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Find video protocols related to scientific articles indexed in Pubmed.
Pulsed transfer etching of PS-PDMS block copolymers self-assembled in 193 nm lithography stacks.
ACS Appl Mater Interfaces
PUBLISHED: 09-04-2014
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This work presents the graphoepitaxy of high-? block copolymers (BCP) in standard industry-like lithography stacks and their transfer into the silicon substrate The process includes conventional 193 nm photolithography, directed self-assembly of polystyrene-block-polydimethylsiloxane (PS-b-PDMS) and pulsed plasma etching to transfer the obtained features into the substrate. PS-b-PDMS has a high Flory-Huggins interaction parameter (high-?) and is capable of achieving sub-10 nm feature sizes. The photolithography stack is fabricated on 300 mm diameter silicon wafers and is composed of three layers: spin-on-carbon (SoC), silicon-containing anti-reflective coating (SiARC) and 193 nm photolithography resist. Sixty-nanometer-deep trenches are first patterned by plasma etching in the SiARC/SoC stack using the resist mask. The PS-b-PDMS is then spread on the substrate surface. Directed self-assembly (DSA) of the BCP is induced by a solvent vapor annealing process and PDMS cylinders parallel to the substrate surface are obtained. The surface chemistry based on SoC permits an efficient etching process into the underlying silicon substrate. The etching process is performed under dedicated pulsed plasma etching conditions. Fifteen nanometer half-pitch dense line/space features are obtained with a height up to 90 nm.
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Viability and gene expression responses to polymeric nanoparticles in human and rat cells.
Cell Biol. Toxicol.
PUBLISHED: 04-01-2014
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Applications of polymeric nanoparticles (NP) in medical fields are rapidly expanding. However, the influence of polymeric NP on cell growth and functions is widely underestimated. Therefore, we have studied cell and polymeric NP interactions by addressing two cell types with two endpoints (viability and gene expressions). Rat NR8383 and human THP-1 monocytic cell lines were exposed to 6 to 200 ?g/mL of Eudragit(®) RL NP for 24 h, and cellular viability was estimated using MTT, WST-1, and trypan blue tests. A decrease of viability was observed with NR8383 cells (down to 70% for 200 ?g/mL), and on the contrary, an increase with THP-1 cells (up to 140% for 200 ?g/mL). Differential expression of genes involved in oxidative damage (NCF1), inflammation (NFKB, TNFA, IL6, IL1B), autophagy (ATG16L), and apoptotic balance (PDCD4, BCL2, CASP8) was analyzed. ATG16L, BCL2, and TNFA were up-regulated in NR8383 cells, which are consistent with an induction of autophagy and inflammation. On the other hand, NCF1, NFKB, and IL1B were down-regulated in THP-1 cells, which may contribute to explain the increase of cellular viability. Our results show that (1) the toxic potency of NP is dependent on the cellular model used and (2) mechanistic toxicology should be the corner stone for the evaluation of NP hazard.
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Unique growth pattern of human mammary epithelial cells induced by polymeric nanoparticles.
Physiol Rep
PUBLISHED: 04-22-2013
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Due to their unique properties, engineered nanoparticles (NPs) have found broad use in industry, technology, and medicine, including as a vehicle for drug delivery. However, the understanding of NPs interaction with different types of mammalian cells lags significantly behind their increasing adoption in drug delivery. In this study, we show unique responses of human epithelial breast cells when exposed to polymeric Eudragit® RS NPs (ENPs) for 1-3 days. Cells displayed dose-dependent increases in metabolic activity and growth, but lower proliferation rates, than control cells, as evidenced in tetrazolium salt (WST-1) and 5-bromo-2-deoxyuridine (BrdU) assays, respectively. Those effects did not affect cell death or mitochondrial fragmentation. We attribute the increase in metabolic activity and growth of cells culture with ENPs to three factors: (1) high affinity of proteins present in the serum for ENPs, (2) adhesion of ENPs to cells, and (3) activation of proliferation and growth pathways. The proteins and genes responsible for stimulating cell adhesion and growth were identified by mass spectrometry and Microarray analyses. We demonstrate a novel property of ENPs, which act to increase cell metabolic activity and growth and organize epithelial cells in the epithelium as determined by Microarray analysis.
