JoVE Visualize What is visualize?
Stop Reading. Start Watching.
Advanced Search
Stop Reading. Start Watching.
Regular Search
Find video protocols related to scientific articles indexed in Pubmed.
EPGA: de novo assembly using the distributions of reads and insert size.
Bioinformatics
PUBLISHED: 11-20-2014
Show Abstract
Hide Abstract
In genome assembly, the primary issue is how to determine upstream and downstream sequence regions of sequence seeds for constructing long contigs or scaffolds. When extending one sequence seed, repetitive regions in the genome always cause multiple feasible extension candidates which increase the difficulty of genome assembly. The universally accepted solution is choosing one based on read overlaps and paired-end (mate-pair) reads. However, this solution faces difficulties with regard to some complex repetitive regions. In addition, sequencing errors may produce false repetitive regions and uneven sequencing depth leads some sequence regions to have too few or too many reads. All the aforementioned problems prohibit existing assemblers from getting satisfactory assembly results.
Related JoVE Video
Gold crescent nanodisk array for nanoantenna-enhanced sensing in subwavelength areas.
Appl Opt
PUBLISHED: 11-18-2014
Show Abstract
Hide Abstract
Benefitting from the antenna effect and localized surface plasmon resonance (LSPR), a metal nanoparticle with a designed morphology has the amazing ability to confine light energy into the required extremely small volume, whose refractive index largely affects the optical properties of the whole metal nanoparticle. In this work, the optical spectra and near-field distribution of a gold nanocrescent array were investigated both experimentally and theoretically. To find out the LSPR wavelength and the enhancement using different morphologies of sharp tips, the spectra of gold nanocrescent arrays with different waist widths (d) were first measured, which were then confirmed and analyzed using the finite difference time-domain method and the hybridization theory. At last, the LSPR of this array with 100 nm diameter dielectric nanodisks was studied for sensing in subwavelength areas. Our results showed that because of its giant nanoantenna-enhanced electromagnetic field at the two tips, this gold nanocrescent array could be a suitable local senor to sense the variation of a local medium in a subwavelength area.
Related JoVE Video
XGlycScan: An Open-source Software For N-linked Glycosite Assignment, Quantification and Quality Assessment of Data from Mass Spectrometry-based Glycoproteomic Analysis.
MOJ Proteom Bioinform
PUBLISHED: 10-28-2014
Show Abstract
Hide Abstract
Mass spectrometry based glycoproteomics has become a major means of identifying and characterizing previously N-linked glycan attached loci (glycosites). In the bottom-up approach, several factors which include but not limited to sample preparation, mass spectrometry analyses, and protein sequence database searches result in previously N-linked peptide spectrum matches (PSMs) of varying lengths. Given that multiple PSM scan map to a glycosite, we reason that identified PSMs are varying length peptide species of a unique set of glycosites. Because associated spectra of these PSMs are typically summed separately, true glycosite associated spectra counts are lost or complicated. Also, these varying length peptide species complicate protein inference as smaller sized peptide sequences are more likely to map to more proteins than larger sized peptides or actual glycosite sequences. Here, we present XGlycScan. XGlycScan maps varying length peptide species to glycosites to facilitate an accurate quantification of glycosite associated spectra counts. We observed that this reduced the variability in reported identifications of mass spectrometry technical replicates of our sample dataset. We also observed that mapping identified peptides to glycosites provided an assessment of search-engine identification. Inherently, XGlycScan reported glycosites reduce the complexity in protein inference. We implemented XGlycScan in the platform independent Java programing language and have made it available as open source. XGlycScan's source code is freely available at https://bitbucket.org/paiyetan/xglycscan/src and its compiled binaries and documentation can be freely downloaded at https://bitbucket.org/paiyetan/xglycscan/downloads. The graphical user interface version can also be found at https://bitbucket.org/paiyetan/xglycscangui/src and https://bitbucket.org/paiyetan/xglycscangui/downloads respectively.
Related JoVE Video
M2Lite: An Open-source, Light-weight, Pluggable and Fast Proteome Discoverer MSF to mzIdentML Tool.
J Bioinform
PUBLISHED: 10-28-2014
Show Abstract
Hide Abstract
Proteome Discoverer is one of many tools used for protein database search and peptide to spectrum assignment in mass spectrometry-based proteomics. However, the inadequacy of conversion tools makes it challenging to compare and integrate its results to those of other analytical tools. Here we present M2Lite, an open-source, light-weight, easily pluggable and fast conversion tool. M2Lite converts proteome discoverer derived MSF files to the proteomics community defined standard - the mzIdentML file format. M2Lite's source code is available as open-source at https://bitbucket.org/paiyetan/m2lite/src and its compiled binaries and documentation can be freely downloaded at https://bitbucket.org/paiyetan/m2lite/downloads.
Related JoVE Video
Critical role of prohibitin in endothelial cell apoptosis caused by glycated low-density lipoproteins and protective effects of grape seed procyanidin B2.
J. Cardiovasc. Pharmacol.
PUBLISHED: 10-25-2014
Show Abstract
Hide Abstract
Elevated level of glycated low-density lipoproteins (glyLDL) is believed to contribute to endothelial dysfunction, which is involved in the pathogenesis and acceleration of diabetic vascular diseases. Grape seed procyanidin B2 (GSPB2) has been reported to possess protective effects against endothelial dysfunction. However, the underlying mechanism remains unclear. Prohibitin (PHB) is a multi-functional protein implicated in cellular survival and apoptosis. In the present study, we showed that glyLDL treatment decreased protein level of PHB, reduced viability and increased apoptosis in human umbilical vein endothelial cells (HUVEC). PHB overexpression or GSPB2 significantly attenuated apoptosis induced by glyLDL. Moreover, PHB siRNA increased HUVEC apoptosis, along with defective mitochondria and increased levels of cytosol cytochrome c concentration, caspase-3 activity, Bax/Bcl-2 ratio, and phosphorylated Akt, while PHB overexpression or GSPB2 restored these changes. Our study identified PHB as an important player responsible for HUVEC apoptosis induced by glyLDL. GSPB2 protected against HUVEC apoptosis at least in part through up-regulating PHB. Targeting PHB could be significant in fighting against diabetic vascular complications.
Related JoVE Video
The complete mitochondrial genome of Parus ater (Passeriformes, Paridae).
Mitochondrial DNA
PUBLISHED: 10-21-2014
Show Abstract
Hide Abstract
Abstract The complete mitochondrial genome sequence of Coal Tit (Parus ater) consisted 16,783?bp, the genome harbored the same gene order with that of other birds, contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and 1 non-coding control region. The all tRNAs can formed typical cloverleaf secondary structures (excluding tRNA(Ser-AGY)). A total of 38 base mismatches appeared, mainly 28 for G-U mismatch, 5 for A-C mismatch, 2 for U-U mismatch. The third loci of codon existed obvious base bias. The control region was between tRNA(Glu) and tRNA(Phe), consisted 1195?bp, no repetitive sequence.
Related JoVE Video
Positive Regulation of Botulinum Neurotoxin Gene Expression by CodY in Clostridium botulinum ATCC 3502.
Appl. Environ. Microbiol.
PUBLISHED: 10-03-2014
Show Abstract
Hide Abstract
Botulinum neurotoxin, produced mainly by the spore-forming bacterium Clostridium botulinum, is the most poisonous biological substance known. Here, we show that CodY, a global regulator conserved in low-G+C Gram-positive bacteria, positively regulates the botulinum neurotoxin gene expression. Inactivation of codY resulted in decreased expression of botA, encoding the neurotoxin, as well as in reduced neurotoxin synthesis. Complementation of the codY mutation in trans rescued neurotoxin synthesis, and overexpression of codY in trans caused elevated neurotoxin production. Recombinant CodY was found to bind to a 30-bp region containing the botA transcription start site, suggesting regulation of the neurotoxin gene transcription through direct interaction. GTP enhanced the binding affinity of CodY to the botA promoter, suggesting that CodY-dependent neurotoxin regulation is associated with nutritional status.
Related JoVE Video
KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring.
Bioinformatics
PUBLISHED: 09-30-2014
Show Abstract
Hide Abstract
We have developed an integrated molecular network learning method, within a well-grounded mathematical framework, to construct differential dependency networks with significant rewiring. This knowledge-fused differential dependency networks (KDDN) method, implemented as a Java Cytoscape app, can be used to optimally integrate prior biological knowledge with measured data to simultaneously construct both common and differential networks, to quantitatively assign model parameters and significant rewiring p-values and to provide user-friendly graphical results. The KDDN algorithm is computationally efficient and provides users with parallel computing capability using ubiquitous multi-core machines. We demonstrate the performance of KDDN on various simulations and real gene expression datasets, and further compare the results with those obtained by the most relevant peer methods. The acquired biologically plausible results provide new insights into network rewiring as a mechanistic principle and illustrate KDDN's ability to detect them efficiently and correctly. Although the principal application here involves microarray gene expressions, our methodology can be readily applied to other types of quantitative molecular profiling data. Availability: Source code and compiled package are freely available for download at http://apps.cytoscape.org/apps/kddn CONTACT: yuewang@vt.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Related JoVE Video
Overexpression of the CaTIP1-1 Pepper Gene in Tobacco Enhances Resistance to Osmotic Stresses.
