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Find video protocols related to scientific articles indexed in Pubmed.
Inhibition of phosphodiesterase10A attenuates morphine-induced conditioned place preference.
Mol Brain
PUBLISHED: 09-25-2014
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BackgroundPhosphodiesterase (PDE) 10A is selectively expressed in medium spiny neurons of the striatum. Nucleus accumbens (NAc) is a key region that mediates drug reward and addiction-related behaviors. To investigate the potential role of PDE10A in the reinforcement properties of morphine, we tested the effect of MP-10, a selective inhibitor of PDE10A, on acquisition, expression, and extinction of morphine-induced conditioned place preference (CPP).ResultsThe results show that 2.5 mg/kg MP-10, administered subcutaneously, significantly inhibited the acquisition of morphine-induced CPP. The same dose of MP-10 alone did not result in the CPP. Moreover, MP-10 did not alter the expression of morphine-induced CPP, but did accelerate the extinction of morphine-induced CPP. Additionally, chronic treatment with 2.5 mg/kg MP-10 decreased expression of phosphorylated CREB (pCREB), activated cAMP response element binding protein, in dorsomedial striatum, in shell of NAc, and in anterior cingulate cortex (ACC) as well as decreased expression of ¿FosB in the shell of NAc and ACC.ConclusionThe results suggest that inhibition of PDE10A may have therapeutic potential in the treatment of opioid addiction.
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Allergen screening bioassays: recent developments in lab-on-a-chip and lab-on-a-disc systems.
Bioanalysis
PUBLISHED: 08-28-2014
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Allergies occur when a person's immune system mounts an abnormal response with or without IgE to a normally harmless substance called an allergen. The standard skin-prick test introduces suspected allergens into the skin with lancets in order to trigger allergic reactions. This test is annoying and sometimes life threatening. New tools such as lab-on-a-chip and lab-on-a-disc, which rely on microfabrication, are designed for allergy testing. These systems provide benefits such as short analysis times, enhanced sensitivity, simplified procedures, minimal consumption of sample and reagents and low cost. This article gives a summary of these systems. In particular, a cell-based assay detecting both the IgE- and non-IgE-type triggers through the study of degranulation in a centrifugal microfluidic system is highlighted.
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p62/sequestosome 1 regulates aggresome formation of pathogenic ataxin-3 with expanded polyglutamine.
Int J Mol Sci
PUBLISHED: 08-25-2014
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The cellular protein quality control system in association with aggresome formation contributes to protecting cells against aggregation-prone protein-induced toxicity. p62/Sequestosome 1 (p62) is a multifunctional protein which plays an important role in protein degradation and aggregation. Although poly-ubiquitination is usually required for p62-mediated protein degradation and aggresome formation, several p62 substrates are processed to form aggregate in an ubiquitination-independent manner. In this study we demonstrate that p62 directly interacts with pathogenic Machado Joseph Disease (MJD)-associated protein ataxin-3 with polyglutamine (polyQ) expansion. Moreover, p62 could regulate the aggresome formation of pathogenic ataxin-3 and protect cells against pathogenic ataxin-3-induced cell death.
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Bcl-2 Decreases the Affinity of SQSTM1/p62 to Poly-Ubiquitin Chains and Suppresses the Aggregation of Misfolded Protein in Neurodegenerative Disease.
Mol. Neurobiol.
PUBLISHED: 08-04-2014
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Poly-ubiquitinated protein aggregate formation is the most striking hallmark of various neurodegenerative diseases such as Alzheimer's disease, Huntington's disease, amyotrophic lateral sclerosis, and prion disease. Mutations of many ubiquitin-associated proteins involved in the regulation of protein aggregation, such as SQSTM1/p62 (p62), parkin, and VCP, are closely linked to neurodegeneration. B-cell lymphoma 2 (Bcl-2) is a key regulator in autophagy, apoptosis, and mitochondria quality control in many cell types including neurons, and it plays important roles in the pathogenesis of neurodegenerative diseases mentioned above. Our previous work showed that Bcl-2 can directly bind to p62, and here we report that Bcl-2 directly interacts with the N-terminus of p62, but not the C-terminus (UBA domain). Interestingly and importantly, Bcl-2 affects the affinity of p62 to poly-ubiquitin chains and suppresses the aggregation of poly-ubiquitinated proteins such as mutant huntingtin associated with Huntington's disease. Our study reveals a role of Bcl-2 that involves in the regulation of misfolded proteins.
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Global discovery of high-NaCl-induced changes of protein phosphorylation.
Am. J. Physiol., Cell Physiol.
PUBLISHED: 06-25-2014
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High extracellular NaCl, such as in the renal medulla, can perturb and even kill cells, but cells mount protective responses that enable them to survive and function. Many high-NaCl-induced perturbations and protective responses are known, but the signaling pathways involved are less clear. Change in protein phosphorylation is a common mode of cell signaling, but there was no unbiased survey of protein phosphorylation in response to high NaCl. We used stable isotopic labeling of amino acids in cell culture coupled to mass spectrometry to identify changes in protein phosphorylation in human embryonic kidney (HEK 293) cells exposed to high NaCl. We reproducibly identify >8,000 unique phosphopeptides in 4 biological replicate samples with a 1% false discovery rate. High NaCl significantly changed phosphorylation of 253 proteins. Western analysis and targeted ion selection mass spectrometry confirm a representative sample of the phosphorylation events. We analyze the affected proteins by functional category to infer how altered protein phosphorylation might signal cellular responses to high NaCl, including alteration of cell cycle, cyto/nucleoskeletal organization, DNA double-strand breaks, transcription, proteostasis, metabolism of mRNA, and cell death.
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Structure elucidation and biological activity of two new trichothecenes from an endophyte, Myrothecium roridum.
J. Agric. Food Chem.
PUBLISHED: 06-17-2014
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Worldwide, many different grains are infected by various fungi that may produce trichothecene mycotoxins. Fungi that produce trichothecenes, as well as the trichothecenes themselves, are potential problems for public health. On the other hand, trichothecenes possess multiple biological activities. Reduced toxicity may result in their applications in the pharmaceutical field. Two new trichothecenes along with seven known trichothecenes were isolated from an endophyte of the herb plant Ajuga decumbens. Their structures were deduced from 1D and 2D NMR data. The results of MTT assays revealed that new trichothecene 2',3'-epoxymyrothecine A, 1, and myrothecine A, 3, exhibited much lower toxicity compared to other trichothecenes. New trichothecene 2',3'-epoxymyrothecine A, 1, could induce phosphorylation of JNK (c-Jun N-terminal protein kinase) protein and the PARP (poly ADP-ribose polymerase) cleavage, and eventually induce apoptosis in cancer cells. These results point out the possibility for application of trichothecenes as chemotherapeutic agent.
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Interleukin 22 protects colorectal cancer cells from chemotherapy by activating the STAT3 pathway and inducing autocrine expression of interleukin 8.
Clin. Immunol.
PUBLISHED: 06-06-2014
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Resistance to chemotherapy is the major cause of colorectal cancer (CRC) treatment failure. The cytokine IL-22, which is produced by T cells and NK cells, is associated with tumorigenesis and tumor progression in cancers. However, the role of IL-22 in chemoresistance has not been investigated. We found that IL-22 levels in tumor tissues and peripheral blood were associated with chemoresistance and indicate poor prognosis for patients who received FOLFOX chemotherapy. In CRC cells, IL-22 was able to attenuate the cytotoxic and apoptosis-inducing effects of 5-FU and OXA by activating the STAT3 pathway and subsequently increasing the expression of anti-apoptotic genes. In addition, IL-22 conferred resistance to 5-FU and OXA by inducing IL-8 autocrine expression through STAT3 activation. Our findings identify IL-22 as a novel chemoresistance cytokine and may be a useful prognostic biomarker for CRC patients receiving FOLFOX chemotherapy.
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Biochemical and biological properties of cortexillin III, a component of Dictyostelium DGAP1-cortexillin complexes.
Mol. Biol. Cell
PUBLISHED: 05-07-2014
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Cortexillins I-III are members of the ?-actinin/spectrin subfamily of Dictyostelium calponin homology proteins. Unlike recombinant cortexillins I and II, which form homodimers as well as heterodimers in vitro, we find that recombinant cortexillin III is an unstable monomer but forms more stable heterodimers when coexpressed in Escherichia coli with cortexillin I or II. Expressed cortexillin III also forms heterodimers with both cortexillin I and II in vivo, and the heterodimers complex in vivo with DGAP1, a Dictyostelium GAP protein. Binding of cortexillin III to DGAP1 requires the presence of either cortexillin I or II; that is, cortexillin III binds to DGAP1 only as a heterodimer, and the heterodimers form in vivo in the absence of DGAP1. Expressed cortexillin III colocalizes with cortexillins I and II in the cortex of vegetative amoebae, the leading edge of motile cells, and the cleavage furrow of dividing cells. Colocalization of cortexillin III and F-actin may require the heterodimer/DGAP1 complex. Functionally, cortexillin III may be a negative regulator of cell growth, cytokinesis, pinocytosis, and phagocytosis, as all are enhanced in cortexillin III-null cells.
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A polyphenylene support for Pd catalysts with exceptional catalytic activity.
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 05-02-2014
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We describe a solid polyphenylene support that serves as an excellent platform for metal-catalyzed reactions that are normally carried out under homogeneous conditions. The catalyst is synthesized by palladium-catalyzed Suzuki coupling which directly results in formation of palladium nanoparticles confined to a porous polyphenylene network. The composite solid is in turn highly active for further Suzuki coupling reactions, including non-activated substrates that are challenging even for molecular catalysts.
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Myrotheciumones: bicyclic cytotoxic lactones isolated from an endophytic fungus of Ajuga decumbens.
Bioorg. Med. Chem. Lett.
PUBLISHED: 03-17-2014
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Two new bicyclic lactones, myrotheciumones A (1) and B (2) which possessed a rare ring-fusion system were isolated from Myrothecium roridum (M. roridum), an endophytic fungus of the medicinal herb plant Ajuga decumbens (A. decumbens) via an in vitro cytotoxicity assay. Structures were deduced from 1D and 2D NMR (Nuclear magnetic resonance) data. Myrotheciumone A's in vitro cytotoxicity and apoptotic activity were evaluated and myrotheciumone A was shown to exert cytotoxicity via inducing apoptosis in cancer cell line.
