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Jiang H, Hou L, Qiao H, Pan S, Zhou B, Liu C, Sun X. Administration of tolerogenic dendritic cells induced by interleukin-10 prolongs rat splenic allograft survival. Transplant Proc 2005; 36:3255-9. [PMID: 15686741 DOI: 10.1016/j.transproceed.2004.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The risk and intensity in splenic graft rejection are greater than in other types of transplants, because the spleen is the largest peripheral lymphoid organ and the immunosuppressive drugs administered can cause splenic dysfunction. In this study, we demonstrate that intravenous injection of interleukin-10-treated donor-type dendritic cells into recipient rats prolongs the survival of splenic allografts. Although the mechanisms are not clear, the induction of tolerance to grafted spleens seems to rely mainly on blockage of expression of the costimulatory molecule CD86, by interleukin-10, leading to enhanced apoptosis of allospecific T cells by immature and tolerogenic dendritic cells. Administration of tolerogenic cells induced by interleukin-10 may thus represent a useful approach for protection of splenic allografts. Further study is required to investigate the operative pathways and to optimize the strategy targeting dendritic cells to induce tolerance in splenic allografts.
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Johnson KC, Conlon MSC, Pan S, Mao Y. 225: Long Term Smoking and Smoking Before the First Full-Term Pregnancy: Critical in Breast Cancer Risk? Am J Epidemiol 2005. [DOI: 10.1093/aje/161.supplement_1.s57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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153
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Chang IF, Szick-Miranda K, Pan S, Bailey-Serres J. Proteomic characterization of evolutionarily conserved and variable proteins of Arabidopsis cytosolic ribosomes. PLANT PHYSIOLOGY 2005; 137:848-62. [PMID: 15734919 PMCID: PMC1065386 DOI: 10.1104/pp.104.053637] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Revised: 11/16/2004] [Accepted: 11/23/2004] [Indexed: 05/18/2023]
Abstract
Analysis of 80S ribosomes of Arabidopsis (Arabidopsis thaliana) by use of high-speed centrifugation, sucrose gradient fractionation, one- and two-dimensional gel electrophoresis, liquid chromatography purification, and mass spectrometry (matrix-assisted laser desorption/ionization time-of-flight and electrospray ionization) identified 74 ribosomal proteins (r-proteins), of which 73 are orthologs of rat r-proteins and one is the plant-specific r-protein P3. Thirty small (40S) subunit and 44 large (60S) subunit r-proteins were confirmed. In addition, an ortholog of the mammalian receptor for activated protein kinase C, a tryptophan-aspartic acid-domain repeat protein, was found to be associated with the 40S subunit and polysomes. Based on the prediction that each r-protein is present in a single copy, the mass of the Arabidopsis 80S ribosome was estimated as 3.2 MD (1,159 kD 40S; 2,010 kD 60S), with the 4 single-copy rRNAs (18S, 26S, 5.8S, and 5S) contributing 53% of the mass. Despite strong evolutionary conservation in r-protein composition among eukaryotes, Arabidopsis 80S ribosomes are variable in composition due to distinctions in mass or charge of approximately 25% of the r-proteins. This is a consequence of amino acid sequence divergence within r-protein gene families and posttranslational modification of individual r-proteins (e.g. amino-terminal acetylation, phosphorylation). For example, distinct types of r-proteins S15a and P2 accumulate in ribosomes due to evolutionarily divergence of r-protein genes. Ribosome variation is also due to amino acid sequence divergence and differential phosphorylation of the carboxy terminus of r-protein S6. The role of ribosome heterogeneity in differential mRNA translation is discussed.
