.
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Wlad H, Ballagi A, Bouakaz L, Gu Z, Janson JC. Rapid two-step purification of a recombinant mouse Fab fragment expressed in Escherichia coli. Protein Expr Purif 2001; 22:325-9. [PMID: 11437609 DOI: 10.1006/prep.2001.1444] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report a rapid, large-scale process for the purification of a recombinant Fab fragment specific for the tobacco mosaic virus coat protein (Fab57P). The fragment is expressed periplasmically in Escherichia coli. The expression level was optimized in 0.3-L fermentors. The highest levels were obtained using the following conditions: (1) low postinduction temperature (21 degrees C), (2) combined use of two beta-lactam antibiotics (carbenicillin and ampicillin), (3) IPTG concentration 0.1 mM, (4) regulated pH 7.2, (5) 17-h induction time, and (6) conditions that reduce mechanical stress. Optimized large-scale fermentations were done in 15- and 300-L capacity fermentors. The recombinant Fab fragment was purified by two chromatographic steps. After disruption of the bacteria using an APV Gaulin homogenizer, the crude E. coli homogenate was directly applied, without centrifugation, to an SP Sepharose Big Beads column. The recombinant Fab fragment was eluted as a single peak in a sodium chloride gradient. The fragment was further purified by affinity adsorption to a column packed with Epoxy-activated Sepharose 6B to which the antigen peptide NH(2)-CGS YNR GSF SQS SGLV-CONH(2) had been coupled through its N-terminal cysteine. The purified Fab57P fragment showed one band in SDS-PAGE. The overall purification yield was 35%.
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107
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Gu Z, Lu X. [Influence of art of changes on the thinking of traditional Chinese medicine]. ZHONGHUA YI SHI ZA ZHI (BEIJING, CHINA : 1980) 2001; 31:160-4. [PMID: 11762366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The most important influence of art of changes on traditional Chinese medicine (TCM) was reflected in the formation of the basic theory of TCM. Some innovations were achieved by using the theory of art of changes to research medicine in later ages. However, the specific therapies and the prognostication of diseases inferred by using the art of mathematics were mostly unreliable. Though the researches on the art of changes were helpful to the exploration of the cause and effect of TMC, yet, its practical significance should be evaluated properly.
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Amara N, Palapattu GS, Schrage M, Gu Z, Thomas GV, Dorey F, Said J, Reiter RE. Prostate stem cell antigen is overexpressed in human transitional cell carcinoma. Cancer Res 2001; 61:4660-5. [PMID: 11406532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Prostate stem cell antigen (PSCA), a homologue of the Ly-6/Thy-1 family of cell surface antigens, is expressed by a majority of human prostate cancers and is a promising target for prostate cancer immunotherapy. In addition to its expression in normal and malignant prostate, we recently reported that PSCA is expressed at low levels in the transitional epithelium of normal bladder. In the present study, we compared the expression of PSCA in normal and malignant urothelial tissues to assess its potential as an immunotherapeutic target in transitional cell carcinoma (TCC). Immunohistochemical analysis of PSCA protein expression was performed on tissue sections from 32 normal bladder specimens, as well as 11 cases of low-grade transitional cell dysplasia, 21 cases of carcinoma in situ (CIS), 38 superficial transitional cell tumors (STCC, stages T(a)-T(1)), 65 muscle-invasive TCCs (ITCCs, stages T(2)-T(4)), and 7 bladder cancer metastases. The level of PSCA protein expression was scored semiquantitatively by assessing both the intensity and frequency (i.e., percentage of positive tumor cells) of staining. We also examined PSCA mRNA expression in a representative sample of normal and malignant human transitional cell tissues. In normal bladder, PSCA immunostaining was weak and confined almost exclusively to the superficial umbrella cell layer. Staining in CIS and STCC was more intense and uniform than that seen in normal bladder epithelium (P < 0.001), with staining detected in 21 (100%) of 21 cases of CIS and 37 (97%) of 38 superficial tumors. PSCA protein was also detected in 42 (65%) of 65 of muscle-invasive and 4 (57%) of 7 metastatic cancers, with the highest levels of PSCA expression (i.e., moderate-strong staining in >50% of tumor cells) seen in 32% of invasive and 43% of metastatic samples. Higher levels of PSCA expression correlated with increasing tumor grade for both STCCs and ITCCs (P < 0.001). Northern blot analysis confirmed the immunohistochemical data, showing a dramatic increase in PSCA mRNA expression in two of five muscle-invasive transitional cell tumors when compared with normal samples. Confocal microscopy demonstrated that PSCA expression in TCC is confined to the cell surface. These data demonstrate that PSCA is overexpressed in a majority of human TCCs, particularly CIS and superficial tumors, and may be a useful target for bladder cancer diagnosis and therapy.