Int J Mol Sci
PUBLISHED: 09-19-2014
Show Abstract
Hide Abstract
Both the gene expression and activity of water channel protein can control transmembrane water movement. We have reported the overexpression of CaTIP1-1, which caused a decrease in chilling tolerance in transgenic plants by increasing the size of the stomatal pore. CaTIP1-1 expression was strongly induced by salt and mannitol stresses in pepper (Capsicum annuum). However, its biochemical and physiological functions are still unknown in transgenic tobacco. In this study, transient expression of CaTIP1-1-GFP in tobacco suspension cells revealed that the protein was localized in the tonoplast. CaTIP1-1 overexpressed in radicle exhibited vigorous growth under high salt and mannitol treatments more than wild-type plants. The overexpression of CaTIP1-1 pepper gene in tobacco enhanced the antioxidant enzyme activities and increased transcription levels of reactive oxygen species-related gene expression under osmotic stresses. Moreover, the viability of transgenic tobacco cells was higher than the wild-type after exposure to stress. The pepper plants with silenced CaTIP1-1 in P70 decreased tolerance to salt and osmotic stresses using the detached leaf method. We concluded that the CaTIP1-1 gene plays an important role in response to osmotic stresses in tobacco.
Related JoVE Video
Calcineurin upregulates local Ca2+ signaling through ryanodine receptor-1 in airway smooth muscle cells.
Am. J. Physiol. Lung Cell Mol. Physiol.
PUBLISHED: 09-19-2014
Show Abstract
Hide Abstract
Local Ca(2+) signals (Ca(2+) sparks) play an important role in multiple cellular functions in airway smooth muscle cells (ASMCs). Protein kinase C? is known to downregulate ASMC Ca(2+) sparks and contraction; however, no complementary phosphatase has been shown to produce opposite effects. Here, we for the first time report that treatment with a specific calcineurin (CaN) autoinhibitory peptide (CAIP) to block CaN activity decreases, whereas application of nickel to activate CaN increases, Ca(2+) sparks in both the presence and absence of extracellular Ca(2+). Treatment with xestospogin-C to eliminate functional inositol 1,4,5-trisphosphate receptors does not prevent CAIP from inhibiting local Ca(2+) signaling. However, high ryanodine treatment almost completely blocks spark formation and prevents the nickel-mediated increase in sparks. Unlike CAIP, the protein phosphatase 2A inhibitor endothall has no effect. Local Ca(2+) signaling is lower in CaN catalytic subunit A? gene knockout (CaN-A?(-/-)) mouse ASMCs. The effects of CAIP and nickel are completely lost in CaN-A?(-/-) ASMCs. Neither CAIP nor nickel produces an effect on Ca(2+) sparks in type 1 ryanodine receptor heterozygous knockout (RyR1(-/+)) mouse ASMCs. However, their effects are not altered in RyR2(-/+) or RyR3(-/-) mouse ASMCs. CaN inhibition decreases methacholine-induced contraction in isolated RyR1(+/+) but not RyR1(-/+) mouse tracheal rings. Supportively, muscarinic contractile responses are also reduced in CaN-A?(-/+) mouse tracheal rings. Taken together, these results provide novel evidence that CaN regulates ASMC Ca(2+) sparks specifically through RyR1, which plays an important role in the control of Ca(2+) signaling and contraction in ASMCs.
Related JoVE Video
UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples.
Bioinformatics
PUBLISHED: 09-10-2014
Show Abstract
Hide Abstract
We develop a novel unsupervised deconvolution method, within a well-grounded mathematical framework, to dissect mixed gene expressions in heterogeneous tumor samples. We implement an R package, UNsupervised DecOnvolution (UNDO), that can be used to automatically detect cell-specific marker genes (MGs) located on the scatter radii of mixed gene expressions, estimate cellular proportions in each sample and deconvolute mixed expressions into cell-specific expression profiles. We demonstrate the performance of UNDO over a wide range of tumor-stroma mixing proportions, validate UNDO on various biologically mixed benchmark gene expression datasets and further estimate tumor purity in TCGA/CPTAC datasets. The highly accurate deconvolution results obtained suggest not only the existence of cell-specific MGs but also UNDO's ability to detect them blindly and correctly. Although the principal application here involves microarray gene expressions, our methodology can be readily applied to other types of quantitative molecular profiling data. Availability and implementation: UNDO is available at http://bioconductor.org/packages.
Related JoVE Video
[Effects of apolipoprotein A1 gene rs670 and rs5069 polymorphisms on the plasma lipid profiles in healthy adolescents with different body mass index].
Zhongguo Yi Xue Ke Xue Yuan Xue Bao
PUBLISHED: 09-02-2014
Show Abstract
Hide Abstract
To investigate the possible effects of apolipoprotein A1 gene (APOA1) rs670 and rs5069 polymorphisms on plasma lipid profiles in healthy adolescents with different body mass index (BMI).
Related JoVE Video
Phenotypic and functional characterization of cytokine-induced killer cells derived from preterm and term infant cord blood.
Oncol. Rep.
PUBLISHED: 09-01-2014
Show Abstract
Hide Abstract
Cord blood has gradually become an important source for hematopoietic stem cell transplantation (HSCT) in the human, particularly in pediatric patients. Adoptive cellular immunotherapy of patients with hematologic malignancies after umbilical cord blood transplant is crucial. Cytokine?induced killer (CIK) cells derived from cord blood are a new type of antitumor immune effector cells in tumor prevention and treatment and have increasingly attracted the attention of researchers. On the other hand, it has been suggested that preterm infant cord blood retains an early differentiation phenotype suitable for immunotherapy. Therefore, we determined the phenotypic and functional characterization of CIK cells derived from preterm infant cord blood (PCB-CIK) compared with CIK cells from term infant cord blood (TCB-CIK). Twenty cord blood samples were collected and classified into two groups based on gestational age. Cord blood mononuclear cells (CBMCs) were isolated, cultured and induced to CIK cells in vitro. We used flow cytometry to detect cell surface markers, FlowJo software to analyze the proliferation profile and intracellular staining to test the secretion of cytokines. Finally, we evaluated the antitumor activity of CIK cells against K562 in vitro. Compared with TCB-CIK, PCB-CIK cells demonstrated faster proliferation and higher expression of activated cell surface markers. The secretion of IL-10 was lower in PCB-CIK cells while the expression of perforin and CD107a had no significant difference between the two cell groups. PCB-CIK cells exhibited a high proliferation rate while the cytotoxic activity had no difference between the PCB-CIK and TCB-CIK cells. Hence preterm infant cord blood may be a potential source for immunotherapy.
Related JoVE Video
In-line phase-contrast imaging based on Tsinghua Thomson scattering x-ray source.
Rev Sci Instrum
PUBLISHED: 09-01-2014
Show Abstract
Hide Abstract
Thomson scattering x-ray sources can produce ultrashort, energy tunable x-ray pulses characterized by high brightness, quasi-monochromatic, and high spatial coherence, which make it an ideal source for in-line phase-contrast imaging. We demonstrate the capacity of in-line phase-contrast imaging based on Tsinghua Thomson scattering X-ray source. Clear edge enhancement effect has been observed in the experiment.
Related JoVE Video
[Short-term curative effect of ribavirin combination therapy with pegylated interferon alfa-2a vs.interferon alfa-2a in patients with chronic hepatitis C].
Zhonghua Gan Zang Bing Za Zhi
PUBLISHED: 09-01-2014
Show Abstract
Hide Abstract
To perform a retrospective cohort study in order to determine the differences in short-term curative effect of ribavirin in combination with interferon alfa (IFNa)-2a vs.pegylated (Peg)-IFNa-2a in patients with chronic hepatitis C (CHC).
Related JoVE Video
[Altered effective connectivity of insula in nicotine addiction].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 08-26-2014
Show Abstract
Hide Abstract
To explore the changes of effective connectivity associated with insula in different nicotine addiction sessions so as to understand its role and function.
Related JoVE Video
Glycoproteins identified from heart failure and treatment models.
Proteomics
PUBLISHED: 08-20-2014
Show Abstract
Hide Abstract
Conduction abnormalities can lead to dyssynchronous contraction, which significantly worsens morbidity and mortality of heart failure. Cardiac resynchronization therapy (CRT) can reverse ventricular remodeling and improve cardiac function. Although the underlying molecular changes are unknown, the use of a canine model of dyssynchronous heart failure (DHF) and CRT has shown that there are global changes across the cardiac proteome. This study determines changes in serum glycoprotein concentration from DHF and CRT compared to normal. We hypothesize that CRT invokes protective or advantageous pathways that can be reflected in the circulating proteome. Two prong discovery approaches were carried out on pooled normal, DHF, and CRT samples composed of individual canine serum to determine the overall protein concentration and the N-linked glycosites of circulating glycoproteins. The level of the glycoproteins was altered in DHF and CRT compared to control sera, with 63 glycopeptides substantially increased in DHF and/or CRT. Among the 32 elevated glycosite-containing peptides in DHF, 13 glycopeptides were reverted to normal level after CRT therapy. We further verify the changes of glycopeptides using label-free LC-MS from individual canine serum. Circulating glycoproteins such as alpha-fetoprotein, alpha-2-macroglobulin, galectin-3-binding protein, and collectin-10 show association to failing heart and CRT treatment model.
