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Find video protocols related to scientific articles indexed in Pubmed.
Regulation of the extrinsic apoptotic pathway by microRNA-21 in alcoholic liver injury.
J. Biol. Chem.
PUBLISHED: 08-12-2014
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IL-6/Stat3 is associated with the regulation of transcription of key cellular regulatory genes (microRNAs) during different types of liver injury. This study evaluated the role of IL-6/Stat3 in regulating miRNA and miR-21 in alcoholic liver disease. By microarray, we identified that ethanol feeding significantly up-regulated 0.8% of known microRNAs in mouse liver compared with controls, including miR-21. Similarly, the treatment of normal human hepatocytes (N-Heps) and hepatic stellate cells (HSCs) with ethanol and IL-6 significantly increased miR-21 expression. Overexpression of miR-21 decreased ethanol-induced apoptosis in both N-Heps and HSCs. The expression level of miR-21 was significantly increased after Stat3 activation in N-Heps and HSCs, in support of the concept that the 5'-promoter region of miR-21 is regulated by Stat3. Using real time PCR, we confirmed that miR-21 activation is associated with ethanol-linked Stat3 binding of the miR-21 promoter. A combination of bioinformatics, PCR array, dual-luciferase reporter assay, and Western blot analysis revealed that Fas ligand (TNF superfamily, member 6) (FASLG) and death receptor 5 (DR5) are the direct targets of miR-21. Furthermore, inhibition of miR-21 by specific Vivo-Morpholino and knock-out of IL-6 in ethanol-treated mice also increased the expression of DR5 and FASLG in vivo during alcoholic liver injury. The identification of miR-21 as an important regulator of hepatic cell survival, transformation, and remodeling in vitro, as well as its upstream modulators and downstream targets, will provide insight into the involvement of altered miRNA expression in contributing to alcoholic liver disease progression and testing novel therapeutic approaches for human alcoholic liver diseases.
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Identification of apolipoprotein C-I as a potential Wilms' tumor marker after excluding inflammatory factors.
Int J Mol Sci
PUBLISHED: 07-15-2014
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Wilms' tumor is one of the most common malignant tumors observed in children, and its early diagnosis is important for late-stage treatment and prognosis. We previously screened and identified protein markers for Wilms' tumor; however, these markers lacked specificity, and some were associated with inflammation. In the current study, serum samples from children with Wilms' tumors were compared with those of healthy controls and patients with systemic inflammatory response syndrome (SIRS). After exclusion of factors associated with inflammation, specific protein markers for Wilms' tumors were identified. After comparing the protein peak values obtained from all three groups, a protein with a m/z of 6438 Da was specified. Purification and identification of the target protein using high-pressure liquid chromatography (HPLC) and two-dimensional liquid chromatography-linearion trap mass spectrometry(2D-LC-LTQ-MS) mass spectrometry, respectively, revealed that it was apolipoprotein C-I (APO C-I). Thus, APO C-I is a specific protein marker for Wilms' tumor.
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Screening and identification of potential biomarkers and establishment of the diagnostic serum proteomic model for the Traditional Chinese Medicine Syndromes of tuberculosis.
J Ethnopharmacol
PUBLISHED: 05-07-2014
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Chemotherapy is the mainstay of modern tuberculosis (TB) control. Traditional Chinese Medicine (TCM) can enhance the effect of anti-TB drug, promote the absorption of the foci in the lung and reduce drug toxicity. In TCM, the determination of treatment is based on ZHENG (also called TCM syndrome). To establish a diagnostic model by using proteomics technology in order to identify potential biomarkers for TCM syndromes of TB.
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Tumor-secreted miR-214 induces regulatory T cells: a major link between immune evasion and tumor growth.
Cell Res.
PUBLISHED: 04-04-2014
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An increased population of CD4(+)CD25(high)Foxp3(+) regulatory T cells (Tregs) in the tumor-associated microenvironment plays an important role in cancer immune evasion. However, the underlying mechanism remains unclear. Here we observed an increased secretion of miR-214 in various types of human cancers and mouse tumor models. Tumor-secreted miR-214 was sufficiently delivered into recipient T cells by microvesicles (MVs). In targeted mouse peripheral CD4(+) T cells, tumor-derived miR-214 efficiently downregulated phosphatase and tensin homolog (PTEN) and promoted Treg expansion. The miR-214-induced Tregs secreted higher levels of IL-10 and promoted tumor growth in nude mice. Furthermore, in vivo studies indicated that Treg expansion mediated by cancer cell-secreted miR-214 resulted in enhanced immune suppression and tumor implantation/growth in mice. The MV delivery of anti-miR-214 antisense oligonucleotides (ASOs) into mice implanted with tumors blocked Treg expansion and tumor growth. Our study reveals a novel mechanism through which cancer cell actively manipulates immune response via promoting Treg expansion.
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Characterisation of Caenorhabditis elegans sperm transcriptome and proteome.
BMC Genomics
PUBLISHED: 02-13-2014
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Although sperm is transcriptionally and translationally quiescent, complex populations of RNAs, including mRNAs and non-coding RNAs, exist in sperm. Previous microarray analysis of germ cell mutants identified hundreds of sperm genes in Caenorhabditis elegans. To take a more comprehensive view on C. elegans sperm genes, here, we isolate highly pure sperm cells and employ high-throughput technologies to obtain sperm transcriptome and proteome.
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DSSylation, a novel protein modification targets proteins induced by oxidative stress, and facilitates their degradation in cells.
Protein Cell
PUBLISHED: 02-11-2014
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Timely removal of oxidatively damaged proteins is critical for cells exposed to oxidative stresses; however, cellular mechanism for clearing oxidized proteins is not clear. Our study reveals a novel type of protein modification that may play a role in targeting oxidized proteins and remove them. In this process, DSS1 (deleted in split hand/split foot 1), an evolutionally conserved small protein, is conjugated to proteins induced by oxidative stresses in vitro and in vivo, implying oxidized proteins are DSS1 clients. A subsequent ubiquitination targeting DSS1-protein adducts has been observed, suggesting the client proteins are degraded through the ubiquitin-proteasome pathway. The DSS1 attachment to its clients is evidenced to be an enzymatic process modulated by an unidentified ATPase. We name this novel protein modification as DSSylation, in which DSS1 plays as a modifier, whose attachment may render target proteins a signature leading to their subsequent ubiquitination, thereby recruits proteasome to degrade them.
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Quantitative proteomics analysis identifies mitochondria as therapeutic targets of multidrug-resistance in ovarian cancer.
Theranostics
PUBLISHED: 01-01-2014
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Doxorubicin is a widely used chemotherapeutic agent for the treatment of a variety of solid tumors. However, resistance to this anticancer drug is a major obstacle to the effective treatment of tumors. As mitochondria play important roles in cell life and death, we anticipate that mitochondria may be related to drug resistance. Here, stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomic strategy was applied to compare mitochondrial protein expression in doxorubicin sensitive OVCAR8 cells and its doxorubicin-resistant variant NCI_ADR/RES cells. A total of 2085 proteins were quantified, of which 122 proteins displayed significant changes in the NCI_ADR/RES cells. These proteins participated in a variety of cell processes including cell apoptosis, substance metabolism, transport, detoxification and drug metabolism. Then qRT-PCR and western blot were applied to validate the differentially expressed proteins quantified by SILAC. Further functional studies with RNAi demonstrated TOP1MT, a mitochondrial protein participated in DNA repair, was involved in doxorubicin resistance in NCI_ADR/RES cells. Besides the proteomic study, electron microscopy and fluorescence analysis also observed that mitochondrial morphology and localization were greatly altered in NCI_ADR/RES cells. Mitochondrial membrane potential was also decreased in NCI_ADR/RES cells. All these results indicate that mitochondrial function is impaired in doxorubicin-resistant cells and mitochondria play an important role in doxorubicin resistance. This research provides some new information about doxorubicin resistance, indicating that mitochondria could be therapeutic targets of doxorubicin resistance in ovarian cancer cells.
