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Find video protocols related to scientific articles indexed in Pubmed.
Proteomic characterization of the outer membrane vesicle of pseudomonas putida KT2440.
J. Proteome Res.
PUBLISHED: 09-19-2014
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Outer membrane vesicles (OMVs) are produced by various pathogenic Gram-negative bacteria such as Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii. In this study, we isolated OMVs from a representative soil bacterium, Pseudomonas putida KT2440, which has a biodegradative activity toward various aromatic compounds. Proteomic analysis identified the outer membrane proteins (OMPs) OprC, OprD, OprE, OprF, OprH, OprG, and OprW as major components of the OMV of P. putida KT2440. The production of OMVs was dependent on the nutrient availability in the culture media, and the up- or down-regulation of specific OMPs was observed according to the culture conditions. In particular, porins (e.g., benzoate-specific porin, BenF-like porin) and enzymes (e.g., catechol 1,2-dioxygenase, benzoate dioxygenase) for benzoate degradation were uniquely found in OMVs prepared from P. putida KT2440 that were cultured in media containing benzoate as the energy source. OMVs of P. putida KT2440 showed low pathological activity toward cultured cells that originated from human lung cells, which suggests their potential as adjuvants or OMV vaccine carriers. Our results suggest that the protein composition of the OMVs of P. putida KT2440 reflects the characteristics of the total proteome of P. putida KT2440.
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Isolation and proteomic characterization of bacterial extracellular membrane vesicles.
Curr. Protein Pept. Sci.
PUBLISHED: 04-15-2014
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The secretion of extracellular membrane vesicles (EMVs) is a common phenomenon that occurs in archaea, bacteria, and mammalian cells. EMVs contain biologically active proteins, which have diverse roles in biological processes. The outer membrane vesicles (OMVs) of Gram-negative bacteria and membrane vesicles (MVs) of Gram-positive bacteria have been discovered in various species. The main issues related to bacterial EMVs are their virulence, biogenesis mechanisms, host cell interaction mechanisms, and their potential use as new vaccine candidates. Recently, proteomics has become an essential tool for the characterization of EMVs. Proteomics is useful for the identification, quantification, and protein-protein interaction analysis of EMV protein components. This review describes the current understanding of secretory EMVs based on proteomic methods and the characteristics of various bacterial secretory EMVs. Finally, evidence for their potential roles and future applications are discussed.
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G-749, a novel FLT3 kinase inhibitor, can overcome drug resistance for the treatment of acute myeloid leukemia.
Blood
PUBLISHED: 02-14-2014
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Aberrant activations of Fms-like tyrosine receptor kinase (FLT) 3 are implicated in the pathogenesis of 20% to 30% of patients with acute myeloid leukemia (AML). G-749 is a novel FLT3 inhibitor that showed potent and sustained inhibition of the FLT3 wild type and mutants including FLT3-ITD, FLT3-D835Y, FLT3-ITD/N676D, and FLT3-ITD/F691L in cellular assays. G-749 retained its inhibitory potency in various drug-resistance milieus such as patient plasma, FLT3 ligand surge, and stromal protection. Furthermore, it displayed potent antileukemic activity in bone marrow blasts from AML patients regardless of FLT3 mutation status, including those with little or only minor responses to AC220 or PKC412. Oral administration of G-749 yielded complete tumor regression and increased life span in animal models. Thus, G-749 appears to be a promising next-generation drug candidate for the treatment of relapsed and refractory AML patients with various FLT3-ITD/FLT3-TKD mutants and further shows the ability to overcome drug resistance.
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Proteogenomic characterization of antimicrobial resistance in extensively drug-resistant Acinetobacter baumannii DU202.
J. Antimicrob. Chemother.
PUBLISHED: 01-31-2014
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To determine the genomic sequence of extensively drug-resistant Acinetobacter baumannii DU202 and to perform proteomic characterization of antibiotic resistance in this strain using genome data.
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Draft Genome Sequence of Petroleum Oil-Degrading Marine Bacterium Pseudomonas taeanensis Strain MS-3, Isolated from a Crude Oil-Contaminated Seashore.
Genome Announc
PUBLISHED: 01-11-2014
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Pseudomonas taeanensis MS-3(T), isolated from a crude oil-contaminated seashore in South Korea, is capable of degrading petroleum oils, such as gasoline, diesel, and kerosene. Here, we report the draft genome sequence of this strain, which consists of 5,477,045 bp, with a G+C content of 60.72%.