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Rojo E, Martín R, Carter C, Zouhar J, Pan S, Plotnikova J, Jin H, Paneque M, Sánchez-Serrano JJ, Baker B, Ausubel FM, Raikhel NV. VPEgamma exhibits a caspase-like activity that contributes to defense against pathogens. Curr Biol 2005; 14:1897-906. [PMID: 15530390 DOI: 10.1016/j.cub.2004.09.056] [Citation(s) in RCA: 212] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Revised: 09/10/2004] [Accepted: 09/10/2004] [Indexed: 12/22/2022]
Abstract
BACKGROUND Caspases are a family of aspartate-specific cysteine proteases that play an essential role in initiating and executing programmed cell death (PCD) in metazoans. Caspase-like activities have been shown to be required for the initiation of PCD in plants, but the genes encoding those activities have not been identified. VPEgamma, a cysteine protease, is induced during senescence, a form of PCD in plants, and is localized in precursor protease vesicles and vacuoles, compartments associated with PCD processes in plants. RESULTS We show that VPEgamma binds in vivo to a general caspase inhibitor and to caspase-1-specific inhibitors, which block the activity of VPEgamma. A cysteine protease inhibitor, cystatin, accumulates to 20-fold higher levels in vpegamma mutants. Homologs of cystatin are known to suppress hypersensitive cell death in plant and animal systems. We also report that infection with an avirulent strain of Pseudomonas syringae results in an increase of caspase-1 activity, and this increase is partially suppressed in vpegamma mutants. Plants overexpressing VPEgamma exhibit a greater amount of ion leakage during infection with P. syringae, suggesting that VPEgamma may regulate cell death progression during plant-pathogen interaction. VPEgamma expression is induced after infection with P. syringae, Botrytis cinerea, and turnip mosaic virus, and knockout of VPEgamma results in increased susceptibility to these pathogens. CONCLUSIONS We conclude that VPEgamma is a caspase-like enzyme that has been recruited in plants to regulate vacuole-mediated cell dismantling during cell death, a process that has significant influence in the outcome of a diverse set of plant-pathogen interactions.
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Luo GS, Liu JG, Lu YC, Pan S, Wang JD. Two‐Phase Electro‐Electrodialysis with an Emulsion as Anolyte. SEP SCI TECHNOL 2005. [DOI: 10.1081/ss-120030482] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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156
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Carter C, Pan S, Zouhar J, Avila EL, Girke T, Raikhel NV. The vegetative vacuole proteome of Arabidopsis thaliana reveals predicted and unexpected proteins. THE PLANT CELL 2004; 16:3285-303. [PMID: 15539469 PMCID: PMC535874 DOI: 10.1105/tpc.104.027078] [Citation(s) in RCA: 445] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Vacuoles play central roles in plant growth, development, and stress responses. To better understand vacuole function and biogenesis we have characterized the vegetative vacuolar proteome from Arabidopsis thaliana. Vacuoles were isolated from protoplasts derived from rosette leaf tissue. Total purified vacuolar proteins were then subjected either to multidimensional liquid chromatography/tandem mass spectrometry or to one-dimensional SDS-PAGE coupled with nano-liquid chromatography/tandem mass spectrometry (nano-LC MS/MS). To ensure maximum coverage of the proteome, a tonoplast-enriched fraction was also analyzed separately by one-dimensional SDS-PAGE followed by nano-LC MS/MS. Cumulatively, 402 proteins were identified. The sensitivity of our analyses is indicated by the high coverage of membrane proteins. Eleven of the twelve known vacuolar-ATPase subunits were identified. Here, we present evidence of four tonoplast-localized soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), representing each of the four groups of SNARE proteins necessary for membrane fusion. In addition, potential cargo of the N- and C-terminal propeptide sorting pathways, association of the vacuole with the cytoskeleton, and the vacuolar localization of 89 proteins of unknown function are identified. A detailed analysis of these proteins and their roles in vacuole function and biogenesis is presented.
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Gu S, Liu Z, Pan S, Jiang Z, Lu H, Amit O, Bradbury EM, Hu CAA, Chen X. Global investigation of p53-induced apoptosis through quantitative proteomic profiling using comparative amino acid-coded tagging. Mol Cell Proteomics 2004; 3:998-1008. [PMID: 15284338 DOI: 10.1074/mcp.m400033-mcp200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
p53-induced apoptosis plays a pivotal role in the suppression of tumorigenesis, and mutations in p53 have been found in more than 50% of human tumors. By comparing the proteome of a human colorectal cancer cell transfected with inducible p53 (DLD-1.p53) with that of the control DLD-1 cell line using amino acid-coded mass tagging (AACT)-assisted mass spectrometry, we have broadly identified proteins that are upregulated at the execution stage of the p53-mediated apoptosis. In cell culturing, the deuterium-labeled (heavy) amino acids were incorporated into the proteome of the induced DLD-1.p53 cells, whereas the DLD-1.vector cells were grown in the unlabeled medium. In high-throughput LC-ESI-MS/MS analyses, the AACT-containing peptides were paired with their unlabeled counterparts, and their relative spectral intensities, reflecting the differential protein expression, were quantified. In addition, our novel AACT-MS method utilized a number of different heavy amino acids as internal markers that significantly increased the peptide sequence coverage for both quantitation and identification purposes. As a result, we were able to identify differentially regulated protein isozymes that would be difficult to distinguish by ICAT-MS methods and to obtain a large dataset of the proteins with altered expression in the late stage of p53-induced apoptosis. The regulated proteins we identified are associated with several distinct functional categories: cell cycle arrest and p53 binding, protein chaperoning, plasma membrane dynamics, stress response, antioxidant enzymes, and anaerobic glycolysis. This result suggests that the p53-induced apoptosis involves the systematic activation of multiple pathways that are glycolysis-relevant, energy-dependent, oxidative stress-mediated, and possibly mediated through interorganelle crosstalks.