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Compact conformations of human protein disulfide isomerase.
PLoS ONE
PUBLISHED: 01-01-2014
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Protein disulfide isomerase (PDI) composed of four thioredoxin-like domains a, b, b', and a', is a key enzyme catalyzing oxidative protein folding in the endoplasmic reticulum. Large scale molecular dynamics simulations starting from the crystal structures of human PDI (hPDI) in the oxidized and reduced states were performed. The results indicate that hPDI adopts more compact conformations in solution than in the crystal structures, which are stabilized primarily by inter-domain interactions, including the salt bridges between domains a and b' observed for the first time. A prominent feature of the compact conformations is that the two catalytic domains a and a' can locate close enough for intra-molecular electron transfer, which was confirmed by the characterization of an intermediate with a disulfide between the two domains. Mutations, which disrupt the inter-domain interactions, lead to decreased reductase activity of hPDI. Our molecular dynamics simulations and biochemical experiments reveal the intrinsic conformational dynamics of hPDI and its biological impact.
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Analysis of age and gender associated N-glycoproteome in human whole saliva.
Clin Proteomics
PUBLISHED: 01-01-2014
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Glycoproteins comprise a large portion of the salivary proteome and have great potential for biomarker discovery and disease diagnosis. However, the rate of production and the concentration of whole saliva change with age, gender and physiological states of the human body. Therefore, a thorough understanding of the salivary glycoproteome of healthy individuals of different ages and genders is a prerequisite for saliva to have clinical utility.
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Phosphoproteomic analysis of protein phosphorylation networks in Tetrahymena thermophila, a Model Single-Celled Organism.
Mol. Cell Proteomics
PUBLISHED: 11-07-2013
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Tetrahymena thermophila is a widely used unicellular eukaryotic model organism in biological research and contains more than 1000 protein kinases and phosphatases with specificity for Ser/Thr/Tyr residues. However, only a few dozen phosphorylation sites in T. thermophila are known, presenting a major obstacle for further understanding the regulatory roles of reversible phosphorylation in this organism. In this study, we used high accuracy mass spectrometry-based proteomics to conduct global and site-specific phosphoproteome profiling of T. thermophila. In total, 1384 phosphopeptides and 2238 phosphorylation sites from 1008 T. thermophila proteins were identified through the combined use of peptide prefractionation, TiO2 enrichment, and 2D-LC-MS/MS analysis. The identified phosphoproteins are implicated in the regulation of various biological processes such as transport, gene expression, and mRNA metabolic process. Moreover, integrated analysis of the T. thermophila phosphoproteome and gene network reveals the potential biological functions for many previously unannotated proteins and predicts several putative kinase-substrate pairs. Our data provide the first global survey of phosphorylation in T. thermophila by using a phosphoproteomic approach, and suggests a wide-ranging regulatory scope of this modification. The provided dataset is a valuable resource for the future understanding of signaling pathways in this important model organism.
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Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630.
Nucleic Acids Res.
PUBLISHED: 10-22-2013
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Rhodococcus opacus strain PD630 (R. opacus PD630), is an oleaginous bacterium, and also is one of few prokaryotic organisms that contain lipid droplets (LDs). LD is an important organelle for lipid storage but also intercellular communication regarding energy metabolism, and yet is a poorly understood cellular organelle. To understand the dynamics of LD using a simple model organism, we conducted a series of comprehensive omics studies of R. opacus PD630 including complete genome, transcriptome and proteome analysis. The genome of R. opacus PD630 encodes 8947 genes that are significantly enriched in the lipid transport, synthesis and metabolic, indicating a super ability of carbon source biosynthesis and catabolism. The comparative transcriptome analysis from three culture conditions revealed the landscape of gene-altered expressions responsible for lipid accumulation. The LD proteomes further identified the proteins that mediate lipid synthesis, storage and other biological functions. Integrating these three omics uncovered 177 proteins that may be involved in lipid metabolism and LD dynamics. A LD structure-like protein LPD06283 was further verified to affect the LD morphology. Our omics studies provide not only a first integrated omics study of prokaryotic LD organelle, but also a systematic platform for facilitating further prokaryotic LD research and biofuel development.
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The discovery and identification of a candidate proteomic biomarker of active tuberculosis.
BMC Infect. Dis.
PUBLISHED: 10-15-2013
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Noninvasive and convenient biomarkers for early diagnosis of tuberculosis (TB) remain an urgent need. The aim of this study was to discover and identify potential biomarkers specific for TB.
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Proteomic studies of isolated lipid droplets from bacteria, C. elegans, and mammals.
Methods Cell Biol.
PUBLISHED: 10-09-2013
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Lipid droplets (LDs) are an intracellular organelle, consisting of a neutral lipid core covered by a monolayer of phospholipids and proteins. It primarily mediates lipid storage, metabolism, and transportation. Recently, research of LDs has emerged as a rapidly developing field due to the strong linkage between ectopic lipid accumulation and metabolic syndromes. Recently, more than 30 proteomic studies of isolated LDs have identified many important LD proteins that have highlighted and have also predicted the potential biological roles of the organelle, motivating the field to develop quite rapidly. This chapter summarizes methods used in proteomic studies for three representative species reported and discusses their advantages and disadvantages. We believe that this chapter provides useful information and methods for future LD proteomic studies especially for LDs in other species.
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Chronic high glucose induced INS-1? cell mitochondrial dysfunction: a comparative mitochondrial proteome with SILAC.
Proteomics
PUBLISHED: 06-28-2013
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As glucose-stimulated insulin secretion of pancreatic ? cell is triggered and promoted by the metabolic messengers derived from mitochondria, mitochondria take a central stage in the normal function of ? cells. ? cells in diabetics were chronically exposed to hyperglycemia stimulation, which have been reported to exert deleterious effects on ?-cell mitochondria. However, the mechanism of the toxic effects of hyperglycemia on ?-cell mitochondria was not clear. In this study, we characterized the biological functional changes of rat INS-1? cells and their mitochondria with chronic exposure to hyperglycemia and created a research model of chronic hyperglycemia-induced dysfunctional ? cells with damaged mitochondria. Then, SILAC-based quantitative proteomic approach was used to compare the mitochondrial protein expression from high glucose treated INS-1? cells and control cells. The expression of some mitochondrial proteins was found with significant changes. Functional classification revealed most of these proteins were related with oxidative phosphorylation, mitochondrial protein biosynthesis, substances metabolism, transport, and cell death. These results presented some useful information about the effect of glucotoxicity on the ?-cell mitochondria.
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Testicular phosphoproteome in perfluorododecanoic acid-exposed rats.
Toxicol. Lett.
PUBLISHED: 04-14-2013
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Perfluorododecanoic acid (PFDoA) is a common environmental pollutant, which has been detected in human sera and has adverse effects on testicular function in animal models. Exploring phosphorylation events in testes helps elucidate the specific phosphorylation signals involved in testicular toxicity of PFDoA. Combining efficient prefractionation of tryptic peptide mixtures using self-packed reversed phase C18 columns with TiO2 and IMAC phosphopeptide enrichment techniques followed by 2D-LC-MS/MS, we identified 4077 unique phosphopeptides from 1777 proteins with a false discovery rate below 1.0% in the testes of rats exposed to PFDoA for 110 days. In addition, 937 novel phosphorylation sites were discovered in testicular proteins. Hundreds of phosphorylated proteins identified might be involved in spermatogenesis and sperm function. With increasing PFDoA dosage, the number of casein kinase 2 kinase-modified peptides significantly increased. Pathway analysis suggested that the mitogen-activated protein kinase pathway and cell division cycle protein 2 (CDC2) may have contributed to sperm activity and testicular function. By in vitro experiments, CDC2 phosphorylation activity was found to be likely involved in PFDoA-induced toxicity in Leydig cells. This study provides the first examination of the whole proteins phosphorylation profile in rat testis and suggests that the MAPK pathway and CDC2 protein phosphorylation are critical for PFDoA testicular toxicity.