Related JoVE Video
Blockade of 2-arachidonoylglycerol hydrolysis produces antidepressant-like effects and enhances adult hippocampal neurogenesis and synaptic plasticity.
Hippocampus
PUBLISHED: 08-12-2014
Show Abstract
Hide Abstract
The endocannabinoid ligand 2-arachidonoylglycerol (2-AG) is inactivated primarily by monoacylglycerol lipase (MAGL). We have shown recently that chronic treatments with MAGL inhibitor JZL184 produce antidepressant- and anxiolytic-like effects in a chronic unpredictable stress (CUS) model of depression in mice. However, the underlying mechanisms remain poorly understood. Adult hippocampal neurogenesis has been implicated in animal models of anxiety and depression and behavioral effects of antidepressants. We tested whether CUS and chronic JZL184 treatments affected adult neurogenesis and synaptic plasticity in the dentate gyrus (DG) of mouse hippocampus. We report that CUS induced depressive-like behaviors and decreased the number of bromodeoxyuridine-labeled neural progenitor cells and doublecortin-positive immature neurons in the DG, while chronic JZL184 treatments prevented these behavioral and cellular deficits. We also investigated the effects of CUS and chronic JZL184 on a form long-term potentiation (LTP) in the DG known to be neurogenesis-dependent. CUS impaired LTP induction, whereas chronic JZL184 treatments restored LTP in CUS-exposed mice. These results suggest that enhanced adult neurogenesis and long-term synaptic plasticity in the DG of the hippocampus might contribute to antidepressant- and anxiolytic-like behavioral effects of JZL184. © 2014 Wiley Periodicals, Inc.
Related JoVE Video
A biomimetic multi-stimuli-response ionic gate using a hydroxypyrene derivation-functionalized asymmetric single nanochannel.
Adv. Mater. Weinheim
PUBLISHED: 08-11-2014
Show Abstract
Hide Abstract
A highly efficient multi-stimuli-response ionic gate that can be activated separately or cooperatively by pH and UV light has been demonstrated by modifying the environmental stimuli-responsive molecule 8-hydroxypyrene-1,3,6-trisulfonate into a track-etched single conical nanochannel. Such a multi-response ionic gate can find applications in areas such as electronics, actuators, and biosensors.
Related JoVE Video
Four lateral mass screw fixation techniques in lower cervical spine following laminectomy: a finite element analysis study of stress distribution.
Biomed Eng Online
PUBLISHED: 08-09-2014
Show Abstract
Hide Abstract
Lateral mass screw fixation (LSF) techniques have been widely used for reconstructing and stabilizing the cervical spine; however, complications may result depending on the choice of surgeon. There are only a few reports related to LSF applications, even though fracture fixation has become a severe complication. This study establishes the three-dimensional finite element model of the lower cervical spine, and compares the stress distribution of the four LSF techniques (Magerl, Roy-Camille, Anderson, and An), following laminectomy -- to explore the risks of rupture after fixation.
Related JoVE Video
Theoretical and experimental studies of distance dependent response of micro-ring resonator-based ultrasonic detectors for photoacoustic microscopy.
J Appl Phys
PUBLISHED: 08-07-2014
Show Abstract
Hide Abstract
We present in this paper a systematic study of the distance dependent detection characteristics of the newly developed micro-ring resonator (MRR)-based ultrasonic detector for photoacoustic microscopy (PAM). A simple analytic model was first developed to study the steady-state response to the continuous ultrasonic waves. While placing the MRR detector at the acoustic far-field provides longer working distance and broader field of view, the detection at acoustic near-field offers the improved sensitivity and broader bandwidth but at the cost of reduction in the field of view. Furthermore, a numerical model was developed to analyze the transient response to the photoacoustic-induced impulsive waves. Notably, far-field detection exhibits a flat wavefront of its response pattern in the time domain while large distortions are clearly visible in the case of near-field detection. Finally, both analytic and numerical models are validated by experimental studies. This work establishes a theoretical framework for quantitatively analyzing the trade-offs between near-field and far-field detection using MRR detector, creating a guideline for optimizing the PAM for various applications in biomedical imaging and diagnostics.
Related JoVE Video
Copper-dependent and -independent hypoxia-inducible factor-1 regulation of gene expression.
Metallomics
PUBLISHED: 08-07-2014
Show Abstract
Hide Abstract
Hypoxia-inducible factor-1 (HIF-1) regulates the expression of the vascular endothelial growth factor (VEGF), a process requiring copper (Cu) participation. HIF-1 is also involved in the expression of more than a hundred of genes, but it is unknown how HIF-1 differentially controls the expression of these genes timely and spatially. The present study was undertaken to test the hypothesis that Cu is not required for the expression of all HIF-1-regulated genes, thus exploring mechanistic insights into the differential control of multiple gene expression by one transcription factor. Human umbilical vein endothelial cells (HUVECs) were treated with siRNA targeting HIF-1? to define the essential role of HIF-1 in the regulation of BCL2/adenovirus E1B 19 kDa protein-interacting protein 3 (BNIP3) and insulin-like growth factor 2 (IGF-2) expression. A Cu chelator, tetraethylenepentamine (TEPA), was used to reduce intracellular availability of Cu. In comparison, a zinc chelator, N,N,N',N'-tetrakis(2-pyridylmethyl) ethylenediamine (TPEN), was used to reduce intracellular zinc concentration. The expression of both BNIP3 and IGF-2 was completely suppressed in the HIF-1? deficient cells. The removal of Cu suppressed the expression of BNIP3, but did not affect that of IGF-2. The reduction of intracellular zinc did not cause the same effect. Further screening identified a group of genes whose expression required Cu and the others did not need Cu. The present study thus demonstrates Cu-dependent and -independent HIF-1 regulation of gene expression, indicating a mechanism for differential control of multiple gene expression by one transcription factor.
Related JoVE Video
Optical logic gates based on electro-optic modulation with Sagnac interferometer.
Appl Opt
PUBLISHED: 08-05-2014
Show Abstract
Hide Abstract
In this work, we present a new structure to realize optical logic operation in a Sagnac interferometer with electro-optical modulation. In the scheme, we divide two counterpropagation signals in a Sagnac loop to two different arms with the electro-optical crystal by using two circulators. Lithium niobate materials whose electro-optical coefficient can be as large as 32.2×10(-12)??m/V make up the arms of the waveguides. Using the transfer matrix of the fiber coupler, we analyze the propagation of signals in this system and obtain the transmission characteristic curves and the extinction ratio. The results indicate that this optical switching has a high extinction ratio of about 60 dB and an ultrafast response time of 2.036 ns. In addition, the results reveal that the change of the dephasing between the two input signals and the modification of the modulation voltage added to the electro-optical crystal leads to the change of the extinction ratio. We also conclude that, in cases of the dephasing of two initial input signals ??=0, we can obtain the various logical operations, such as the logical operations D=A¯·B, D=A·B¯, C=A+B, and D=A?B in ports C and D of the system by adjusting the modulation voltage. When ???0, we obtain the arithmetic operations D=A+B, C=A?B, D=A·B¯, and C=A¯·B in ports C and D. This study is significant for the design of all optical networks by adjusting the modulation voltage.
Related JoVE Video
A Mn(III)/TEMPO-co-mediated tandem azidation-1,2-carbon migration reaction of allylic silyl ethers.
Chem. Commun. (Camb.)
PUBLISHED: 08-04-2014
Show Abstract
Hide Abstract
A novel Mn(III)/TEMPO-co-mediated tandem azidation-1,2-carbon migration reaction of allylic silyl ethers with an unactivated C=C bond has been explored, generating ?-aryl-alkyl ?-azido ketones with an ?-quaternary stereocenter.
Related JoVE Video
Photoacoustic probe using a microring resonator ultrasonic sensor for endoscopic applications.
Opt Lett
PUBLISHED: 08-01-2014
Show Abstract
Hide Abstract
We designed an all-optical photoacoustic (PA) probe for endoscopic applications by employing an optically transparent, coverslip-type, polymeric microring resonator ultrasonic sensor. We experimentally quantified the axial, tangential, and radial resolutions and angular sensitive stability of this probe. Using this probe, we achieved volumetric imaging of several phantoms. Our all-optical probe design offers clear benefit in integrating PA endoscope with other optical endoscopic imaging modalities to facilitate the transformation from bench to bedside.
Related JoVE Video
A graphene oxide-based enzyme-free signal amplification platform for homogeneous DNA detection.