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Czarnecka-Verner E, Pan S, Salem T, Gurley WB. Plant class B HSFs inhibit transcription and exhibit affinity for TFIIB and TBP. PLANT MOLECULAR BIOLOGY 2004; 56:57-75. [PMID: 15604728 DOI: 10.1007/s11103-004-2307-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant heat shock transcription factors (HSFs) are capable of transcriptional activation (class A HSFs) or both, activation and repression (class B HSFs). However, the details of mechanism still remain unclear. It is likely, that the regulation occurs through interactions of HSFs with general transcription factors (GTFs), as has been described for numerous other transcription factors. Here, we show that class A HSFs may activate transcription through direct contacts with TATA-binding protein (TBP). Class A HSFs can also interact weakly with TFIIB. Conversely, class B HSFs inhibit promoter activity through an active mechanism of repression that involves the C-terminal regulatory region (CTR) of class B HSFs. Deletion analysis revealed two sites in the CTR of soybean GmHSFB1 potentially involved in protein-protein interactions with GTFs: one is the repressor domain (RD) located in the N-terminal half of the CTR, and the other is a TFIIB binding domain (BD) that shows affinity for TFIIB and is located C-terminally from the RD. A Gal4 DNA binding domain-RD fusion repressed activity of LexA-activators, while Gal4-BD proteins synergistically activated strong and weak transcriptional activators. In vitro binding studies were consistent with this pattern of activity since the BD region alone interacted strongly with TFIIB, and the presence of RD had an inhibitory effect on TFIIB binding and transcriptional activation.
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Jiang H, Liu C, Xu J, Sun B, Pan S, Qiao H, Luo L, Sun X. Gene transfer of interleukin-4 delays acute rejection of splenic allografts in rats. Transplant Proc 2004; 36:1600-3. [PMID: 15251393 DOI: 10.1016/j.transproceed.2004.05.041] [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: 10/26/2022]
Abstract
Spleen transplantation is the treatment of choice for some diseases, such as hemophilia A. However, the risk and intensity of rejection after spleen transplantation is greater and more difficult to control than other types of transplant. In the present study, we demonstrated that perfusion of IL-4 expression plasmids into donor spleens pretransplantation led to overexpression of IL-4 and downregulation of IFN-gamma in situ, associated with delayed acute rejection of the allograft. Gene transfer of IL-4 may represent a potential therapeutic approach to induce tolerance to splenic allografts.
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Luo M, Cohen CR, Narayansingh MJ, Pan S, McKinnon L, Brunham RC, Plummer FA. Identification of a novel HLA-DQA1 null allele, DQA1*0403N, from an East African woman. ACTA ACUST UNITED AC 2004; 63:609-11. [PMID: 15140045 DOI: 10.1111/j.0001-2815.2004.00231.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We report a novel DQA1 allele (DQA1*0403N) identified during sequence-based HLA-DQA1 typing of a Kenyan population. The new allele is identical to DQA1*0401 at exon 2 except for a single-nucleotide substitution at codon 53, changing it from lysine to a stop codon (CAA-->TAA). The substitution at codon 53 was confirmed by sequencing two separate polymerase chain reaction products and by sequencing multiple clones obtained following TOPO-TA cloning. The resulting stop codon at position of codon 53 in exon 2 is predicted to produce a non-functional DQA1 alpha-chain. The new allele has been named by the WHO nomenclature committee as DQA1*0403N. This is the first report of a null allele detected in the DQA1 gene.