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Inactivation of Caenorhabditis elegans aminopeptidase DNPP-1 restores endocytic sorting and recycling in tat-1 mutants.
Mol. Biol. Cell
PUBLISHED: 02-20-2013
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In Caenorhabditis elegans, the P4-ATPase TAT-1 and its chaperone, the Cdc50 family protein CHAT-1, maintain membrane phosphatidylserine (PS) asymmetry, which is required for membrane tubulation during endocytic sorting and recycling. Loss of tat-1 and chat-1 disrupts endocytic sorting, leading to defects in both cargo recycling and degradation. In this study, we identified the C. elegans aspartyl aminopeptidase DNPP-1, loss of which suppresses the sorting and recycling defects in tat-1 mutants without reversing the PS asymmetry defect. We found that tubular membrane structures containing recycling cargoes were restored in dnpp-1 tat-1 double mutants and that these tubules overlap with RME-1-positive recycling endosomes. The restoration of the tubular structures in dnpp-1 tat-1 mutants requires normal functions of RAB-5, RAB-10, and RME-1. In tat-1 mutants, we observed alterations in membrane surface charge and targeting of positively charged proteins that were reversed by loss of dnpp-1. DNPP-1 displays a specific aspartyl aminopeptidase activity in vitro, and its enzymatic activity is required for its function in vivo. Our data reveal the involvement of an aminopeptidase in regulating endocytic sorting and recycling and suggest possible roles of peptide signaling and/or protein metabolism in these processes.
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Isolation and identification of mannose-binding proteins and estimation of their abundance in sera from hepatocellular carcinoma patients.
Proteomics
PUBLISHED: 02-11-2013
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The interaction of glycan-binding proteins (GBPs) and glycans plays a significant biological role that ranges from cell-cell recognition to cell trafficking, and glycoprotein targeting. The anomalies of GBPs related to the types and/or quantities were not clearly known in cancer incidence. It is imperative to identify and annotate the GBPs related with the canceration. Here the mannose-binding proteins (MBPs) from the clinical sera were isolated and identified by the mannose-magnetic particle conjugates and the high-accuracy MS analysis. Seventy-five MBPs from normal donors sera and 79 MBPs from hepatocellular carcinoma patients sera were identified and annotated. By using the stringent criteria of exponentially modified protein abundance index (emPAI) quantification, 12 MBPs were estimated to be significantly upregulated (emPAI ratio > 4) and nine MBPs were estimated to be significantly downregulated (emPAI ratio < 0.25) in the hepatocellular carcinoma sera. Real-time quantitative PCR, Western blotting, and protein microarrays were also used to confirm the altered MBPs expression level and the specific binding between the isolated MBPs and mannose. The sequence recognition motifs and structure preference of the isolated MBPs were characterized. The functional enrichment analysis revealed that over 57% of the isolated MBPs were binding protein and the upregulated MBPs were involved in cell death, tumor progression, and macromolecular complex remodeling.
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Integrative proteomic and transcriptomic analyses reveal multiple post-transcriptional regulatory mechanisms of mouse spermatogenesis.
Mol. Cell Proteomics
PUBLISHED: 01-16-2013
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Mammalian spermatogenesis consists of many cell types and biological processes and serves as an excellent model for studying gene regulation at transcriptional and post-transcriptional levels. Many key proteins, miRNAs, and perhaps piRNAs have been shown to be involved in post-transcriptional regulation of spermatogenesis. However, a systematic method for assessing the relationship between protein and mRNA expression has not been available for studying mechanisms of post-transcriptional regulation. In the present study, we used the iTRAQ-based quantitative proteomic approach to identify 2008 proteins in mouse type A spermatogonia, pachytene spermatocytes, round spermatids, and elongative spermatids with high confidence. Of these proteins, 1194 made up four dynamically changing clusters, which reflect the mitotic amplification, meiosis, and post-meiotic development of germ cells. We identified five major regulatory mechanisms termed "transcript only," "transcript degradation," "translation repression," "translation de-repression," and "protein degradation" based on changes in protein level relative to changes in mRNA level at the mitosis/meiosis transition and the meiosis/post-meiotic development transition. We found that post-transcriptional regulatory mechanisms are related to the generation of piRNAs and antisense transcripts. Our results provide a valuable inventory of proteins produced during mouse spermatogenesis and contribute to elucidating the mechanisms of the post-transcriptional regulation of gene expression in mammalian spermatogenesis.
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Histone modification mapping in human brain reveals aberrant expression of histone H3 lysine 79 dimethylation in neural tube defects.
Neurobiol. Dis.
PUBLISHED: 01-11-2013
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Neural tube defects (NTDs) are severe, common birth defects that result from failure of neural tube closure, but their pathological mechanisms are not yet fully understood. Histone modifications have an important role in gene regulation during fetal development. We therefore hypothesized that the human NTDs may be partly caused by an imbalance in metabolism, perhaps caused by nutritional deficiencies, that leads to aberrant histone modifications. Here, we report a screen of fetal brain histone modifications using 2D nano-LC strong cation exchange reverse phase (SCX/RP) MS/MS and the identification of 61 unique post-translational modification sites on histones H1, H2a, H2b, H3, and H4. Of these, 38 sites are novel (not already found in the Uniprot database). Furthermore, we compared the histone modification patterns between normal brains and NTD brains special of which maternal folate levels were lower than of normal control. The results showed that histone H3 lysine 79 dimethylation (H3K79me2) and a novel identified site, H2bK5 monomethylation (H2bK5me1), were completely absent in individuals with NTDs. Follow-up Western blotting validated the decreased H3K79me2 expression in brains with NTDs, but the amplified samples experiments displayed that decreased H3K79me2 expression was not suitable for all samples with NTDs. Furthermore, folate-free treated mouse embryonic stem cells induced the decreased H3K79me2 level. Subsequently, our ChIP results in normal fetal brain tissues showed that H3K79me2 binds to SUFU, RARA and ITGA3 which induce NTDs phenotype after knockout in mice, and in NTDs brain tissues the bindings of H3K79me2 to these three genes were significantly altered. Taken together, our study indicated that low folate treatment might attenuate H3K79 dimethylation, further affect its regulate activation on target genes, some of which are NTDs-resulting associated, lastly interrupt early embryo developing. Our study increases the understanding of normal fetal brain histone modifications and provides a platform for investigating histone modifications in neural disease and also has an insight into a potential role of aberrant histone modification in etiology of NTDs.
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Phosphoproteome analysis reveals an important role for glycogen synthase kinase-3 in perfluorododecanoic acid-induced rat liver toxicity.
Toxicol. Lett.
PUBLISHED: 01-11-2013
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Perfluorododecanoic acid (PFDoA) is a member of the perfluoroalkyl acid (PFAA) family and has broad applications and a wide distribution in the environment. Here, we used TiO(2)-based phosphopeptide enrichment coupled with LC-MS/MS analysis to identify phosphopeptides in rat livers that were influenced by PFDoA treatment. We identified a total of 1443 unique phosphopeptides from among 769 phosphoproteins identified in normal and PFDoA-treated rat livers, 849 unique phosphorylation sites were also identified. Of these sites, 143 were considered to be novel phosphorylation sites. Many phosphoproteins were found to be associated with hepatic injuries and diseases, such as hepatotoxicity, regeneration, fatty liver, neoplasms and carcinoma. Furthermore, 25 of the identified phosphoproteins were found to be related to glycogen synthase kinase-3 (GSK3), either directly or indirectly. Western blot and qPCR results suggested that chronic PFDoA exposure inhibited insulin signal pathways and that inhibition of GSK3 might contribute to the observed increases of lipid levels in the liver.