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Proteomic characterization of plasmid pLA1 for biodegradation of polycyclic aromatic hydrocarbons in the marine bacterium, Novosphingobium pentaromativorans US6-1.
PLoS ONE
PUBLISHED: 01-01-2014
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Novosphingobium pentaromativorans US6-1 is a halophilic marine bacterium able to degrade polycyclic aromatic hydrocarbons (PAHs). Genome sequence analysis revealed that the large plasmid pLA1 present in N. pentaromativorans US6-1 consists of 199 ORFs and possess putative biodegradation genes that may be involved in PAH degradation. 1-DE/LC-MS/MS analysis of N. pentaromativorans US6-1 cultured in the presence of different PAHs and monocyclic aromatic hydrocarbons (MAHs) identified approximately 1,000 and 1,400 proteins, respectively. Up-regulated biodegradation enzymes, including those belonging to pLA1, were quantitatively compared. Among the PAHs, phenanthrene induced the strongest up-regulation of extradiol cleavage pathway enzymes such as ring-hydroxylating dioxygenase, putative biphenyl-2,3-diol 1,2-dioxygenase, and catechol 2,3-dioxygenase in pLA1. These enzymes lead the initial step of the lower catabolic pathway of aromatic hydrocarbons through the extradiol cleavage pathway and participate in the attack of PAH ring cleavage, respectively. However, N. pentaromativorans US6-1 cultured with p-hydroxybenzoate induced activation of another extradiol cleavage pathway, the protocatechuate 4,5-dioxygenase pathway, that originated from chromosomal genes. These results suggest that N. pentaromativorans US6-1 utilizes two different extradiol pathways and plasmid pLA1 might play a key role in the biodegradation of PAH in N. pentaromativorans US6-1.
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Green lighting upconversion luminescence of Yb3+, Er3+ co-doped BaMoO4.
J Nanosci Nanotechnol
PUBLISHED: 11-12-2013
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A green lighting upconversion (UC) system was successfully achieved from Er3+/Yb3+ co-doped BaMoO4 synthesized by the complex citrate-gel method. Under 980 nm laser excitation, the Er3+/Yb3+ co-doped BaMoO4 emitted strong green luminescence around 530 and 550 nm and weak red luminescence near 660 nm, which corresponded to the intra 4f-4f transitions in Er3+. Optimal doping concentrations of Er3+/Yb3+ into the BaMoO4 matrix were investigated. Moreover, based on excitation power dependence, the UC luminescent mechanism in the Er3+/Yb3+ co-doped BaMoO4 was presented in detail.
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Enhancement of conductive pathway of functionalized CNT dispersed poly(methylmethacrylate) nanocomposites.
J Nanosci Nanotechnol
PUBLISHED: 07-19-2013
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Poly(methylmethacrylate) (PMMA) beads were coated with pristine multi-walled carbon nanotube (MWNT) using various mixing medium and then nanocomposite were fabricated. Results were compared with acid functionalized MWNT (f-MWNT) coated PMMA bead nanocomposites. In addition, a combination of different mixing medium was also used to compare and to optimize the homogeneously dispersed MWNT and f-MWNT coating on PMMA beads. A homogeneous coating of nanotubes on the PMMA beads were observed in a DMF solution and confirmed by optical microscopy, SEM, Raman mapping, and sheet resistance measurements. Moreover, percolation and electrical properties were also compared with respect to nanotubes dispersion in the PMMA resin matrix. Nanocomposites prepared by coating PMMA beads with pristine CNT exhibited improvement of electro conductive pathway i.e., lowering percolation threshold below 0.1 wt% of MWNT content. The result was also compared with acid treated MWNT coated PMMA beads and acid treated dispersed MWNT in PMMA resins. The ultra-low electrical surface resistance of nanocomposites using trace amounts of MWNT coating on PMMA beads has not been reported so far.
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The E2F1 oncogene transcriptionally regulates NELL2 in cancer cells.
DNA Cell Biol.