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Gu Z, Xiao J, Lou S. [The mechanical chemical attachment of artificial cartilage (PVA-hydrogel) to metal substrate (or underlying bone)]. SHENG WU YI XUE GONG CHENG XUE ZA ZHI = JOURNAL OF BIOMEDICAL ENGINEERING = SHENGWU YIXUE GONGCHENGXUE ZAZHI 2001; 18:185-7. [PMID: 11450530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The biocompatibility and tribological characteristics of PVA-hydrogel are excellent, but it is very difficult to make the artificial cartilage material (PVA-hydrogel) attach to the underlying bone. In this study, PVA-hydrogel is attached to the metal fibre mesh by means of micro-mechanical interlock methods at first, then the surface of metal fibre mesh is bonded to the underlying bone by the bone cement(PMMA). In this way, the artificial cartilage can be firmly attached to the underlying bone(or metal substrate). Microstructure analysis and mechanical tests show that the attachment between artificial cartilage and the metal substrate is firm.
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Sun Y, Chen D, Wei K, Wu F, Gu Z, Chen H, Li F. [Synthesis of nanocrystalline Y2O3:Eu3+ and study on spectral characteristics]. GUANG PU XUE YU GUANG PU FEN XI = GUANG PU 2001; 21:339-342. [PMID: 12947662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nano-Y2O3:Eu3+ was synthesized with oxalic acid as precipitate agent while adding little surfactant controlling the condition of the reaction. We obtained nanoscale powder. The particle diameter was 15-19 nm. The agglomerate size was less 1.0 micron. Compared with the ordinary powder of Y2O3:Eu3+, the peak of emission spectrum of nano-Y2O3:Eu3+ is at lambda em = 612 nm under 254 nm excitation, blue-shift 6 nm. Excitation spectrum has no difference. The phosphor was measured by PMS-3 chromatic detector and its luminescent chromatic coordinate parameters were x = 0.6479, y = 0.3442. The quenching concentration increases from micro-Y2O3:Eu3+'s 6% to 9% and the intensity of luminescence increases with the grain size growing.
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111
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Gu Z, Su Z, Janson JC. Urea gradient size-exclusion chromatography enhanced the yield of lysozyme refolding. J Chromatogr A 2001; 918:311-8. [PMID: 11407577 DOI: 10.1016/s0021-9673(01)00766-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Protein refolding is still a bottleneck for large-scale production of valuable proteins expressed as inclusion bodies in Escherichia coli. Usually biologically active proteins cannot be obtained with high yield at a high concentration after refolding. In order to meet the challenge of protein refolding a urea gradient gel filtration-refolding system was developed in this article. A Superdex 75 column was pre-equilibrated with a linear decreased urea gradient, the denatured protein experienced the gradual decrease in urea concentration as it went through the column. The refolding of denatured lysozyme showed this method could significantly increase the activity recovery of denatured lysozyme at high protein concentration. The activity recovery of 90% was obtained from the initial protein concentration up to 17 mg/ml within 40 min.