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Pan S, Tay JH, He YX, Tay STL. The effect of hydraulic retention time on the stability of aerobically grown microbial granules. Lett Appl Microbiol 2004; 38:158-63. [PMID: 14746549 DOI: 10.1111/j.1472-765x.2003.01479.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS The aim of this study is to evaluate the effect of hydraulic retention time (HRT) on the development of aerobically grown microbial granules. METHODS AND RESULTS Five column-shaped sequential aerobic sludge blanket reactors (SASBRs) were seeded with aerobically grown microbial granules and operated in a cyclic mode at different HRTs. At the shortest HRT of 1 h, the strong hydraulic pressure triggered biomass washout and led to reactor failure. At the longest HRT of 24 h, which represented the weakest hydraulic selection in this study, aerobic granules were gradually substituted by bioflocs because of the lower frequency of volumetric exchange. Within the optimum range of HRTs from 2 to 12 h, however, aerobic granules became stabilized in the presence of adequate hydraulic selection in the reactors, with good mixed liquor volatile suspended solids (MLVSS) retention, high volumetric chemical oxygen demand (COD) removal, low sludge volume index (SVI) values, good effluent quality, low sludge production rate, stronger and more compact structures, high cell hydrophobicity and high ratios of extracellular polysaccharides (PS) to extracellular proteins (PN). CONCLUSIONS HRTs between 2 and 12 h provided the hydraulic selection pressures favourable for the formation and maintenance of stable aerobic granules with good settleability and activity. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first systematic study on the effect of HRT on heterotrophic aerobic granules. The results of the investigation are useful in understanding how aerobic granules can be applied for wastewater treatment.
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Tay JH, Tay STL, Ivanov V, Pan S, Jiang HL, Liu QS. Biomass and porosity profiles in microbial granules used for aerobic wastewater treatment. Lett Appl Microbiol 2003; 36:297-301. [PMID: 12680942 DOI: 10.1046/j.1472-765x.2003.01312.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To obtain biomass and porosity profiles for aerobically grown granules of different diameters and to determine a suitable range of granule diameters for application in wastewater treatment. METHODS AND RESULTS Microbial granules were cultivated in an aerobic granulated sludge reactor with model wastewaters containing acetate, or ethanol plus acetate, or glucose as the main carbon source. Granules were formed by retaining microbial aggregates using a settling time of 2 min. Sampled granules had diameters ranging from 0.45 to 3 mm. Microbial biomass in the granules was detected with the nucleic acid stain SYTO 9 and confocal laser scanning microscopy. The thickness of the microbial biomass layer was proportional to the granule diameter, and had a maximum value of 0.8 mm. The thickness of the microbial biomass layer correlated with the penetration depth of 0.1 microm fluorescent beads into the granule. CONCLUSIONS The microbial biomass and porosity studies suggest that aerobically grown microbial granules should have diameters less than a critical diameter of 0.5 mm, if deployed for wastewater treatment applications. This critical diameter is based on the assumption that whole granules should have a porous biomass-filled matrix. SIGNIFICANCE AND IMPACT OF THE STUDY This work could contribute to the development of aerobic granulation technology for effective biological wastewater treatment.
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Pan S, Gu S, Bradbury EM, Chen X. Single peptide-based protein identification in human proteome through MALDI-TOF MS coupled with amino acids coded mass tagging. Anal Chem 2003; 75:1316-24. [PMID: 12659191 DOI: 10.1021/ac020482s] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Identification of proteins with low sequence coverage using mass spectrometry (MS) requires tandem MS/MS peptide sequencing. It is very challenging to obtain a complete or to interpret an incomplete tandem MS/MS spectrum from fragmentation of a weak peptide ion signal for sequence assignment. Here, we have developed an effective and high-throughput MALDI-TOF-based method for the identification of membrane and other low-abundance proteins with a simple, one-dimensional separation step. In this approach, several stable isotope-labeled amino acid precursors were selected to mass-tag, in parallel, the human proteome of human skin fibroblast cells in a residue-specific manner during in vivo cell culturing. These labeled residues can be recognized by their characteristic isotope patterns in MALDI-TOF MS spectra. The isotope pattern of particular peptides induced by the different labeled precursors provides information about their amino acid compositions. The specificity of peptide signals in a peptide mass mapping is thus greatly enhanced, resolving a high degree of mass degeneracy of proteolytic peptides derived from the complex human proteome. Further, false positive matches in database searching can be eliminated. More importantly, proteins can be accurately identified through a single peptide with its m/z value and partial amino acid composition. With the increased solubility of hydrophobic proteins in SDS, we have demonstrated that our approach is effective for the identification of membrane and low-abundant proteins with low sequence coverage and weak signal intensity, which are often difficult for obtaining informative fragment patterns in tandem MS/MS peptide sequencing analysis.