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Extracellular HSP70/HSP70-PCs Promote Epithelial-Mesenchymal Transition of Hepatocarcinoma Cells.
PLoS ONE
PUBLISHED: 01-01-2013
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Extracellular heat shock protein 70 and peptide complexes (eHSP70/HSP70-PCs) regulate a variety of biological behaviors in tumor cells. Whether eHSP70/HSP70-PCs are involved in the epithelial-mesenchymal transition (EMT) of tumor cells remains unclear.
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Identification of the major functional proteins of prokaryotic lipid droplets.
J. Lipid Res.
PUBLISHED: 12-15-2011
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Storage of cellular triacylglycerols (TAGs) in lipid droplets (LDs) has been linked to the progression of many metabolic diseases in humans, and to the development of biofuels from plants and microorganisms. However, the biogenesis and dynamics of LDs are poorly understood. Compared with other organisms, bacteria seem to be a better model system for studying LD biology, because they are relatively simple and are highly efficient in converting biomass to TAG. We obtained highly purified LDs from Rhodococcus sp. RHA1, a bacterium that can produce TAG from many carbon sources, and then comprehensively characterized the LD proteome. Of the 228 LD-associated proteins identified, two major proteins, ro02104 and PspA, constituted about 15% of the total LD protein. The structure predicted for ro02104 resembles that of apolipoproteins, the structural proteins of plasma lipoproteins in mammals. Deletion of ro02104 resulted in the formation of supersized LDs, indicating that ro02104 plays a critical role in cellular LD dynamics. The putative ? helix of the ro02104 LD-targeting domain (amino acids 83-146) is also similar to that of apolipoproteins. We report the identification of 228 proteins in the proteome of prokaryotic LDs, identify a putative structural protein of this organelle, and suggest that apolipoproteins may have an evolutionarily conserved role in the storage and trafficking of neutral lipids.
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Bioinformatics analysis of proteomic profiles during the process of anti-Thy1 nephritis.
Mol. Cell Proteomics
PUBLISHED: 12-07-2011
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Anti-Thy1 nephritis is a well-established experimental mesangial proliferative nephritis model. Exploring the molecular mechanisms of pathophysiology in anti-Thy1 nephritis may elucidate the pathogeneses of mesangial proliferation. We examined the roles and acting mechanisms of differentially expressed proteins (DEPs) by bioinformatics analysis of glomeruli proteomic profiles during the course of anti-Thy1 nephritis. In total, 108 DEPs were found by two-dimensional fluorescence difference gel electrophoresis (2D-DIGE), and 40 DEPs were identified by matrix-assisted laser desorption ionization/time of flight and liquid chromatography-MS. DEPs were classified into five clusters (Clusters 1-5), according to their expression trends using Cluster 3.0 software, involved in regulating biological processes such as the stress response, cell proliferation, apoptosis, energy metabolism, transport, and the actin cytoskeleton. The expression patterns of ten DEPs, distributed across five clusters, including AKR1A1, AGAT, ATP6V1B2, HIBADH, MDH1, MPST, NIT2, PRDX6, PSMB7, and TPI1, were validated by Western blotting. Based on Western blotting and immunohistochemistry, we also found that the DEP FHL2, which was primarily expressed in the mesangial region, was down-regulated on days 3 and 5, and up-regulated on day 10. In vitro, we found that FHL2 overexpression induced mesangial cell proliferation by increasing the number of S-phase cells and decreasing G2/M-phase cells, whereas inhibiting FHL2 had the opposite effect. This study explored novel DEPs and their expression patterns during anti-Thy1 nephritis, and elucidated FHL2s effect on mesangial cell proliferation. These results will contribute to our understanding of the pathogenesis of mesangial proliferation.
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Nitric oxide and protein S-nitrosylation are integral to hydrogen peroxide-induced leaf cell death in rice.
Plant Physiol.
PUBLISHED: 11-21-2011
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Nitric oxide (NO) is a key redox-active, small molecule involved in various aspects of plant growth and development. Here, we report the identification of an NO accumulation mutant, nitric oxide excess1 (noe1), in rice (Oryza sativa), the isolation of the corresponding gene, and the analysis of its role in NO-mediated leaf cell death. Map-based cloning revealed that NOE1 encoded a rice catalase, OsCATC. Furthermore, noe1 resulted in an increase of hydrogen peroxide (H(2)O(2)) in the leaves, which consequently promoted NO production via the activation of nitrate reductase. The removal of excess NO reduced cell death in both leaves and suspension cultures derived from noe1 plants, implicating NO as an important endogenous mediator of H(2)O(2)-induced leaf cell death. Reduction of intracellular S-nitrosothiol (SNO) levels, generated by overexpression of rice S-nitrosoglutathione reductase gene (GSNOR1), which regulates global levels of protein S-nitrosylation, alleviated leaf cell death in noe1 plants. Thus, S-nitrosylation was also involved in light-dependent leaf cell death in noe1. Utilizing the biotin-switch assay, nanoliquid chromatography, and tandem mass spectrometry, S-nitrosylated proteins were identified in both wild-type and noe1 plants. NO targets identified only in noe1 plants included glyceraldehyde 3-phosphate dehydrogenase and thioredoxin, which have been reported to be involved in S-nitrosylation-regulated cell death in animals. Collectively, our data suggest that both NO and SNOs are important mediators in the process of H(2)O(2)-induced leaf cell death in rice.
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Proteome of skeletal muscle lipid droplet reveals association with mitochondria and apolipoprotein a-I.
J. Proteome Res.
PUBLISHED: 09-15-2011
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The lipid droplet (LD) is a universal organelle governing the storage and turnover of neutral lipids. Mounting evidence indicates that elevated intramuscular triglyceride (IMTG) in skeletal muscle LDs is closely associated with insulin resistance and Type 2 Diabetes Mellitus (T2DM). Therefore, the identification of the skeletal muscle LD proteome will provide some clues to dissect the mechanism connecting IMTG with T2DM. In the present work, we identified 324 LD-associated proteins in mouse skeletal muscle LDs through mass spectrometry analysis. Besides lipid metabolism and membrane traffic proteins, a remarkable number of mitochondrial proteins were observed in the skeletal muscle LD proteome. Furthermore, imaging by fluorescence microscopy and transmission electronic microscopy (TEM) directly demonstrated that mitochondria closely adhere to LDs in vivo. Moreover, our results revealed for the first time that apolipoprotein A-I (apo A-I), the principal apolipoprotein of high density lipoprotein (HDL) particles, was also localized on skeletal muscle LDs. Further studies verified that apo A-I was expressed endogenously by skeletal muscle cells. In conclusion, we report the protein composition and characterization of skeletal muscle LDs and describe a novel LD-associated protein, apo A-I.
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Castration inhibits biliary proliferation induced by bile duct obstruction: novel role for the autocrine trophic effect of testosterone.
Am. J. Physiol. Gastrointest. Liver Physiol.