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Gu Z, Jiang Q, Zhang G. Extracellular signal-regulated kinase 1/2 activation in hippocampus after cerebral ischemia may not interfere with postischemic cell death. Brain Res 2001; 901:79-84. [PMID: 11368953 DOI: 10.1016/s0006-8993(01)02275-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To investigate the effect of the activation of extracellular signal-regulated kinase 1/2 (ERK1/2) on cerebral ischemic injury, temporospatial alterations of active (diphosphorylated) ERK1/2 immunoreactivity in hippocampus was examined. Western blot showed that diphosphorylated ERK1/2 were decreased at 10 min of cerebral ischemia but increased rapidly (within 2 min) and transiently (within 4 h) during reperfusion. Immunohistochemistry showed that little diphosphorylated ERK1/2 immunoreactivity was seen in CA1 pyramidal cell bodies after ischemia, while strong immunoreactivity were seen in neuronal bodies in CA3/DG and in fiber systems in both CA1 and CA3 regions. Cerebral ventricular infusion of PD98059, a specific inhibitor of ERK kinase, completely prevented ERK1/2 activation after ischemia but had no effect on the survival of pyramidal cells in CA1 subfield. The results suggest that ERK1/2 activation in hippocampus after brain ischemia may not interfere with the postischemic cell death in CA1 region.
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Zhao P, Zhong M, Song X, Lu Y, Wang D, Gu Z, Chen L. [Expression of heparanase gene and the metastatic activity of lung cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2001; 4:88-90. [PMID: 21044460 DOI: 10.3779/j.issn.1009-3419.2001.02.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND To investigate the relationship between the expression of heparanase gene and the metastatic activity of lung cancer. METHODS Using the primers of heparanase gene, the expression of heparanase gene was detected by reverse transcriptase-polymerase chain reaction (RT-PCR) in two giant cell lung cancer cell lines with different metastatic activity and 56 primary tumor tissues of lung cancer and normal lung tissues. RESULTS Both cell lines and 80% (20/25) of primary tumor tissues of lung cancer with lymph node metastasis showed positive expression of heparanase gene, whereas 6.5% (2/31) primary tumor tissues of lung cancer without lymph node metastasis was positive and the normal lung tissues were all negative. The positive rate for expression of heparanase gene was significantly higher in the tumor tissues with lymph node metastasis than that without lymph node metastasis (P<0.001), higher in squamous cell carcinoma (47.2%, 17/36) than that in adenocarcinoma (20%, 4/20)(P<0.05), and remarkably higher in the poorly differentiated tumors (65%, 13/20) than that in the well-mediate differentiated tumors (22.2%, 8/36)(P<0.01). CONCLUSIONS The preliminary results suggest that the expression of heparanase gene may be one of the reliable markers for the metastastic activity gained by the lung cancer cells and could be used clinically in predicting the prognosis of patients.
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Gu Z, Jiang Q, Zhang G. c-Jun N-terminal kinase activation in hippocampal CA1 region was involved in ischemic injury. Neuroreport 2001; 12:897-900. [PMID: 11303755 DOI: 10.1097/00001756-200104170-00006] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
To clarify the role of c-Jun N-terminal kinase (NK) activation in brain ischemia, temporospatial alteration of active (diphosphorylated) JNK1/2 immunoreactivity in hippocampus after brain ischemia in rat was investigated. Western immunoblot study showed that JNK1/2 diphosphorylation level was increased biphasically in CA1 but not CA3/dentate gyrus (DG) after 10 min of ischemia. Cerebral ventricular infusion of JNK1/2 antisense oligonucleotides not only significantly decreased JNK1/2 protein expression and the activation level but also significantly decreased CA1 pyramidal cell death (demonstrated by cresyl violet staining) and DNA fragmentation (demonstrated by in situ end-labeling of DNA). These results suggest that JNK1/2 were selectively activated and involved in the selective cell death in hippocampal CA1 subfield after cerebral ischemia.