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Gu S, Pan S, Bradbury EM, Chen X. Precise peptide sequencing and protein quantification in the human proteome through in vivo lysine-specific mass tagging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:1-7. [PMID: 12504328 DOI: 10.1016/s1044-0305(02)00799-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Proteomics studies demand new scalable and automatable MS-based methods with higher specificity and accuracy. Here we describe an accurate and efficient method for both precise quantification and comprehensive de novo identification of peptide sequences in complex mixtures. The unique feature of this method is based on the incorporation of deuterium-labeled (heavy) lysines into proteins through in vivo cell culturing, which introduces specific mass tags at the carboxyl termini of proteolytic peptides when cleaved by certain proteases. The mass shift between the unlabeled and the deuterated lysine (lys-d4) assigns a mass signature to all lysine-containing peptides in any pool of proteolytic peptides. Lys-d4 tags can also serve as internal markers in MS/MS fragment spectra when they are buried in some peptide sequences due to miscleavages. This signal specificity circumvents the mass accuracy limitations in determining particular amino acid residues for de novo sequencing. Further, this strategy of lysine-specific tagging was successfully implemented to measure the differential protein expression of human skin fibroblast cells in response to heat shock.
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Tay JH, Pan S, Tay STL, Ivanov V, Liu Y. The effect of organic loading rate on the aerobic granulation: the development of shear force theory. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2003; 47:235-240. [PMID: 12906295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The effect of organic loading rate (OLR) on aerobic granulation was studied by adopting three column-shaped, sequential aerobic sludge blanket reactors (SASBR). The reactors had been fed with laboratory prepared, synthetic dextrose-nutrient broth substrate. Experimental results showed clearly that the formation, characteristics and stability of aerobic granules had a close relationship with the strength of OLR applied. Aerobic granules appeared firstly under the OLR of 4 kg COD x (m3 x day)(-1). The system stabilization was demonstrated by its little-changed amount and morphology of granules. The characteristics of the stabilized granules were: 5.4 mm in mean diameter, 1.29 in roundness, 118 mg O2 x (mg VSS x hr)(-1) in SPOUR. The respective biomass SVI was 50 mL x (g MLVSS)(-1) and the averaged COD removal rate was 95%. Under the OLR of 8 kg COD x (m3 x day)(-1), granules appeared two days later than those for 4 kg COD x (m3 x day)(-1) and they always coexisted with flocs. The formed granule bed was not as compact as that under 4 kg COD x (m3 x day)(-1). There were no granules formed under the OLR of 1 kg COD x (m3 x day)(-1). Instead, flocs with rather loose structure dominated reactor mixed-liquor. The respective SVI's were 65 and 138 mL x (g MLVSS)(-1) under OLR of 8 and 1 kg COD x (m3 x day)(-1). It was proposed that the growth and maintenance of aerobic granules follow the shear force balance theory. Under the OLR of 4 kg COD x (m3 x day)(-1), a balance was reached between the aeration shear force and organic loading rate. Under this favored condition aerobic granules formed quickly and, became stabilized with the experimental parameters remained unchanged.
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Gu S, Pan S, Bradbury EM, Chen X. Use of deuterium-labeled lysine for efficient protein identification and peptide de novo sequencing. Anal Chem 2002; 74:5774-85. [PMID: 12463361 DOI: 10.1021/ac0204350] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we describe a method for protein identification and de novo peptide sequencing. Through in vivo cell culturing, the deuterium-labeled lysine residue (Lys-d4) introduces a 4-Da mass tag at the carboxyl terminus of proteolytic peptides when cleaved by certain proteases. The 4-Da mass difference between the unlabeled and the deuterated lysine assigns a mass signature to all lysine-containing peptides in any pool of proteolytic peptides for protein identification directly through peptide mass mapping. Furthermore, it was used to distinguish between N- and C-terminal fragments for accurate assignments of daughter ions in tandem MS/MS spectra for sequence assignment. This technique simplifies the labeling scheme and the interpretation of the MS/MS spectra by assigning different series of fragment ions correctly and easily and is very useful in de novo peptide sequencing. We have also successfully implemented this approach to the analysis of protein mixtures derived from the human proteome.