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Total synthesis and RXR?-mediated transcription studies of neriifolone B and related compounds.
Bioorg. Med. Chem.
PUBLISHED: 03-13-2014
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Neriifolone B (1), a natural product containing a novel 4',4'-dimethyl-4',5'-dihydropyran-6-one[2',3':3,4]xanthone skeleton, was found to be a potent inhibitor of transcription mediated by retinoid X receptor ? (RXR?). The first total synthesis of neriifolone B (1) was achieved in 14 steps with an overall yield of 7.1%. A Claisen rearrangement was employed as the key step in the sequence. The activity of six natural xanthones and eight compounds related to neriifolone B (1) against RXR?-mediated transcription was evaluated. Two neriifolone B analogs, 17 and 11?, were potent inhibitors of RXR? transcriptional activity. Preliminary structure-activity relationship studies are discussed briefly.
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Multimethylation of Rickettsia OmpB catalyzed by lysine methyltransferases.
J. Biol. Chem.
PUBLISHED: 02-04-2014
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Methylation of rickettsial OmpB (outer membrane protein B) has been implicated in bacterial virulence. Rickettsial methyltransferases RP789 and RP027-028 are the first biochemically characterized methyltransferases to catalyze methylation of outer membrane protein (OMP). Methylation in OMP remains poorly understood. Using semiquantitative integrated liquid chromatography-tandem mass spectroscopy, we characterize methylation of (i) recombinantly expressed fragments of Rickettsia typhi OmpB exposed in vitro to trimethyltransferases of Rickettsia prowazekii RP027-028 and of R. typhi RT0101 and to monomethyltransferases of R. prowazekii RP789 and of R. typhi RT0776, and (ii) native OmpBs purified from R. typhi and R. prowazekii strains Breinl, RP22, and Madrid E. We found that in vitro trimethylation occurs at relatively specific locations in OmpB with consensus motifs, KX(G/A/V/I)N and KT(I/L/F), whereas monomethylation is pervasive throughout OmpB. Native OmpB from virulent R. typhi contains mono- and trimethyllysines at locations well correlated with methylation in recombinant OmpB catalyzed by methyltransferases in vitro. Native OmpBs from highly virulent R. prowazekii strains Breinl and RP22 contain multiple clusters of trimethyllysine in contrast to a single cluster in OmpB from mildly virulent R. typhi. Furthermore, OmpB from the avirulent strain Madrid E contains mostly monomethyllysine and no trimethyllysine. The native OmpB from Madrid E was minimally trimethylated by RT0101 or RP027-028, consistent with a processive mechanism of trimethylation. This study provides the first in-depth characterization of methylation of an OMP at the molecular level and may lead to uncovering the link between OmpB methylation and rickettsial virulence.
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Histamine H3 receptors aggravate cerebral ischaemic injury by histamine-independent mechanisms.
Nat Commun
PUBLISHED: 01-28-2014
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The role of the histamine H3 receptor (H3R) in cerebral ischaemia/reperfusion (I/R) injury remains unknown. Here we show that H3R expression is upregulated after I/R in two mouse models. H3R antagonists and H3R knockout attenuate I/R injury, which is reversed by an H3R-selective agonist. Interestingly, H1R and H2R antagonists, a histidine decarboxylase (HDC) inhibitor and HDC knockout all fail to compromise the protection by H3R blockade. H3R blockade inhibits mTOR phosphorylation and reinforces autophagy. The neuroprotection by H3R antagonism is reversed by 3-methyladenine and siRNA for Atg7, and is diminished in Atg5?/? mouse embryonic fibroblasts. Furthermore, the peptide Tat-H3R(CT414-436), which blocks CLIC4 binding with H3Rs, or siRNA for CLIC4, further increases I/R-induced autophagy and protects against I/R injury. Therefore, H3R promotes I/R injury while its antagonism protects against ischaemic injury via histamine-independent mechanisms that involve suppressing H3R/CLIC4 binding-activated autophagy, suggesting that H3R inhibition is a therapeutic target for cerebral ischaemia.
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NF-?B activation and cell death after intracerebral hemorrhage in patients.
Neurol. Sci.
PUBLISHED: 01-23-2014
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Nuclear factor-?B (NF-?B) plays an important role in secondary damage after intracerebral hemorrhage (ICH). We explored NF-?B activation and the relationship between NF-?B and cell death in the perihematomal brain tissue of patients after ICH. According to the interval between onset of hemorrhage and specimen collection, 53 cases of patients with basal ganglia hemorrhage were divided into six experimental groups: 0-6, 7-12, 13-24, 25-48, 49-96, and >96 h group. Brain tissues of the experimental groups and control group were collected. IL-1?, TNF-?, and NF-?B p65 expressions at the protein level were detected by immunohistochemistry. Cell death was detected by terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling (TUNEL) assay. All of the detection items of immunohistochemistry and TUNEL showed significant differences between the experimental groups and control group. At the protein level, nuclear NF-?B p65, IL-1?, and TNF-? achieved maximum values at 13-48, 0-24, and 13-48 h, respectively. Maximum cell death was reached at 13-48 h. NF-?B activation increased dramatically in perihematomal brain tissue after ICH. NF-?B activation was closely related with cell death and had an important function in secondary brain damage after ICH in patients.
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Prognostic significance of systemic inflammation-based lymphocyte- monocyte ratio in patients with lung cancer: based on a large cohort study.
PLoS ONE
PUBLISHED: 01-01-2014
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Increasing evidence indicates cancer-related inflammatory biomarkers show great promise for predicting the outcome of cancer patients. The lymphocyte- monocyte ratio (LMR) was demonstrated to be independent prognostic factor mainly in hematologic tumor. The aim of the present study was to investigate the prognostic value of LMR in operable lung cancer. We retrospectively enrolled a large cohort of patients with primary lung cancer who underwent complete resection at our institution from 2006 to 2011. Inflammatory biomarkers including lymphocyte count and monocyte count were collected from routinely performed preoperative blood tests and the LMR was calculated. Survival analyses were calculated for overall survival (OS) and disease-free survival (DFS). A total of 1453 patients were enrolled in the study. The LMR was significantly associated with OS and DFS in multivariate analyses of the whole cohort (HR = 1.522, 95% CI: 1.275-1.816 for OS, and HR = 1.338, 95% CI: 1.152-1.556 for DFS). Univariate subgroup analyses disclosed that the prognostic value was limited to patients with non-small-cell lung cancer (NSCLC) (HR: 1.824, 95% CI: 1.520-2.190), in contrast to patients with small cell lung cancer (HR: 1.718, 95% CI: 0.946-3.122). Multivariate analyses demonstrated that LMR was still an independent prognostic factor in NSCLC. LMR can be considered as a useful independent prognostic marker in patients with NSCLC after complete resection. This will provide a reliable and convenient biomarker to stratify high risk of death in patients with operable NSCLC.
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Tumor-associated neutrophils as a new prognostic factor in cancer: a systematic review and meta-analysis.
PLoS ONE
PUBLISHED: 01-01-2014
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Tumor-associated neutrophils (TAN) have been reported in a variety of malignancies. We conducted an up-to-date meta-analysis to evaluate the prognostic role of TAN in cancer.
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BAG5 protects against mitochondrial oxidative damage through regulating PINK1 degradation.
PLoS ONE
PUBLISHED: 01-01-2014
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Mutations in PTEN-induced kinase 1 (PINK1) gene cause PARK6 familial Parkinsonism, and loss of the stability of PINK1 may also contribute to sporadic Parkinson's disease (PD). Degradation of PINK1 occurs predominantly through the ubiquitin proteasome system (UPS), however, to date, few of the proteins have been found to regulate the degradation of PINK1. Using the yeast two-hybrid system and pull-down methods, we identified bcl-2-associated athanogene 5 (BAG5), a BAG family member, directly interacted with PINK1. We showed that BAG5 stabilized PINK1 by decreasing the ubiquitination of PINK1. Interestingly, BAG5 rescued MPP(+)- and rotenone-induced mitochondria dysfunction by up-regulating PINK1 in vitro. In PINK1-null mice and MPTP-treated mice, BAG5 significantly increased in the substantia nigra pars compacta (SNpc) although PINK1 was decreased. Our findings indicated that BAG5, as a key protein to stabilize PINK1, is a promising therapeutic tool for preventing mitochondrial dysfunction following oxidative stress.
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Gambogenic acid kills lung cancer cells through aberrant autophagy.
PLoS ONE
PUBLISHED: 01-01-2014
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Lung cancer is one of the most common types of cancer and causes 1.38 million deaths annually, as of 2008 worldwide. Identifying natural anti-lung cancer agents has become very important. Gambogenic acid (GNA) is one of the active compounds of Gamboge, a traditional medicine that was used as a drastic purgative, emetic, or vermifuge for treating tapeworm. Recently, increasing evidence has indicated that GNA exerts promising anti-tumor effects; however, the underlying mechanism remains unclear. In the present paper, we found that GNA could induce the formation of vacuoles, which was linked with autophagy in A549 and HeLa cells. Further studies revealed that GNA triggers the initiation of autophagy based on the results of MDC staining, AO staining, accumulation of LC3 II, activation of Beclin 1 and phosphorylation of P70S6K. However, degradation of p62 was disrupted and free GFP could not be released in GNA treated cells, which indicated a block in the autophagy flux. Further studies demonstrated that GNA blocks the fusion between autophagosomes and lysosomes by inhibiting acidification in lysosomes. This dysfunctional autophagy plays a pro-death role in GNA-treated cells by activating p53, Bax and cleaved caspase-3 while decreasing Bcl-2. Beclin 1 knockdown greatly decreased GNA-induced cell death and the effects on p53, Bax, cleaved caspase-3 and Bcl-2. Similar results were obtained using a xenograft model. Our findings show, for the first time, that GNA can cause aberrant autophagy to induce cell death and may suggest the potential application of GNA as a tool or viable drug in anticancer therapies.
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The ubiquitin proteasome system as a potential target for the treatment of neurodegenerative diseases.
Curr. Pharm. Des.
