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Find video protocols related to scientific articles indexed in Pubmed.
Thiobacimonas profunda gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from the deep-sea water.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 10-31-2014
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A bacterial strain, JLT2016T, was isolated from a sample of Southeastern Paci?c deep-sea water. Cells were Gram-stain-negative, aerobic, devoid of flagella, motile by gliding, rod-shaped. Colonies were mucoid and creamy-coloured. Growth occurred at 1.0-11.0% (w/v) NaCl, 10-40 °C and pH 4.0-9.0. The major fatty acids were summed in feature 8 (C18:1?7c and/or C18:1?6c) (60.5%), cyclo-C19:0?8c (10.9%), C16:0 (9.0%). Polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two sphingoglycolipid. The DNA G+C content was 67.1 mol%. The closest relative of strain JLT2016T was Salipiger mucosus A3T (96.7% 16S rRNA gene sequence identity). The results of phylogenetic analyses with different treeing algorithms indicated this strain belonged to the Roseobacter clade in the order Rhodobacterales. Based on the polyphasic analysis, strain JLT2016T is considered to represent a novel genus and species, for which the name Thiobacimonas profunda gen. nov., sp. nov. is proposed. The type strain is JLT2016T (= LMG 27365T= CGMCC 1.12377T).
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[Effect of (E)-2-(4-bromophenyl )-1-(3,4-dihydroxyphenyl )ethanone oxime on proliferation and activation of mice lymphocytes].
Sichuan Da Xue Xue Bao Yi Xue Ban
PUBLISHED: 10-25-2014
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To study the effects of (E)-2-(4-bromophenyl)-1-(3, 4-dihydroxyphenyl) ethanone oxime (BDEO) on the proliferation and activation of the mice' s splenic lymphocytes and the peripheral blood lymphocytes induced by Concanavalin A (Con A) in vitro and in vivo, and its molecular mechanism.
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Association between a polymorphism in miR-34b/c and susceptibility to cancer--a meta-analysis.
Asian Pac. J. Cancer Prev.
PUBLISHED: 09-18-2014
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MicroRNAs (miRNAs) act as tumor suppressors or promoters in neoplasia by regulating relative gene expression. The association between a single nucleotide polymorphism (SNP) rs4938723 in miR-34b/c and susceptibility to cancers was inconsistent in previous studies. In this study, we conducted a literature search of PubMed, Web of Science and Embase to identify all relevant studies in this meta-analysis with 6,036 cases and 6,204 controls. We found that the miR-34b/c rs4938723 polymorphism was significantly associated with increased risk of cancers in the heterozygous model (TC versus TT, OR=1.09, 95% CI=1.01-1.18, P=0.02). Subgroup analysis also revealed increased risk for Asian ethnicity in the heterozygous model (TC versus TT, OR=1.12, 95% CI=1.02-1.22, P=0.02), but decreased risk of colorectal cancer in homozygote model (CC versus TT, OR=0.66, 95% CI=0.47-0.92, P=0.02) and in the recessive model (CC versus TC+TT, OR=0.67, 95% CI=0.48-0.93, P=0.02) by cancer type. The current meta-analysis indicated that the miR-34b/c rs4938723 polymorphism may decrease susceptibility to colorectal cancer. Well-designed studies with larger sample size are required to further validate the results.
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QT restitution properties during exercise in male patients with coronary artery disease.
Ann Noninvasive Electrocardiol
PUBLISHED: 08-29-2014
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The hypothesis of action potential duration restitution (APDR) suggests that wave break is mainly determined by the steepness of APDR curve. The purpose of this study was to investigate the QT restitution properties by a noninvasive method, exercise ECG test, in patients with and without left anterior descending coronary artery disease (CAD).
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More favorable response to cardiac resynchronization therapy in women than in men.
Circ Arrhythm Electrophysiol
PUBLISHED: 08-21-2014
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Data on sex difference in response to cardiac resynchronization therapy (CRT) remain controversial. We conducted a meta-analysis to summarize all published studies to determine whether sex-based differences in response to CRT exist.
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Polysaccharopeptide enhanced the anti-cancer effect of gamma-tocotrienol through activation of AMPK.
BMC Complement Altern Med
PUBLISHED: 08-16-2014
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Prostate cancer (PCa) frequently relapses after hormone ablation therapy. Unfortunately, once progressed to the castration resistant stage, the disease is regarded as incurable as prostate cancer cells are highly resistant to conventional chemotherapy.
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MicroRNA-581 promotes hepatitis B virus surface antigen expression by targeting Dicer and EDEM1.
Carcinogenesis
PUBLISHED: 06-09-2014
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Hepatitis B virus surface antigen (HBsAg) is an important risk factor for hepatocellular carcinoma (HCC) and is downregulated during hepatocarcinogenesis. MicroRNAs (miRNAs) are frequently deregulated in HCC tissues. However, whether the deregulation of certain miRNAs in HCC has an impact on HBsAg expression remains unclear. We found here that microRNA-581 (miR-581), which is deregulated during hepatocarcinogenesis, promoted HBsAg expression. Additionally, miR-581 targeted Dicer and endoplasmic reticulum degradation-enhancing alpha-mannosidase-like protein 1 (EDEM1) and repressed their expression. Although Dicer cannot process HBV transcripts, Dicer knockdown led to increased HBsAg secretion, most likely due to a reduction in the levels of Dicer-processed 7SL RNA fragments. Moreover, Dicer-processed 7SL RNA fragments partially inhibited the ability of miR-581 to stimulate HBsAg expression. Furthermore, we found that forced EDEM1 expression inhibited miR-581-mediated induction of HBsAg. Finally, transfection of miR-581 into HepG2.2.15 cells promoted cell proliferation and led to upregulation of genes involved in development, cell proliferation and protein secretion. Altogether, we conclude that miR-581 promotes HBsAg expression by targeting Dicer and EDEM1. Our findings suggest that downregulation of miR-581 during hepatocarcinogenesis may lead to a reduction in HBsAg expression and impede HCC development.
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Effects of transplantation of olfactory ensheathing cells in chronic spinal cord injury: a systematic review and meta-analysis.
Eur Spine J
PUBLISHED: 06-08-2014
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The debate on the effects and outcome of olfactory ensheathing cell (OEC) transplantation for the treatment of spinal cord injury (SCI) has remained unresolved for nearly 20 years. This study aimed to evaluate the safety and efficacy of OEC transplantation in chronic SCI patients.
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Impacts of different draw solutions on a novel anaerobic forward osmosis membrane bioreactor (AnFOMBR).
Water Sci. Technol.
PUBLISHED: 05-22-2014
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Two anaerobic forward osmosis (FO) membrane bioreactors (AnFOMBRs), Rchloride and Rsulfate, were operated for 100 days using NaCl and Na2SO4 as the draw solution, respectively. The operating conditions were identical for both systems, with a solids retention time of 30 d, hydraulic retention time of 8 h and using cellulose triacetate FO membrane. High rejection performance of FO membranes resulted in salinity accumulation in the bioreactors. Rchloride and Rsulfate reached a stable conductivity of about 35 and 11 mS/cm, respectively, at the end of the experimental run. Hypersalinity of Rchloride undesirably impacted biological growth; mixed liquor volatile suspended solids in Rchloride was much lower at 376 mg/L, whereas that of Rsulfate was 1,170 mg/L. Organic removals were excellent due to reduced organic loadings at low fluxes and thus, Rsulfate and Rchloride achieved secondary total organic carbon (TOC) removal efficiencies of at least 75%. Both AnFOMBRs started with an initial flux of 5 LMH. Flux for Rchloride stabilized at 0.25 LMH, while Rsulfate at 0.96 LMH. The high salinities of both reactors negatively impacted methanogenic growth. Application of the fluorescence in-situ hybridization (FISH) technique confirmed the ousting of methanogens by sulfate reducing bacteria from the anaerobic consortium. Sparsely located methanogens were detected in Rchloride but none were detected in Rsulfate.
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Pelagibaca abyssi sp. nov., of the family Rhodobacteraceae, isolated from deep-sea water.