Analyst
PUBLISHED: 07-25-2014
Show Abstract
Hide Abstract
A graphene oxide (GO) based enzyme-free signal amplification platform for homogeneous DNA sensing is developed with simplicity and high sensitivity. In the absence of the target DNA, labeled hairpin probe 1 (H1) and probe 2 (H2) were adsorbed on the surface of GO, resulting in the fluorescence quenching of the dyes and minimizing the background fluorescence. The addition of the target DNA facilitated the formation of double-stranded DNA (dsDNA) between H1 and H2, causing the probes to separate from GO and release the target DNA through a strand displacement reaction. Meanwhile, the whole reaction started anew. This is an excellent isothermal signal amplification technique without the involvement of enzymes. By monitoring the change of the fluorescence intensity, the target DNA not only can be determined in buffer solution, but also can be detected in 1% serum solution spiked with a series of concentrations of the target DNA. In addition, the consumption amount of the probes in this method is lower than that in traditional molecular beacon methods.
Related JoVE Video
Imaging cellular ultrastructure by PALM, iPALM, and correlative iPALM-EM.
Methods Cell Biol.
PUBLISHED: 06-30-2014
Show Abstract
Hide Abstract
Many biomolecules in cells can be visualized with high sensitivity and specificity by fluorescence microscopy. However, the resolution of conventional light microscopy is limited by diffraction to ~200-250 nm laterally and >500 nm axially. Here, we describe superresolution methods based on single-molecule localization analysis of photoswitchable fluorophores (PALM: photoactivated localization microscopy) as well as our recent three-dimensional (3D) method (iPALM: interferometric PALM) that allows imaging with a resolution better than 20 nm in all three dimensions. Considerations for their implementations, applications to multicolor imaging, and a recent development that extend the imaging depth of iPALM to ~750 nm are discussed. As the spatial resolution of superresolution fluorescence microscopy converges with that of electron microscopy (EM), direct imaging of the same specimen using both approaches becomes feasible. This could be particularly useful for cross validation of experiments, and thus, we also describe recent methods that were developed for correlative superresolution fluorescence and EM.
Related JoVE Video
[Therapeutic effect of saxagliptin in rat models of nonalcoholic fatty liver and type 2 diabetes].
Nan Fang Yi Ke Da Xue Xue Bao
PUBLISHED: 06-28-2014
Show Abstract
Hide Abstract
To observe the therapeutic effect of saxagliptin in a rat model of nonalcoholic fatty liver and type 2 diabetes and investigate the possible mechanism.
Related JoVE Video
[Effect of paeonol on adhesive function of rat vascular endothelial cells induced by lipopolysaccharide and co-cultured with smooth muscle cells].
Zhongguo Zhong Yao Za Zhi
PUBLISHED: 06-25-2014
Show Abstract
Hide Abstract
To observe the changes in the adhesive function of vascular endothelial cells (VEC) and rat monocytes induced by lipopolysaccharide (LPS) and co-cultured with smooth muscle cells (SMC) and the intervention effect of paeonol (Pae).
Related JoVE Video
[Prediction of efficacy of neoadjuvant radiochemotherapy based on depth of invasion in T3 rectal cancer].
Zhonghua Wei Chang Wai Ke Za Zhi
PUBLISHED: 06-24-2014
Show Abstract
Hide Abstract
To investigate the association of mesorectal invasion depth before neoadjuvant radiochemotherapy with pathological outcome and to provide evidence for individualized treatment in T3 rectal cancer.
Related JoVE Video
Collagen scaffolds combined with collagen-binding ciliary neurotrophic factor facilitate facial nerve repair in mini-pigs.
J Biomed Mater Res A
PUBLISHED: 06-20-2014
Show Abstract
Hide Abstract
The preclinical studies using animal models play a very important role in the evaluation of facial nerve regeneration. Good models need to recapitulate the distance and time for axons to regenerate in humans. Compared with the most used rodent animals, the structure of facial nerve in mini-pigs shares more similarities with humans in microanatomy. To evaluate the feasibility of repairing facial nerve defects by collagen scaffolds combined with ciliary neurotrophic factor (CNTF), 10-mm-long gaps were made in the buccal branch of mini-pigs' facial nerve. Three months after surgery, electrophysiological assessment and histological examination were performed to evaluate facial nerve regeneration. Immunohistochemistry and transmission electron microscope observation showed that collagen scaffolds with collagen binding (CBD)-CNTF could promote better axon regeneration, Schwann cell migration, and remyelination at the site of implant device than using scaffolds alone. Electrophysiological assessment also showed higher recovery rate in the CNTF group. In summary, combination of collagen scaffolds and CBD-CNTF showed promising effects on facial nerve regeneration in mini-pig models. © 2014 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2014.
Related JoVE Video
Alternative sigma factors SigF, SigE, and SigG are essential for sporulation in Clostridium botulinum ATCC 3502.
Appl. Environ. Microbiol.
PUBLISHED: 06-13-2014
Show Abstract
Hide Abstract
Clostridium botulinum produces heat-resistant endospores that may germinate and outgrow into neurotoxic cultures in foods. Sporulation is regulated by the transcription factor Spo0A and the alternative sigma factors SigF, SigE, SigG, and SigK in most spore formers studied to date. We constructed mutants of sigF, sigE, and sigG in C. botulinum ATCC 3502 and used quantitative reverse transcriptase PCR and electron microscopy to assess their expression of the sporulation pathway on transcriptional and morphological levels. In all three mutants the expression of spo0A was disrupted. The sigF and sigE mutants failed to induce sigG and sigK beyond exponential-phase levels and halted sporulation during asymmetric cell division. In the sigG mutant, peak transcription of sigE was delayed and sigK levels remained lower than that in the parent strain. The sigG mutant forespore was engulfed by the mother cell and possessed a spore coat but no peptidoglycan cortex. The findings suggest that SigF and SigE of C. botulinum ATCC 3502 are essential for early sporulation and late-stage induction of sigK, whereas SigG is essential for spore cortex formation but not for coat formation, as opposed to previous observations in B. subtilis sigG mutants. Our findings add to a growing body of evidence that regulation of sporulation in C. botulinum ATCC 3502, and among the clostridia, differs from the B. subtilis model.
Related JoVE Video
Construction of Full-Length cDNA Library and Development of EST-Derived Simple Sequence Repeat (EST-SSR) Markers in Senecio scandens.
Biochem. Genet.
PUBLISHED: 06-10-2014
Show Abstract
Hide Abstract
Senecio scandens Buch.-Ham. ex D. Don (Compositae) is a crucial source of Chinese traditional medicine with antibacterial properties. We constructed a cDNA library and obtained expressed sequence tags (ESTs) to show the distribution of gene ontology annotations for mRNAs, using an individual plant with superior antibacterial characteristics. Analysis of comparative genomics indicates that the putative uncharacterized proteins (21.07%) might be derived from "molecular function unknown" clones or rare transcripts. Furthermore, the Compositae had high cross-species transferability of EST-derived simple sequence repeats (EST-SSR), based on valid amplifications of 206 primer pairs developed from the newly assembled expressed sequence tag sequences in Artemisia annua L. Among those EST-SSR markers, 52 primers showed polymorphic amplifications between individuals with contrasting diverse antibacterial traits. Our sequence data and molecular markers will be cost-effective tools for further studies such as genome annotation, molecular breeding, and novel transcript profiles within Compositae species.
Related JoVE Video
Protective effects of osthole on intestinal ischemia-reperfusion injury in mice.
Exp Clin Transplant
PUBLISHED: 06-09-2014
Show Abstract
Hide Abstract
The purpose of this study was to evaluate the effect of intravenous injection of osthole on intestinal ischemia-reperfusion injury and parameters of oxidative stress.
Related JoVE Video
Survival analysis of patients with non-small cell lung cancer who underwent surgical resection following 4 lung cancer resection guidelines.
BMC Cancer
PUBLISHED: 06-05-2014
Show Abstract
Hide Abstract
To compare survival of patients with non-small cell lung cancer (NSCLC) who underwent surgical resection and lymph node sampling based on guidelines proposed by the American College of Surgeons Oncology Group (ACOSOG), National Comprehensive Cancer Network (NCCN), the OSI Pharmaceutical RADIANT trial, and the International Association for the Study of Lung Cancer (IASLC).
Related JoVE Video
Efficacy comparison of the anterior low small incision and the traditional incision for treatment of thyroid adenoma.
Pak J Med Sci
PUBLISHED: 05-28-2014
Show Abstract
Hide Abstract
To compare the clinical efficacy and surgical effects of the anterior low small incision and the traditional incision in the treatments of thyroid adenomas.
Related JoVE Video
Hes1, a Notch signaling downstream target, regulates adult hippocampal neurogenesis following traumatic brain injury.
Brain Res.