PUBLISHED: 10-29-2013
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Neurodegenerative diseases are severe disorders characterized by progressive neurodegeneration in specific brain regions. The ubiquitin-proteasome system (UPS) is closely linked to neurodegenerative disease. In most cases, UPS impairment and dysregulation of the UPS components are frequently observed. Moreover, toxin-induced neurodegeneration produces neuronal cell death accompanied by decreased UPS function. These studies suggest an involvement of the UPS in these diseases. In this review, we summarize the changes to UPS components in neurodegenerative diseases and the association between the UPS and disease pathology. Dysfunction of the UPS results in the abnormal accumulation of proteins; thus, the UPS plays a critical role in disease pathogenesis. Drugs targeting specific components of the UPS may provide promising strategies for disease treatment.
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Comparative study of the anatomic segmentectomy versus lobectomy for clinical stage IA peripheral lung cancer by video assistant thoracoscopic surgery.
J Cancer Res Ther
PUBLISHED: 10-19-2013
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The objective of this study was to compare the completely thoracoscopic anatomic segmentectomy with lobectomy to treat stage I(A) peripheral lung cancer <2 cm.
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Cyclophilin d modulates mitochondrial acetylome.
Circ. Res.
PUBLISHED: 09-23-2013
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Mice lacking cyclophilin D (CypD(-/-)), a mitochondrial chaperone protein, have altered cardiac metabolism. As acetylation has been shown to regulate metabolism, we tested whether changes in protein acetylation might play a role in these metabolic changes in CypD(-/-) hearts.
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The BAG2 protein stabilises PINK1 by decreasing its ubiquitination.
Biochem. Biophys. Res. Commun.
PUBLISHED: 08-30-2013
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Mutations in the PTEN-induced putative kinase 1 (PINK1) gene cause an autosomal recessive form of Parkinson disease (PD). Thus far, little is known about what can regulate the ubiquitin proteasome pathway of PINK1. Here, we report BAG2 (Bcl-2-associated athanogene family protein 2), a member of the BAG family, which directly binds with and stabilises PINK1 by decreasing its ubiquitination. Moreover, we found that BAG2 also binds with the pathogenic R492X PINK1 mutation directly and more tightly. Moreover, BAG2 stabilises the R492X PINK1 mutation by decreasing its ubiquitination to a greater extent than the wild-type species. Our data correlate BAG2 to PINK1 for the first time, strengthening the important role of BAG2 in PD-related neurodegeneration.
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Focused ion beam nanoscale patterned transmission-enhanced fiber-optic tips.
J Nanosci Nanotechnol
PUBLISHED: 08-02-2013
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The angled and tapered antireflection and transmission-enhanced fiber-optic tips were designed, fabricated, and characterized based on nanoscale surface modification using the nano-precision focused ion beam (FIB). The developed optical fiber tips showed combined functions of antireflection and transmission enhancement for higher detection efficiency or signal-to-noise ratio because the FIB-milled nanoholes into the fiber tip endfaces could act as tapered air-filled nanopillars, changing the light propagation direction, enhancing the scattering effect, and allowing more photons to transmit along/near the glass/air interface to enhance the local evanescent field for sensing/detection.
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A lab-in-a-droplet bioassay strategy for centrifugal microfluidics with density difference pumping, power to disc and bidirectional flow control.
Lab Chip
PUBLISHED: 07-25-2013
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In this paper, we present a lab-in-a-droplet bioassay strategy for a centrifugal microfluidics or lab-on-a-disc (LOAD) platform with three important advancements including density difference pumping, power to disc and bidirectional flow control. First, with the water based bioassay droplets trapped in a micro-channel filled with mineral oil, centrifugal force due to the density difference between the water and oil phases actuates droplet movement while the oil based medium remains stationary. Second, electricity is coupled to the rotating disc through a split-core transformer, thus enabling on-chip real-time heating in selected areas as desired and wireless programmable functionality. Third, an inertial mechanical structure is proposed to achieve bidirectional flow control within the spinning disc. The droplets can move back and forth between two heaters upon changing the rotational speed. Our platform is an essential and versatile solution for bioassays such as those involving DNA amplification, where localized temperature cycling is required. Finally, without the loss of generality, we demonstrate the functionality of our platform by performing real-time polymerase chain reaction (RT-PCR) in a linear microchannel made with PTFE (Teflon) micro-tubing.
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Cerebral ischemia-reperfusion-induced autophagy protects against neuronal injury by mitochondrial clearance.
Autophagy
PUBLISHED: 06-12-2013
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Cerebral ischemia-reperfusion (I-R) is a complex pathological process. Although autophagy can be evoked by ischemia, its involvement in the reperfusion phase after ischemia and its contribution to the fate of neurons remains largely unknown. In the present investigation, we found that autophagy was activated in the reperfusion phase, as revealed in both mice with middle cerebral artery occlusion and oxygen-glucose deprived cortical neurons in culture. Interestingly, in contrast to that in permanent ischemia, inhibition of autophagy (by 3-methyladenine, bafilomycin A 1, Atg7 knockdown or in atg5(-/-) MEF cells) in the reperfusion phase reinforced, rather than reduced, the brain and cell injury induced by I-R. Inhibition of autophagy either with 3-methyladenine or Atg7 knockdown enhanced the I-R-induced release of cytochrome c and the downstream activation of apoptosis. Moreover, MitoTracker Red-labeled neuronal mitochondria increasingly overlapped with GFP-LC3-labeled autophagosomes during reperfusion, suggesting the presence of mitophagy. The mitochondrial clearance in I-R was reversed by 3-methyladenine and Atg7 silencing, further suggesting that mitophagy underlies the neuroprotection by autophagy. In support, administration of the mitophagy inhibitor mdivi-1 in the reperfusion phase aggravated the ischemia-induced neuronal injury both in vivo and in vitro. PARK2 translocated to mitochondria during reperfusion and Park2 knockdown aggravated ischemia-induced neuronal cell death. In conclusion, the results indicated that autophagy plays different roles in cerebral ischemia and subsequent reperfusion. The protective role of autophagy during reperfusion may be attributable to mitophagy-related mitochondrial clearance and inhibition of downstream apoptosis. PARK2 may be involved in the mitophagy process.
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High NaCl- and urea-induced posttranslational modifications that increase glycerophosphocholine by inhibiting GDPD5 phosphodiesterase.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 04-15-2013
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Glycerophosphocholine (GPC) is high in cells of the renal inner medulla where high interstitial NaCl and urea power concentration of the urine. GPC protects inner medullary cells against the perturbing effects of high NaCl and urea by stabilizing intracellular macromolecules. Degradation of GPC is catalyzed by the glycerophosphocholine phosphodiesterase activity of glycerophosphodiester phosphodiesterase domain containing 5 (GDPD5). We previously found that inhibitory posttranslational modification (PTM) of GDPD5 contributes to high NaCl- and urea-induced increase of GPC. The purpose of the present studies was to identify the PTM(s). We find at least three such PTMs in HEK293 cells: (i) Formation of a disulfide bond between C25 and C571. High NaCl and high urea increase reactive oxygen species (ROS). The ROS increase disulfide bonding between GDPD5-C25 and -C571, which inhibits GDPD5 activity, as supported by the findings that the antioxidant N-acetylcysteine prevents high NaCl- and urea-induced inhibition of GDPD5; GDPD5-C25S/C571S mutation or over expression of peroxiredoxin increases GDPD5 activity; H2O2 inhibits activity of wild type GDPD5, but not of GDPD5-C25S/C571S; and peroxiredoxin is relatively low in the renal inner medulla where GPC is high. (ii) Dephosphorylation of GDPD5-T587. GDPD5 threonine 587 is constitutively phosphorylated. High NaCl and high urea dephosphorylate GDPD5-T587. Mutation of GDPD5-T587 to alanine, which cannot be phosphorylated, decreases GPC-PDE activity of GDPD5. (iii) Alteration at an unknown site mediated by CDK1. Inhibition of CDK1 protein kinase reduces GDE-PDE activity of GDPD5 without altering phosphorylation at T587, and CDK1/5 inhibitor reduces activity of GDPD5- C25S/C571S-T587A.
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Effects of caudal sufentanil supplemented with levobupivacaine on blocking spermatic cord traction response in pediatric orchidopexy.
J Anesth
PUBLISHED: 04-07-2013
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Caudal block is one of the most commonly used anesthetic techniques in subumbilical and genitourinary procedures. However, traditional administration of caudal levobupivacaine was inadequate on blocking peritoneal response during spermatic cord traction. The aim of this study was to evaluate whether the addition of caudal sufentanil to levobupivacaine provided better analgesia for children undergoing orchidopexy.
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Intrinsic apoptotic pathway and G2/M cell cycle arrest involved in tubeimoside I-induced EC109 cell death.
Chin. J. Cancer Res.
PUBLISHED: 03-13-2013
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Squamous esophageal carcinoma is highly prevalent in developing countries, especially in China. Tu Bei Mu (TBM), a traditional folk medicine, has been used to treat esophageal squamous cell carcinoma (ESCC) for a long term. tubeimoside I (TBMS1) is the main component of TBM, exhibiting great anticancer potential. In this study, we investigated the mechanism of TBMS1 cytotoxic effect on EC109 cells.
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Global analysis of neuronal phosphoproteome regulation by chondroitin sulfate proteoglycans.
PLoS ONE
PUBLISHED: 02-13-2013
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Chondroitin sulfate proteoglycans (CSPGs) are major components of the extracellular matrix which mediate inhibition of axonal regeneration after injury to the central nervous system (CNS). Several neuronal receptors for CSPGs have recently been identified; however, the signaling pathways by which CSPGs restrict axonal growth are still largely unknown. In this study, we applied quantitative phosphoproteomics to investigate the global changes in protein phosphorylation induced by CSPGs in primary neurons. In combination with isobaric Tags for Relative and Absolute Quantitation (iTRAQ) labeling, strong cation exchange chromatography (SCX) fractionation, immobilized metal affinity chromatography (IMAC) and LC-MS/MS, we identified and quantified 2214 unique phosphopeptides corresponding to 1118 phosphoproteins, with 118 changing significantly in abundance with CSPG treatment. The proteins that were regulated by CSPGs included key components of synaptic vesicle trafficking, axon guidance mediated by semaphorins, integrin signaling, cadherin signaling and EGF receptor signaling pathways. A significant number of the regulated proteins are cytoskeletal and related proteins that have been implicated in regulating neurite growth. Another highly represented protein category regulated by CSPGs is nucleic acid binding proteins involved in RNA post-transcriptional regulation. Together, by screening the overall phosphoproteome changes induced by CSPGs, this data expand our understanding of CSPG signaling, which provides new insights into development of strategies for overcoming CSPG inhibition and promoting axonal regeneration after CNS injury.