Antonie Van Leeuwenhoek
PUBLISHED: 04-04-2014
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A Gram-stain negative, oval-shaped, aerobic, catalase and oxidase-positive bacterium, designated JLT2014(T), was isolated from a deep-seawater sample (obtained at a 2,000 m depth) of the Southeastern Pacific Ocean. The dominant fatty acids were identified as C18:1?7c/C18:1?6c, C16:0 and C10:0 3-OH, which altogether represented 60.1 % of the total. The predominant respiratory quinone was identified as Q-10. The G+C content of genomic DNA was determined to be 66.4 mol %. The major polar lipids were identified as phosphatidylethanolamine and diphosphatidylglycerol. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel isolate can be affiliated with the Roseobacter clade within the family Rhodobacteraceae. Strain JLT2014(T) exhibited highest 16S rRNA gene sequence similarity value to Pelagibaca bermudensis HTCC2601(T) (sequence similarity value: 97.6 %). The DNA-DNA relatedness value between strain JLT2014(T) and P. bermudensis HTCC2601(T) was 46.9 ± 2 %. Based on phenotypic properties and phylogenetic analysis, the name Pelagibaca abyssi sp. nov. is proposed, with JLT2014(T)(=LMG 27363(T)=CGMCC 1.12376(T)) as the type strain.
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Regulation of active DNA demethylation by an ?-crystallin domain protein in Arabidopsis.
Mol. Cell
PUBLISHED: 04-03-2014
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DNA methylation patterns are dynamically controlled by DNA methylation and active DNA demethylation, but the mechanisms of regulation of active DNA demethylation are not well understood. Through forward genetic screens for Arabidopsis mutants showing DNA hypermethylation at specific loci and increased silencing of reporter genes, we identified IDM2 (increased DNA methylation 2) as a regulator of DNA demethylation and gene silencing. IDM2 dysfunction causes DNA hypermethylation and silencing of reporter genes and some endogenous genes. These effects of idm2 mutations are similar to those of mutations in IDM1, a regulator of active DNA demethylation. IDM2 encodes an ?-crystallin domain protein in the nucleus. IDM2 and IDM1 interact physically and partially colocalize at discrete subnuclear foci. IDM2 is required for the full activity of H3K18 acetylation but not H3K23 acetylation of IDM1 in planta. Our results suggest that IDM2 functions in active DNA demethylation and in antisilencing by regulating IDM1.
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Effects of Nardostachys chinensis on spontaneous ventricular arrhythmias in rats with acute myocardial infarction.
J. Cardiovasc. Pharmacol.
PUBLISHED: 03-26-2014
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To investigate the effects and mechanisms of Nardostachys chinensis (NC) on spontaneous ventricular arrhythmias in rats with hyper-acute myocardial infarction (AMI).
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Ras-induced epigenetic inactivation of the RRAD (Ras-related associated with diabetes) gene promotes glucose uptake in a human ovarian cancer model.
J. Biol. Chem.
PUBLISHED: 03-19-2014
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RRAD (Ras-related associated with diabetes) is a small Ras-related GTPase that is frequently inactivated by DNA methylation of the CpG island in its promoter region in cancer tissues. However, the role of the methylation-induced RRAD inactivation in tumorigenesis remains unclear. In this study, the Ras-regulated transcriptome and epigenome were profiled by comparing T29H (a Ras(V12)-transformed human ovarian epithelial cell line) with T29 (an immortalized but non-transformed cell line) through reduced representation bisulfite sequencing and digital gene expression. We found that Ras(V12)-mediated oncogenic transformation was accompanied by RRAD promoter hypermethylation and a concomitant loss of RRAD expression. In addition, we found that the RRAD promoter was hypermethylated, and its transcription was reduced in ovarian cancer versus normal ovarian tissues. Treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine resulted in demethylation in the RRAD promoter and restored RRAD expression in T29H cells. Additionally, treatment with farnesyltransferase inhibitor FTI277 resulted in restored RRAD expression and inhibited DNA methytransferase expression and activity in T29H cells. By employing knockdown and overexpression techniques in T29 and T29H, respectively, we found that RRAD inhibited glucose uptake and lactate production by repressing the expression of glucose transporters. Finally, RRAD overexpression in T29H cells inhibited tumor formation in nude mice, suggesting that RRAD is a tumor suppressor gene. Our results indicate that Ras(V12)-mediated oncogenic transformation induces RRAD epigenetic inactivation, which in turn promotes glucose uptake and may contribute to ovarian cancer tumorigenesis.
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Association between a lumican promoter polymorphism and high myopia in the Chinese population: a meta-analysis of case-control studies.
Ophthalmologica
PUBLISHED: 02-08-2014
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To evaluate the relationship between lumican polymorphisms and high myopia in Chinese populations.
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Posterior short segment pedicle screw fixation and TLIF for the treatment of unstable thoracolumbar/lumbar fracture.
BMC Musculoskelet Disord
PUBLISHED: 02-06-2014
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Currently, Posterior Short Segment Pedicle Screw Fixation is a popular procedure for treating unstable thoracolumbar/lumbar burst fracture. But progressive kyphosis and a high rate of hardware failure because of lack of the anterior column support remains a concern. The efficacy of different methods remains debatable and each technique has its advantages and disadvantages.
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Differences of various region-of-interest methods for measuring dopamine transporter availability using 99mTc-TRODAT-1 SPECT.
ScientificWorldJournal
PUBLISHED: 02-01-2014
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This study was to investigate whether various region-of-interest (ROI) methods for measuring dopamine transporter (DAT) availabilities by single photon emission computed tomography (SPECT) are statistically different, whether results of medical research are thereby influenced, and causes of these differences. Eighty-four healthy adults with (99m)Tc-TRODAT-1 SPECT and magnetic resonance imaging (MRI) scans were included. Six major analysis approaches were compared: (1) ROI drawn on the coregistered MRI; (2) ROIs drawn on the SPECT images; (3) standard ROI templates; (4) threshold-ROIs; (5) atlas-based mappings with coregistered MRI; and (6) atlas-based mappings with SPECT images. Using the atlas-based approaches we assessed the influence of striatum ROIs by slice-wise and voxel-wise comparisons. In (5) and (6), three partial-volume correction (PVC) methods were also explored. The results showed that DAT availabilities obtained from different methods were closely related but quite different and leaded to significant differences in determining the declines of DAT availability per decade (range: 5.95-11.99%). Use of 3D whole-striatum or more transverse slices could avoid biases in measuring the striatal DAT declines per decade. Atlas-based methods with PVC may be the preferable methods for medical research.
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Pacificamonas flava gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from the Southeastern Pacific.
Curr. Microbiol.
PUBLISHED: 01-23-2014
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Strain JLT2015(T) was isolated from surface seawater of the Southeastern Pacific. The strain was Gram-negative, aerobic, motile by gliding, and rod shaped. The dominant fatty acids were C18:1?7c, C16:0, and C16:1?7c. The major respiratory ubiquinone was Q-10, and the predominant polyamine pattern was spermidine. The components of the polar lipid profile were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and sphingoglycolipid. The DNA G+C content was 64.2 %. Phylogenetic analysis based on 16S rRNA gene sequence revealed strain JLT2015(T) belonged to belong to the family Sphingomonadaceae, exhibiting 94.7 % 16S rRNA gene sequence similarity with Novosphingobium pentaromativorans. On the basis of the taxonomic data presented, together with phylogenetic and genetic characteristics, strain JLT2015(T) is considered to represent a novel genus, for which the name Pacificamonas flava gen. nov., sp. nov. is proposed. The type strain of Pacificamonas flava is JLT2015(T) (=LMG27364(T) = CGMCC1.12401(T)).
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Controlled attenuation parameter for the detection of steatosis severity in chronic liver disease: a meta-analysis of diagnostic accuracy.
J. Gastroenterol. Hepatol.
PUBLISHED: 01-12-2014
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Controlled attenuation parameter (CAP) is a novel ultrasound-based elastography method for detection of steatosis severity. This meta-analysis aimed to assess the performance of CAP.
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An Rrp6-like protein positively regulates noncoding RNA levels and DNA methylation in Arabidopsis.
Mol. Cell
PUBLISHED: 01-02-2014
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Rrp6-mediated nuclear RNA surveillance tunes eukaryotic transcriptomes through noncoding RNA degradation and mRNA quality control, including exosomal RNA decay and transcript retention triggered by defective RNA processing. It is unclear whether Rrp6 can positively regulate noncoding RNAs and whether RNA retention occurs in normal cells. Here we report that AtRRP6L1, an Arabidopsis Rrp6-like protein, controls RNA-directed DNA methylation through positive regulation of noncoding RNAs. Discovered in a forward genetic screen, AtRRP6L1 mutations decrease DNA methylation independently of exosomal RNA degradation. Accumulation of Pol V-transcribed scaffold RNAs requires AtRRP6L1 that binds to RNAs in vitro and in vivo. AtRRP6L1 helps retain Pol V-transcribed RNAs in chromatin to enable their scaffold function. In addition, AtRRP6L1 is required for genome-wide Pol IV-dependent siRNA production that may involve retention of Pol IV transcripts. Our results suggest that AtRRP6L1 functions in epigenetic regulation by helping with the retention of noncoding RNAs in normal cells.