PUBLISHED: 09-08-2011
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Increased cholangiocyte growth is critical for the maintenance of biliary mass during liver injury by bile duct ligation (BDL). Circulating levels of testosterone decline following castration and during cholestasis. Cholangiocytes secrete sex hormones sustaining cholangiocyte growth by autocrine mechanisms. We tested the hypothesis that testosterone is an autocrine trophic factor stimulating biliary growth. The expression of androgen receptor (AR) was determined in liver sections, male cholangiocytes, and cholangiocyte cultures [normal rat intrahepatic cholangiocyte cultures (NRICC)]. Normal or BDL (immediately after surgery) rats were treated with testosterone or antitestosterone antibody or underwent surgical castration (followed by administration of testosterone) for 1 wk. We evaluated testosterone serum levels; intrahepatic bile duct mass (IBDM) in liver sections of female and male rats following the administration of testosterone; and secretin-stimulated cAMP levels and bile secretion. We evaluated the expression of 17?-hydroxysteroid dehydrogenase 3 (17?-HSD3, the enzyme regulating testosterone synthesis) in cholangiocytes. We evaluated the effect of testosterone on the proliferation of NRICC in the absence/presence of flutamide (AR antagonist) and antitestosterone antibody and the expression of 17?-HSD3. Proliferation of NRICC was evaluated following stable knock down of 17?-HSD3. We found that cholangiocytes and NRICC expressed AR. Testosterone serum levels decreased in castrated rats (prevented by the administration of testosterone) and rats receiving antitestosterone antibody. Castration decreased IBDM and secretin-stimulated cAMP levels and ductal secretion of BDL rats. Testosterone increased 17?-HSD3 expression and proliferation in NRICC that was blocked by flutamide and antitestosterone antibody. Knock down of 17?-HSD3 blocks the proliferation of NRICC. Drug targeting of 17?-HSD3 may be important for managing cholangiopathies.
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Quantitative proteomics analysis of parthenogenetically induced pluripotent stem cells.
Protein Cell
PUBLISHED: 07-01-2011
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Parthenogenetic embryonic stem (pES) cells isolated from parthenogenetic activation of oocytes and embryos, also called parthenogenetically induced pluripotent stem cells, exhibit pluripotency evidenced by both in vitro and in vivo differentiation potential. Differential proteomic analysis was performed using differential in-gel electrophoresis and isotope-coded affinity tag-based quantitative proteomics to investigate the molecular mechanisms underlying the developmental pluripotency of pES cells and to compare the protein expression of pES cells generated from either the in vivo-matured ovulated (IVO) oocytes or from the in vitro-matured (IVM) oocytes with that of fertilized embryonic stem (fES) cells derived from fertilized embryos. A total of 76 proteins were upregulated and 16 proteins were downregulated in the IVM pES cells, whereas 91 proteins were upregulated and 9 were downregulated in the IVO pES cells based on a minimal 1.5-fold change as the cutoff value. No distinct pathways were found in the differentially expressed proteins except for those involved in metabolism and physiological processes. Notably, no differences were found in the protein expression of imprinted genes between the pES and fES cells, suggesting that genomic imprinting can be corrected in the pES cells at least at the early passages. The germline competent IVM pES cells may be applicable for germ cell renewal in aging ovaries if oocytes are retrieved at a younger age.
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Identification of potential serum biomarkers for Wilms tumor after excluding confounding effects of common systemic inflammatory factors.
Mol. Biol. Rep.
PUBLISHED: 05-10-2011
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Wilms tumor is the most common pediatric tumor of the kidney. Previous studies have identified several serum biomarkers for Wilms tumor; however, they lack sufficient specificity and may not adequately distinguish Wilms tumor from confounding conditions. To date, no specific protein biomarker has been confirmed for this pediatric tumor. To identify novel serum biomarkers for Wilms tumor, we used proteomic technologies to perform protein profiling of serum samples from pre-surgery and post-surgery patients with Wilms tumor and healthy controls. Some common systemic inflammatory factors were included to control for systemic inflammation. By comparing protein peaks among the three groups of sera, we identified two peaks (11,526 and 4,756 Da) showing significant differential expression not only between pre-surgery and control sera but also between pre-surgery and post-surgery sera. These two peaks were identified as serum amyloid A1 (SAA1) and apolipoprotein C-III (APO C-III). Western blot analysis confirmed that both proteins were expressed at higher levels in pre-surgery sera than in post-surgery and control sera. Using the method of leave-1-out for cross detection, we demonstrate that detection of these two candidate biomarkers had high sensitivity and specificity in discriminating pre-surgery sera from post-surgery and normal control sera. Taken together, these findings suggest that SAA1 and APO C-III are two potential biomarkers for Wilms tumor.
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Xbp1-mediated histone H4 deacetylation contributes to DNA double-strand break repair in yeast.
Cell Res.
PUBLISHED: 04-05-2011
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Xbp1 has been shown to regulate the cell cycle as a transcriptional repressor in budding yeast Saccharomyces cerevisiae. In this study, we demonstrated that Xbp1 regulates DNA double-strand break (DSB) repair in S. cerevisiae. Xbp1 physically and genetically interacts with the histone deacetylase Rpd3 complex. Chromatin immunoprecipitation revealed that Xbp1 is required for efficient deacetylation of histone H4 flanking DSBs by the Rpd3 complex. Deletion of XBP1 leads to the delayed deacetylation of histone H4, which is coupled with increased nucleosome displacement, increased DNA end resection and decreased non-homologous end-joining (NHEJ). In response to DNA damage, Xbp1 is upregulated in a Mec1-Rad9-Rad53 checkpoint pathway-dependent manner and undergoes dephosphorylation. Cdk1, a central regulator of S. cerevisiae cell cycle, is responsible for Xbp1 phosphorylation at residues Ser146, Ser271 and Ser551. Substitution of these serine residues with alanine not only increases the association of Xbp1 with the Rpd3 complex and its recruitment to a DSB, but also promotes DSB repair. Together, our findings reveal a role for Xbp1 in DSB repair via NHEJ through regulation of histone H4 acetylation and nucleosome displacement in a positive feedback manner.
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Regulation of biliary proliferation by neuroendocrine factors: implications for the pathogenesis of cholestatic liver diseases.
Am. J. Pathol.
PUBLISHED: 02-02-2011
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The proliferation of cholangiocytes occurs during the progression of cholestatic liver diseases and is critical for the maintenance and/or restoration of biliary mass during bile duct damage. The ability of cholangiocytes to proliferate is important in many different human pathologic conditions. Recent studies have brought to light the concept that proliferating cholangiocytes serve as a unique neuroendocrine compartment in the liver. During extrahepatic cholestasis and other pathologic conditions that trigger ductular reaction, proliferating cholangiocytes acquire a neuroendocrine phenotype. Cholangiocytes have the capacity to secrete and respond to a variety of hormones, neuropeptides, and neurotransmitters, regulating their surrounding cell functions and proliferative activity. In this review, we discuss the regulation of cholangiocyte growth by neuroendocrine factors in animal models of cholestasis and liver injury, which includes a discussion of the acquisition of neuroendocrine phenotypes by proliferating cholangiocytes and how this relates to cholangiopathies. We also review what is currently known about the neuroendocrine phenotypes of cholangiocytes in human cholestatic liver diseases (ie, cholangiopathies) that are characterized by ductular reaction.
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Preparative isolation of alkaloids from Corydalis bungeana Turcz. by high-speed counter-current chromatography using stepwise elution.