PUBLISHED: 05-19-2014
Show Abstract
Hide Abstract
Hairy and enhancer of split 1 (Hes1), a downstream target of Notch signaling, has long been recognized as crucial in inhibiting neuronal differentiation. However, the role of Hes1 following traumatic brain injury (TBI) in adult neurogenesis in the mouse dentate gyrus (DG) remains partially understood. Here, we investigate the role of Hes1 in regulating neurogenesis in the DG of the adult hippocampus after TBI by up- or downregulating Hes1 expression. First, adenovirus-mediated gene transfection was employed to upregulate Hes1 in vivo. The mice were then subjected to TBI, and the hippocampal tissue was collected for Western blot analysis at designated times, pre- and post-injury. Moreover, the brain slices were stained for BrdU and doublecortin (DCX). We show that enhancing Hes1 inhibits the proliferation and differentiation of neural precursor cells (NPCs) in the DG of the hippocampus soon after TBI. Second, downregulation of Hes1 via RNA interference (RNAi) results in a significant increase in neuronal production and promotes the differentiation of NPCs into mature neurons in the DG, as assessed by BrdU and NeuN double staining. Furthermore, a Morris water maze (MWM) test clearly confirmed that the knockdown of Hes1 improves the spatial learning and memory capacity of adult mice following injury. Taken together, these observations suggest that Hes1 represents a negative regulator of adult neurogenesis post-TBI and that the precise space-time regulation of Hes1 expression in the DG may promote the recovery of neural function following TBI.
Related JoVE Video
Forest type affects the coupled relationships of soil C and N mineralization in the temperate forests of northern China.
Sci Rep
PUBLISHED: 05-16-2014
Show Abstract
Hide Abstract
Decomposition of soil organic matter (SOM) is sensitive to vegetation and climate change. Here, we investigated the influence of changes in forest types on the mineralization of soil carbon (C) and nitrogen (N), and their temperature sensitivity (Q10) and coupling relationships by using a laboratory soil incubation experiments. We sampled soils from four forest types, namely, a primary Quercus liaotungensis forest (QL), Larix principis-rupprechtii plantation (LP), Pinus tabulaeformis plantation (PT), and secondary shrub forest (SS) in temperate northern China. The results showed that soil C and N mineralization differed significantly among forest types. Soil C and N mineralization were closely coupled in all plots, and C:N ratios of mineralized SOM ranged from 2.54 to 4.12. Forest type significantly influenced the Q10 values of soil C and N mineralization. The activation energy (Ea) of soil C and N mineralization was negatively related to the SOM quality index in all forest types. The reverse relationships suggested that the carbon quality-temperature (CQT) hypothesis was simultaneously applicable to soil C and N mineralization. Our findings show that the coupled relationships of soil C and N mineralization can be affected by vegetation change.
Related JoVE Video
Senescence impairs direct conversion of human somatic cells to neurons.
Nat Commun
PUBLISHED: 05-13-2014
Show Abstract
Hide Abstract
Recent reports have shown that fibroblasts can be converted to neurons by forced expression of transcription factors. However, the mechanisms underlying this conversion remain unclear. Here, we show that the efficiency of neuronal conversion of embryonic human fibroblasts aged in culture is lower than that in cells in early culture stages. Moreover, depletion of p16(Ink4a) and p19(Arf) involved in the activation of cellular senescence is sufficient to convert human fibroblast and epithelial cells into neurons. The induced neurons express neuron-specific proteins, generate action potentials and neurotransmitter receptor-mediated currents. Genome-wide transcriptional analysis shows that the induced neurons have a profile different from fibroblasts and similar to that of control neurons induced by established methods. We further noted that expression of p53 blocks the neuronal conversion, whereas expression of human telomerase reverse transcriptase (hTERT) induces it. Our results indicate that overcoming senescence is a crucial step for neuronal conversion of somatic cells.
Related JoVE Video
Extreme surface propensity of halide ions in water.
Nat Commun
PUBLISHED: 05-09-2014
Show Abstract
Hide Abstract
Water possesses an extremely high polarity, making it a unique solvent for salts. Indeed, aqueous electrolyte solutions are ubiquitous in the atmosphere, biology, energy applications and industrial processes. For many processes, chemical reactions at the water surface are rate determining, and the nature and concentration of the surface-bound electrolytes are of paramount importance, as they determine the water structure and thereby surface reactivity. Here we investigate the dynamics of water molecules at the surface of sodium chloride and sodium iodide solutions, using surface-specific femtosecond vibrational spectroscopy. We quantify the interfacial ion density through the reduced energy transfer rates between water molecules resulting from the lowered effective interfacial density of water molecules, as water is displaced by surface active ions. Our results reveal remarkably high surface propensities for halogenic anions, higher for iodide than for chloride ions, corresponding to surface ion concentrations several times that of the bulk.
Related JoVE Video
Predicting protein functions by using unbalanced bi-random walk algorithm on protein-protein interaction network and functional interrelationship network.
Curr. Protein Pept. Sci.
PUBLISHED: 05-07-2014
Show Abstract
Hide Abstract
Accurate annotation of protein functions is still a big challenge for understanding life in the post-genomic era. Recently, some methods have been developed to solve the problem by incorporating functional similarity of GO terms into protein-protein interaction (PPI) network, which are based on the observation that a protein tends to share some common functions with proteins that interact with it in PPI network, and two similar GO terms in functional interrelationship network usually co-annotate some common proteins. However, these methods annotate functions of proteins by considering at the same level neighbors of proteins and GO terms respectively, and few attempts have been made to investigate their difference. Given the topological and structural difference between PPI network and functional interrelationship network, we firstly investigate at which level neighbors of proteins tend to have functional associations and at which level neighbors of GO terms usually co-annotate some common proteins. Then, an unbalanced Bi-random walk (UBiRW) algorithm which iteratively walks different number of steps in the two networks is adopted to find protein-GO term associations according to some known associations. Experiments are carried out on S. cerevisiae data. The results show that our method achieves better prediction performance not only than methods that only use PPI network data, but also than methods that consider at the same level neighbors of proteins and of GO terms.
Related JoVE Video
Crystal structures of apparent saccharide sensors from histidine kinase receptors prevalent in a human gut symbiont.
FEBS J.
PUBLISHED: 04-24-2014
Show Abstract
Hide Abstract
The adult human gut is a complicated ecosystem in which host-bacterium symbiosis plays an important role. Bacteroides thetaiotaomicron is a predominant member of the gut microflora, providing the human digestive tract with a large number of glycolytic enzymes. Expression of many of these enzymes appears to be controlled by histidine kinase receptors that are fused into unusual hybrid two-component systems that share homologous periplasmic sensor domains. These sensor domains belong to the third most populated (HK3) family based on a previous unpublished bioinformatics analysis of predicted histidine kinase sensors. Here, we present the crystal structures of two sensor domains representative of the HK3 family. Each sensor is folded into three domains: two-seven-bladed ?-propeller domains and one ?-sandwich domain. Both sensors form dimers in crystals, and one sensor appears to be physiologically relevant. The folding characteristics in the individual domains, the domain organization, and the oligomeric architecture are all unique to HK3 sensors. Sequence analysis of the HK3 sensors indicates that these sensor domains are shared among other signaling molecules, implying combinatorial molecular evolution.
Related JoVE Video
Rapid fabrication of hierarchically structured supramolecular nanocomposite thin films in one minute.
Nat Commun
PUBLISHED: 04-24-2014
Show Abstract
Hide Abstract
Functional nanocomposites containing nanoparticles of different chemical compositions may exhibit new properties to meet demands for advanced technology. It is imperative to simultaneously achieve hierarchical structural control and to develop rapid, scalable fabrication to minimize degradation of nanoparticle properties and for compatibility with nanomanufacturing. Here we show that the assembly kinetics of supramolecular nanocomposites in thin films are governed by the energetic cost arising from defects, the chain mobility and the activation energy for inter-domain diffusion. By optimizing only one parameter, the solvent fraction in the film, the assembly kinetics can be precisely tailored to produce hierarchically structured thin films of supramolecular nanocomposites in one minute. Moreover, the strong wavelength-dependent optical anisotropy in the nanocomposite highlights their potential applications for light manipulation and information transmission. The present study may open a new avenue in designing manufacture-friendly continuous processing for the fabrication of functional nanocomposite thin films.
Related JoVE Video
Inhibition of autophagy potentiates the efficacy of Gli inhibitor GANT-61 in MYCN-amplified neuroblastoma cells.
BMC Cancer
PUBLISHED: 04-14-2014
Show Abstract
Hide Abstract
Aberrant Hedgehog (Hh) signaling is often associated with neuroblastoma (NB), a childhood malignancy with varying clinical outcomes due to different molecular characteristics. Inhibition of Hh signaling with small molecule inhibitors, particularly with GANT-61, significantly suppresses NB growth. However, NB with MYCN amplification is less sensitive to GANT-61 than those without MYCN amplification.
Related JoVE Video
Collagen scaffolds modified with CNTF and bFGF promote facial nerve regeneration in minipigs.
Biomaterials
PUBLISHED: 04-10-2014
Show Abstract
Hide Abstract
Most experiments of peripheral nerve repair after injury have been conducted in the rodent model but the translation of findings from rodent studies to clinical practice is needed partly because the nerve regeneration must occur over much longer distances in humans than in rodents. The reconstruction of long distance nerve injuries still represents a great challenge to surgeons who is engaged in peripheral nerve surgery. Here we used the functional nerve conduit (collagen scaffolds incorporated with neurocytokines CNTF and bFGF) to bridge a 35 mm long facial nerve gap in minipig models. At 6 months after surgery, electrophysiology assessment and histological examination were conducted to evaluate the regeneration of peripheral facial nerves. Based on functional and histological observations, the results indicated that the functional collagen scaffolds promoted nerve reconstruction. The number and arrangement of regenerated nerve fibers, myelination, and nerve function reconstruction was better in the CNTF + bFGF conduit group than the single factor CNTF or bFGF conduit group. The functional composite conduit, which exhibited favorable mechanical properties, may promote facial nerve regeneration in minipigs effectively.