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Abstract
AIMS To determine the optimal size of aerobically grown granules for wastewater treatment by measuring specific layers within the granules. METHODS AND RESULTS A variety of biological layers were detected by oligonucleotide probes, specific fluorochromes, and fluorescent microspheres. The channels in the granule matrix penetrated to depths of 900 microm. A layer of obligate anaerobic bacteria was detected at a depth of 800 microm below the granule surface. Dead cells were also observed in the granule interior. CONCLUSIONS Aerobically grown granules contained layers of aerobic and anaerobic micro-organisms. SIGNIFICANCE AND IMPACT OF THE STUDY The optimal diameter of the aerobic granule is less than 1600 microm. This is twice the distance from the granule surface to the anaerobic layer. This approach can be used to optimize the thickness of other microbial aggregates such as flocs, colonies and biofilms.
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Abstract
Relatively little attention has been paid to the aetiology of male breast cancer and the current understanding of female breast cancer, primarily related to reproductive events, cannot be readily transferred to understanding the cancer in males. However, since male breast cancer occurs in the absence of factors related to childbearing and menstruation, its aetiology may provide special insights into the causes of breast cancer in women. We examined lifestyle risk factors for male breast cancer as part of a Canadian, multi-site, population-based, case-control study. Eighty-one newly diagnosed, histologically confirmed cases and 1905 male controls aged 42-74 were analysed using unconditional logistic regression. Increased risks were found for men with a mother or sister with breast cancer (adjusted odds ratio (OR) 3.65, 95% confidence interval (95% CI) 1.62-8.19). Higher physical activity levels (moderate, and strenuous recreational plus occupational) were associated with a decreased risk of male breast cancer (highest quartile, adjusted OR 0.48, 95% CI 0.26-0.91). Similarly, higher risks were associated with higher weight 2 years before interview (2.19, 95% CI 1.08-4.43), maximum weight (OR 2.66) and higher body mass index (OR 1.60). Higher vegetable consumption and coffee consumption were associated with decreased risk, whereas higher beta-carotene, vitamin E and calcium supplementation were associated with statistically significant increased risk. The small number of cases and multiple comparisons preclude strong conclusions, but our study is consistent with studies suggesting obesity and family history increase risk, and physical activity decreases risk of breast cancer.
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Luo M, Embree J, Ramdahin S, Ndinya-Achola J, Njenga S, Bwayo JB, Pan S, Mao X, Cheang M, Stuart T, Brunham RC, Plummer FA. HLA-A and HLA-B in Kenya, Africa: allele frequencies and identification of HLA-B*1567 and HLA-B*4426. TISSUE ANTIGENS 2002; 59:370-80. [PMID: 12144620 DOI: 10.1034/j.1399-0039.2002.590503.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
HLA-A and HLA-B alleles of a population from Kenya, Africa were examined by sequencing exon 2 and exon 3 DNA and typing using a Taxonomy-based Sequence-analysis (TBSA) method. Extensive diversities were observed at both HLA-A and HLA-B loci in this population. Forty-one HLA-A alleles were identified from 159 unrelated individuals. The most frequently observed alleles were A*6802 (11.64%), A*02011/09 (9.75%), A*7401/02 (9.43%), A*3001 (7.86%), A*3002 (7.23%) and A*3601 (6.6%). Forty-nine HLA-B alleles were identified in 161 unrelated individuals, including two novel alleles, B*1567 and B*4426. The most frequently observed HLA-B alleles were B*5301 (9.01%), B*5801 (8.38%), B*4201 (7.76%), B*1503 (7.14%), B*1801 (6.21%), and B*5802 (5.90%). The most frequently observed HLA-A-B haplotypes were A*3601-B*5301 (3.55%) and A*3001-B*4201 (3.19%), followed by A*7401/02-B*5801 (2.84%), A*7401/02-B*5802 (2.84%) and A*02011/09-B*1503 (2.13%). Linkage disequilibrium and chi2 analysis showed the association of these HLA-A-B haplotypes at the antigen level to be significant. The frequencies of HLA-A and HLA-B alleles from the Kenyan population were compared with that of a population from Cameroon. The difference in allele and haplotype frequency distributions partly reflected the different ethnic composition of these two African populations.