J Sep Sci
PUBLISHED: 01-12-2011
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High-speed counter-current chromatography (HSCCC) was successfully applied for the preparative separation and purification of alkaloids from Corydalis bungeana Turcz. (Kudiding in Chinese) for the first time. After the measurement of partition coefficient of seven target alkaloids in the nine two-phase solvent systems composed of CHCl(3)-MeOH-(0.1?M; 0.2?M; 0.3?M) HCl (4:1.5:2; 4:2:2; 4:3:2, v/v), CHCl(3)-MeOH-0.2?M HCl (4:2:2, v/v) and CHCl(3)-MeOH-0.3?M HCl (4:3:2, v/v) were finally selected for the HSCCC separation using the first upper phase as the stationary phase and the stepwise elution of the two lower mobile phases. Consequently, sanguinarine (10?mg), corynoline (25?mg), protopine (20?mg), corynoloxine (18?mg), and 12-hydroxycorynoline (8?mg) were obtained from 200?mg of crude alkaloid extracts with purities of 94-99% as determined by HPLC. Their chemical structures were characterized on the basis of (1)H-NMR, (13)C-NMR, and LC-ESI-Q-TOF-MS/MS analyses.
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Ser149 is another potential PKA phosphorylation target of Cdc25B in G2/M transition of fertilized mouse eggs.
J. Biol. Chem.
PUBLISHED: 01-06-2011
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It is well documented that protein kinase A (PKA) acts as a negative regulator of M phase promoting factor (MPF) by phosphorylating cell division cycle 25 homolog B (Cdc25B) in mammals. However, the molecular mechanism remains unclear. In this study, we identified PKA phosphorylation sites in vitro by LC-MS/MS analysis, including Ser(149), Ser(229), and Ser(321) of Cdc25B, and explored the role of Ser(149) in G(2)/M transition of fertilized mouse eggs. The results showed that the overexpressed Cdc25B-S149A mutant initiated efficient MPF activation by direct dephosphorylation of Cdc2-Tyr(15), resulting in triggering mitosis prior to Cdc25B-WT. Conversely, overexpression of the phosphomimic Cdc25B-S149D mutant showed no significant difference in comparison with the control groups. Furthermore, we found that Cdc25B-Ser(149) was phosphorylated at G(1) and S phases, whereas dephosphorylated at G(2) and M phases, and the phosphorylation of Cdc25B-Ser(149) was modulated by PKA in vivo. In addition, we examined endogenous and exogenous Cdc25B, which were expressed mostly in the cytoplasm at the G(1) and S phases and translocated to the nucleus at the G(2) phase. Collectively, our findings provide evidence that Ser(149) may be another potential PKA phosphorylation target of Cdc25B in G(2)/M transition of fertilized mouse eggs and Cdc25B as a direct downstream substrate of PKA in mammals, which plays important roles in the regulation of early development of mouse embryos.
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Simvastatin stimulates apoptosis in cholangiocarcinoma by inhibition of Rac1 activity.
Dig Liver Dis
PUBLISHED: 01-03-2011
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Simvastatin is a cholesterol-lowering drug that is widely used to prevent and treat atherosclerotic cardiovascular disease. Simvastatin exhibits numerous pleiotropic effects including anti-cancer activity. However, the effect of simvastatin on cholangiocarcinoma has not been evaluated.
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Acyl-biotinyl exchange chemistry and mass spectrometry-based analysis of palmitoylation sites of in vitro palmitoylated rat brain tubulin.
Protein J.
PUBLISHED: 10-27-2010
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Research has shown that the palmitoyl group of ?-tubulin mediates the hydrophobic interaction between microtubules and intracellular membranes and that palmitoylated tubulin plays a role in signal transduction. There are 20 cysteine residues per ?/? tubulin heterodimer. C376 of ?-tubulin was reported to be predominantly palmitoylated and C20, C213 and C305 of ?-tubulin were palmitoylated at lower levels. The previous method used for the analysis of the palmitoylation sites on ?-tubulin was based on ³H-labeling, enzymolysis, purification and sequencing. This approach, although efficient, is laborious. Mass spectrometry (MS), especially tandem MS, has been shown to be a successful method for identification of various post-translational modifications of proteins. We report here a convenient MS-based method to comprehensively analyze the palmitoylation sites of the ?/? tubulin heterodimer. Acyl-biotinyl exchange chemistry and streptavidin agarose affinity purification were applied to enrich palmitoylated peptides from tubulin. After nano-LC-MS/MS analysis, database searching and manual analysis of the spectra revealed that 11 cysteine residues of the ?/? tubulin heterodimer were palmitoylated.
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Mammalian mitochondrial proteomics: insights into mitochondrial functions and mitochondria-related diseases.
Expert Rev Proteomics
PUBLISHED: 06-12-2010
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Mitochondria are organelles that are essential for cell life and death. A huge range of pathologies, including neurodegenerative diseases, cancer, diabetes and aging, have been reported to be associated with mitochondrial dysfunction. Therefore, identification of mitochondrial proteins that are differentially expressed in these pathologies will help to further our understanding of these diseases. In recent years, great achievements have been made in mammalian mitochondrial proteomics. Here we provide an overview of the current state of knowledge with respect to the whole mitochondrial proteome, the mitochondrial subproteome, mitochondrial complexes and mitochondrial post-translational modifications. Applications of comparative mitochondrial proteomics to various pathologies that have provided clues for understanding the relationship between mitochondrial dysfunction and pathogenesis are described. We conclude that mitochondrial proteomics can be used not only to map all the components of mitochondria, but can also provide information for discovering therapeutic targets for mitochondria-related diseases.
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Proteomic analysis of aqueous humor from patients with primary open angle glaucoma.
Mol. Vis.
PUBLISHED: 05-13-2010
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Primary open angle glaucoma (POAG) is a leading cause of irreversible blindness on a global level. Researchers have yet to specify the exact mechanisms of POAG; the respective relationships between POAG and elevated intraocular pressure (IOP), as well as optic neuropathy, remain particularly unclear. It is known, however, that the expression profile for some proteins in the aqueous humor (AH) changes in some diseases, and that AH changes play important roles in elevated IOP. To identify the possible roles of these AH proteins in POAG, a proteomic analysis of the AH compositions of POAG patients eyes was performed and compared with those derived from paired, non-POAG cataract (control) eyes.
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The profile of mitochondrial proteins and their phosphorylation signaling network in INS-1 beta cells.
J. Proteome Res.
PUBLISHED: 04-13-2010
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Mitochondria have important roles in cellular physiological functions and various diseases. In pancreatic beta cells, mitochondria play a central role in glucose-stimulated insulin secretion (GSIS). To reveal the potential functions of mitochondria in the GSIS process in beta cells, shotgun proteomics was applied to profiling mitochondrial proteins and their potential phosphorylation sites in rat INS-1 cells. More than 800 proteins were assigned to mitochondria. In addition, 84 different mitochondrial phosphoproteins were identified, and 52 upstream kinases of mitochondrial phosphoproteins were predicted using bioinformatics tools. Regulation networks of mitochondrial phosphoproteins were constructed by integrating mitochondrial protein interaction networks and mitochondrial phosphorylation signaling, providing a preliminary survey of how phosphorylation signaling regulates mitochondrial function in beta cells. We present integrated resources including the protein composition and signaling pathways of mitochondria which can be used to understand the role of mitochondria in GSIS.
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Enhanced MALDI-TOF MS analysis of phosphopeptides using an optimized DHAP/DAHC matrix.
J. Biomed. Biotechnol.
PUBLISHED: 03-21-2010
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Selecting an appropriate matrix solution is one of the most effective means of increasing the ionization efficiency of phosphopeptides in matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). In this study, we systematically assessed matrix combinations of 2, 6-dihydroxyacetophenone (DHAP) and diammonium hydrogen citrate (DAHC), and demonstrated that the low ratio DHAP/DAHC matrix was more effective in enhancing the ionization of phosphopeptides. Low femtomole level of phosphopeptides from the tryptic digests of alpha-casein and beta-casein was readily detected by MALDI-TOF-MS in both positive and negative ion mode without desalination or phosphopeptide enrichment. Compared with the DHB/PA matrix, the optimized DHAP/DAHC matrix yielded superior sample homogeneity and higher phosphopeptide measurement sensitivity, particularly when multiple phosphorylated peptides were assessed. Finally, the DHAP/DAHC matrix was applied to identify phosphorylation sites from alpha-casein and beta-casein and to characterize two phosphorylation sites from the human histone H1 treated with Cyclin-Dependent Kinase-1 (CDK1) by MALDI-TOF/TOF MS.