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Li Y, Pei Y, Zhang X, Gu Z, Zhou Z, Yuan W, Zhou J, Zhu J, Gao X. PEGylated PLGA nanoparticles as protein carriers: synthesis, preparation and biodistribution in rats. J Control Release 2001; 71:203-11. [PMID: 11274752 DOI: 10.1016/s0168-3659(01)00218-8] [Citation(s) in RCA: 356] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The aim of the present work was to assess the merits of PEGylated poly(lactic-co-glycolic acid) (PEG-PLGA) nanoparticles as protein and peptide drugs (PPD) carriers. PEG-PLGA copolymer, which could be used to prepare the stealth nanoparticles or long-circulating nanoparticles, was synthesized with methoxypolyethyleneglycol (MePEG) and PLGA. The structure of PEG-PLGA was confirmed with (1)H NMR and Fourier transform infrared (FTIR) spectrum, and molecular weight was determined by gel permeation chromatography (GPC). Bovine serum albumin (BSA), chosen as model protein, was encapsulated within the stealth nanoparticles with the double emulsion method. The particles were characterized in terms of size, zeta potential and in vitro release of the protein. The biological fate of the BSA-loaded nanoparticles following intravenous administration was determined over 24 h in rats. The experimental results showed that PEG-PLGA could be obtained by ring-opening polymerization of lactide and glycolide in the presence of MePEG. (1)H NMR and FTIR spectrum were consistent with the structure of PEG-PLGA copolymer. Molecular weight determined by GPC was 50800. The stealth nanoparticles loading BSA could be prepared by the double emulsion technique. The entrapment efficiency was 48.6%, particle size about 200 nm and zeta potential -16.1 mV. BSA release from the stealth nanoparticles showed an initial burst release and then sustained release. PEG-PLGA nanoparticles could extend half-life of BSA from 13.6 min of loaded in PLGA nanoparticles to 4.5 h and obviously change the protein biodistribution in rats compared with that of PLGA nanoparticles. Thus, PEG-PLGA nanoparticles could be an effective carrier for PPD delivery.
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Luo H, Shi Z, Li N, Gu Z, Zhuang Q. Investigation of the electrochemical and electrocatalytic behavior of single-wall carbon nanotube film on a glassy carbon electrode. Anal Chem 2001; 73:915-20. [PMID: 11289436 DOI: 10.1021/ac000967l] [Citation(s) in RCA: 509] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The electrochemical behavior of a film of single-wall carbon nanotubes (SWNTs) functionalized with carboxylic acid groups was studied extensively on a glassy carbon (GC) electrode. One stable couple corresponding to the redox of the carboxylic acid group, which was supported by XPS and IR experiments, was observed. The electrode process involved four electrons, while the rate-determining step was a one-electron reduction. The SWNT film-modified electrode showed favorable electrocatalytic behavior toward the oxidation of biomolecules such as dopamine, epinephrine, and ascorbic acid.
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Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Deslattes Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X. The sequence of the human genome. Science 2001; 291:1304-51. [PMID: 11181995 DOI: 10.1126/science.1058040] [Citation(s) in RCA: 7747] [Impact Index Per Article: 336.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.
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Abstract
The completion of the human genome will greatly accelerate the development of a new branch of science--evolutionary genomics. We can now directly address important questions about the evolutionary history of human genes and their regulatory sequences. Computational analyses of the human genome will reveal the number of genes and repetitive elements, the extent of gene duplication and compositional heterogeneity in the human genome, and the extent of domain shuffling and domain sharing among proteins. Here we present some first glimpses of these features.