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Combination of ranibizumab with photodynamic therapy vs ranibizumab monotherapy in the treatment of age-related macular degeneration: a systematic review and meta-analysis of randomized controlled trials.
Int J Ophthalmol
PUBLISHED: 01-01-2014
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To compare the efficacy and safety of combination of ranibizumab with photodynamic therapy (PDT) vs ranibizumab monotherapy in the treatment of age-related macular degeneration (AMD).
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Protocol: a beginner's guide to the analysis of RNA-directed DNA methylation in plants.
Plant Methods
PUBLISHED: 01-01-2014
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DNA methylation is a conserved epigenetic mark that controls genome stability, development and environmental responses in many eukaryotes. DNA methylation can be guided by non-coding RNAs that include small interfering RNAs and scaffold RNAs. Although measurement of DNA methylation and regulatory non-coding RNAs is desirable for many biologists who are interested in exploring epigenetic regulation in their areas, conventional methods have limitations and are technically challenging. For instance, traditional siRNA detection through RNA hybridization requires relatively large amount of small RNAs and involves radioactive isotopes. An alternative approach is RT-qPCR that employs stem loop primers during reverse transcription; however, it requires a prerequisite that the exact sequences of siRNAs should be known.
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Effects of metformin on the cerebral metabolic changes in type 2 diabetic patients.
ScientificWorldJournal
PUBLISHED: 01-01-2014
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Metformin, a widely used antidiabetic drug, has numerous effects on human metabolism. Based on emerging cellular, animal, and epidemiological studies, we hypothesized that metformin leads to cerebral metabolic changes in diabetic patients. To explore metabolism-influenced foci of brain, we used 2-deoxy-2-[(18)F]fluoro-D-glucose (FDG) positron emission tomography for type 2 diabetic patients taking metformin (MET, n = 18), withdrawing from metformin (wdMET, n = 13), and not taking metformin (noMET, n = 9). Compared with the noMET group, statistical parametric mapping showed that the MET group had clusters with significantly higher metabolism in right temporal, right frontal, and left occipital lobe white matter and lower metabolism in the left parahippocampal gyrus, left fusiform gyrus, and ventromedial prefrontal cortex. In volume of interest (VOI-) based group comparisons, the normalized FDG uptake values of both hypermetabolic and hypometabolic clusters were significantly different between groups. The VOI-based correlation analysis across the MET and wdMET groups showed a significant negative correlation between normalized FDG uptake values of hypermetabolic clusters and metformin withdrawal durations and a positive but nonsignificant correlation in the turn of hypometabolic clusters. Conclusively, metformin affects cerebral metabolism in some white matter and semantic memory related sites in patients with type 2 diabetes.
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Apoptotic genes expression in placenta of clubfoot-like fetus pregnant rats.
Int J Clin Exp Pathol
PUBLISHED: 01-01-2014
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To investigate the apoptotic gene expression of placenta in an all-trans-retinoic acid (ATRA) induced fetus congenital clubfoot pregnant rat model.
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Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 11-18-2013
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DNA methylation is important for the silencing of transposons and other repetitive elements in many higher eukaryotes. However, plant and mammalian genomes have evolved to contain repetitive elements near or inside their genes. How these genes are kept from being silenced by DNA methylation is not well understood. A forward genetics screen led to the identification of the putative chromatin regulator Enhanced Downy Mildew 2 (EDM2) as a cellular antisilencing factor and regulator of genome DNA methylation patterns. EDM2 contains a composite Plant Homeo Domain that recognizes both active and repressive histone methylation marks at the intronic repeat elements in genes such as the Histone 3 lysine 9 demethylase gene Increase in BONSAI Methylation 1 (IBM1) and is necessary for maintaining the expression of these genes by promoting mRNA distal polyadenylation. Because of its role in maintaining IBM1 expression, EDM2 is required for preventing CHG methylation in the bodies of thousands of genes. Our results thus increase the understanding of antisilencing, genome methylation patterns, and regulation of alternative RNA processing by intronic heterochromatin.
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Muir-Torre Syndrome in a Middle-Aged Chinese Patient with Sebaceous Carcinoma of the Eyelid.
Semin Ophthalmol
PUBLISHED: 10-15-2013
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Abstract Muir-Torre syndrome is a rare, autosomal dominant condition characterized by the presence of a skin tumor of sebaceous differentiation and visceral malignancies. We reviewed the case of a 46-year-old Chinese man who had a bleeding mass over the right upper eyelid. He had a history of colon cancer and a family history satisfying the Amsterdam criteria for hereditary non-polyposis colorectal cancer syndrome with germline mutation in the MutS homolog-2 gene. The eyelid lesion was excised completely and submitted for histopathologic examination which showed sebaceous carcinoma. Frozen section and conjunctival map biopsy showed no residual malignancy or local metastasis. Post-operative positron-emission tomography with combined computed tomography did not reveal any residual or visceral malignancy. He had no recurrence in the 32-month follow-up period. We should consider Muir-Torre syndrome in patients with sebaceous carcinoma, especially in the presence of personal and/or family history of visceral malignancies.
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A large-area diffuse air discharge plasma excited by nanosecond pulse under a double hexagon needle-array electrode.
Spectrochim Acta A Mol Biomol Spectrosc
PUBLISHED: 10-06-2013
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A large-area diffuse air discharge plasma excited by bipolar nanosecond pulse is generated under a double hexagon needle-array electrode at atmospheric pressure. The images of the diffuse discharge, electric characteristics, and the optical emission spectra emitted from the diffuse air discharge plasma are obtained. Based on the waveforms of pulse voltage and current, the power consumption, and the power density of the diffuse air discharge plasma are investigated under different pulse peak voltages. The electron density and the electron temperature of the diffuse plasma are estimated to be approximately 1.42×10(11)cm(-3) and 4.4eV, respectively. The optical emission spectra are arranged to determine the rotational and vibrational temperatures by comparing experimental with simulated spectra. Meanwhile, the rotational and vibrational temperatures of the diffuse discharge plasma are also discussed under different pulse peak voltages and pulse repetition rates, respectively. In addition, the diffuse air discharge plasma can form an area of about 70×50mm(2) on the surface of dielectric layer and can be scaled up to the required size.
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Gramella flava sp. nov., a novel member of the family Flavobacteriaceae isolated from the Southeastern Pacific.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 09-18-2013
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A novel Gram-negative, yellow-pigmented, aerobic, motile by gliding, rod-shaped marine bacterium (JLT2011T) was isolated from surface seawater. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JLT2011T could be assigned to the genus Gramella, and was most closely related to Gramella gaetbulicola with 96.2% similarity. The genomic DNA G+C content was 42.1%. The predominant fatty acids were C16:0, iso-C15:0, C18:0 and summed feature 3 (C16:1?6c/ C16:1?7c). The major menaquinone was MK-6. The major components of the polar lipid profile were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG) and sphingoglycolipid (SGL). On the basis of phenotypic, genotypic and taxonomic data presented, strain JLT2011T is considered to represent a novel species of Gramella, for which the name Gramella flava sp. nov. is proposed; the type strain is JLT2011T (=CGMCC 1.12375T=LMG 27360T).
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Meta-analysis of the association between a polymorphism in microRNA-196a2 and susceptibility to colorectal cancer.
Onkologie
PUBLISHED: 09-16-2013
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To accurately evaluate the impact of the C/T polymorphism in microRNA (miRNA)-196a2 on the colorectal cancer (CRC) risk, by meta-analysis.
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Parvularcula oceanus sp. nov., isolated from deep-sea water of the Southeastern Pacific Ocean.
Antonie Van Leeuwenhoek
PUBLISHED: 09-13-2013
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A Gram-negative, aerobic, motile by single polar flagellum, short rod-shaped bacterium was isolated from a deep-seawater sample of the Southeastern Pacific Ocean. Growth was found to occur at 10-40 °C, at pH 4.0-10.0 and in the presence of 0-9.0 % (w/v) NaCl. The phylogenetic tree based on 16S rRNA gene sequences showed that strain JLT2013(T) fell within a clade comprising species of the genus Parvularcula and formed a coherent cluster with Parvularcula lutaonensis CC-MMS-1(T) (neighbour-joining phylogenetic tree) or Parvularcula dongshanensis SH25(T) (maximum-likelihood and maximum-parsimony phylogenetic trees). Sequence similarity analyses based on 16S rRNA gene sequences revealed that strain JLT2013(T) shows high sequence similarity to P. lutaonensis CC-MMS-1(T) (96.7 %), P. dongshanensis SH25(T) (96.0 %) and Parvularcula bermudensis HTCC2503(T) (95.2 %). The major cellular fatty acids were identified as C12:0 (34.3 %), summed feature 8 (C18:1 ?7c and/or C18:1 ?6c) (10.9 %), C16:0 (10.0 %) and C17:1 ?6c (7.2 %). The polar lipids were found to include diphosphatidylglycerol, phosphatidylglycerol, three sphingoglycolipids and three unknown glycolipids. Strain JLT2013(T) was found to contain Q-10 as the predominant quinone. The DNA G+C content was determined to be 66.3 mol%. In the light of the phenotypic characteristics, chemotaxonomic features and phylogenetic evidence gathered in this study, strain JLT2013(T) (=LMG 27362(T) = CGMCC 1.12400(T)) should be classified as a novel species in the genus Parvularcula, for which the name Parvularcula oceanus sp. nov. is proposed.