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A novel derivatization-based liquid chromatography tandem mass spectrometry method for quantitative characterization of naphthenic acid isomer profiles in environmental waters.
J Chromatogr A
PUBLISHED: 01-09-2013
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A method for quantitative characterization of naphthenic acid (NA) isomer groups by carbon number and extent of cyclization was developed and validated with water samples from northern Alberta. Following solid phase extraction, NAs undergo derivatization with N-(3-dimethylaminopropyl)-N-ethylcarbodiimide (EDC) allowing detection by positive electrospray ionization tandem mass spectrometry (+ESI)-MS/MS. NA-EDC derivatives produce a common product ion by MS/MS, regardless of structure of the starting NA. Thus, approximately constant relative response factors (RRFs) were assumed for the various isomer groups that elute at a given point in the elution gradient (supported by calculated RRFs for individual model NAs), facilitating quantification using a single standard (1-pyrenebutyric acid). To reduce the impact of major background fatty acids on NA data, the method employed an optimized liquid chromatography method that separated straight chain (Z=0) analytes from other NAs. Method validation was performed at two spiking levels (7.72?g and 38.6?g total refined Merichem per 500mL of reagent water) and good accuracy (mean recoveries of 82.4±2.5% and 93.0±2.6%, respectively; range ~50-130%) and precision (<17% RSD) were achieved at both spiking levels for all 60 NA isomer groups. The method also performed well in an independent method comparison study in which method accuracy values of 107%, 120%, and 121% were obtained for 2 spiked reagent waters (1mg/L and 50mg/L NAs) and spiked Athabasca River water (0.035mg/L NAs), respectively. Application of the method to samples from northern Alberta revealed that NA concentrations decreased in the order: process water (52.8mg/L)>tailings pond water (30.6mg/L)>well water (0.086mg/L)>surface water (0.007mg/L), and that samples were distinguishable by NA isomer profile using Principal components analysis.
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SKF83959 is a potent allosteric modulator of sigma-1 receptor.
Mol. Pharmacol.
PUBLISHED: 01-07-2013
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SKF83959 (3-methyl-6-chloro-7,8-hydroxy-1-[3-methylphenyl]-2,3,4,5-tetrahydro-1H-3-benzazepine), an atypical dopamine receptor-1 (D(1) receptor) agonist, has shown many D(1) receptor-independent effects, such as neuroprotection, blockade of Na(+) channel, and promotion of spontaneous glutamate release, which resemble the effects of the sigma-1 receptor activation. In the present work, we explored the potential modulation of SKF83959 on the sigma-1 receptor. The results indicated that SKF83959 dramatically promoted the binding of (3)H(+)-pentazocine (a selective sigma-1 receptor agonist) to the sigma-1 receptor in brain and liver tissues but produced no effect on (3)H-progesterone binding (a sigma-1 receptor antagonist). The saturation assay and the dissociation kinetics assay confirmed the allosteric effect. We further demonstrated that the SKF83959 analogs, such as SCH22390 [(R)-(1)-7-chloro-8- hydroxy-3-methyl-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine hydrochloride] and SKF38393 [(+/-)-1-phenyl-2,3,4,5-tetrahydro-(1H)-3-benzazepine-7,8-diol hydrobromide], also showed the similar allosteric effect on the sigma-1 receptor in the liver tissue but not in the brain tissue. Moreover, all three tested chemicals elicited no significant effect on (3)H-1,3-di(2-tolyl)-guanidine ((3)H-DTG) binding to the sigma-2 receptor. The present data uncovered a new role of SKF83959 and its analogs on the sigma-1 receptor, which, in turn, may reveal the underlying mechanism for the D(1) receptor-independent effect of the drug.
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Identification of CHIP as a Novel Causative Gene for Autosomal Recessive Cerebellar Ataxia.
PLoS ONE
PUBLISHED: 01-01-2013
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Autosomal recessive cerebellar ataxias are a group of neurodegenerative disorders that are characterized by complex clinical and genetic heterogeneity. Although more than 20 disease-causing genes have been identified, many patients are still currently without a molecular diagnosis. In a two-generation autosomal recessive cerebellar ataxia family, we mapped a linkage to a minimal candidate region on chromosome 16p13.3 flanked by single-nucleotide polymorphism markers rs11248850 and rs1218762. By combining the defined linkage region with the whole-exome sequencing results, we identified a homozygous mutation (c.493CT) in CHIP (NM_005861) in this family. Using Sanger sequencing, we also identified two compound heterozygous mutations (c.389AT/c.441GT; c.621C>G/c.707GC) in CHIP gene in two additional kindreds. These mutations co-segregated exactly with the disease in these families and were not observed in 500 control subjects with matched ancestry. CHIP colocalized with NR2A, a subunit of the N-methyl-D-aspartate receptor, in the cerebellum, pons, medulla oblongata, hippocampus and cerebral cortex. Wild-type, but not disease-associated mutant CHIPs promoted the degradation of NR2A, which may underlie the pathogenesis of ataxia. In conclusion, using a combination of whole-exome sequencing and linkage analysis, we identified CHIP, encoding a U-box containing ubiquitin E3 ligase, as a novel causative gene for autosomal recessive cerebellar ataxia.
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Rotenone directly induces BV2 cell activation via the p38 MAPK pathway.
PLoS ONE
PUBLISHED: 01-01-2013
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Parkinsons disease (PD) is the second most common neurodegenerative disease. Although its pathogenesis is still unclear, increasing evidence suggests that mitochondrial dysfunction induced by environmental toxins, such as mitochondrial complex I inhibitors, plays a significant role in the disease process. The microglia in PD brains are highly activated, and inflammation is also an essential element in PD pathogenesis. However, the means by which these toxins activate microglia is still unclear. In the present study, we found that rotenone, a mitochondrial complex I inhibitor, could directly activate microglia via the nuclear factor kappa B (NF-?B) signaling pathway, thereby inducing significantly increased expression of inflammatory cytokines. We further observed that rotenone induced caspase-1 activation and mature IL-1? release, both of which are strictly dependent on p38 mitogen-activated protein kinase (MAPK). The activation of p38 is associated with the presence of reactive oxygen species (ROS) produced by rotenone. Removal of these ROS abrogated the activation of the microglia. Therefore, our data suggest that the environmental toxin rotenone can directly activate microglia through the p38 MAPK pathway.
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The MAT locus genes play different roles in sexual reproduction and pathogenesis in Fusarium graminearum.
PLoS ONE
PUBLISHED: 01-01-2013
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Sexual reproduction plays a critical role in the infection cycle of Fusarium graminearum because ascospores are the primary inoculum. As a homothallic ascomycete, F. graminearum contains both the MAT1-1 and MAT1-2-1 loci in the genome. To better understand their functions and regulations in sexual reproduction and pathogenesis, in this study we assayed the expression, interactions, and mutant phenotypes of individual MAT locus genes. Whereas the expression of MAT1-1-1 and MAT12-1 rapidly increased after perithecial induction and began to decline after 1 day post-perithecial induction (dpi), the expression of MAT1-1-2 and MAT1-1-3 peaked at 4 dpi. MAT1-1-2 and MAT1-1-3 had a similar expression profile and likely are controlled by a bidirectional promoter. Although none of the MAT locus genes were essential for perithecium formation, all of them were required for ascosporogenesis in self-crosses. In outcrosses, the mat11-1-2 and mat11-1-3 mutants were fertile but the mat1-1-1 and mat1-2-1 mutants displayed male- and female-specific defects, respectively. The mat1-2-1 mutant was reduced in FgSO expression and hyphal fusion. Mat1-1-2 interacted with all other MAT locus transcription factors, suggesting that they may form a protein complex during sexual reproduction. Mat1-1-1 also interacted with FgMcm1, which may play a role in controlling cell identity and sexual development. Interestingly, the mat1-1-1 and mat1-2-1 mutants were reduced in virulence in corn stalk rot assays although none of the MAT locus genes was important for wheat infection. The MAT1-1-1 and MAT1-2-1 genes may play a host-specific role in colonization of corn stalks.
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Functional analysis of the kinome of the wheat scab fungus Fusarium graminearum.
PLoS Pathog.
PUBLISHED: 10-24-2011
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As in other eukaryotes, protein kinases play major regulatory roles in filamentous fungi. Although the genomes of many plant pathogenic fungi have been sequenced, systematic characterization of their kinomes has not been reported. The wheat scab fungus Fusarium graminearum has 116 protein kinases (PK) genes. Although twenty of them appeared to be essential, we generated deletion mutants for the other 96 PK genes, including 12 orthologs of essential genes in yeast. All of the PK mutants were assayed for changes in 17 phenotypes, including growth, conidiation, pathogenesis, stress responses, and sexual reproduction. Overall, deletion of 64 PK genes resulted in at least one of the phenotypes examined, including three mutants blocked in conidiation and five mutants with increased tolerance to hyperosmotic stress. In total, 42 PK mutants were significantly reduced in virulence or non-pathogenic, including mutants deleted of key components of the cAMP signaling and three MAPK pathways. A number of these PK genes, including Fg03146 and Fg04770 that are unique to filamentous fungi, are dispensable for hyphal growth and likely encode novel fungal virulence factors. Ascospores play a critical role in the initiation of wheat scab. Twenty-six PK mutants were blocked in perithecia formation or aborted in ascosporogenesis. Additional 19 mutants were defective in ascospore release or morphology. Interestingly, F. graminearum contains two aurora kinase genes with distinct functions, which has not been reported in fungi. In addition, we used the interlog approach to predict the PK-PK and PK-protein interaction networks of F. graminearum. Several predicted interactions were verified with yeast two-hybrid or co-immunoprecipitation assays. To our knowledge, this is the first functional characterization of the kinome in plant pathogenic fungi. Protein kinase genes important for various aspects of growth, developmental, and infection processes in F. graminearum were identified in this study.
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The HDF1 histone deacetylase gene is important for conidiation, sexual reproduction, and pathogenesis in Fusarium graminearum.