Related JoVE Video
Tissue Proteomics Using Chemical Immobilization and Mass Spectrometry.
Anal. Biochem.
PUBLISHED: 04-02-2014
Show Abstract
Hide Abstract
Proteomics analysis is important for characterizing tissues to gain biological and pathological insights, which could lead to the identification of disease-associated proteins for disease diagnostics or targeted therapy. However, tissues are commonly embedded in optimal cutting temperature compound (OCT) or they are formalin-fixed and paraffin-embedded (FFPE) in order to maintain tissue morphology for histology evaluation. Although several tissue proteomics analyses have been performed on FFPE tissues using advanced mass spectrometry technologies, high throughput proteomic analysis of OCT-embedded tissues has been difficult due to the interference of OCT in the mass spectrometry analysis. In addition, molecules other than proteins present in tissues further complicate tissue proteomic analysis. Herein, we report the development of a method using Chemical Immobilization of Proteins for Peptide Extraction (CIPPE). In this method, proteins are chemically immobilized onto a solid support; interferences from tissues and OCT embedding are removed by extensive washing of proteins conjugated on the solid support. Peptides are then released from the solid phase by proteolysis, enabling mass spectrometry analysis. This method was first validated by eliminating OCT interference from a standard protein, human serum albumin, where all the unique peaks contributed by OCT contamination were eradicated. Finally, this method was applied for the proteomic analysis of frozen and OCT-embedded tissues using iTRAQ labeling and 2D liquid chromatography tandem mass spectrometry. The data showed reproducible extraction and quantitation of 10,284 proteins from 3,996 protein groups and a minimal impact of OCT embedding on the analysis of the global proteome of the stored tissue samples.
Related JoVE Video
Determination of Hg(2+) by on-line separation and pre-concentration with atmospheric-pressure solution-cathode glow discharge atomic emission spectrometry.
Anal. Chim. Acta
PUBLISHED: 03-30-2014
Show Abstract
Hide Abstract
A simple and sensitive method to determine Hg(2+) was developed by combining solution-cathode glow discharge atomic emission spectrometry (SCGD-AES) with flow injection (FI) based on on-line solid-phase extraction (SPE). We synthesized l-cysteine-modified mesoporous silica and packed it in an SPE microcolumn, which was experimentally determined to possess a good mercury adsorption capacity. An enrichment factor of 42 was achieved under optimized Hg(2+) elution conditions, namely, an FI flow rate of 2.0 mL min(-1) and an eluent comprised of 10% thiourea in 0.2 mol L(-1) HNO3. The detection limit of FI-SCGD-AES was determined to be 0.75 ?g L(-1), and the precision of the 11 replicate Hg(2+) measurements was 0.86% at a concentration of 100 ?g L(-1). The proposed method was validated by determining Hg(2+) in certified reference materials such as human hair (GBW09101b) and stream sediment (GBW07310).
Related JoVE Video
CXCL10 mRNA expression predicts response to neoadjuvant chemoradiotherapy in rectal cancer patients.
Tumour Biol.
PUBLISHED: 03-25-2014
Show Abstract
Hide Abstract
Chemoradiotherapy has been commonly used as neoadjuvant therapy for rectal cancer to allow for less aggressive surgical approaches and to improve quality of life. In cancer, it has been reported that CXCL10 has an anti-tumor function. However, the association between CXCL10 and chemoradiosensitivity has not been fully investigated. We performed this study to investigate the relationship between CXCL10 expression and chemoradiosensitivity in rectal cancer patients. Ninety-five patients with rectal cancer who received neoadjuvant chemoradiotherapy (NCRT) were included. Clinical parameters were compared with the outcome of NCRT and CXCL10 messenger RNA (mRNA) expression between the pathological complete response (pCR) group and non-pathological complete response (npCR) group. CXCL10 mRNA and protein expressions between groups were analyzed using the Student's t test and chi-square test. The mean mRNA level of CXCL10 in the pCR group was significantly higher than that in the npCR group (p?=?0.010). In the pCR group, 73.7 % of the patients had high CXCL10 mRNA expression, and 61.4 % of the patients in the npCR group had low CXCL10 mRNA expression. Subjects with high CXCL10 mRNA expression demonstrated a higher sensitivity to NCRT (p?=?0.011). The receiver operating characteristic curve showed that the diagnostic performance of CXCL10 mRNA expression had an area under the curve of 0.720 (95 % confidence interval, 0.573-0.867). There were no differences between the pCR and npCR groups in CXCL10 protein expression (p?>?0.05). High CXCL10 mRNA expression is associated with a better tumor response to NCRT in rectal cancer patients and may predict the outcome of NCRT in this malignancy.
Related JoVE Video
Beneficial effects of phlorizin on diabetic nephropathy in diabetic db/db mice.
J. Diabetes Complicat.
PUBLISHED: 03-18-2014
Show Abstract
Hide Abstract
This study observes the effects of phlorizin on diabetic nephrology in db/db diabetic mice and explores possible underlying mechanisms.
Related JoVE Video
Reduced tolerance to abiotic stress in transgenic Arabidopsis overexpressing a Capsicum annuum multiprotein bridging factor 1.
BMC Plant Biol.
PUBLISHED: 03-17-2014
Show Abstract
Hide Abstract
The pepper fruit is the second most consumed vegetable worldwide. However, low temperature affects the vegetative development and reproduction of the pepper, resulting in economic losses. To identify cold-related genes regulated by abscisic acid (ABA) in pepper seedlings, cDNA representational difference analysis was previously performed using a suppression subtractive hybridization method. One of the genes cloned from the subtraction was homologous to Solanum tuberosum MBF1 (StMBF1) encoding the coactivator multiprotein bridging factor 1. Here, we have characterized this StMBF1 homolog (named CaMBF1) from Capsicum annuum and investigated its role in abiotic stress tolerance.
Related JoVE Video
Antennal transcriptome analysis and comparison of olfactory genes in two sympatric defoliators, Dendrolimus houi and Dendrolimus kikuchii (Lepidoptera: Lasiocampidae).
Insect Biochem. Mol. Biol.
PUBLISHED: 03-15-2014
Show Abstract
Hide Abstract
The Yunnan pine and Simao pine caterpillar moths, Dendrolimus houi Lajonquière and Dendrolimus kikuchii Matsumura (Lepidoptera: Lasiocampidae), are two closely related and sympatric pests of coniferous forests in southwestern China, and olfactory communication systems of these two insects have received considerable attention because of their economic importance. However, there is little information on the molecular aspect of odor detection about these insects. Furthermore, although lepidopteran species have been widely used in studies of insect olfaction, few work made comparison between sister moths on the olfactory recognition mechanisms. In this study, next-generation sequencing of the antennal transcriptome of these two moths were performed to identify the major olfactory genes. After comparing the antennal transcriptome of these two moths, we found that they exhibit highly similar transcripts-associated GO terms. Chemosensory gene families were further analyzed in both species. We identified 23 putative odorant binding proteins (OBP), 17 chemosensory proteins (CSP), two sensory neuron membrane proteins (SNMP), 33 odorant receptors (OR), and 10 ionotropic receptors (IR) in D. houi; and 27 putative OBPs, 17 CSPs, two SNMPs, 33 ORs, and nine IRs in D. kikuchii. All these transcripts were full-length or almost full-length. The predicted protein sequences were compared with orthologs in other species of Lepidoptera and model insects, including Bombyx mori, Manduca sexta, Heliothis virescens, Danaus plexippus, Sesamia inferens, Cydia pomonella, and Drosophila melanogaster. The sequence homologies of the orthologous genes in D. houi and D. kikuchii are very high. Furthermore, the olfactory genes were classed according to their expression level, and the highly expressed genes are our target for further function investigation. Interestingly, many highly expressed genes are ortholog gene of D. houi and D. kikuchii. We also found that the Classic OBPs were further separated into three groups according to their motifs, which will help future functional researches. Surprisingly, no pheromone receptor was identified in the two Dendrolimus species, which may indicate a special pheromone identification mechanism in Dendrolimus. Our work allows for further functional studies of pheromones and host volatile recognition genes, and give novel candidate targets for pest management.
Related JoVE Video
A Bio-inspired, Sensitive, and Selective Ionic Gate Driven by Silver (I) Ions.
Small
PUBLISHED: 03-11-2014
Show Abstract
Hide Abstract
By grafting specific response DNA on the interior surface of ion track-etched conical nanochannels, a highly sensitive and selective ionic gate that can be driven by silver (I) ions is demonstrated. The switches between the OFF-state and the ON-state are mainly dependent on silver (I) ions and cysteine. Such a biomimetic nanodevice shows potential for application in sensing, pharmaceuticals, and sterilization.