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SIRT5: a safeguard against oxidative stress-induced apoptosis in cardiomyocytes.
Cell. Physiol. Biochem.
PUBLISHED: 09-03-2013
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SIRT5 is located in the mitochondria, and plays a crucial role in the regulation of metabolic process and cellular apoptosis. Cardiomyocytes are abundant in mitochondria. However, the role of SIRT5 in oxidative stress-induced apoptosis is still unknown in cardiomyocytes.
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RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 09-03-2013
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DNA methylation-dependent heterochromatin formation is a conserved mechanism of epigenetic silencing of transposons and other repeat elements in many higher eukaryotes. Genes adjacent to repetitive elements are often also subjected to this epigenetic silencing. Consequently, plants have evolved antisilencing mechanisms such as active DNA demethylation mediated by the REPRESSOR OF SILENCING 1 (ROS1) family of 5-methylcytosine DNA glycosylases to protect these genes from silencing. Some transposons and other repeat elements have found residence in the introns of genes. It is unclear how these intronic repeat elements-containing genes are regulated. We report here the identification of ANTI-SILENCING 1 (ASI1), a bromo-adjacent homology domain and RNA recognition motif-containing protein, from a forward genetic screen for cellular antisilencing factors in Arabidopsis thaliana. ASI1 is required to prevent promoter DNA hypermethylation and transcriptional silencing of some transgenes. Genome-wide DNA methylation analysis reveals that ASI1 has a similar role to that of the histone H3K9 demethylase INCREASE IN BONSAI METHYLATION 1 (IBM1) in preventing CHG methylation in the bodies of thousands of genes. We found that ASI1 is an RNA-binding protein and ensures the proper expression of IBM1 full-length transcript by associating with an intronic heterochromatic repeat element of IBM1. Through mRNA sequencing, we identified many genes containing intronic transposon elements that require ASI1 for proper expression. Our results suggest that ASI1 associates with intronic heterochromatin and binds the gene transcripts to promote their 3 distal polyadenylation. The study thus reveals a unique mechanism by which higher eukaryotes deal with the collateral effect of silencing intronic repeat elements.
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A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis.
PLoS Genet.
PUBLISHED: 09-01-2013
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Cytosine DNA methylation is a stable epigenetic mark that is frequently associated with the silencing of genes and transposable elements (TEs). In Arabidopsis, the establishment of DNA methylation is through the RNA-directed DNA methylation (RdDM) pathway. Here, we report the identification and characterization of RDM16, a new factor in the RdDM pathway. Mutation of RDM16 reduced the DNA methylation levels and partially released the silencing of a reporter gene as well as some endogenous genomic loci in the DNA demethylase ros1-1 mutant background. The rdm16 mutant had morphological defects and was hypersensitive to salt stress and abscisic acid (ABA). Map-based cloning and complementation test led to the identification of RDM16, which encodes a pre-mRNA-splicing factor 3, a component of the U4/U6 snRNP. RNA-seq analysis showed that 308 intron retention events occurred in rdm16, confirming that RDM16 is involved in pre-mRNA splicing in planta. RNA-seq and mRNA expression analysis also revealed that the RDM16 mutation did not affect the pre-mRNA splicing of known RdDM genes, suggesting that RDM16 might be directly involved in RdDM. Small RNA expression analysis on loci showing RDM16-dependent DNA methylation suggested that unlike the previously reported putative splicing factor mutants, rdm16 did not affect small RNA levels; instead, the rdm16 mutation caused a decrease in the levels of Pol V transcripts. ChIP assays revealed that RDM16 was enriched at some Pol V target loci. Our results suggest that RDM16 regulates DNA methylation through influencing Pol V transcript levels. Finally, our genome-wide DNA methylation analysis indicated that RDM16 regulates the overall methylation of TEs and gene-surrounding regions, and preferentially targets Pol IV-dependent DNA methylation loci and the ROS1 target loci. Our work thus contributes to the understanding of RdDM and its interactions with active DNA demethylation.
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Selenium Attenuates High Glucose-Induced ROS/TLR-4 Involved Apoptosis of Rat Cardiomyocyte.
Biol Trace Elem Res
PUBLISHED: 08-30-2013
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The potential mechanism of high glucose-induced cardiomyocyte apoptosis and seleniums protective effects were investigated in this study. Myocytes isolated from neonate rats were cultured in high-glucose medium (25.5 mmol/L glucose) to mimic sustained hyperglycemia. Before high-glucose incubation, myocytes were pretreated by sodium selenite solution. Cell apoptosis was evaluated by annexin V/propidium iodide (PI) staining and caspase activation. Expression of Toll-like receptor 4 (TLR-4) and myeloid differentiation factor 88 (MyD-88) was examined at both mRNA and protein levels. The intracellular reactive oxygen species (ROS) production and glutathione peroxidase (GPx) activity in myocytes were also detected. We found high glucose-induced cell apoptosis and activation of TLR-4/MyD-88/caspase-8/caspase-3 signaling, accompanied by increased production of ROS. Selenium pretreatment attenuated apoptosis in high glucose-incubated myocytes, and mechanically, this protective effect was found to be associated with attenuating oxidative status by increasing activity of GPx, decreasing the generation of ROS, as well as inhibition of the activation of TLR-4/MyD-88/caspase-8/caspase-3 signaling in myocytes. These results suggest that activation of TLR-4/MyD-88 signaling pathway plays an important role in high glucose-induced cardiomyocyte apoptosis. Additionally, by modulating TLR-4/MyD-88 signaling pathway, which is linked to ROS formation, selenium exerts its antioxidative and antiapoptotic effects in high glucose-incubated myocytes.
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SIRT4 prevents hypoxia-induced apoptosis in H9c2 cardiomyoblast cells.
Cell. Physiol. Biochem.
PUBLISHED: 08-18-2013
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Apoptosis plays a critical role in cardiomyocyte loss during ischaemic heart injury. A detailed understanding of the mechanism involved has a substantial impact on the optimization and development of treatment strategies. Here, we report that the expression of SIRT4, a mitochondrial sirtuin, is markedly down-regulated in hypoxia-induced apoptosis of H9c2 cardiomyoblast cells.
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YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity.
Nucleic Acids Res.
PUBLISHED: 08-14-2013
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As a typical endoribonuclease, YoeB mediates cellular adaptation in diverse bacteria by degrading mRNAs on its activation. Although the catalytic core of YoeB is thought to be identical to well-studied nucleases, this enzyme specifically targets mRNA substrates that are associated with ribosomes in vivo. However, the molecular mechanism of mRNA recognition and cleavage by YoeB, and the requirement of ribosome for its optimal activity, largely remain elusive. Here, we report the structure of YoeB bound to 70S ribosome in pre-cleavage state, revealing that both the 30S and 50S subunits participate in YoeB binding. The mRNA is recognized by the catalytic core of YoeB, of which the general base/acid (Glu46/His83) are within hydrogen-bonding distance to their reaction atoms, demonstrating an active conformation of YoeB on ribosome. Also, the mRNA orientation involves the universally conserved A1493 and G530 of 16S rRNA. In addition, mass spectrometry data indicated that YoeB cleaves mRNA following the second position at the A-site codon, resulting in a final product with a 3-phosphate at the newly formed 3 end. Our results demonstrate a classical acid-base catalysis for YoeB-mediated RNA hydrolysis and provide insight into how the ribosome is essential for its specific activity.
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Hepatitis B surface antigen inhibits MICA and MICB expression via induction of cellular miRNAs in hepatocellular carcinoma cells.