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Jiang Q, Gu Z, Zhang G, Jing G. N-methyl-D-aspartate receptor activation results in regulation of extracellular signal-regulated kinases by protein kinases and phosphatases in glutamate-induced neuronal apototic-like death. Brain Res 2000; 887:285-92. [PMID: 11134617 DOI: 10.1016/s0006-8993(00)03003-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Extracellular signal-regulated kinases (ERK1/ERK2) have been shown transiently activated and involved in excitotoxicity. We searched for upstream molecules responsible for the regulation of glutamate-induced ERK1/ERK2 activation and ERK1/ERK2-mediated apototic-like death in cultured rat cortical neurons. ERK1/ERK2 activation (monitored by anti-active ERK1/ERK2 antibody) was almost completely prevented by blockage of NMDA receptor (NMDA-R) or elimination of extracellular Ca(2+), but not any other glutamate receptor or L-type voltage-gated Ca(2+) channel. It was prevented largely by inhibition of protein kinase C (PKC), protein-tyrosine kinases (PTK), respectively, but mildly by that of CaM kinase II. Combined inhibition of CaM kinase II (but not PTK) and PKC had an additive effect. Reversion of ERK1/ERK2 activation was largely prevented by inhibition of protein phosphatase (PP) 1 or protein tyrosine phosphatase (PTP). Combined inhibition of PP 1 and PTP had no additive effect. Glutamate-induced apoptotic-like death (determined by DAPI staining) was largely prevented by inhibition of NMDA-R, PKC, CaM kinase II, PTK and MEK1/MEK2 (ERK1/ERK2 kinase), respectively. Combined inhibition of CaM kinase II (but not PKC or PTK) and MEK1/MEK2 had an additive effect. Glutamate-induced apoptotic-like death was promoted by inhibition of PP1 and PTP, respectively. The above results suggested that in glutamate-induced cortical neurotoxicity ERK1/ERK2 activation be mainly mediated by NMDA-R. Subsequently, a pathway dependent on both PKC and PTK was mainly involved, which was also mainly responsible for ERK1/ERK2-mediated apoptotic-like death, and a CaM kinase II-dependent pathway was relatively mildly involved. Reversion of ERK1/ERK2 activation was mainly mediated by a pathway dependent on both PP1 and PTP, which might be involved in the restrain of glutamate-induced neurotoxicity.
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Gu Z, Wang H, Nekrutenko A, Li WH. Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence. Gene 2000; 259:81-8. [PMID: 11163965 DOI: 10.1016/s0378-1119(00)00434-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The densities of repetitive elements in the human genome were calculated in each GC content class using non-overlapping windows of 50kb. The density of Alu is two to three times higher in GC-rich regions than in AT-rich regions, while the opposite is true for LINE1. In contrast, LINE2 and other elements, such as DNA transposons, are more uniformly distributed in the genome. The number of Alus in the human genome was estimated to be 1.4 million, higher than previous estimates. About 40% of the autosomes and approximately 51% of the X and Y chromosomes are occupied by repetitive elements. In total, the human genome is estimated to contain more than 4 million repetitive elements. The GC contents (%) of repetitive elements and their flanking regions were also calculated. The GC contents of almost all kinds of repeats are positively correlated with the window GC contents, suggesting that a repetitive sequence is subject to the same mutation pressure as its surrounding regions, so it tends to have the same GC content as its surrounding regions. This observation supports the regional mutation hypothesis. The only two exceptions are AluYa and AluYb8, the two youngest Alu subfamilies. The GC content of AluYb8 is negatively correlated with that of its surrounding regions, while AluYa shows no correlation, suggesting different insertion patterns for these two young Alu subfamilies. This suggestion was supported by the fact that the average genetic distance between members of AluYb8 in each GC window class is positively correlated with the GC content of the window, but no correlation was found for AluYa. AluYa is more frequent in Y chromosome than in other chromosomes; the same is true for LTR retroviruses. This pattern might be correlated with the evolutionary history of Y chromosome.