Related JoVE Video
Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks.
BMC Syst Biol
PUBLISHED: 02-24-2014
Show Abstract
Hide Abstract
Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context-specific and dynamic in nature. To systematically characterize the selectively activated regulatory components and mechanisms, modeling tools must be able to effectively distinguish significant rewiring from random background fluctuations. While differential networks cannot be constructed by existing knowledge alone, novel incorporation of prior knowledge into data-driven approaches can improve the robustness and biological relevance of network inference. However, the major unresolved roadblocks include: big solution space but a small sample size; highly complex networks; imperfect prior knowledge; missing significance assessment; and heuristic structural parameter learning.
Related JoVE Video
Highly efficient multifluorenyl host materials with unsymmetrical molecular configurations and localized triplet States for green and red phosphorescent devices.
Adv. Mater. Weinheim
PUBLISHED: 02-13-2014
Show Abstract
Hide Abstract
Highly efficient green and red electro-phosphorescence is achieved in devices with the host material DPESPODEF3. The multiple fluorenyl moieties of the host material are arranged such that it has an unsymmetrical molecular configuration, and its triplet-state location is tuned such that it has independent energy (ET) and charge transfer (CT) channels. As a result, DPESPODEF3 can suppress triplet-triplet annihilation and triplet-polaron quenching. In the resulting green and red phosphorescent devices, impressive external quantum efficiencies of ca. 20% and 16% and power efficiencies of ca. 75 and 20 lm W(-1) , respectively, are observed.
Related JoVE Video
Cloning, molecular characterization and expression analysis of insulin-like growth factor binding protein-2 (IGFBP-2) cDNA in goldfish, Carassius auratus.
Fish Physiol. Biochem.
PUBLISHED: 02-11-2014
Show Abstract
Hide Abstract
In the present study, a full-length cDNA encoding the insulin-like growth factor binding protein-2 (IGFBP-2) was cloned from the liver of goldfish (Carassius auratus) by rapid amplification of cDNA ends technique. The goldfish IGFBP-2 cDNA sequence was 1,513 bp long and had an open reading frame of 825 bp encoding a predicted polypeptide of 274 amino acid residues. Semi-quantitative RT-PCR results revealed that goldfish IGFBP-2 mRNA was expressed in all detected tissues. In liver, central nervous system and pituitary gland, goldfish IGFBP-2 expressed at high levels, followed by anterior intestine, middle intestine and kidney. In posterior intestine, ovary, skin, fat, spleen, muscle and gill, the goldfish IGFBP-2 expression levels were very low. Fasting and refeeding experiment showed that the mRNA expression of goldfish IGFBP-2 was up-regulated significantly in liver compared to the fed group and restored rapidly to normal level after refed. However, the mRNA expressions of IGFBP-2 in hypothalamus and pituitary of goldfish were insensitive to fasting. Furthermore, the mRNA expressions of IGFBP-2 in hypothalamus, pituitary and liver were varied in periprandial changes and significantly down-regulated at 2 and 4 h after meal. These results imply that the IGFBP-2 mRNA expression may be associated with anabolic and catabolic metabolism and regulated by metabolic factors in goldfish.
Related JoVE Video
Simultaneous determination and pharmacokinetic study of three isoflavones from Trifolium pratense extract in rat plasma by LC-MS/MS.
Biomed. Chromatogr.
PUBLISHED: 01-31-2014
Show Abstract
Hide Abstract
A highly selective and sensitive liquid chromatography-tandem mass spectrometry has been developed and validated for simultaneous determination of three isoflavones - ononin, formononetin and biochanin A - in rat plasma using lysionotin as internal standard (IS). The plasma samples were pretreated and extracted by liquid-liquid extraction. Chromatographic separation was accomplished on a C18 column with the column temperature of 30?°C and a mobile phase of methanol-0.1% formic acid (75:25, v/v). The detection was accomplished by multiple-reaction monitoring scanning with positive/negative ion-switching electrospray ionization mode. The optimized mass transition ion pairs (m/z) for quantitation were 431.3/269.1 for ononin, 267.1/252.2 for formononetin, 283.2/268.2 for biochanin A and 343.2/313.3 for IS. The total run time was 8.0?min. Full validation of the assay was implemented, including selectivity, sensitivity, linearity, precision, accuracy, recovery, matrix effect and stability. This is the first report on simultaneous determination of the three major isoflavones in rat plasma after intragastric administration of Trifolium pratense extract. The results provided a significant basis for the clinical application of this herb Trifolium pratense. Copyright © 2014 John Wiley & Sons, Ltd.
Related JoVE Video
A discrete time-varying internal model-based approach for high precision tracking of a multi-axis servo gantry.
ISA Trans
PUBLISHED: 01-27-2014
Show Abstract
Hide Abstract
In this paper, we consider the discrete time-varying internal model-based control design for high precision tracking of complicated reference trajectories generated by time-varying systems. Based on a novel parallel time-varying internal model structure, asymptotic tracking conditions for the design of internal model units are developed, and a low order robust time-varying stabilizer is further synthesized. In a discrete time setting, the high precision tracking control architecture is deployed on a Voice Coil Motor (VCM) actuated servo gantry system, where numerical simulations and real time experimental results are provided, achieving the tracking errors around 3.5‰ for frequency-varying signals.
Related JoVE Video
Determination of trace heavy metals in environmental and biological samples by solution cathode glow discharge-atomic emission spectrometry and addition of ionic surfactants for improved sensitivity.
Talanta
PUBLISHED: 01-10-2014
Show Abstract
Hide Abstract
Solution cathode glow discharge-atomic emission spectrometry (SCGD-AES) was evaluated for its ability to determine toxic heavy metals, including cadmium (Cd), mercury (Hg), lead (Pb), and chromium (Cr), in environmental and biological samples. A significant enhancement in heavy metal signal was observed by addition of a small amount of cetyltrimethylammoniumchloride (CTAC, C16H33 (CH3)3NCl) to the samples. The net intensity of atomic emission lines of Cd, Hg, Pb, and Cr increased by 2.1-, 4.8-, 6.6-, and 2.6-fold, respectively, after addition of 0.15% CTAC to the test solutions. The effects of ionic surfactants (CTAC) compared with non-ionic surfactants, e.g., Triton x-45 and Triton x-100, on the sensitivity of Cd, Hg, Pb, and Cr were also investigated in the present study. The enhancement effect is in the order Triton x-45
Related JoVE Video
Effects of partially replacing dietary soybean meal or cottonseed meal with completely hydrolyzed feather meal (defatted rice bran as the carrier) on production, cytokines, adhesive gut bacteria, and disease resistance in hybrid tilapia (Oreochromis niloticus ? × O. aur
Fish Shellfish Immunol.
PUBLISHED: 01-02-2014
Show Abstract
Hide Abstract
We formulated experimental diets for hybrid tilapia to investigate the effects of replacing dietary soybean meal (SBM) or cottonseed meal (CSM) by completely hydrolyzed feather meal (defatted rice bran as the carrier; abbreviated as CHFM), with emphasis on fish growth, the composition of adhesive gut bacteria, intestinal and hepatic immune responses, and disease resistance. A series of four isonitrogenous (33% crude protein) and isolipidic (6% crude lipid) diets were formulated to replace the isonitrogenous percentages of CSM or SBM by 6% or 12% CHFM. Quadruplicate groups of healthy and uniformly sized hybrid tilapia were assigned to each experimental diet. Fish were hand fed three times a day for 8 weeks at a rearing temperature of 25-28°C. The growth performance of hybrid tilapia fed diets with partial replacement of dietary SBM or CSM with CHFM was comparable to the group of fish fed the control diet. The CHFM-containing diets affected the intestinal autochthonous bacterial community in similar ways. All CHFM-containing diets stimulated the expression of heat shock protein 70 in the intestine but suppressed its expression in the liver. Only the CHFM6/SBM diet stimulated the expression of interleukin-1? in intestine, and no effects were observed in all diets to the expression of interleukin-1? in liver. Thus, regarding the immune response in the intestine and liver, CHFM is a good alternative protein source that induces less stress in the host. CHFM did not affect disease resistance to Aeromonas hydrophila infection in hybrid tilapia. These data suggest that CHFM is a good alternative to partially replace SBM and CSM in tilapia feed.
Related JoVE Video
A cross-sectional study of avian influenza in one district of guangzhou, 2013.