Carcinogenesis
PUBLISHED: 08-05-2013
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Hepatitis B surface antigen (HBsAg) seropositivity is an important risk factor for hepatocellular carcinoma (HCC), and HBsAg-transgenic mice have been reported to spontaneously develop HCC. The major histocompatibility complex class I-related molecules A and B (MICA and MICB) are NKG2D ligands that play important roles in tumor immune surveillance. In the present study, we found that HBsAg overexpression in HepG2 cells led to upregulation of 133 and downregulation of 9 microRNAs (miRNAs). Interestingly, several HBsAg-induced miRNAs repressed the expression of MICA and MICB via targeting their 3-untranslated regions. In addition, the expression of MICA and MICB was significantly reduced upon HBsAg overexpression, which was partially restored by inhibiting the activities of HBsAg-induced miRNAs. Moreover, HBsAg-overexpressing HCC cells exhibited reduced sensitivity to natural killer cell-mediated cytolysis. Taken together, our data suggest that HBsAg supresses the expression of MICA and MICB via induction of cellular miRNAs, thereby preventing NKG2D-mediated elimination of HCC cells.
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The PRP6-like splicing factor STA1 is involved in RNA-directed DNA methylation by facilitating the production of Pol V-dependent scaffold RNAs.
Nucleic Acids Res.
PUBLISHED: 07-22-2013
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DNA methylation is a conserved epigenetic marker in plants and animals. In Arabidopsis, DNA methylation can be established through an RNA-directed DNA methylation (RdDM) pathway. By screening for suppressors of ros1, we identified STA1, a PRP6-like splicing factor, as a new RdDM regulator. Whole-genome bisulfite sequencing suggested that STA1 and the RdDM pathway share a large number of common targets in the Arabidopsis genome. Small RNA deep sequencing demonstrated that STA1 is predominantly involved in the accumulation of the siRNAs that depend on both Pol IV and Pol V. Moreover, the sta1 mutation partially reduces the levels of Pol V-dependent RNA transcripts. Immunolocalization assay indicated that STA1 signals are exclusively present in the Cajal body and overlap with AGO4 in most nuclei. STA1 signals are also partially overlap with NRPE1. Localization of STA1 to AGO4 and NRPE1 signals is probably related to the function of STA1 in the RdDM pathway. Based on these results, we propose that STA1 acts downstream of siRNA biogenesis and facilitates the production of Pol V-dependent RNA transcripts in the RdDM pathway.
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Brain abscess after endosaccular embolisation of a cerebral aneurysm.
J Clin Neurosci
PUBLISHED: 07-08-2013
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Endovascular embolization has become an important treatment option for cerebral aneurysms, along with surgical clipping. But few literatures mentioned infectious complications after coiling of aneurysms. We present a patient with a brain abscess that developed after endosaccular embolization of a left middle cerebral artery aneurysm. The brain abscess was located adjacent to the aneurysm and discovered more than 2months after embolization. We discuss the clinical implications of this rare complication and review the literature for infections related to the coils used for embolization of aneurysms.
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Interface structure and corrosion resistance of Ti/Cr nanomultilayer film prepared by magnetron sputtering on depleted uranium.
ACS Appl Mater Interfaces
PUBLISHED: 07-03-2013
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Uranium has broadened utility in military and civilization; however, it is extremely apt to oxidation corrosion. Ti/Cr nanomultilayer film was prepared by unbalanced magnetron sputtering on the surface of depleted uranium (DU) to improve its corrosion resistance. The SEM morphologies show that Ti/Cr multilayer film has fine grain and high density. The Auger electron spectroscopy is used to investigate the depth profiles of Ti, U, and O elements of interface between DU substrate and the Ti interlayer, and indicates that the mutual diffusion area of U and Ti is formed at the interface. The TEM cross-section microstructure shows that the multilayer film has alternative Ti and Cr layers and form a perfect modulation structure. The modulation period is measured to be 4.8 nm in TEM morphology, the thickness ratio of Ti to Cr could be estimated to be about 1:2. Potentiodynamic polarization curves show that, after depositing Ti/Cr nanomultilayer film, the corrosion potential increases while the corrosion current density decreases obviously. The surface of Ti/Cr nanomultilayer film exhibits a pseudo passivation behavior when the polarization potential increased from -50 to 400 mV. It was indicated that, after depositing Ti/Cr nanomultilayer film by unbalanced magnetron sputtering, the corrosion resistance of DU was effectively improved.
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An uniform DBD plasma excited by bipolar nanosecond pulse using wire-cylinder electrode configuration in atmospheric air.
Spectrochim Acta A Mol Biomol Spectrosc
PUBLISHED: 07-01-2013
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In this study, a bipolar nanosecond pulsed power supply with 15ns rising time is employed to generate an uniform dielectric barrier discharge using the wire-cylinder electrode configuration in atmospheric air. The images, waveforms of pulse voltage and discharge current, and the optical emission spectra of the discharges are recorded. The rotational and vibrational temperatures of plasma are determined by comparing the simulated spectra with the experimental spectra. The effects of pulse peak voltage, pulse repetition rate and quartz tube diameter on the emission intensities of N2 (C(3)?u?B(3)?g, 0-0) and N2(+)B(2)?u(+)?X(2)?g(+),0-0 and the rotational and vibrational temperatures have been investigated. It is found that the uniform plasma with low gas temperature can be obtained, and the emission intensities of N2 (C(3)?u?B(3)?g, 0-0) and N2(+)B(2)?u(+)?X(2)?g(+),0-0 rise with increasing the pulse peak voltage and pulse repetition rate, while decrease as the increase of quartz tube diameter. In addition, under the condition of 28kV pulse peak voltage, 150Hz pulse repetition rate and 7mm quartz tube diameter, the plasma gas temperature is determined to be 330K. The results also indicate that the plasma gas temperature keep almost constant when increasing the pulse peak voltage and pulse repetition rate but increase with the increase of the quartz tube diameter.
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MALDI mass spectrometry for nucleic acid analysis.
Top Curr Chem
PUBLISHED: 06-14-2013
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With the discovery of several matrices which enable the ionization of DNA and RNA, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become a powerful platform for the study of nucleic acid sequence changes (e.g., mutations, single nucleotide polymorphisms (SNPs), insertion/deletion, alternative splicing, etc.), amount changes (e.g., copy number variation, gene expression, allele expression, etc.), as well as modifications (e.g., methylation of genomic DNA, post transcriptional modification of tRNAs and rRNAs). Two major strategies have been employed to characterize these changes. Primer extension reactions are designed for genotyping of known polymorphic sites and determining the levels of gene or allele expressions. Base-specific cleavage reactions are used for discovery of unknown polymorphisms and characterization of modifications. These two assays usually generate nucleic acid fragments less than 30 bases in length, which is the ideal mass range for MALDI-MS. Here we review the basic concepts of these assays, sample analysis techniques, and their applications published in recent years.
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[Sequences analysis of jlFABP2 and the correlation between polymorphisms and body weight gain in Cyprinus carpio var. jian].
Yi Chuan
PUBLISHED: 06-05-2013
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Two replicate intestine fatty acid binding protein genes (jlFABP2a and jlFABP2b) were cloned from Cyprinus carpio var. jian using PCR. Both ORFs were 399 bp in length sharing 92.2% similarity with each other, and 88.0% and 90.5% with their counterpart in zebrafish, respectively. The gene structure of jlFABP2s was same as other FABPs, which contained four exons and three introns. Sequences and lengths of introns between 2a and 2b. were obviously different Phylogenetic tree displayed that two jlFABP2s corresponded to one zebrafish FABP2 which matches the fact that the chromosome number of common carp was twice of zebrafish. Real time-PCR showed that jlFABP2 genes mainly expressed in intestine and the expression level was very significantly higher than other tissues such as brain, liver, muscle, kidney, and gonad (P<0.01). The expression level of jlFABP2a was significantly (male, P<0.05) or very significantly (females, P<0.01) higher than 2b in intestine; and 2b was expressed slightly higher than 2a in other tissues. It seemed that 2a expressed specifically in intestine, while 2b expressed ubiquitously. Twelve and four SNP loci were found at jlFABP2a and 2b introns through comparison sequences from 8 individuals, respectively. Genotypes of I1-A15G, I1-A99G, I2-C487T, and I3-A27T on jlFABP2a were detected using PCR-RFLP in selection population of C. carpio var. jian. The SNP genotypes and individual weight gain correlation indicated that four SNPs were significantly (P<0.05 or P<0.01) associated with adult weight gain. Diplotype analysis displayed that individuals with genotype AGGGCCXX or AGGGXXAT grew faster than other individuals by 15%. The individuals with these two genotypes only occupied 9% in total selection populations, indicating the presence of large selection space. The 4 SNPs detected in this experiment can be used in C. carpio var. Jian growth selection breeding plan.
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[Glutathione S-transferase polymorphisms and male infertility].