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Zhu H, Hunter TC, Pan S, Yau PM, Bradbury EM, Chen X. Residue-specific mass signatures for the efficient detection of protein modifications by mass spectrometry. Anal Chem 2002; 74:1687-94. [PMID: 12033261 DOI: 10.1021/ac010853p] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Currently available mass spectrometric (MS) techniques lack specificity in identifying protein modifications because molecular mass is the only parameter used to characterize these changes. Consequently, the suspected modified peptides are subjected to tandem MS/MS sequencing that may demand more time and sample. We report the use of stable isotope-enriched amino acids as residue-specific "mass signatures" for the rapid and sensitive detection of protein modifications directly from the peptide mass map (PMM) without enrichment of the modified peptides. These mass signatures are easily recognized through their characteristic spectral patterns and provide fingerprints for peptides containing the same content of specific amino acid residue(s) in a PMM. Without the need for tandem MS/MS sequencing, a peptide and its modified form(s) can readily be identified through their identical fingerprints, regardless of the nature of modifications. In this report, we demonstrate this strategy for the detection of methionine oxidation and protein phosphorylation. More interestingly, the phosphorylation of a histone protein, H2A.X, obtained from human skin fibroblast cells, was effectively identified in response to low-dose radiation. In general, this strategy of residue-specific mass tagging should be applicable to other posttranslational modifications.
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Zhu H, Pan S, Gu S, Bradbury EM, Chen X. Amino acid residue specific stable isotope labeling for quantitative proteomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2002; 16:2115-2123. [PMID: 12415544 DOI: 10.1002/rcm.831] [Citation(s) in RCA: 160] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Various stable isotope labeling (SIL) techniques have recently emerged to improve the efficiency and accuracy of protein quantitation by mass spectrometry (MS). We have developed a mass-tagging strategy to incorporate stable isotope tagged amino acids into cellular proteins in a residue-specific manner during cell growth. In this study, we further extend this residue-specific SIL approach to the accurate quantitation of protein abundances in different cell populations. For proteins whose expression levels are the same in cells grown in the normal and labeled media, the relative areas of the normal (light) and labeled (heavy) isotopic peaks are linearly correlated with the cells mixing ratios. This approach was first used to determine the effect of the zinc-responsive transcription factor Zap1 on the yeast proteome. Ten protein spots from a PAGE gel were chosen randomly and their differential protein expression levels in wild-type and zap1delta cells were readily determined by the isotopic ratio. Methionine synthase (Met6) was identified to be up-regulated more than four times in the zap1delta mutant strain whereas the expression level of other nine proteins remained unchanged. Further, we applied this strategy to study the cellular response to radiation in human skin fibroblast cells. Analyzing one protein band randomly selected from SDS-PAGE, the expression level of a novel protein was found to increase two-fold in response to radiation whereas the expression level of a control protein remained unchanged. This strategy is generally applicable using any particular type of amino acid as the labeling precursors for accurate quantitation of protein relative abundances.
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172
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Ji S, Chen H, Wang H, Yan H, Pan S. [Administration of leukemic granulocyte colony-stimulating factor to donors: the changes in donor bone marrow cell composition and the transplantation outcome]. ZHONGHUA NEI KE ZA ZHI 2001; 40:834-7. [PMID: 16206675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
OBJECTIVE To investigate the change of bone marrow cell composition the effect of graft on hemopoietic reconstitution and the incidence of acute graft-versus-host disease (aGVHD) with granulocyte colony-stimulating factor G-CSF administration to donors before marrow harvesting. METHODS Twenty-four patients with myeloid leukemia underwent allogeneic bone marrow transplantation. The donors of twelve patients (study group) were given G-CSF 250 microg/d for seven days prior to harvesting. The marrow cell composition, the outcome of subsequent engraftment and the occurrence of aGVHD were compared with those in twelve patients without G-CSF (control group). RESULTS The bone marrow stimulated by G-CSF yielded higher number of nucleated cells, CD34+ cells, CFU-GM and CFU-MK (P < 0.01). The number of T lymphocyte subsets in the graft stimulated with G-CSF was different from that in the control group. The number of CD4+ cells was decreased and that of CD8+ increased. The CD4+/CD8+ ratio was reduced markedly (P < 0.01). The change of CD34+, CD4+, CD8+ percentage and CFU-GM, CFU-MK proliferation in donor bone marrow with and without G-CSF was compared. The same characteristic change as above graft was observed. Hemopoietic reconstitution in the study group after allo-BMT was accelerated. In the study group the days of granulocyte count exceeding 0.5 x 10(9)/L and platelet count exceeding 20 x 10(9)/L were 16 days (range 11 - 23 days) and 17 days (range 14 - 25 days) (in the control group 20.5 day, range 14 - 29 days and 23 days, range 17 - 32 days P < 0.05). Grade II - IV aGVHD did not occur in patients of the study group but in 3 patients of the control group. CONCLUSION The bone marrow harvested from donor with G-CSF stimulation can accelerate hemopoietic recovery and decrease the incidence of severe aGVHD. The accelerated hematopoietic recovery is associated with increased number of CD34+, CFU-GM and CFU-MK in the graft.