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Mechanisms of Biliary Damage.
J Cell Death
PUBLISHED: 03-17-2010
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Bile duct damage is present in virtually all cholangiopathies, which share the biliary epithelial cells (i.e. cholangiocytes) as a common pathogenic target. Cholangiocyte cell death largely occurs through the process of apoptosis. In this review, we will summarize the mechanisms through which biliary damage occurs in a variety of animal and in vitro models, such as extrahepatic cholestasis induced by bile duct ligation (BDL), cytotoxin- and hepatotoxin-induced liver injury, and biliary atresia. Although we have increased our knowledge of the factors that regulate cholangiocyte cell death mechanisms during cholangiopathies, especially in experimental models, there is still a lack of effective treatment modalities for these biliary disorders. However, future studies will hopefully provide for new therapeutic modalities for the prevention or restoration of biliary mass and function lost during the progression of cholangiopathies.
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Proteomic analysis of mitochondria from Caenorhabditis elegans.
Proteomics
PUBLISHED: 08-12-2009
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Mitochondria play essential roles in cell physiological processes including energy production, metabolism, ion homeostasis, cell growth, aging and apoptosis. Proteomic strategies have been applied to the study of mitochondria since 1998; these studies have yielded decisive information about the diverse physiological functions of the organelle. As an ideal model biological system, the nematode Caenorhabditis elegans has been widely used in the study of several diseases, such as metabolic diseases and cancer. However, the mitochondrial proteome of C. elegans remains elusive. In this study, we purified mitochondria from C. elegans and performed a comprehensive proteomic analysis using the shotgun proteomic approach. A total of 1117 proteins have been identified with at least two unique peptides. Their physicochemical and functional characteristics, subcellular locations, related biological processes, and associations with human diseases, especially Parkinsons disease, are discussed. An orthology comparison was also performed between C. elegans and four other model organisms for a general depiction of the conservation of mitochondrial proteins during evolution. This study will provide new clues for understanding the role of mitochondria in the physiological and pathological processes of C. elegans.
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Analysis of the urine proteome of human contrast-induced kidney injury using two-dimensional fluorescence differential gel electrophoresis/matrix-assisted laser desorption time-of-flight mass spectrometry/liquid chromatography mass spectrometry.
Am. J. Nephrol.
PUBLISHED: 07-02-2009
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The pathogenesis of contrast-induced nephropathy (CIN) remains unclear and is defined by changes in serum creatinine which is not a sensitive biomarker for acute kidney injury. Search for differentially expressed urinary protein or peptide could contribute to further understanding of the disease and may provide new biomarkers.
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RUVBL2, a novel AS160-binding protein, regulates insulin-stimulated GLUT4 translocation.
Cell Res.
PUBLISHED: 06-16-2009
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In fat and muscle cells, insulin-stimulated glucose uptake is mainly mediated by glucose transporter 4 (GLUT4), which translocates from intracellular compartments to the cell surface in response to insulin stimulation. AS160 is one of the substrates of Akt and plays important roles in insulin-regulated GLUT4 translocation. In this study, RuvB-like protein 2 (RUVBL2) is identified as a new AS160-binding protein using mammalian tandem affinity purification (TAP) combined with mass spectrometry. In 3T3-L1 adipocytes, RUVBL2 is highly expressed and is mainly distributed in the cytosol. Depletion of RUVBL2 in adipocytes inhibits insulin-stimulated GLUT4 translocation and glucose uptake through reducing insulin-stimulated AS160 phosphorylation. However, introduction of human RUVBL2 can reverse this inhibitory effect. These data suggest that RUVBL2 plays an important role in insulin-stimulated GLUT4 translocation through its interaction with AS160.
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Sequential phosphorylation of Nedd1 by Cdk1 and Plk1 is required for targeting of the gammaTuRC to the centrosome.
J. Cell. Sci.
PUBLISHED: 06-09-2009
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Nedd1 is a new member of the gamma-tubulin ring complex (gammaTuRC) and targets the gammaTuRC to the centrosomes for microtubule nucleation and spindle assembly in mitosis. Although its role is known, its functional regulation mechanism remains unclear. Here we report that the function of Nedd1 is regulated by Cdk1 and Plk1. During mitosis, Nedd1 is firstly phosphorylated at T550 by Cdk1, which creates a binding site for the polo-box domain of Plk1. Then, Nedd1 is further phosphorylated by Plk1 at four sites: T382, S397, S637 and S426. The sequential phosphorylation of Nedd1 by Cdk1 and Plk1 promotes its interaction with gamma-tubulin for targeting the gammaTuRC to the centrosome and is important for spindle formation. Knockdown of Plk1 by RNAi decreases Nedd1 phosphorylation and attenuates Nedd1 accumulation at the spindle pole and subsequent gamma-tubulin recruitment at the spindle pole for microtubule nucleation. Taken together, we propose that the sequential phosphorylation of Nedd1 by Cdk1 and Plk1 plays a pivotal role in targeting gammaTuRC to the centrosome by promoting the interaction of Nedd1 with the gammaTuRC component gamma-tubulin, during mitosis.
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ISG56 is a negative-feedback regulator of virus-triggered signaling and cellular antiviral response.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 04-28-2009
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IFN-stimulated gene 56 (ISG56) is one of the first identified proteins induced by viruses and type I IFNs. In this study, we identified ISG56 as a virus-induced protein associated with MITA, an adapter protein involved in virus-triggered induction of type I IFNs. Overexpression of ISG56 inhibited Sendai virus-triggered activation of IRF3, NF-kappaB, and the IFN-beta promoter, whereas knockdown of ISG56 had opposite effects. Consistently, overexpression of ISG56 reversed cytoplasmic poly(I:C)-induced inhibition of vesicular stomatitis virus (VSV) replication, whereas knockdown of ISG56 inhibited VSV replication. Competitive coimmunoprecipitation experiments indicated that ISG56 disrupted the interactions between MITA and VISA or TBK1, two components in the virus-triggered IFN signaling pathways. These results suggest that ISG56 is a mediator of negative-feedback regulation of virus-triggered induction of type I IFNs and cellular antiviral responses.
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Discovery and identification of potential biomarkers of pediatric acute lymphoblastic leukemia.
Proteome Sci
PUBLISHED: 03-16-2009
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Acute lymphoblastic leukemia (ALL) is a common form of cancer in children. Currently, bone marrow biopsy is used for diagnosis. Noninvasive biomarkers for the early diagnosis of pediatric ALL are urgently needed. The aim of this study was to discover potential protein biomarkers for pediatric ALL.
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Preliminary quantitative profile of differential protein expression between rat L6 myoblasts and myotubes by stable isotope labeling with amino acids in cell culture.