Zhonghua Nan Ke Xue
PUBLISHED: 05-25-2013
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The pathogenesis of male infertility involves the interactions between environmental and genetic factors. An individuals susceptibility to male infertility is influenced by his internal abilities of metabolizing and detoxicating endogenous and exogenous chemicals. Glutathione-S-transferases (GSTs), such as enzymes, are involved in the cellular detoxication of various physiological and xenobiotic substances. Studies show that the polymorphism of the GSTs gene is correlated with male infertility. GSTs polymorphism-related susceptibilities to male infertility were found similar but with some inconsistencies within the same community, and inconsistent with some similarities among different communities. Therefore, further studies are to be done on the differences in GSTs polymorphism-related susceptibility to male infertility in different communities.
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Clinical utility of endoscopic ultrasound elastography for identification of malignant pancreatic masses: a meta-analysis.
J. Gastroenterol. Hepatol.
PUBLISHED: 05-16-2013
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Endoscopic ultrasound (EUS) elastography is not used for detection but rather for characterization of solid pancreatic masses. A meta-analysis was used to assess the accuracy of EUS elastography for identification of malignant pancreatic masses.
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Isolation and synthesis of a bioactive benzenoid derivative from the fruiting bodies of Antrodia camphorata.
Molecules
PUBLISHED: 05-15-2013
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A new enynyl-benzenoid, antrocamphin O (1,4,7-dimethoxy-5-methyl-6-(3-methylbut-3-en-1-ynyl)benzo[d][1,3]dioxide), and the known benzenoids antrocamphin A and 7-dimethoxy-5-methyl-1,3-benzodioxole, were isolated from the fruiting bodies of Antrodia camphorata (Taiwanofungus camphoratus). The structure of antrocamphin O was unambiguously assigned by the analysis of spectral data (including 1D and 2D NMR, high-resolution MS, IR, and UV) and total synthesis. Compound 1 was prepared through the Sonogashira reaction of 5-iodo-4,7-dimethoxy-6-methylbenzene and 2-methylbut-1-en-3-yne as the key step. The benzenoids were tested for cytotoxicity against the HT29, HTC15, DLD-1, and COLO 205 colon cancer cell lines, and activities are reported herein.
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Draft Genome Sequence of Strain JLT2015T, Belonging to the Family Sphingomonadaceae of the Alphaproteobacteria.
Genome Announc
PUBLISHED: 05-11-2013
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Strain JLT2015(T) was isolated from the southeastern Pacific, as a representative of a new genus of the family Sphingomonadaceae of the Alphaproteobacteria. Here, we present the draft genome sequence of strain JLT2015(T), which provides insight into the oligotrophic strategy of this organism.
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DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 05-01-2013
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DNA methylation is an important epigenetic mark in many eukaryotic organisms. De novo DNA methylation in plants can be achieved by the RNA-directed DNA methylation (RdDM) pathway, where the plant-specific DNA-dependent RNA polymerase IV (Pol IV) transcribes target sequences to initiate 24-nt siRNA production and action. The putative DNA binding protein DTF1/SHH1 of Arabidopsis has been shown to associate with Pol IV and is required for 24-nt siRNA accumulation and transcriptional silencing at several RdDM target loci. However, the extent and mechanism of DTF1 function in RdDM is unclear. We show here that DTF1 is necessary for the accumulation of the majority of Pol IV-dependent 24-nt siRNAs. It is also required for a large proportion of Pol IV-dependent de novo DNA methylation. Interestingly, there is a group of RdDM target loci where 24-nt siRNA accumulation but not DNA methylation is dependent on DTF1. DTF1 interacts directly with the chromatin remodeling protein CLASSY 1 (CLSY1), and both DTF1 and CLSY1 are associated in vivo with Pol IV but not Pol V, which functions downstream in the RdDM effector complex. DTF1 and DTF2 (a DTF1-like protein) contain a SAWADEE domain, which was found to bind specifically to histone H3 containing H3K9 methylation. Taken together, our results show that DTF1 is a core component of the RdDM pathway, and suggest that DTF1 interacts with CLSY1 to assist in the recruitment of Pol IV to RdDM target loci where H3K9 methylation may be an important feature. Our results also suggest the involvement of DTF1 in an important negative feedback mechanism for DNA methylation at some RdDM target loci.
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A covalent reporter of ?-lactamase activity for fluorescent imaging and rapid screening of antibiotic-resistant bacteria.
Chemistry
PUBLISHED: 04-30-2013
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Bacterial resistance to antibiotics poses a great clinical challenge in fighting serious infectious diseases due to complicated resistant mechanisms and time-consuming testing methods. Chemical reaction-directed covalent labeling of resistance-associated bacterial proteins in the context of a complicated environment offers great opportunity for the in-depth understanding of the biological basis conferring drug resistance, and for the development of effective diagnostic approaches. In the present study, three fluorogenic reagents LRBL1-3 for resistant bacteria labeling have been designed and prepared on the basis of fluorescence resonance energy transfer (FRET). The hydrolyzed probes could act as reactive electrophiles to attach the enzyme, ?-lactamase, and thus facilitated the covalent labeling of drug resistant bacterial strains. SDS electrophoresis and MALDI-TOF mass spectrometry characterization confirmed that these probes were sensitive and specific to ?-lactamase and could therefore serve for covalent and localized fluorescence labeling of the enzyme structure. Moreover, this ?-lactamase-induced covalent labeling provides quantitative analysis of the resistant bacterial population (down to 5%) by high resolution flow cytometry, and allows single-cell detection and direct observation of bacterial enzyme activity in resistant pathogenic species. This approach offers great promise for clinical investigations and microbiological research.
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Two ?6-desaturase-like genes in common carp (Cyprinus carpio var. Jian): structure characterization, mRNA expression, temperature and nutritional regulation.
Gene
PUBLISHED: 04-19-2013
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?6-Desaturase is the rate-limiting enzyme involved in highly unsaturated fatty acid (HUFA) biosynthesis. There is very little information on the evolution and functional characterization of ?6Fad-a and ?6Fad-b in common carp (Cyprinus carpio var. Jian). In the present study, the genomic sequences and structures of two putative ?6-desaturase-like genes in common carp genome were obtained. We investigated the mRNA expression patterns of ?6Fad-a and ?6Fad-b in tissue, hatching carp embryos, larvae by temperature shock and juveniles under nutritional regulation. Our results showed that the two ?6Fad genes had identical coding exon structures, being comprised of 12 coding exons, and with introns of distinct size and sequence composition. They were not allelic variants of a single gene. Both ?6Fad genes were highly expressed in liver, intestine (pyloric caeca) and brain. The ?6Fad-a and ?6Fad-b mRNAs showed an increase in expression from newly hatched to 25 days after hatching. The expression levels of ?6Fad-a were obviously regulated by temperature, whereas ?6Fad-b was not affected by temperature. The regulation of ?6Fad-a and ?6Fad-b in response to dietary fatty acid composition was determined in liver, brain and intestine (pyloric caeca) of common carp fed with diets: diet1with fish oil (FO) rich in n-3 HUFA, diet2 with corn oil (CO, 18:2n-6) and diet3 with linseed oil (LO, 18:3n-3). The differential expression of ?6Fad-a and ?6Fad-b genes in liver, brain and intestine in common carps was fed with different oil sources, respectively. Further work is in progress to determine the mechanism of differential expression of the ?6Fad-a and ?6Fad-b genes in different tissues and the roles of transcription factors in regulating HUFA synthesis.
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The influencing factors of nanosecond pulse homogeneous dielectric barrier discharge in air.
Spectrochim Acta A Mol Biomol Spectrosc
PUBLISHED: 04-11-2013
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In this paper, a bipolar nanosecond high pulse voltage with 20 ns rising time was employed to generate homogeneous dielectric barrier discharges using the plate-plate electrode configuration in air at atmospheric pressure. The effects of pulse peak voltage, gas discharge gap, and dielectric plates made by different materials or thicknesses on the discharge homogeneity, voltage-current waveform, and optical emission spectra were investigated. Results show that aforementioned parameters have a strongly impact on the discharge homogeneity and the optical emission spectra, but it is hard to identify definitely their influences on the discharge voltage-current waveform. Homogeneous discharges were easily observed when using low permittivity dielectric plate and the emission intensity of N2 (C(3)?u?B(3)?g, 0-0, 337.1 nm) increases with the rising of pulse peak voltage and the permittivity of dielectric material but decreases with the increasing of gas discharge gap and the dielectric plate thickness. The rotational and vibrational temperatures (Trot and Tvib) were determined at Trot=350±5 K and Tvib=3045 K via fitting the simulative spectra of N2 (C(3)?u?B(3)?g, 0-2) with the measured one.
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Effect of dielectric material on bipolar nanosecond pulse diffuse dielectric barrier discharge in air at atmospheric pressure.