PUBLISHED: 07-05-2013
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NELL2 was first identified as a mammalian homolog of the chicken NEL protein. It was expressed in neurons and has been suggested to play a role in cell survival. However, no clear evidence has yet been available for functions of NELL2. In this study, we found two E2F1 binding sites located in the NELL2 promoter region. We examined the expression of NELL2 and E2F1 in human breast cancer cells (MDA-MB231, MCF7) and bladder cancer cells (5637, UC5). In MDA-MB231 and 5637, the expression levels of NELL2 and E2F1 were higher. To examine the interaction between E2F1 and NELL2, the binding activity was checked by a promoter assay and chromatin immunoprecipitation. From the results, we suggest that NELL2 is a novel target gene of E2F1, which is a key regulator of cell proliferation. We reveal that expression of NELL2 is regulated by E2F1, specifically, mRNA and protein levels of NELL2 are elevated upon activation of exogenous E2F1. Moreover, cells overexpressing NELL2 increased their invasive ability and an enhancement of the effect was observed when NELL2 and E2F1 were coexpressed in MDA-MB231 cells. Therefore, we suggest a novel activity for NELL2 in cancer progression through the regulation of E2F1.
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Lipocalin-2 negatively modulates the epithelial-to-mesenchymal transition in hepatocellular carcinoma through the epidermal growth factor (TGF-beta1)/Lcn2/Twist1 pathway.
Hepatology
PUBLISHED: 04-12-2013
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Lipocalin-2 (Lcn2) is preferentially expressed in hepatocellular carcinoma (HCC). However, the functional role of Lcn2 in HCC progression is still poorly understood, particularly with respect to its involvement in invasion and metastasis. The purpose of this study was to investigate whether Lcn2 is associated with the epithelial-mesenchymal transition (EMT) in HCC and to elucidate the underlying signaling pathway(s). Lcn2 was preferentially expressed in well-differentiated HCC versus liver cirrhosis tissues, and its expression was positively correlated with the stage of HCC. The characteristics of EMT were reversed by adenoviral transduction of Lcn2 into SH-J1 cells, including the down-regulation of N-cadherin, vimentin, alpha-smooth muscle actin, and fibronectin, and the concomitant up-regulation of CK8, CK18, and desmoplakin I/II. Knockdown of Lcn2 by short hairpin RNA (shRNA) in HKK-2 cells expressing high levels of Lcn2 was associated with EMT. Epidermal growth factor (EGF) or transforming growth factor beta1 (TGF-?1) treatment resulted in down-regulation of Lcn2, accompanied by an increase in Twist1 expression and EMT in HCC cells. Stable Lcn2 expression in SH-J1 cells reduced Twist1 expression, inhibited cell proliferation and invasion in vitro, and suppressed tumor growth and metastasis in a mouse model. Furthermore, EGF or TGF-?1 treatment barely changed EMT marker expression in SH-J1 cells ectopically expressing Lcn2. Ectopic expression of Twist1 induced EMT marker expression even in cells expressing Lcn2, indicating that Lcn2 functions downstream of growth factors and upstream of Twist1. Conclusion: Together, our findings indicate that Lcn2 can negatively modulate the EMT in HCC cells through an EGF (or TGF-?1)/Lcn2/Twist1 pathway. Thus, Lcn2 may be a candidate metastasis suppressor and a potential therapeutic target in HCC.
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Analysis of tear cytokines and clinical correlations in Sjögren syndrome dry eye patients and non-Sjögren syndrome dry eye patients.
Am. J. Ophthalmol.
PUBLISHED: 04-01-2013
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To compare concentrations of tear cytokines in 3 groups composed of Sjögren syndrome (SS) dry eye, non-Sjögren syndrome (non-SS) dry eye, and normal subjects. Correlations between ocular surface parameters and tear cytokines were also investigated.
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Susceptibility for breast cancer in young patients with short rare minisatellite alleles of BORIS.
BMB Rep
PUBLISHED: 11-02-2010
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In this study, we characterized two blocks of minisatellites in the 5 upstream region of the BORIS gene (BORIS-MS1, -MS2). BORIS-MS2 was found to be polymorphic; therefore, this locus could be useful as a marker for DNA fingerprinting. We assessed the association between BORIS-MS2 and breast cancer by a case-control study with 428 controls and 793 breast cancers cases. Rare alleles in the younger group (age, <40) were associated with a statistically significant increased risk of breast cancer (odds ratio, 4.84; 95% confidence interval, 1.06-22.22; and P = 0.026). A statistically significant association between the short rare alleles and cancer was identified in the younger group (8.02; 1.01-63.83; P = 0.021). Kaplan-Meier estimates showed that poor prognosis was associated with patients who contained the rare alleles. Our data suggest that the short rare alleles of BORIS-MS2 could be used to identify the risk for breast cancer in young patients.
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Short rare MUC6 minisatellites-5 alleles influence susceptibility to gastric carcinoma by regulating gene.
Hum. Mutat.