PLoS ONE
PUBLISHED: 01-01-2014
Show Abstract
Hide Abstract
Since Feb, 2013, more than 100 human beings had been infected with novel H7N9 avian influenza virus. As of May 2013, several H7N9 viruses had been found in retail live bird markets (LBMs) in Guangdong province of southern China where several human cases were confirmed later. However, the real avian influenza virus infection status especially H7N9 in Guangzhou remains unclear. Therefore, a cross-sectional study of avian influenza in commercial poultry farms, the wholesale LBM and retail LBMs in one district of Guangzhou was conducted from October to November, 2013. A total of 1505 cloacal and environmental samples from 52 commercial poultry farms, 1 wholesale LBM and 18 retail LBMs were collected and detected using real-time RT-PCR for type A, H7, H7N9 and H9 subtype avian influenza virus, respectively. Of all the flocks randomly sampled, 6 farms, 12 vendors of the wholesale LBM and 18 retail LBMs were type A avian influenza virus positive with 0, 3 and 11 positive for H9, respectively. The pooled prevalence and individual prevalence of type A avian influenza virus were 33.9% and 7.9% which for H9 subtype was 7.6% and 1.6%, respectively. None was H7 and H7N9 subtype virus positive. Different prevalence and prevalence ratio were found in different poultry species with partridges having the highest prevalence for both type A and H9 subtype avian influenza virus. Our results suggest that LBM may have a higher risk for sustaining and transmission of avian influenza virus than commercial poultry farms. The present study also indicates that different species may play different roles in the evolution and transmission of avian influenza virus. Therefore, risk-based surveillance and management measures should be conducted in future in this area.
Related JoVE Video
Changes of rabbit meniscus influenced by hyaline cartilage injury of osteoarthritis.
Int J Clin Exp Med
PUBLISHED: 01-01-2014
Show Abstract
Hide Abstract
Osteoarthritis (OA) is a common disease in the elderly population. Most of the previous OA-related researches focused on articular cartilage degeneration, osteophyte formation and synovitis etc. However, the role of the meniscus in these pathological changes has not been given enough attention. The goal of our study was to find the pathological changes of the meniscus in OA knee and determine their relationship.
Related JoVE Video
Cellular capacities for high-light acclimation and changing lipid profiles across life cycle stages of the green alga Haematococcus pluvialis.
PLoS ONE
PUBLISHED: 01-01-2014
Show Abstract
Hide Abstract
The unicellular microalga Haematococcus pluvialis has emerged as a promising biomass feedstock for the ketocarotenoid astaxanthin and neutral lipid triacylglycerol. Motile flagellates, resting palmella cells, and cysts are the major life cycle stages of H. pluvialis. Fast-growing motile cells are usually used to induce astaxanthin and triacylglycerol biosynthesis under stress conditions (high light or nutrient starvation); however, productivity of biomass and bioproducts are compromised due to the susceptibility of motile cells to stress. This study revealed that the Photosystem II (PSII) reaction center D1 protein, the manganese-stabilizing protein PsbO, and several major membrane glycerolipids (particularly for chloroplast membrane lipids monogalactosyldiacylglycerol and phosphatidylglycerol), decreased dramatically in motile cells under high light (HL). In contrast, palmella cells, which are transformed from motile cells after an extended period of time under favorable growth conditions, have developed multiple protective mechanisms--including reduction in chloroplast membrane lipids content, downplay of linear photosynthetic electron transport, and activating nonphotochemical quenching mechanisms--while accumulating triacylglycerol. Consequently, the membrane lipids and PSII proteins (D1 and PsbO) remained relatively stable in palmella cells subjected to HL. Introducing palmella instead of motile cells to stress conditions may greatly increase astaxanthin and lipid production in H. pluvialis culture.
Related JoVE Video
[Effects and mechanism of osthole on intestinal ischemia-reperfusion injury in mice].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 12-31-2013
Show Abstract
Hide Abstract
To explore the protective role of osthole in intestinal ischemia-reperfusion (I/R) injury in mice and examine its underlying mechanism.
Related JoVE Video
Variant rs1421085 in the FTO gene contribute childhood obesity in Chinese children aged 3-6 years.
Obes Res Clin Pract
PUBLISHED: 12-17-2013
Show Abstract
Hide Abstract
Summary: Objective: Childhood obesity has become a public health crisis worldwide due to an alarming increase in its prevalence. Numerous studies have demonstrated that the common variants (rs1421085 and rs17817449) of the fat mass and obesity associated (FTO) gene are associated with the obesity in adult and children in European. However, these two variants of FTO gene in childhood obesity have not been established in Chinese populations.Methods: In this population-based case-control study, 158 obese preschooler and 397 normal population controls aged 3-6 years were recruited between June 2007 and April 2008 from 6 kindergartens of Huai-an city in Jiangsu Province, China. All the children were conducted the body examinations and provided blood sample to detect the serum lipid levels and FTO rs1421085 T>C and rs17817449 T>G genetic variances.Results: In the association analysis between the FTO gene variant and risk of childhood obesity, compared with the rs1421085TT wide-type genotype, rs1421085 CC and CT/CC genotypes were associated with 59% and 71% increased risks of childhood obesity (adjusted OR = 1.59, 95%CI = 1.00-2.53 for CC; adjusted OR = 1.71, 95%CI = 1.10-2.65 for CT/CC), while the rs17817449 T > G variant was not associated with the significantly increased risk of childhood obesity. In addition, the higher level of serum TG (>0.64 mmol/l) was associated with 93% increased risk of childhood obesity (adjusted OR = 1.93, 95%CI = 1.30-2.87), and the higher serum HDL-C level (>1.14 mmol/l) was associated with 45% decreased risk of childhood obesity (adjusted OR = 0.55, 95%CI = 0.37-0.81). But the quantitative phenotypes analysis regarding the levels of TC, TG, HDL-C, and LDL-C were not found to be significantly associated with the variants of rs1421085 and rs17817449 both in the cases and controls.Conclusion: The FTO rs1421085 T>C polymorphism may modulate the magnitude of dyslipidemia in Chinese early-onset obesity.
Related JoVE Video
[Effects of an insertion/deletion polymorphism of angiotensin converting enzyme gene on the changes of serum lipid ratios and blood pressure induced by a high-carbohydrate and low-fat diet].
Sichuan Da Xue Xue Bao Yi Xue Ban
PUBLISHED: 12-12-2013
Show Abstract
Hide Abstract
To investigate the effects of an insertion/deletion (I/D) polymorphism at the intron 16 of the gene of angiotensin converting enzyme (ACE) on the changes of serum lipid ratios and blood pressure induced by a high-carbohydrate and low-fat (HC/LF) diet in healthy Chinese Han youth.
Related JoVE Video
[Evaluation of induction chemotherapy with vinorelbine plus cisplatin (NP) or docetaxel plus cisplatin (TP) combined with concurrent chemoradiotherapy for patients with locally advanced nasopharyngeal carcinoma].
Zhonghua Zhong Liu Za Zhi
PUBLISHED: 12-10-2013
Show Abstract
Hide Abstract
To compare the efficacy and side effects of induction chemotherapy with vinorelbine plus cisplatin (NP) or docetaxel plus cisplatin (TP) combined with concurrent chemoradiotherapy in treating locally advanced nasopharyngeal carcinoma (NPC).
Related JoVE Video
Kimuras disease or IgG4-related disease? A case-based review.
Clin. Rheumatol.
PUBLISHED: 12-07-2013
Show Abstract
Hide Abstract
Kimuras disease usually presents with benign painless soft tissue swelling around the head and neck areas with eosinophilia and high immunoglobulin E (IgE) levels. IgG4-related disease is characterized by fibrosis and sclerosis of the involved organs, with infiltration of IgG4-positive plasma cells. There are some similar clinical manifestations of these two diseases, with eosinophilia or high IgE levels often found in patients with IgG4-related disease. However, the relation between these two diseases is not well known. We report a 23-year-old man who had multiple neck lumps for longer than 1 year. He had remarkable eosinophilia and elevated serum IgE levels. Biopsy of his lymph nodes suggested the diagnosis of both Kimuras disease and IgG4-related disease. In this article, we discuss the relationship between Kimuras disease and IgG4-related disease. We also suggest a possible model ("allergen-specific immunotherapy") to illustrate our view that an increase in IgG4-positive plasma cells is an epiphenomenon of Kimuras disease.
Related JoVE Video
AISAIC: a software suite for accurate identification of significant aberrations in cancers.
Bioinformatics
PUBLISHED: 11-29-2013
Show Abstract
Hide Abstract
?Accurate identification of significant aberrations in cancers (AISAIC) is a systematic effort to discover potential cancer-driving genes such as oncogenes and tumor suppressors. Two major confounding factors against this goal are the normal cell contamination and random background aberrations in tumor samples. We describe a Java AISAIC package that provides comprehensive analytic functions and graphic user interface for integrating two statistically principled in silico approaches to address the aforementioned challenges in DNA copy number analyses. In addition, the package provides a command-line interface for users with scripting and programming needs to incorporate or extend AISAIC to their customized analysis pipelines. This open-source multiplatform software offers several attractive features: (i) it implements a user friendly complete pipeline from processing raw data to reporting analytic results; (ii) it detects deletion types directly from copy number signals using a Bayes hypothesis test; (iii) it estimates the fraction of normal contamination for each sample; (iv) it produces unbiased null distribution of random background alterations by iterative aberration-exclusive permutations; and (v) it identifies significant consensus regions and the percentage of homozygous/hemizygous deletions across multiple samples. AISAIC also provides users with a parallel computing option to leverage ubiquitous multicore machines.Availability and implementation:?AISAIC is available as a Java application, with a users guide and source code, at https://code.google.com/p/aisaic/.
Related JoVE Video

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.

How does it work?

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

Video X seems to be unrelated to Abstract Y...

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.