Mol. Plant Microbe Interact.
PUBLISHED: 09-29-2011
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Head blight caused by Fusarium graminearum is an important disease of wheat and barley. Its genome contains chromosomal regions with higher genetic variation and enriched for genes expressed in planta, suggesting a role of chromatin modification in the regulation of infection-related genes. In a previous study, the FTL1 gene was characterized as a novel virulence factor in the head blight fungus. FTL1 is homologous to yeast SIF2, which is a component of the Set3 complex. Many members of the yeast Set3 complex, including Hos2 histone deacetylase (HDAC), are conserved in F. graminearum. In this study, we characterized the HDF1 gene that is orthologous to HOS2. HDF1 physically interacted with FTL1 in yeast two-hybrid assays. Deletion of HDF1 resulted in a significant reduction in virulence and deoxynivalenol (DON) production. The ?hdf1 mutant failed to spread from the inoculation site to other parts of wheat heads or corn stalks. It was defective in sexual reproduction and significantly reduced in conidiation. Expression of HDF1 was highest in conidia in comparison with germlings and hyphae. Deletion of HDF1 also resulted in a 60% reduction in HDAC activity. Microarray analysis revealed that 149 and 253 genes were down- and upregulated, respectively, over fivefold in the ?hdf1 mutant. Consistent with upregulation of putative catalase and peroxidase genes, the ?hdf1 mutant was more tolerant to H(2)O(2) than the wild type. Deletion of the other two class II HDAC genes had no obvious effect on vegetative growth and resulted in only a minor reduction in conidiation and virulence in the ?hdf2 mutant. Overall, our results indicate that HDF1 is the major class II HDAC gene in F. graminearum. It may interact with FTL1 and function as a component in a well-conserved HDAC complex in the regulation of conidiation, DON production, and pathogenesis.
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Oxidized DJ-1 interacts with the mitochondrial protein BCL-XL.
J. Biol. Chem.
PUBLISHED: 08-18-2011
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Parkinson disease (PD)- and cancer-associated protein, DJ-1, mediates cellular protection via many signaling pathways. Deletions or mutations in the DJ-1 gene are directly linked to autosomal recessive early-onset PD. DJ-1 has potential roles in mitochondria. Here, we show that DJ-1 increases its mitochondrial distribution in response to ultraviolet B (UVB) irradiation and binds to Bcl-X(L). The interactions between DJ-1 and Bcl-X(L) are oxidation-dependent. DJ-1(C106A), a mutant form of DJ-1 that is unable to be oxidized, binds Bcl-X(L) much less than DJ-1 does. Moreover, DJ-1 stabilizes Bcl-X(L) protein level by inhibiting its ubiquitination and degradation through ubiquitin proteasome system (UPS) in response to UVB irradiation. Furthermore, under UVB irradiation, knockdown of DJ-1 leads to increases of Bcl-X(L) ubiquitination and degradation upon UVB irradiation, thereby increasing mitochondrial Bax, caspase-3 activation and PARP cleavage. These data suggest that DJ-1 protects cells against UVB-induced cell death dependent on its oxidation and its association with mitochondrial Bcl-X(L).
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Modeling and analysis of localized biosensing and index sensing by introducing effective phase shift in microfiber Bragg grating (µFBG).
Opt Express
PUBLISHED: 06-07-2011
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We report a novel micro-fiber Bragg grating (µFBG) sensor that takes advantage of the degeneracy of stop-band and rapid emergence of spectral modes when an effective phase shift occurs. The phase shift can be enabled by a range of perturbations in a central segment of the grating, including monolayer immobilization of bio-molecules or change in refractive index in the surrounding, thereby constituting the possibility of a highly sensitive sensor with the merit of scalable performance. The use of µFBG ensures strong evanescent field coupling to the surrounding in order to maximize signal transduction. Simulation results indicate very favorable sensor signal characteristics such as large wavelength shift and sharp reflection dips. A general relation between the peak position within the stop-band and the amount of effective phase shift is also provided, and may generally serve as helpful guideline for FBG sensor design. A typical µFBG sensor device may detect surface protein/DNA adsorption with limit-of-detection (LOD) as low as 3.3 pg.mm(-2) for surface mass density and 51.8 fg for total mass. For refractive index (RI) sensing, the LOD is 2.5×10(-6) refractive index unit (RIU).
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Fatty acids as natural specific inhibitors of the proto-oncogenic protein Shp2.
Bioorg. Med. Chem. Lett.
PUBLISHED: 05-11-2011
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Src homology-2 domain-containing protein tyrosine phosphatase (Shp2), a novel proto-oncogenic protein, is an important target in cancer therapy research. Approximately 2000 plant extracts were screened to find its natural specific inhibitors, with the ethyl acetate (EtOAc) active extract of the root of Angelica dahurica showing considerable inhibitory effects (IC(50)=21.6 mg/L). Bioguided isolation of EtOAc extract led to 13 compounds, including 10 fatty acids and derivatives. All these compounds were isolated from the plant for the first time. The inhibitory effects of these compounds on the enzyme activities of Shp2, VH1-related human protein (VHR), and hematopoietic protein tyrosine phosphatase (HePTP) were investigated. 8Z,11Z-Feptadecadienoic acid (4), 14Z,17Z-tricosadienoic acid (5), caffeic acid (9), and 2-hydroxy-3-[(1-oxododecyl) oxy]propyl-?-d-glucopyranoside (11) showed considerable selective inhibition of Shp2 activity. After treatment of HepG2 cells with the compounds, only compound 5, a polyunsaturated fatty acid, strongly induced poly (ADP-ribose) polymerase (PARP) cleavage in a dose- and time-dependent manner and increased the activities of caspase-3, caspase-8, and caspase-9 at 100 ?M. Compound 5 also inhibited colony formation of HepG2 cells in a dose-dependent manner. Thus, this study reported fatty acids as specific Shp2 inhibitors and provided the molecular basis of one active compound as novel potential anticancer drug.
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The endoplasmic reticulum (ER)-associated degradation system regulates aggregation and degradation of mutant neuroserpin.
J. Biol. Chem.
PUBLISHED: 04-20-2011
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Familial encephalopathy with neuroserpin inclusion bodies is a neurodegenerative disorder characterized by the accumulation of neuroserpin polymers in the endoplasmic reticulum (ER) of cortical and subcortical neurons in the CNS because of neuroserpin point mutations. ER-associated degradation (ERAD) is involved in mutant neuroserpin degradation. In this study, we demonstrate that two ER-associated E3 ligases, Hrd1 and gp78, are involved in the ubiquitination and degradation of mutant neuroserpin. Overexpression of Hrd1 and gp78 decreases the mutant neuroserpin protein level, whereas Hrd1 and gp78 knockdown increases mutant neuroserpin stability. Moreover, ERAD impairment by mutant valosin-containing protein increases the mutant neuroserpin protein level and aggregate formation. Thus, these findings identify mutant neuroserpin as an ERAD target and show that Hrd1 and gp78 mediate mutant neuroserpin turnover through the ERAD pathway.
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Identification of proteins and phosphoproteins using pulsed Q collision induced dissociation (PQD).
J. Am. Soc. Mass Spectrom.
PUBLISHED: 03-02-2011
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Pulsed Q collision induced dissociation (PQD) was developed to facilitate detection of low-mass reporter ions from labeling reagents (e.g., iTR?Q) in peptide quantification using an LTQ mass spectrometer (MS). Despite the large number of linear ion traps worldwide, the use and optimization of PQD for protein identification have been limited, in part due to less effective ion fragmentation relative to the collision induced dissociation (CID). PQD expands the m/z coverage of fragment ions to the lower m/z range by circumventing the typical low mass cut-off of an ion trap MS. Since database searching relies on the matching between theoretical and observed spectra, it is not clear how ion intensity and peak number might affect the outcomes of a database search. In this report, we systematically evaluated the attributes of PQD mass spectra, performed intensity optimization, and assessed the benefits of using PQD on the identification of peptides and phosphopeptides from an LTQ. Based on head-to-head comparisons between CID (higher intensity) and PQD (better m/z coverage), peptides identified using PQD generally have Xcorr scores lower than those using CID. Such score differences were considerably diminished by the use of 0.1% m-nitrobenzyl alcohol (m-NBA) in mobile phases. The ion intensities of both CID and PQD were adversely affected by increasing m/z of the precursor, with PQD more sensitive than CID. In addition to negating the 1/3 rule, PQD enhances direct bond cleavage and generates patterns of fragment ions different from those of CID, particularly for peptides with a labile functional group (e.g., phosphopeptides). The higher energy fragmentation pathway of PQD on peptide fragmentation was further compared to those of CID and the quadrupole-type activation in parallel experiments.
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Characterization of potential S-nitrosylation sites in the myocardium.
Am. J. Physiol. Heart Circ. Physiol.
PUBLISHED: 01-28-2011
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S-nitrosylation (SNO) is a reversible protein modification that has the ability to alter the activity of target proteins. However, only a small number of SNO proteins have been found in the myocardium, and even fewer specific sites of SNO have been identified. Therefore, this study aims to characterize potential SNO sites in the myocardium. We utilized a modified version of the SNO-resin-assisted capture technique in tandem with mass spectrometry. In brief, a modified biotin switch was performed using perfused mouse heart homogenates incubated with or without the S-nitrosylating agent S-nitrosoglutathione. Our modified SNO-resin-assisted capture protocol identified 116 unique SNO-modified proteins under basal conditions, and these represent the constitutive SNO proteome. These constitutive SNO proteins are likely to be physiologically relevant targets, since nitric oxide has been shown to play an important role in the regulation of normal cardiovascular physiology. Following S-nitrosoglutathione treatment, we identified 951 unique SNO proteins, many of which contained multiple SNO sites. These proteins show the potential for SNO. This study provides novel information regarding the constitutive SNO proteome of the myocardium, as well as potential myocardial SNO sites, and yields additional information on the SNO sites for many key proteins involved in myocardial contraction, metabolism, and cellular signaling.
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A comparison of Twist and E-cadherin protein expression in primary non-small-cell lung carcinoma and corresponding metastases.