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Chang CC, Chen SH, Pan S, Fang CL, Lien GS. Endoscopic mucosal resection with a cap-fitted endoscope for early gastric carcinoma with focal submucosal invasion in a patient with decompensated liver cirrhosis. J Formos Med Assoc 2001; 100:841-3. [PMID: 11802527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Prognosis for patients with early gastric cancer who undergo gastric resection is far better than that for patients with advanced disease. However, patients with advanced liver cirrhosis may not be suitable for general anesthesia and major surgery. We used a less invasive endoscopic mucosal resection (EMR) with a cap-fitted endoscope to resect an early gastric cancer in a 58-year-old male with decompensated liver cirrhosis. Although postoperative pathology revealed that the tumor had focal invasion to the submucosa, the patient had an uneventful course and was well during 4 years' follow-up. This method may be effective for the treatment of early gastric cancer with focal submucosal invasion when patients are not suitable for major surgery.
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Guo P, Xu L, Pan S, Brekken RA, Yang ST, Whitaker GB, Nagane M, Thorpe PE, Rosenbaum JS, Su Huang HJ, Cavenee WK, Cheng SY. Vascular endothelial growth factor isoforms display distinct activities in promoting tumor angiogenesis at different anatomic sites. Cancer Res 2001; 61:8569-77. [PMID: 11731444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The gene for the major angiogenic factor, vascular endothelial growth factor (VEGF), encodes several spliced isoforms. We reported previously that overexpression of two VEGF isoforms, VEGF(121) and VEGF(165), by human glioma U87 MG cells induced tumor-associated intracerebral hemorrhage, whereas expression of a third form, VEGF(189), did not cause vessel rupture. Here, we test whether these VEGF isoforms have distinct activities for enhancing vascularization and growth of gliomas in mice. U87 MG cells that overexpressed VEGF(165) or VEGF(189) grew more rapidly than the parental cells in both s.c. and intracranial (i.c.) locations. However, cells that overexpressed VEGF(121) only showed enhancement of i.c. tumor growth but had a minimal effect on s.c. glioma progression. At both anatomical sties, VEGF(165) and VEGF(189) strongly augmented neovascularization, whereas VEGF(121) only increased vessel density in brain tumors. In each type of glioma, expression of VEGF receptors -1 and -2 largely phenocopied the tumor vasculature, because increased VEGF/VEGF receptor-activated microvessel densities were strongly correlated with the angiogenicity and tumorigenicity elicited by the VEGF isoforms at both anatomical sites. One notable difference between the sites was the expression of vitronectin, a prototypic ligand of alpha(v)beta(3) and alpha(v)beta(5) integrins, detected in i.c. but not in s.c., gliomas. Endothelial cell migration stimulated by VEGF(121) was potentiated by vitronectin to a greater extent than that stimulated by VEGF(165). This data demonstrates that VEGF isoforms have distinct activities at different anatomical sites and suggest that the microenvironment of different tissues affects the function of VEGF isoforms.
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175
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Lu B, Zhou L, Pan S. [Clinical and pathological characteristics of heroin spongiform leukoencephalopathy in China]. ZHONGHUA NEI KE ZA ZHI 2001; 40:753-6. [PMID: 11930682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
OBJECTIVE To observe the clinical, image and pathological characteristics of Heroin Spongiform Leukoencephalopathy(HSLE). METHODS Clinical, CT and MRI analysis of 28 cases, brain autopsies of 2 cases and brain biopsies of 8 cases with HE, Loyez and Congo Red staining and observation through electron microscope. RESULTS The clinic, image and pathologic characteristics of HSLE: (1) the history of inhalation of heated heroin vapor; (2) among 28 cases with HSLE, recurrence of HSLE was found in 17 cases during the abstinence, in 8 cases 1-2 month after abstinence, in 2 cases 4 month after abstinence and in 1 case after inhaling large amount of heroin; (3) the majority of cases were described with the acute onset characterized by cerebellar signs; (4) pyramidal tract lesion was frequently involved, but sensory system usually remained normal; (5) CSF test was normal; (6) CT and MRI revealed extensive symmetric white matter lesions in cerebra and cerebellum; (7) spongiform vacuoles degeneration of white matter was the main morphological change. CONCLUSIONS Spongiform leukoencephalopathy may be considered if a patient who had a history of inhaling heated heroin vapor showed acute cerebellar signs. Spongiform vacuoles degeneration of cerebral white matter was the main pathological change.
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