Spectrochim Acta A Mol Biomol Spectrosc
PUBLISHED: 04-02-2013
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In this paper, dielectric plates made by ceramic, quartz and polytetrafluoroethylene (PTFE) respectively are employed to generate low gas temperature, diffuse dielectric barrier discharge plasma by using a needle-plate electrode configuration in air at atmospheric pressure. Both discharge images and the optical emission spectra are obtained while ceramic, quartz and PTFE are used as dielectric material. Plasma gas temperature is also calculated by comparing the experimental emission spectra with the best fitted spectra of N2 (C(3)?u?B(3)?g 1-3) and N2 (C(3)?u?B(3)?g 0-2). The effects of different pulse peak voltages and gas gap distances on the emission intensity of N2 (C(3)?u?B(3)?g, 0-0, 337.1 nm) and the plasma area on dielectric surface are investigated while ceramic, quartz and PTFE are used as dielectric material. It is found that the permittivity of dielectric material plays an important role in the discharge homogeneity, plasma gas temperature, emission spectra intensity of the discharge, etc. Dielectric with higher permittivity i.e., ceramic means brighter discharge luminosity and stronger emission spectra intensity of N2 (C(3)?u?B(3)?g, 0-0, 337.1 nm) among the three dielectric materials. However, more homogeneous, larger plasma area on dielectric surface and lower plasma gas temperature can be obtained under dielectric with lower permittivity i.e., PTFE. The emission spectra intensity and plasma gas temperature of the discharge while the dielectric plate is made by quartz are smaller than that while ceramic is used as dielectric material and bigger than that when PTFE is used as dielectric material.
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Hepatic stellate cells promote tumor progression by enhancement of immunosuppressive cells in an orthotopic liver tumor mouse model.
Lab. Invest.
PUBLISHED: 03-28-2013
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The immunosuppressive properties of hepatic stellate cells (HSCs) contribute to the occurrence and development of hepatocellular carcinoma (HCC). The accumulation of cells with immune suppressive activities, such as myeloid-derived suppressor cells (MDSCs) and regulatory T cells (Tregs) is a key mechanism for tumor immune evasion. However, the impact of HSCs on immune cell populations in tumor-bearing hosts is unclear. In this study, we established an orthotopic liver tumor mouse model for studying the complex tumor-host interactions in HCC. The activated HSCs promoted HCC growth not only induced tumor angiogenesis and lymphangiogenesis, but also significantly increased the suppressive immune cell population of Tregs and MDSCs in the spleen, bone marrow, and tumor tissues of the tumor-bearing mice. Murine HCC cell line H22-activated HSCs also expanded the expression of Tregs and MDSCs in vitro. In conclusion, our study suggests a novel role for HSCs in the HCC microenvironment. HSCs can promote HCC progression by enhancement of the immunosuppressive cell population. Targeting HSCs, which is a new concept in adjuvant immunotherapy, may be introduced in the near future to improve the outcome of patients with HCC.Laboratory Investigation advance online publication, 2 December 2013; doi:10.1038/labinvest.2013.139.
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Identifying Ki-67 specific miRNA-mRNA interactions in malignant astrocytomas.
Neurosci. Lett.
PUBLISHED: 03-16-2013
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Background: Ki-67 is an excellent indicator of glioma cell growth. However, limited information is available regarding the mechanisms underlying abnormal expression of Ki-67 in glioma tissue. The aim of this study is to identify Ki-67 specific miRNA-mRNA interactions on basis of miRNA and mRNA expression profilings. Methods: We performed a large-scale miRNA (n=829) and mRNA (n=29,421) expression profiling in primary glioblastoma multiforme (pGBM) and anaplastic astrocytoma (AA) tissues (with an aim to investigate Ki-67 related miRNAs and mRNAs). From target prediction databases, the targeting relationships between Ki-67 specific miRNAs and mRNAs were established, and functions of these mRNAs were analyzed by DAVID. The functional verifications of the candidate miRNA were also performed in LN229 cell line. Results: High expression level of Ki-67 protein predicted a shorter survival time for patients with AA. Integrated analysis of profiling data from pGBM and AA revealed 4 Ki-67 positively and 5 negatively correlated miRNAs, along with the top 12 Ki-67 positively and 2 negatively correlated mRNAs. By means of target prediction, we found that the target mRNAs employed by miR-218 were the most significant among Ki-67 specific mRNAs. Up-regulation of miR-218 was further demonstrated to reduce Ki-67 expression, promote apoptosis, and induce G0/G1 phase cell cycle arrest in LN229 cells. Conclusions: Ki-67 protein may be regulated by specific miRNA-mRNA interactions which may contribute to the proliferation of glioma cells.
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In vivo evaluation of the interaction between titanium dioxide nanoparticle and rat liver DNA.
Toxicol Ind Health
PUBLISHED: 02-26-2013
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Titanium dioxide nanoparticles (TiO2 NPs) are massively produced and widely used in daily life, which may pose potential risk to human health via uncharacterized interaction between DNAs. This research aims to examine the interaction between DNA and three types of TiO2 NPs of different sizes and crystallines. The interaction between TiO2 NPs and liver DNA molecules obtained from Sprague-Dawley rats was systematically evaluated in vivo using atomic force microscopy, transmission electron microscopy, various spectroscopic techniques and gel electrophoresis. We found that TiO2 NPs (diameter <25 nm and <100 nm) in anatase crystalline can covalently interact with liver DNA by either inserting itself in between DNA base pairs or binding to DNA nucleotide via P-O-Ti-O bond. Such interaction may not be NP size-dependent but may be crystalline phase-dependent, because such interaction did not occur in rutile crystal phase, in which the DNA damage was potentially caused by reactive oxygen species.
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Influence of body mass index on recurrence and quality of life in atrial fibrillation patients after catheter ablation: a meta-analysis and systematic review.
Clin Cardiol
PUBLISHED: 01-30-2013
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Accumulating evidence has demonstrated that overweight and obesity, expressed as high body mass index (BMI), are associated with the development of atrial fibrillation (AF) and quality of life (QoL) in AF patients. However, the role of high BMI as a risk factor for prognosis and QoL in AF patients undergoing ablation remains controversial.
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The role of phenethyl isothiocyanate on bladder cancer ADM resistance reversal and its molecular mechanism.
Anat Rec (Hoboken)
PUBLISHED: 01-20-2013
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Adramycin (ADM) resistance is an essential aspect of bladder cancer treatment failure and phenethyl isothiocyanate (PEITC) has been found to exhibit antitumor properties; however, the effect and potential mechanism of PEITC on bladder cancer ADM resistance reversal is not fully clear. The aim of this study was to explore the role of PEITC in bladder cancer cells ADM resistance reversal and the underlying molecular mechanisms. In this report, we identified the role of PEITC on ADM resistance reversal of human bladder carcinoma T24/ADM cells, including an increased drug sensitivity to ADM, cell apoptosis rates, intracellular accumulation of Rhodamine-123 (Rh-123), an increased expression of DNA topoisomerase II (Topo-II), and a decreased expression of multidrug resistance gene (MDR1), multidrug resistance-associated protein (MRP1), bcl-2 and glutathione s transferase ? (GST-?).We also found that there was a decreased expression of NF-?B, Survivin, Twist, and p-Akt, and an increased expression of PTEN and p-JNK after PEITC treatment for T24/ ADM cells. The results indicated that PEITC might be used as a potential therapeutic strategy to ADM resistance through blocking Akt and activating MAPK pathway in human bladder carcinoma.
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Decreased dicer expression enhances SRP-mediated protein targeting.
PLoS ONE
PUBLISHED: 01-16-2013
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We have shown that Dicer processes 7SL RNA into different fragments ranging from ?20 to more than 200 nucleotides. Here we addressed the molecular functions of these 7SL RNA fragments and found that some of them functioned as dominant-negative regulators of the full-length 7SL RNA, interfering with signal recognition particle (SRP) complex formation. Transfection of these 7SL RNA fragments inhibited the expression of cell surface glycoproteins, the targeting of a reporter protein to the endoplasmic reticulum, and the secretion of secreted alkaline phosphatase. These results suggest that some Dicer-processed 7SL RNA fragments interfered with SRP-mediated protein targeting. Moreover, we showed that Dicer knockdown enhanced SRP-mediated protein targeting and that transfection of a mixture of the 7SL RNA fragments partially restored this effect. Our data indicate that Dicer can fine-tune the efficiency of SRP-mediated protein targeting via processing a proportion of 7SL RNA into fragments of different lengths.
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B-type natriuretic Peptide and prognosis of end-stage renal disease: a meta-analysis.
PLoS ONE
PUBLISHED: 01-01-2013
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The prognostic importance of B-type natriuretic peptide (BNP) or N-terminal pro BNP (NT-proBNP) in patients with end-stage renal disease (ESRD) remains controversial.