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Richard N, Salomon H, Oliveira M, Rando R, Mansour T, Gu Z, Wainberg MA. Selection of resistance-conferring mutations in HIV-1 by the nucleoside reverse transcriptase inhibitors (+/-)dOTC and (+/-)dOTFC. Antivir Chem Chemother 2000; 11:359-65. [PMID: 11227993 DOI: 10.1177/095632020001100602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The patterns of resistance-conferring mutations that are selected in HIV-1 reverse transcriptase (RT) by the racemates of 2'-dideoxy-3'-oxa-4'-thiocytidine (+/-)dOTC and its fluorinated derivative (+/-)dOTFC were characterized. Genotypic and phenotypic analyses of HIV-1 clinical isolates and HXB2D variants selected with (+/-)dOTC and (+/-)dOTFC were performed in primary cells and in the MT-2 T cell line. HIV-1 variants selected with (+/-)dOTC or (+/-)dOTFC displayed fivefold decreased susceptibility to the respective compounds. A substitution of methionine to valine was identified at position 184 (M184V) in variants selected with (+/-)dOTC. In contrast, a mutation of lysine to arginine at position 65 (K65R) was found in variants selected with (+/-)dOTFC. These patterns of selected mutations differ from those seen with the individual enantiomers. Studies with mutated recombinant HXB2D-M184V and -K65R confirmed that these mutations are important for phenotypic resistance in MT-2 cells. Clinical isolates that display resistance to (-)2'-deoxy-3'-thiacytidine (3TC) also showed cross-resistance to (+/-)dOTC and (+/-)dOTFC. These studies demonstrate that similar genotypes may be selected by the dOTC and dOTFC compounds to those with the structurally related drug 3TC.
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Gu Z, Gilbert DJ, Valentine VA, Jenkins NA, Copeland NG, Zambetti GP. The p53-inducible gene EI24/PIG8 localizes to human chromosome 11q23 and the proximal region of mouse chromosome 9. CYTOGENETICS AND CELL GENETICS 2000; 89:230-3. [PMID: 10965130 DOI: 10.1159/000015620] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Activation of the p53 tumor suppressor leads to either a cell cycle arrest or to apoptosis and the factors that influence these responses are poorly understood. It is clear, however, that p53 regulates these processes by inducing a series of downstream target genes. One recently identified p53-target gene, EI24 (alias PIG8), induces apoptosis when ectopically expressed. To better understand the biological properties of EI24 and its potential relevance to disease, in particular cancer, we determined the chromosomal location and pattern of gene expression of EI24. EI24 is widely expressed in adult tissues and throughout mouse embryogenesis. The genomic locus of EI24 was mapped to the proximal region of mouse chromosome 9 and human chromosome 11q23-->q24, a region frequently altered in human cancers. These results suggest that EI24 may play an important role in the p53 tumor suppressor pathway.
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Peng P, Weng X, Gu Z. [Detection of the asymptomatic infection by human papillomavirus in pregnant women and neonates]. ZHONGHUA FU CHAN KE ZA ZHI 2000; 35:523-6. [PMID: 11775940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
OBJECTIVE To investigate the state of human papillomavirus (HPV) infection in similar average-aged pregnant women of different gestational periods, in the puerperium and neonates. METHODS Polymerase chain reaction (PCR) assay was employed to detect HPV-6, 11, 16 and 18 DNA in 30 pregnant women in the first trimester, 42 in the second and 31 in the third (who were followed up to their puerperium), and 30 non-pregnant women asking for intrauterine device in our out-patient clinic were taken as controls. Average age in the four groups showed no significant difference (P > 0.05). Samples from cervical, vaginal exfoliated cells, maternal peripheral blood and nasopharyngeal secretion of the newborns were examined respectively. RESULTS (1) In the first trimester, HPV-DNA was detected in the cervical, vaginal exfoliated cells of 5 cases and in the maternal peripheral blood of 7 cases. (2) In the second trimester, HPV-DNA was detected in the cervical, vaginal exfoliated cells of 12 cases and in the maternal peripheral blood of 11 cases. (3) In the third trimester, HPV-DNA was detected