Eur J Cardiothorac Surg
PUBLISHED: 01-10-2011
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The metastasis of solid tumors is directly or indirectly responsible for most cancer-related deaths. It has already been known that in non-small-cell lung carcinoma cells, up-regulation of Twist (a highly conserved basic helix-loop-helix transcription factor) can promote epithelial-mesenchymal transition through down-regulation of E-cadherin. The main aim of this study was to determine whether the expression of Twist and E-cadherin differs between primary and metastatic lung carcinoma and to correlate Twist and E-cadherin expression in primary and metastatic non-small-cell lung carcinoma.
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Simultaneous measurement of protein oxidation and S-nitrosylation during preconditioning and ischemia/reperfusion injury with resin-assisted capture.
Circ. Res.
PUBLISHED: 12-30-2010
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Redox modifications play an important role in many cellular processes, including cell death. Ischemic preconditioning (IPC) has been shown to involve redox signaling. Protein S-nitrosylation (SNO) is increased following myocardial IPC, and SNO is thought to provide cardioprotection, in part, by reducing cysteine oxidation during ischemia/reperfusion (IR) injury.
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Refractive index sensing based on higher-order mode reflection of a microfiber Bragg grating.
Opt Express
PUBLISHED: 12-18-2010
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A fiber Bragg grating written in a photosensitive microfiber using KrF excimer laser via a uniform phase mask is demonstrated. We have successfully fabricated two Bragg gratings in microfibers having different diameters. In the reflection spectrum of a microfiber Bragg grating (MFBG), we observed two reflection peaks,which agrees with our numerical simulation results. Compared with the fundamental mode reflection, the higher-order reflection mode is more sensitive to the refractive index (RI) variation of the surrounding fluid due to its larger evanescent field. The measured maximum sensitivity is ~102 nm/RIU (RI unit) at an RI value of 1.378 in an MFBG with a diameter of 6 ?m.
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The ?-adrenoceptor antagonist, propranolol, induces human gastric cancer cell apoptosis and cell cycle arrest via inhibiting nuclear factor ?B signaling.
Oncol. Rep.
PUBLISHED: 11-03-2010
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In a recent clinical observation, the growth of endothelial tumors, such as nasopharyngeal carcinoma, was repressed by the non-selective-adrenergic antagonist propranolol. In this study, we evaluated whether ?-adrenoceptors (?-ARs), nuclear factor ?B (NF-?B), vascular endothelial growth factor (VEGF), cyclooxygenase-2 (COX-2), matrix metalloproteinase-2 (MMP-2) and matrix metalloproteinase-9 (MMP-9) were involved in modulating cell apoptosis and cell cycle arrest by propranolol in human gastric adenocarcinoma cell lines (SGC-7901 and BGC-823) in vitro. Our results showed that the propranolol treatment inhibited cell proliferation in a concentration-dependent manner, suggesting the involvement of ?-ARs in this cellular response. Propranolol-induced growth inhibition was associated with G0/G1 arrest and G2/M arrest depending upon the concentration. In addition, propranolol also induced apoptosis in both cell lines, as determined by Annexin V staining assay. Furthermore, propranolol decreased the level of NF-?B and then downregulated VEGF, Cox-2, MMP-2 and MMP-9 expression. Collectively, these results suggested that propranolol repressed gastric cancer cell growth through the inhibition of ?-ARs and the downstream NF-?B-VEGF/MMP-2/9/COX-2 pathway.
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Quantitative protein and mRNA profiling shows selective post-transcriptional control of protein expression by vasopressin in kidney cells.
Mol. Cell Proteomics
PUBLISHED: 10-12-2010
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Previous studies in yeast have supported the view that post-transcriptional regulation of protein abundances may be more important than previously believed. Here we ask the question: "In a physiological regulatory process (the response of mammalian kidney cells to the hormone vasopressin), what fraction of the expressed proteome undergoes a change in abundance and what fraction of the regulated proteins have corresponding changes in mRNA levels?" In humans and other mammals, vasopressin fulfills a vital homeostatic role (viz. regulation of renal water excretion) by regulating the water channel aquaporin-2 in collecting duct cells. To address the question posed, we utilized large-scale quantitative protein mass spectrometry (LC-MS/MS) employing stable isotopic labeling in cultured mpkCCD cells (SILAC) coupled with transcriptomic profiling using oligonucleotide expression arrays (Affymetrix). Preliminary studies analyzing two nominally identical control samples by SILAC LC-MS/MS yielded a relative S.D. of 13% (for ratios), establishing the precision of the SILAC approach in our hands. We quantified nearly 3000 proteins with nontargeted SILAC LC-MS/MS, comparing vasopressin- versus vehicle-treated samples. Of these proteins 786 of them were quantified in each of 3 experiments, allowing statistical analysis and 188 of these showed significant vasopressin-induced changes in abundance, including aquaporin-2 (20-fold increase). Among the proteins with statistically significant abundance changes, a large fraction (at least one-third) was found to lack changes in the corresponding mRNA species (despite sufficient statistical power), indicating that post-transcriptional regulation of protein abundance plays an important role in the vasopressin response. Bioinformatic analysis of the regulated proteins (versus all transcripts) shows enrichment of glutathione S-transferase isoforms as well as proteins involved in organization of the actin cytoskeleton. The latter suggests that long-term regulatory processes may contribute to actomyosin-dependent trafficking of the water channel aquaporin-2. The results provide impetus for increased focus on translational regulation and regulation of protein degradation in physiological control in mammalian epithelial cells.
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Nucleocytoplasmic shuttling of dysbindin-1, a schizophrenia-related protein, regulates synapsin I expression.
J. Biol. Chem.
PUBLISHED: 10-04-2010
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Dysbindin-1 is a 50-kDa coiled-coil-containing protein encoded by the gene DTNBP1 (dystrobrevin-binding protein 1), a candidate genetic factor for schizophrenia. Genetic variations in this gene confer a susceptibility to schizophrenia through a decreased expression of dysbindin-1. It was reported that dysbindin-1 regulates the expression of presynaptic proteins and the release of neurotransmitters. However, the precise functions of dysbindin-1 are largely unknown. Here, we show that dysbindin-1 is a novel nucleocytoplasmic shuttling protein and translocated to the nucleus upon treatment with leptomycin B, an inhibitor of exportin-1/CRM1-mediated nuclear export. Dysbindin-1 harbors a functional nuclear export signal necessary for its nuclear export, and the nucleocytoplasmic shuttling of dysbindin-1 affects its regulation of synapsin I expression. In brains of sandy mice, a dysbindin-1-null strain that displays abnormal behaviors related to schizophrenia, the protein and mRNA levels of synapsin I are decreased. These findings demonstrate that the nucleocytoplasmic shuttling of dysbindin-1 regulates synapsin I expression and thus may be involved in the pathogenesis of schizophrenia.
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Parkin mono-ubiquitinates Bcl-2 and regulates autophagy.
J. Biol. Chem.
PUBLISHED: 10-02-2010
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Parkin is an E3 ubiquitin ligase that mediates the ubiquitination of protein substrates. The mutations in the parkin gene can lead to a loss of function of parkin and cause autosomal recessive juvenile onset parkinsonism. Recently, parkin was reported to be involved in the regulation of mitophagy. Here, we identify the Bcl-2, an anti-apoptotic and autophagy inhibitory protein, as a substrate for parkin. Parkin directly binds to Bcl-2 via its C terminus and mediates the mono-ubiquitination of Bcl-2, which increases the steady-state levels of Bcl-2. Overexpression of parkin, but not its ligase-deficient forms, decreases autophagy marker LC3 conversion, whereas knockdown of parkin increases LC3 II levels. In HeLa cells, a parkin-deficient cell line, knockdown of parkin does not change LC3 conversion. Moreover, overexpression of parkin enhances the interactions between Bcl-2 and Beclin 1. Our results provide evidence that parkin mono-ubiquitinates Bcl-2 and regulates autophagy via Bcl-2.
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Dendritic cell nuclear protein-1, a novel depression-related protein, upregulates corticotropin-releasing hormone expression.
Brain
PUBLISHED: 08-07-2010
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The recently discovered dendritic cell nuclear protein-1 is the product of a novel candidate gene for major depression. The A allele encodes full-length dendritic cell nuclear protein-1, while the T allele encodes a premature termination of translation at codon number 117 on chromosome 5. In the present study we investigate whether the two forms of dendritic cell nuclear protein-1 might act on corticotropin-releasing hormone, which plays a crucial role in the stress response and in the pathogenesis of depression. The messenger RNA expression of dendritic cell nuclear protein-1 appeared to be increased in the laser micro-dissected paraventricular nucleus of patients with depression compared with control subjects. Dendritic cell nuclear protein-1 was also found to be co-localized with corticotropin-releasing hormone in paraventricular nucleus neurons. Moreover, full-length dendritic cell nucleus protein-1 bound to and transactivated the promoter of corticotropin-releasing hormone in human embryonic kidney 293 cells. We propose that full-length dendritic cell nucleus protein-1 may play a role in the pathogenesis of depressive disorders by enhancing corticotropin-releasing hormone expression in the hypothalamic paraventricular nucleus.
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Stoichiometry of STAT3 and mitochondrial proteins: Implications for the regulation of oxidative phosphorylation by protein-protein interactions.
J. Biol. Chem.
PUBLISHED: 06-17-2010
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The signal transducer and activator of transcription 3 (STAT3) is a transcription factor and downstream product of cytokine and growth factor pathways. Among members of the STAT family, STAT3 has garnered particular interest due to its role in cancer and development. Recently, it was proposed that STAT3 regulates cardiac ATP generation in vivo through protein interaction with the mitochondrial complexes of oxidative phosphorylation, specifically Complexes I/II. For this mechanism to work effectively, the cellular ratio of Complexes I/II and STAT3 must approach one. However, using three different proteomic approaches in cardiac tissue, we determined the ratio of Complexes I/II and STAT3 to be approximately 10(5). This finding suggests that direct protein interaction between Complexes I/II and STAT3 cannot be required for optimal ATP production, nor can it dramatically modulate oxidative phosphorylation in vivo. Thus, STAT3 is likely altering mitochondrial function via transcriptional regulation or indirect signaling pathways that warrant further investigation.
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New steroidal glycosides isolated as CDL inhibitors of activated platelets.