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Performance of shear wave elastography for differentiation of benign and malignant solid breast masses.
PLoS ONE
PUBLISHED: 01-01-2013
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To perform a meta-analysis assessing the ability of shear wave elastography (SWE) to identify malignant breast masses.
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Functional metagenomic investigations of microbial communities in a shallow-sea hydrothermal system.
PLoS ONE
PUBLISHED: 01-01-2013
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Little is known about the functional capability of microbial communities in shallow-sea hydrothermal systems (water depth of <200 m). This study analyzed two high-throughput pyrosequencing metagenomic datasets from the vent and the surface water in the shallow-sea hydrothermal system offshore NE Taiwan. This system exhibited distinct geochemical parameters. Metagenomic data revealed that the vent and the surface water were predominated by Epsilonproteobacteria (Nautiliales-like organisms) and Gammaproteobacteria (Thiomicrospira-like organisms), respectively. A significant difference in microbial carbon fixation and sulfur metabolism was found between the vent and the surface water. The chemoautotrophic microorganisms in the vent and in the surface water might possess the reverse tricarboxylic acid cycle and the Calvin-Bassham-Benson cycle for carbon fixation in response to carbon dioxide highly enriched in the environment, which is possibly fueled by geochemical energy with sulfur and hydrogen. Comparative analyses of metagenomes showed that the shallow-sea metagenomes contained some genes similar to those present in other extreme environments. This study may serve as a basis for deeply understanding the genetic network and functional capability of the microbial members of shallow-sea hydrothermal systems.
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MicroRNA-34a inhibits migration and invasion of colon cancer cells via targeting to Fra-1.
Carcinogenesis
PUBLISHED: 12-22-2011
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MicroRNA-34a (miR-34a), a transcriptional target of p53, is a well-known tumor suppressor gene. Here, we identified Fra-1 as a new target of miR-34a and demonstrated that miR-34a inhibits Fra-1 expression at both protein and messenger RNA levels. In addition, we found that p53 indirectly regulates Fra-1 expression via a miR-34a-dependant manner in colon cancer cells. Overexpression of miR-34a strongly inhibited colon cancer cell migration and invasion, which can be partially rescued by forced expression of the Fra-1 transcript lacking the 3-untranslated region. The expression of matrix metalloproteinase (MMP)-1 and MMP-9, two enzymes involved in cell migration and invasion, was decreased in miR-34a-transfected cells, and this can be rescued by Fra-1 overexpression. Moreover, we found that miR-34a was downregulated in 25 of 40 (62.5%) colon cancer tissues, as compared with the adjacent normal colon tissues and that the expression of miR-34a was correlated with the DNA-binding activity of p53. Unexpectedly, the DNA-binding activity of p53 was not inversely correlated with Fra-1 expression, and a significant statistical inverse correlation between miR-34a and Fra-1 expression was only observed in 14 of 40 (35%) colon cancer tissues. Taken together, our in vitro data suggest that p53 regulates Fra-1 expression, and eventually cell migration/invasion, via a miR-34a-dependent manner. However, in vivo data indicate that the p53-miR-34a pathway is not the major regulator of Fra-1 expression in human colon cancer tissues.
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Antioxidation and tyrosinase inhibition of polyphenolic curcumin analogs.
Biosci. Biotechnol. Biochem.
PUBLISHED: 12-07-2011
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A series of polyphenolic curcumin analogs were synthesized and their inhibitory effects on mushroom tyrosinase and the inhibition of 1,1-diphenyl-2-picryl-hydrazyl (DPPH) free radical formation were evaluated. The results indictated that the analogs possessing m-diphenols and o-diphenols exhibited more potent inhibitory activity on tyrosinase than reference compound rojic acid, and that the analogs with o-diphenols exhibited more potent inhibitory activity of DPPH free-radical formation than reference compound vitamin C. The inhibition kinetics, analyzed by Lineweaver-Burk plots, revealed that compounds B(2) and C(2) bearing o-diphenols were non-competitive inhibitors, while compounds B(11) and C(11) bearing m-diphenols were competitive inhibitors. In particular, representative compounds C(2) and B(11) showed no side effects at a dose of 2,000 mg/kg in a preliminary evaluation of acute toxicity in mice. These results suggest that such polyphenolic curcumin analogs might serve as lead compounds for further design of new potential tyrosinase inhibitors.
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Association between left atrial size and atrial fibrillation recurrence after single circumferential pulmonary vein isolation: a systematic review and meta-analysis of observational studies.
Europace
PUBLISHED: 11-23-2011
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Left atrial (LA) enlargement is associated with atrial fibrillation (AF). However, it is controversial whether dilated atrium can predict post-ablation AF recurrence. We undertook a systematic review and meta-analysis to analyse the association between LA diameter and AF recurrence after single circumferential pulmonary vein isolation (CPVI) and explore the potential mechanism.
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[Neuroendoscopic treatment for 372 cases of intracranial lesions].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 11-19-2011
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To explore the application of neuroendoscopic treatment for intracranial lesions.
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Relationship between magnetic resonance imaging and molecular pathology in patients with glioblastoma multiforme.
Chin. Med. J.
PUBLISHED: 11-02-2011
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Glioblastoma multiforme (GBM) is the most common and lethal primary brain tumor in adults. Magnetic resonance imaging (MRI) is routinely used in the diagnosis, characterization and clinical management of GBM. The diagnosis and treatment of GBM is largely guided by histopathology and immunohistochemistry. This study aimed to identify the relationship between magnetic resonance features and molecular pathology of GBM.
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Macrophage migration inhibitory factor reduces apoptosis in cerebral arteriovenous malformations.
Neurosci. Lett.
PUBLISHED: 10-05-2011
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Purpose: To investigate the expression of macrophage migration inhibitory factor (MIF) in human brain arteriovenous malformations (AVM). Materials and methods: Twelve AVM specimens were obtained from patients who did not received preoperative embolization. MIF levels were measured by Western blot and matrix metalloproteinase 9 (MMP9) levels were measured by reverse transcription PCR. The expression of MIF in brain AVMs was also evaluated by immunohistochemistry and was correlated with apoptosis and the expression of cleaved caspase-3 and MMP9. Results: The expression of MIF, MMP9, and cleaved caspase-3 was elevated in brain AVM vessels. High levels of MIF were primarily found in the endothelium and adventitia, whereas apoptotic cells were concentrated in the smooth muscle layer. Conclusions: Abnormal apoptosis may be involved in the pathogenesis of brain AVM. In addition, increased MIF expression could play an important role regulating the homeostasis of AVM vessels.
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Lipid binding to the carotenoid binding site in photosynthetic reaction centers.
J. Am. Chem. Soc.
PUBLISHED: 09-21-2011
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Lipid binding to the carotenoid binding site near the inactive bacteriochlorophyll monomer was probed in the reaction centers of carotenoid-less mutant, R-26 from Rhodobacter sphaeroides. Recently, a marked light-induced change of the local dielectric constant in the vicinity of the inactive bacteriochlorophyll monomer was reported in wild type that was attributed to structural changes that ultimately lengthened the lifetime of the charge-separated state by 3 orders of magnitude (Deshmukh, S. S.; Williams, J. C.; Allen, J. P.; Kalman, L. Biochemistry 2011, 50, 340). Here in the R-26 reaction centers, the combination of light-induced structural changes and lipid binding resulted in a 5 orders of magnitude increase in the lifetime of the charge-separated state involving the oxidized dimer and the reduced primary quinone in proteoliposomes. Only saturated phospholipids with fatty acid chains of 12 and 14 carbon atoms long were bound successfully at 8 °C by cooling the reaction center protein slowly from room temperature. In addition to reporting a dramatic increase of the lifetime of the charge-separated state at physiologically relevant temperatures, this study reveals a novel lipid binding site in photosynthetic reaction center. These results shed light on a new potential application of the reaction center in energy storage as a light-driven biocapacitor since the charges separated by ?30 Å in a low-dielectric medium can be prevented from recombination for hours.
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[Tamoxifen combined with coenzyme Q10 for idiopathic oligoasthenospermia].
Zhonghua Nan Ke Xue
PUBLISHED: 08-10-2011
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To investigate the effects of tamoxifen (TMX) combined with coenzyme Q10 (CoQ10) on idiopathic oligoasthenospermia.
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Acute renal failure after topical fortified gentamicin and vancomycin eyedrops.
J Ocul Pharmacol Ther
PUBLISHED: 06-24-2011
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To report a case of acute renal failure after topical fortified gentamicin and vancomycin eyedrops in the treatment of endophthalmitis.
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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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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.