Proteomics
PUBLISHED: 03-03-2009
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Defining the mechanisms governing myogenesis has advanced in recent years. Skeletal-muscle differentiation is a multi-step process controlled spatially and temporally by various factors at the transcription level. To explore those factors involved in myogenesis, stable isotope labeling with amino acids in cell culture (SILAC), coupled with high-accuracy mass spectrometry (LTQ-Orbitrap), was applied successfully. Rat L6 cell line is an excellent model system for studying muscle myogenesis in vitro. When mononucleate L6 myoblast cells reach confluence in culture plate, they could transform into multinucleate myotubes by serum starvation. By comparing protein expression of L6 myoblasts and terminally differentiated multinucleated myotubes, 1170 proteins were quantified and 379 proteins changed significantly in fully differentiated myotubes in contrast to myoblasts. These differentially expressed proteins are mainly involved in inter-or intracellular signaling, protein synthesis and degradation, protein folding, cell adhesion and extracellular matrix, cell structure and motility, metabolism, substance transportation, etc. These findings were supported by many previous studies on myogenic differentiation, of which many up-regulated proteins were found to be involved in promoting skeletal muscle differentiation for the first time in our study. In summary, our results provide new clues for understanding the mechanism of myogenesis.
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Discovery and identification of potential biomarkers of papillary thyroid carcinoma.
Mol. Cancer
PUBLISHED: 03-01-2009
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Thyroid carcinoma is the most common endocrine malignancy and a common cancer among the malignancies of head and neck. Noninvasive and convenient biomarkers for diagnosis of papillary thyroid carcinoma (PTC) as early as possible remain an urgent need. The aim of this study was to discover and identify potential protein biomarkers for PTC specifically.
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Epigenetic regulation of miR-34a expression in alcoholic liver injury.
Am. J. Pathol.
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Epigenetic changes are associated with the regulation of transcription of key cell regulatory genes [micro RNAs (miRNAs)] during different types of liver injury. This study evaluated the role of methylation-associated miRNA, miR-34a, in alcoholic liver diseases. We identified that ethanol feeding for 4 weeks significantly up-regulated 0.8% of known miRNA compared with controls, including miR-34a. Treatment of normal human hepatocytes (N-Heps) and cholangiocytes [human intrahepatic biliary epithelial cells (HiBECs)] with ethanol and lipopolysaccharide induced a significant increase of miR-34a expression. Overexpression of miR-34a decreased ethanol-induced apoptosis in both N-Heps and HiBECs. In support of the concept that the 5-promoter region of miR-34a was noted to be embedded within a CpG island, the expression level of miR-34a was significantly increased after demethylation treatment in N-Heps and HiBECs. By methylation-specific PCR, we confirmed that miR-34a activation is associated with ethanol-linked hypomethylation of the miR-34a promoter. A combination of bioinformatics, dual-luciferase reporter assay, mass spectrometry, and Western blot analysis revealed that caspase-2 and sirtuin 1 are the direct targets of miR-34a. Furthermore, modulation of miR-34a also altered expression of matrix metalloproteases 1 and 2, the mediators involved in hepatic remodeling during alcoholic liver fibrosis. These findings provide the basis for an exciting field in which the epigenomic microRNAs of hepatic cells may be manipulated with potential therapeutic benefits in human alcoholic liver diseases.
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MS-Simulator: predicting y-ion intensities for peptides with two charges based on the intensity ratio of neighboring ions.
J. Proteome Res.
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For the identification of peptides with tandem mass spectrometry (MS/MS), many software tools rely on the comparison between an experimental spectrum and a theoretically predicted spectrum. Consequently, the accurate prediction of the theoretical spectrum from a peptide sequence can potentially improve the peptide identification performance and is an important problem for mass spectrometry based proteomics. In this study a new approach, called MS-Simulator, is presented for predicting the y-ion intensities in the spectrum of a given peptide. The new approach focuses on the accurate prediction of the relative intensity ratio between every two adjacent y-ions. The theoretical spectrum can then be derived from these ratios. The prediction of a ratio is a closed-form equation that involves up to five consecutive amino acids nearby the two y-ions and the two peptide termini. Compared with another existing spectrum prediction tool MassAnalyzer, the new approach not only simplifies the computation, but also improves the prediction accuracy.
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Mitochondria in the pathogenesis of diabetes: a proteomic view.
Protein Cell
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Diabetes mellitus is a complex metabolic disorder characterized by chronic hyperglycemia due to absolute or relative lack of insulin. Though great efforts have been made to investigate the pathogenesis of diabetes, the underlying mechanism behind the development of diabetes and its complications remains unexplored. Cumulative evidence has linked mitochondrial modification to the pathogenesis of diabetes and its complications and they are also observed in various tissues affected by diabetes. Proteomics is an attractive tool for the study of diabetes since it allows researchers to compare normal and diabetic samples by identifying and quantifying the differentially expressed proteins in tissues, cells or organelles. Great progress has already been made in mitochondrial proteomics to elucidate the role of mitochondria in the pathogenesis of diabetes and its complications. Further studies on the changes of mitochondrial protein specifically post-translational modifications during the diabetic state using proteomic tools, would provide more information to better understand diabetes.
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Proteomic study and marker protein identification of Caenorhabditis elegans lipid droplets.
Mol. Cell Proteomics
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Lipid droplets (LDs) are a neutral lipid storage organelle that is conserved across almost all species. Many metabolic syndromes are directly linked to the over-storage of neutral lipids in LDs. The study of LDs in Caenorhabditis elegans (C. elegans) has been difficult because of the lack of specific LD marker proteins. Here we report the purification and proteomic analysis of C. elegans lipid droplets for the first time. We identified 306 proteins, 63% of these proteins were previously known to be LD-proteins, suggesting a similarity between mammalian and C. elegans LDs. Using morphological and biochemical analyses, we show that short-chain dehydrogenase, DHS-3 is almost exclusively localized on C. elegans LDs, indicating that it can be used as a LD marker protein in C. elegans. These results will facilitate further mechanistic studies of LDs in this powerful genetic system, C. elegans.
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Purification, identification and profiling of serum amyloid A proteins from sera of advanced-stage cancer patients.
J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.
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Surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF-MS) is a powerful tool for screening potential biomarkers of various pathological conditions. However, low resolution and mass accuracy of SELDI-TOF-MS remain a major obstacle for determination of biological identities of potential protein biomarkers. We report here a refined workflow that combines ZipTip desalting, acetonitrile precipitation, high-performance liquid chromatography (HPLC) separation and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) analysis for the profiling, purification and identification of the targeted serum proteins found by SELDI-TOF-MS. By using this workflow, we purified ten targeted proteins from the sera of patients with various types of advanced stage (stage III-IV) cancers. These proteins were identified as isoforms of the human serum amyloid protein A (SAA) family with or without truncations at their N-terminals. This was confirmed by Western blot analysis. Different SAA expression patterns were observed by MALDI-TOF-MS profiling. SAA has long been reported as a biomarker for various cancer types such as lung cancer, ovarian cancer, and breast cancer. However, in this study we found increased SAA expression in the sera of advanced-stage cancer patients with different cancer types. Our results suggest that maybe SAA should not be used alone as a biomarker for any specific cancer type.
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Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells.
Nat. Cell Biol.
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Accumulating evidence has shown that dysfunctional mitochondria can be selectively removed by mitophagy. Dysregulation of mitophagy is implicated in the development of neurodegenerative disease and metabolic disorders. How individual mitochondria are recognized for removal and how this process is regulated remain poorly understood. Here we report that FUNDC1, an integral mitochondrial outer-membrane protein, is a receptor for hypoxia-induced mitophagy. FUNDC1 interacted with LC3 through its typical LC3-binding motif Y(18)xxL(21), and mutation of the LC3-interaction region impaired its interaction with LC3 and the subsequent induction of mitophagy. Knockdown of endogenous FUNDC1 significantly prevented hypoxia-induced mitophagy, which could be reversed by the expression of wild-type FUNDC1, but not LC3-interaction-deficient FUNDC1 mutants. Mechanistic studies further revealed that hypoxia induced dephosphorylation of FUNDC1 and enhanced its interaction with LC3 for selective mitophagy. Our findings thus offer insights into mitochondrial quality control in mammalian cells.
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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.