Molecules
PUBLISHED: 04-24-2010
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Three new compounds were isolated from the dried bulbs of Allium macrostemon Bunge. Their structures were elucidated from their spectral data as (25R)-26-O-beta-D-glucopyranosyl-5alpha-furostane-3beta,12beta,22,26-tetraol-3-O-beta-D-glucopyranos-yl (1-->2) [beta-D-glucopyranosyl (1-->3)]-beta-D-glucopyranosyl (1-->4)-beta-D-galactopyranoside (1), (25R)-26-O-beta-D-glucopyranosyl-5alpha-furostane-3beta,12alpha,22,26-tetraol-3-O-beta-D-glucopyranosyl (1-->2) [beta-D-glucopyranosyl (1-->3)]-beta-D-glucopyranosyl (1-->4)-beta-D-galacto- pyranoside (2) and (25R)-26-O-beta-D-glucopyranosyl-5beta-furostane-3beta,12alpha,22,26-tetraol-3-O-beta-D-glucopyranosyl (1-->2)-beta-D-galactopyranoside (3), respectively. The inhibition effect of all compounds on CD40 ligand (CD40L) expression on the membrane of activated platelets stimulated by ADP was tested. Compounds 1 and 2 exhibited significant inhibitory activities in a dose dependent manner (P < 0.05), suggesting their potential application as CD40L inhibitors.
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Administration of embryonic stem cells generates effective antitumor immunity in mice with minor and heavy tumor load.
Cancer Immunol. Immunother.
PUBLISHED: 04-15-2010
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The history of immunizing animals with fetal tissues to generate an antitumor response dates back a century ago. Subsequent reports supported the idea that vaccination with embryonic materials could generate cancer-specific immunity and protect animals from transplantable and chemically induced tumors. In our study, we found C57 BL/6 mice vaccinated with embryonic stem cells (ESCs) received obvious antitumor immunity, which protected them from the formation and development of lung cancer. Furthermore, we investigated the antitumor effects of administration of ESCs in mice with minor and/or heavy tumor load. The tumor growth was monitored, the proliferation of lymphocytes and secretion of cytokines were examined, and finally the tissue sections were approached by immunohistochemical and apoptosis staining. The results suggested that mice injected with ESCs received obvious tumor inhibition and retardation due to significant lymphocyte proliferation and cytokine secretion, which help to rebuild the hosts immunity against cancer to some extent and comprise the main part of antitumor immunity. Moreover, mice with minor tumor load received stronger antitumor effect compared with mice with heavy tumor load, may be due to relatively intact immune system. Thus, besides their function as prophylactic vaccines, administration of ESCs could be a potential treatment for cancer, which obviously prevent and control the proliferation and development of malignant tumors.
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Simultaneous removal of phenanthrene and lead from artificially contaminated soils with glycine-?-cyclodextrin.
J. Hazard. Mater.
PUBLISHED: 02-10-2010
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Preparation of glycine-?-cyclodextrin (GCD) was carried out by the reaction of ?-cyclodextrin with glycine in the presence of KOH and epichlorohydrin. The enhanced solubilization behavior of phenanthrene and lead carbonate by GCD was studied, and the desorption behavior of phenanthrene and lead from co-contaminated soil was also investigated. The results showed that GCD has obvious solubilization for phenanthrene and lead carbonate. The solubility of phenanthrene in 30 g/L of GCD was enhanced about 30-fold. And the apparent aqueous solubilities of lead carbonate are also obviously increased with increasing GCD concentration, when the concentration of GCD reached 20 g/L, the aqueous lead concentration was 2945 mg/L. GCD could simultaneously increase the apparent aqueous solubility of phenanthrene and complex with lead. The desorption process of GCD for phenanthrene and lead from co-contaminated soil followed the pseudo-second-order kinetic model. The removal efficiencies of phenanthrene and lead in soil increased dramatically with increasing GCD concentrations. At concentration of 40 g/L, GCD has a removal efficiency of 85.8% and 78.8% for lead and phenanthrene, respectively, from the combined contaminated soil. The use of GCD as an extractant to enhance the removal of heavy and hydrophobic organic contaminants (HOCs) from co-contaminated soils appears as a promising remediation method.
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DJ-1, a cancer and Parkinsons disease associated protein, regulates autophagy through JNK pathway in cancer cells.
Cancer Lett.
PUBLISHED: 02-05-2010
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Autophagy mediates cellular self-digestion to degrade cytoplasmic proteins and organelles and plays important roles in tumorigenesis. DJ-1 is an oncogene product in association with cancers and tumorigenesis. In this study, we show that knockdown of DJ-1 induces autophagy through activating JNK pathway to promote Beclin 1 transcription, whereas overexpression of DJ-1 inhibits these processes. Moreover, inhibition of JNK pathway by SP600125 blocks autophagy activation and p62 degradation induced by knockdown of DJ-1. Our findings suggest that DJ-1 regulates autophagy in a JNK-dependent manner. Thus, the involvement of DJ-1 in autophagy regulation may be involved in tumorigenesis.
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Quantitative phosphoproteomic analysis reveals vasopressin V2-receptor-dependent signaling pathways in renal collecting duct cells.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 02-05-2010
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Vasopressins action in renal cells to regulate water transport depends on protein phosphorylation. Here we used mass spectrometry-based quantitative phosphoproteomics to identify signaling pathways involved in the short-term V2-receptor-mediated response in cultured collecting duct cells (mpkCCD) from mouse. Using Stable Isotope Labeling by Amino acids in Cell culture (SILAC) with two treatment groups (0.1 nM dDAVP or vehicle for 30 min), we carried out quantification of 2884 phosphopeptides. The majority (82%) of quantified phosphopeptides did not change in abundance in response to dDAVP. Analysis of the 273 phosphopeptides increased by dDAVP showed a predominance of so-called "basophilic" motifs consistent with activation of kinases of the AGC family. Increases in phosphorylation of several known protein kinase A targets were found. In addition, increased phosphorylation of targets of the calmodulin-dependent kinase family was seen, including autophosphorylation of calmodulin-dependent kinase 2 at T286. Analysis of the 254 phosphopeptides decreased in abundance by dDAVP showed a predominance of so-called "proline-directed" motifs, consistent with down-regulation of mitogen-activated or cyclin-dependent kinases. dDAVP decreased phosphorylation of both JNK1/2 (T183/Y185) and ERK1/2 (T183/Y185; T203/Y205), consistent with a decrease in activation of these proline-directed kinases in response to dDAVP. Both ERK and JNK were able to phosphorylate residue S261of aquaporin-2 in vitro, a site showing a decrease in phosphorylation in response to dDAVP in vivo. The data support roles for multiple vasopressin V2-receptor-dependent signaling pathways in the vasopressin signaling network of collecting duct cells, involving several kinases not generally accepted to regulate collecting duct function.
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Phosphoproteomic profiling reveals vasopressin-regulated phosphorylation sites in collecting duct.
J. Am. Soc. Nephrol.
PUBLISHED: 01-14-2010
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Protein phosphorylation is an important component of vasopressin signaling in the renal collecting duct, but the database of known phosphoproteins is incomplete. We used tandem mass spectrometry to identify vasopressin-regulated phosphorylation events in isolated rat inner medullary collecting duct (IMCD) suspensions. Using multiple search algorithms to identify the phosphopeptides from spectral data, we expanded the size of the existing collecting duct phosphoproteome database from 367 to 1187 entries. Label-free quantification in vasopressin- and vehicle-treated samples detected a significant change in the phosphorylation of 29 of 530 quantified phosphopeptides. The targets include important structural, regulatory, and transporter proteins. The vasopressin-regulated sites included two known sites (Ser-486 and Ser-499) present in the urea channel UT-A1 and one previously unknown site (Ser-84) on vasopressin-sensitive urea channels UT-A1 and UT-A3. In vitro assays using synthetic peptides showed that purified protein kinase A (PKA) could phosphorylate all three sites, and immunoblotting confirmed the PKA dependence of Ser-84 and Ser-486 phosphorylation. These results expand the known list of collecting duct phosphoproteins and highlight the utility of targeted phosphoproteomic approaches.
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Mediator of DNA damage checkpoint 1 (MDC1) contributes to high NaCl-induced activation of the osmoprotective transcription factor TonEBP/OREBP.
PLoS ONE
PUBLISHED: 01-11-2010
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Hypertonicity, such as induced by high NaCl, increases the activity of the transcription factor TonEBP/OREBP whose target genes increase osmoprotective organic osmolytes and heat shock proteins.
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Studying the influence of operation parameters on heavy and alkali metals partitioning in flue gases.
Waste Manag Res
PUBLISHED: 09-01-2009
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In order to study the distribution and partitioning of heavy and alkali metals in the flue gases of a sewage sludge incinerator, an experiment was carried out in a pilot scale combustor. The results indicated that it was feasible to separate part of metals from flue gases by collecting fly ash at different temperatures. On the basis of their separation temperature, heavy and alkali metals could be divided into three groups: group A included Zn, K and P, which converted from gaseous phase to liquid or solid when temperature was above 600 degrees C. Pb and Cu were the metals of group B, with optimum transformation temperature of 400 degrees C. Na and As belonged to group C, with conversion temperatures of 300 degrees C. Moreover, the effect of temperature gradient on heavy and alkali metal gas-solid transformation was also experimentally investigated. It was observed that the temperature gradient could promote the gas-solid conversion of heavy and alkali metals. However, too high a temperature gradient would suppress the formation of fine particles. The peak of conversion rate for K, Pb and Na occurred at 434 degrees C s(-1), while that of P and Cu was 487 degrees C s(-1).
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NGFI-B nuclear orphan receptor Nurr1 interacts with p53 and suppresses its transcriptional activity.
Mol. Cancer Res.
PUBLISHED: 08-11-2009
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Nurr1 is a member of the NGFI-B nuclear orphan receptor family which includes two other members, Nur77 and Nor-1. Nurr1 is essential for the development and survival of dopaminergic neurons. It was reported that Nurr1 has antiapoptotic functions, however, the mechanisms by which Nurr1 mediates these effects remain unknown. Here, we show that overexpression of Nurr1 decreases Bax expression whereas knockdown of Nurr1 increases Bax expression. Nurr1 also interacts with p53 and represses its assembly. Furthermore, Nurr1 represses p53 transcriptional activity in interaction-dependent and dose-dependent manners. Moreover, Nurr1 protects cells from doxorubicin-induced apoptosis. These findings provide evidence that Nurr1 promotes cell survival through its interacting with and repressing p53, thus implicating that Nurr1 may play an important role in carcinogenesis and other diseases.