PUBLISHED: 05-28-2010
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The human MUC6 gene, which is reported to be expressed in the stomach and gall bladder, is clustered on chromosome 11p15.5 with other secreted mucins. In this study, the genomic structure of MUC6 has been analyzed and five VNTR (minisatellites; MS1-MS5) were identified. These minisatellites were analyzed in genomic DNA extracted from 1,103 controls, 470 gastric cancer patients, and multigenerational families. Five novel minisatellites were found to be polymorphic and transmitted through meiosis by Mendelian inheritance in families. We evaluated allelic variation in these minisatellites to determine if such variation affected the susceptibility to gastric cancer. A significant association (odds ratio [OR]=7.08) between short rare MUC6-MS5 alleles and relative risks were observed for gastric cancer (95% confidence interval [CI], 1.43-35.19; P=0.005). To investigate the function of minisatellite alleles of MUC6-MS5, we examined the effects on gene expression from luciferase reporters when inserted with minisatellites. Interestingly, when the shortest allele (7TR) was inserted in the promoter, the expression level decreased over 20-fold (P<0.001) in normal and cancer cell lines. Furthermore, the cancer-specific rare allele (TR8) also showed decreased expression levels in cancer cells. Therefore, we suggest that the short rare MUC6-MS5 alleles may be related to cancer development by the regulation of MUC6 expression.
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Expression signature of E2F1 and its associated genes predict superficial to invasive progression of bladder tumors.
J. Clin. Oncol.
PUBLISHED: 04-26-2010
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In approximately 20% of patients with superficial bladder tumors, the tumors progress to invasive tumors after treatment. Current methods of predicting the clinical behavior of these tumors prospectively are unreliable. We aim to identify a molecular signature that can reliably identify patients with high-risk superficial tumors that are likely to progress to invasive tumors.
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Short rare hTERT-VNTR2-2nd alleles are associated with prostate cancer susceptibility and influence gene expression.
BMC Cancer
PUBLISHED: 03-04-2010
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The hTERT (human telomerase reverse transcriptase) gene contains five variable number tandem repeats (VNTR) and previous studies have described polymorphisms for hTERT-VNTR2-2nd. We investigated how allelic variation in hTERT-VNTR2-2nd may affect susceptibility to prostate cancer.
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Foveal ganglion cell layer damage in ischemic diabetic maculopathy: correlation of optical coherence tomographic and anatomic changes.
Ophthalmology
PUBLISHED: 02-06-2009
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To describe the morphologic features of ischemic diabetic maculopathy by high-resolution optical coherence tomography (OCT) and their correlation with the damaged foveal avascular zone (FAZ) on fluorescein angiography (FA).
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Reliability of RTVue, Visante, and slit-lamp adapted ultrasonic pachymetry for central corneal thickness measurement.
Yonsei Med. J.
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To evaluate reliability of Fourier-domain optical coherence tomography (OCT) (RTVue), time-domain OCT (Visante), and slit-lamp adapted ultrasonic pachymetry (SL-US) in the measurement of central corneal thickness (CCT).
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Histone deacetylase 6 functions as a tumor suppressor by activating c-Jun NH2-terminal kinase-mediated beclin 1-dependent autophagic cell death in liver cancer.
Hepatology
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Ubiquitin-binding histone deacetylase 6 (HDAC6) is uniquely endowed with tubulin deacetylase activity and plays an important role in the clearance of misfolded protein by autophagy. In cancer, HDAC6 has become a target for drug development due to its major contribution to oncogenic cell transformation. In the present study we show that HDAC6 expression was down-regulated in a large cohort of human hepatocellular carcinoma (HCC) patients, and that low expression of HDAC6 was significantly associated with poor prognosis of HCC patients in 5-year overall, disease-free, and recurrence-free survival. Notably, we observed that ectopic overexpression of HDAC6 suppressed tumor cell growth and proliferation in various liver cancer cells, and elicited increased LC3B-II conversion and autophagic vacuole formation without causing apoptotic cell death or cell cycle inhibition. In addition, the sustained overexpression of HDAC6 reduced the in vivo tumor growth rate in a mouse xenograft model. It was also found that HDAC6 mediated autophagic cell death by way of Beclin 1 and activation of the LC3-II pathway in liver cancer cells, and that HDAC6 overexpression activated c-Jun NH2-terminal kinase (JNK) and increased the phosphorylation of c-Jun. In contrast, the induction of Beclin 1 expression was blocked by SP600125 (a specific inhibitor of JNK) or by small interfering RNA directed against HDAC6.
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What is Visualize?

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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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

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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.