in the cervical, vaginal exfoliated cells of 23 cases and in the maternal peripheral blood of 18 cases. (4) In the puerperium, HPV-DNA was detected in samples of cervical, vaginal exfoliated cells of 8 cases and maternal peripheral blood of 7 cases. (5) In the control group, HPV-DNA was detected in the cervical, vaginal exfoliated cells of 8 cases and in the maternal peripheral blood of 6 cases. (6) Consecutive examinations were carried out in 31 pregnant women from the third trimester, through labor to 6 weeks of postpartum. HPV-DNA was positive in the cervical, vaginal samples of 17, 21 and 8 cases, respectively, according to the perinatal periods, and in the maternal peripheral blood of 14, 13 and 7 cases, respectively. The result through the above gestational stages was fluctuated in the cervical, vaginal samples of 6 cases and in the maternal peripheral blood of 7 cases. (7) Successive examinations in infants at time of birth, 48-72 h and 6 weeks after birth showed positive HPV-DNA in the nasopharyngeal secretion of 13, 6 cases and 1 case with respect to the examining periods. (8) The positive cases were mainly infected by HPV-16, 18. CONCLUSIONS (1) Infective rate of HPV is statistically significant in the third trimester, but no significant difference exists among the first trimester, the second trimester, the puerperium or the non-pregnancies. (2) Examining consecutively, the HPV positive rate is found to be decreased after delivery, the positive expression of HPV during the gestational periods exhibited fluctuation. (3) Infective rate of HPV in the neonatal nasopharyngeal specimens tends to decrease with time after delivery.
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Murugesan N, Gu Z, Stein PD, Spergel S, Mathur A, Leith L, Liu EC, Zhang R, Bird E, Waldron T, Marino A, Morrison RA, Webb ML, Moreland S, Barrish JC. Biphenylsulfonamide endothelin receptor antagonists. 2. Discovery of 4'-oxazolyl biphenylsulfonamides as a new class of potent, highly selective ET(A) antagonists. J Med Chem 2000; 43:3111-7. [PMID: 10956219 DOI: 10.1021/jm000105c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis and structure-activity relationship (SAR) studies of a series of 4'-oxazolyl-N-(3,4-dimethyl-5-isoxazolyl)[1, 1'-biphenyl]-2-sulfonamide derivatives as endothelin-A (ET(A)) receptor antagonists are described. The data reveal a remarkable improvement in potency and metabolic stability when the 4'-position of the biphenylsulfonamide is substituted with an oxazole ring. Additional 2'-substitution of an acylaminomethyl group further increased the binding activity and provided one of the first subnanomolar ET(A)-selective antagonists in the biphenylsulfonamide series (17, ET(A) K(i) = 0.2 nM). Among the compounds described, 3 (N-(3,4-dimethyl-5-isoxazolyl)-4'-(2-oxazolyl)[1, 1'-biphenyl]-2-sulfonamide; BMS-193884) had the optimum pharmacological profile and was therefore selected as a clinical candidate for studies in congestive heart failure.
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Xie M, Lu Q, Zhu L, Gu Z. [Comparison of the effects of xianyu tablet and its component on electrophoretic mobility of serum LDL and expression of ET-1 mRNA and iNOS mRNA of vessel wall in atherosclerotic rabbits]. ZHONG YAO CAI = ZHONGYAOCAI = JOURNAL OF CHINESE MEDICINAL MATERIALS 2000; 23:474-6. [PMID: 12575163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
Xiaoyu tablet, a compound preparation of Chinese herbal medicines, consists of Radix Salviae Miltiorrhizae(SM) and Fructus Crataegi(FC) extracts. To determine whether the proved recipe was reasonable, the effects of Xiaoyu tablet and its component on electrophoretic mobility of serum LDL and expression of ET-1 mRNA and iNOS mRNA of vessel wall in atherosclerotic rabbits were observed. The results indicated that inhibition of expression iNOS mRNA in vessel wall by Xiaoyu tablet was the same as its single extract of SM or FC, but Xiaoyu talbet was superior to SM or FC extract in reduction of electrophoretic mobility of serum LDL and inhibition of ET-1 mRNA expression in vessel wall. These results suggested that there was obvious synergism on prevention and treatment of atherosclerosis when both of the Chinese herbal medicines were simultaneously used.
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