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Gp78, an ER associated E3, promotes SOD1 and ataxin-3 degradation.
Hum. Mol. Genet.
PUBLISHED: 08-06-2009
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Superoxide dismutase-1 (SOD1) and ataxin-3 are two neurodegenerative disease proteins in association with familial amyotrophic lateral sclerosis and Machado-Joseph disease/spinocerebellar ataxia type 3. Both normal and mutant types of SOD1 and ataxin-3 are degraded by the proteasome. It was recently reported that these two proteins are associated with the endoplasmic reticulum (ER). Mammalian gp78 is an E3 ubiquitin ligase involved in ER-associated degradation (ERAD). Here, we show that gp78 interacts with both SOD1 and ataxin-3. Overexpression of gp78 promotes the ubiquitination and degradation of these two proteins, whereas knockdown of gp78 stabilizes them. Moreover, gp78 represses aggregate formation of mutant SOD1 and protect cells against mutant SOD1-induced cell death. Furthermore, gp78 is increased in cells transfected with these two mutant proteins as well as in ALS mice. Thus, our results suggest that gp78 functions in the regulation of SOD1 and ataxin-3 to target them for ERAD.
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Degradation of TDP-43 and its pathogenic form by autophagy and the ubiquitin-proteasome system.
Neurosci. Lett.
PUBLISHED: 07-28-2009
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TAR DNA-binding protein-43 (TDP-43) is a nuclear protein functioning in the regulation of transcription and mRNA splicing. TDP-43 is accumulated in ubiquitinated inclusions in frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U) and amyotrophic lateral sclerosis (ALS) diseased brains. However, the pathways involved in the clearance of TDP-43 and its pathogenic form (TDP-25), a truncated form of TDP-43, are still not elucidated. In this study, we demonstrated that the protein levels of TDP-43 and TDP-25 were increased in cells treated with a proteasome inhibitor, MG132, or an autophagy inhibitor, 3-MA, whereas, they were decreased in cells treated with an enhancer of autophagy, trehalose. Furthermore, more protein level changes of TDP-25 than TDP-43 were observed in cells treated with above inhibitors or enhancer. Thus, our data suggest that TDP-43 and TDP-25 are degraded by both proteasome and autophagy with TDP-25 being more regulated.
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Holey fiber design for single-polarization single-mode guidance.
Appl Opt
PUBLISHED: 07-14-2009
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We propose a holey fiber design to achieve single-polarization single-mode (SPSM) guidance. The photonic crystal fiber (PCF) has a triangular-lattice with elliptical airholes in the microstructured cladding and circular airholes in the core. The SPSM guidance can be obtained by designing the PCF structure such that the fundamental space-filling mode (FSM) of the core region is positioned between the indices of the two nondegenerate orthogonally polarized FSMs of the microstructured cladding.
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A novel strategy for MALDI-TOF MS analysis of small molecules.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 04-27-2009
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Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) does not work efficiently on small molecules (usually with molecular weight below 500 Da) because of the interference of matrix-related peaks in low m/z region. The previous methods developed for this problem focused on reducing the peaks caused by the traditional matrices. Here, we report a novel strategy to analyze small molecules in a high and interference-free mass range by using metal-phthalocyanines (MPcs) as matrices which should be capable of forming matrix-analyte adducts. The mass of the target analyte was calculated by subtracting the mass of MPc from the mass of the MPc-analyte adduct. MPcs were also detectable and could serve as internal standards. Various MPcs with aromatic or aliphatic groups and different metal centers were then synthesized and explored. Aluminum-phthalocyanines (AlPcs), gallium-phthalocyanines (GaPcs), and indium-phthalocyanines (InPcs) were efficient matrices to form MPc-analyte adducts in either the positive or negative ion mode. The detection limits varied from 17 to 75 fmol, depending on analyte types. The mechanism of adducts formation was also proposed. Collectively, our strategy provides a novel and efficient way to analyze small molecules by MALDI-TOF MS.
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[Mechanism study of protobioside on tumor cell proliferation].
Zhongguo Zhong Yao Za Zhi
PUBLISHED: 03-02-2009
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To investigate the anti-proliferative effect of Protobioside on the HepG2 cells and its mechanism.
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Proteomic identification of altered apolipoprotein patterns in pulmonary hypertension and vasculopathy of sickle cell disease.
Blood
PUBLISHED: 02-28-2009
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Pulmonary arterial hypertension (PAH) is emerging as a major complication and independent risk factor for death among adults with sickle cell disease (SCD). Using surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF MS), we searched for biomarkers of PAH in plasma specimens from 27 homozygous sickle cell anemia (HbSS) patients with PAH and 28 without PAH. In PAH patients, analysis consistently showed lower abundance of a 28.1-kDa peak (P < .001), identified by high-resolution mass spectrometry as the oxidant-scavenging protein apolipoprotein A-I (apoA-I), which correlated with clinical assays of apoA-I (r = .58, P < .001) and high-density lipoprotein (HDL) levels (r = .50, P = .001). Consistent with endothelial dysfunction that may mediate this effect in PAH, HbSS patients with lower apoA-I levels also displayed impaired vasodilatory responses to acetylcholine (mean +/- SEM, 189% +/- 34% [n = 13] vs 339% +/- 51% [n = 13], P < .001). As a group, patients with SCD demonstrated significantly lower apoA-I levels than African-American control subjects. The PAH cohort was further characterized by high levels of apolipoproteins A-II and B and serum amyloid A, and low levels of haptoglobin dimers and plasminogen. These results imply a relationship of apolipoproteins to the development of PAH vasculopathy in SCD, potentially involving an unexpected mechanistic parallel to atherosclerosis, another proliferative vasculopathy.
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Decoy methods for assessing false positives and false discovery rates in shotgun proteomics.
Anal. Chem.
PUBLISHED: 02-10-2009
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The potential of getting a significant number of false positives (FPs) in peptide-spectrum matches (PSMs) obtained by proteomic database search has been well-recognized. Among the attempts to assess FPs, the concomitant use of target and decoy databases is widely practiced. By adjusting filtering criteria, FPs and false discovery rate (FDR) can be controlled at a desired level. Although the target-decoy approach is gaining in popularity, subtle differences in decoy construction (e.g., reversing vs stochastic methods), rate calculation (e.g., total vs unique PSMs), or searching (separate vs composite) do exist among various implementations. In the present study, we evaluated the effects of these differences on FP and FDR estimations using a rat kidney protein sample and the SEQUEST search engine as an example. On the effects of decoy construction, we found that, when a single scoring filter (XCorr) was used, stochastic methods generated a higher estimation of FPs and FDR than sequence reversing methods, likely due to an increase in unique peptides. This higher estimation could largely be attenuated by creating decoy databases similar in effective size but not by a simple normalization with a unique-peptide coefficient. When multiple filters were applied, the differences seen between reversing and stochastic methods significantly diminished, suggesting multiple filterings reduce the dependency on how a decoy is constructed. For a fixed set of filtering criteria, FDR and FPs estimated by using unique PSMs were almost twice those using total PSMs. The higher estimation seemed to be dependent on data acquisition setup. As to the differences between performing separate or composite searches, in general, FDR estimated from the separate search was about three times that from the composite search. The degree of difference gradually decreased as the filtering criteria became more stringent. Paradoxically, the estimated true positives in separate search were higher when multiple filters were used. By analyzing a standard protein mixture, we demonstrated that the higher estimation of FDR and FPs in the separate search likely reflected an overestimation, which could be corrected with a simple merging procedure. Our study illustrates the relative merits of different implementations of the target-decoy strategy, which should be worth contemplating when large-scale proteomic biomarker discovery is to be attempted.
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Adsorption of uranium (VI) from aqueous solution onto cross-linked chitosan.
J. Hazard. Mater.
PUBLISHED: 01-13-2009
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Cross-linked chitosan (CCTS) was synthesized by the reaction of chitosan with epichlorohydrin under alkaline conditions. Adsorption of uranium (VI) from aqueous solution onto cross-linked chitosan was investigated in a batch system. Adsorption isotherm and adsorption kinetic studies of uranium (VI) onto cross-linked chitosan were carried out. The influence factors on uranium (VI) adsorption were also investigated and described in detail, such as contact time, pH value and initial uranium (I) concentration. Langmuir and Freundlich adsorption models were used for the mathematical description of the adsorption equilibrium. Equilibrium data agreed very well with the Langmuir model. Adsorption kinetics data were tested using pseudo-first-order and pseudo-second-order models. Kinetic studies showed that the adsorption followed a pseudo-second-order kinetic model, indicating that the chemical adsorption was the rate-limiting step. Results also showed that cross-linked chitosan was favourable adsorbent.
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An Efficient Dynamic Programming Algorithm for Phosphorylation Site Assignment of Large-Scale Mass Spectrometry Data.
Proceedings (IEEE Int Conf Bioinformatics Biomed)
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Phosphorylation site assignment of large-scale data from high throughput tandem mass spectrometry (LC-MS/MS) data is an important aspect of phosphoproteomics. Correct assignment of phosphorylated residue(s) is important for functional interpretation of the data within a biological context. Common search algorithms (Sequest etc.) for mass spectrometry data are not designed for accurate site assignment; thus, additional algorithms are needed. In this paper, we propose a linear-time and linear-space dynamic programming strategy for phosphorylation site assignment. The algorithm, referred to as PhosSA, optimizes the objective function defined as the summation of peak intensities that are associated with theoretical phosphopeptide fragmentation ions. Quality control is achieved through the use of a post-processing criteria whose value is indicative of the signal-to-noise (S/N) properties and redundancy of the fragmentation spectra. The algorithm is tested using experimentally generated data sets of peptides with known phosphorylation sites while varying the fragmentation strategy (CID or HCD) and molar amounts of the peptides. The algorithm is also compatible with various peptide labeling strategies including SILAC and iTRAQ. PhosSA is shown to achieve > 99% accuracy with a high degree of sensitivity. The algorithm is extremely fast and scalable (able to process up to 0.5 million peptides in an hour). The implemented algorithm is freely available at http://helixweb.nih.gov/ESBL/PhosSA/ for academic purposes.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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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.