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p-Sulfonato-calix[n]arenes inhibit staphylococcal bicomponent leukotoxins by supramolecular interactions.
Biochem. J.
PUBLISHED: 01-04-2013
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PVL (Panton-Valentine leukocidin) and other Staphylococcus aureus ?-stranded pore-forming toxins are important virulence factors involved in various pathologies that are often necrotizing. The present study characterized leukotoxin inhibition by selected SCns (p-sulfonato-calix[n]arenes): SC4, SC6 and SC8. These chemicals have no toxic effects on human erythrocytes or neutrophils, and some are able to inhibit both the activity of and the cell lysis by leukotoxins in a dose-dependent manner. Depending on the type of leukotoxins and SCns, flow cytometry revealed IC50 values of 6-22 ?M for Ca2+ activation and of 2-50 ?M for cell lysis. SCns were observed to affect membrane binding of class S proteins responsible for cell specificity. Electrospray MS and surface plasmon resonance established supramolecular interactions (1:1 stoichiometry) between SCns and class S proteins in solution, but not class F proteins. The membrane-binding affinity of S proteins was Kd=0.07-6.2 nM. The binding ability was completely abolished by SCns at different concentrations according to the number of benzenes (30-300 ?M; SC8>SC6?SC4). The inhibitory properties of SCns were also observed in vivo in a rabbit model of PVL-induced endophthalmitis. These calixarenes may represent new therapeutic avenues aimed at minimizing inflammatory reactions and necrosis due to certain virulence factors.
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The hedgehog receptor patched is involved in cholesterol transport.
PLoS ONE
PUBLISHED: 04-08-2011
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Sonic hedgehog (Shh) signaling plays a crucial role in growth and patterning during embryonic development, and also in stem cell maintenance and tissue regeneration in adults. Aberrant Shh pathway activation is involved in the development of many tumors, and one of the most affected Shh signaling steps found in these tumors is the regulation of the signaling receptor Smoothened by the Shh receptor Patched. In the present work, we investigated Patched activity and the mechanism by which Patched inhibits Smoothened.
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Stability study of the human G-protein coupled receptor, Smoothened.
Biochim. Biophys. Acta
PUBLISHED: 02-10-2010
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Smoothened is a member of the G-protein coupled receptor (GPCR) family responsible for the transduction of the Hedgehog signal to the intracellular effectors of the Hedgehog signaling pathway. Aberrant regulation of this receptor is implicated in many cancers but also in neurodegenerative disorders. Despite the pharmacological relevance of this receptor, very little is known about its functional mechanism and its physiological ligand. In order to characterize this receptor for basic and pharmacological interests, we developed the expression of human Smoothened in the yeast Saccharomyces cerevisiae and Smoothened was then purified. Using Surface Plasmon Resonance technology, we showed that human Smoothened was in a native conformational state and able to interact with its antagonist, the cyclopamine, both at the yeast plasma membrane and after purification. Thermostability assays on purified human Smoothened showed that this GPCR is relatively stable in the classical detergent dodecyl-beta-d-maltoside (DDM). The fluorinated surfactant C(8)F(17)TAC, which has been proposed to be less aggressive towards membrane proteins than classical detergents, increased Smoothened thermostability in solution. Moreover, the replacement of a glycine by an arginine in the third intracellular loop of Smoothened coupled to the use of the fluorinated surfactant C(8)F(17)TAC during the mutant purification increased Smoothened thermostability even more. These data will be very useful for future crystallization assays and structural characterization of the human receptor Smoothened.
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Heterologous expression of human membrane receptors in the yeast Saccharomyces cerevisiae.
Methods Mol. Biol.
PUBLISHED: 01-26-2010
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Due to their implication in numerous diseases like cancer, cystic fibrosis, epilepsy, hyperinsulinism, heart failure, hypertension, and Alzheimer disease, membrane proteins (MPs) represent around 50% of drug targets. However, only 204 crystal structures of MPs have been solved. Structural analysis requires large quantities of pure and active proteins. The majority of medically and pharmaceutically relevant MPs are present in tissues at low concentration, which makes heterologous expression in large-scale production-adapted cells a prerequisite for structural studies. The yeast Saccharomyces cerevisiae is a convenient host for the production of mammalian MPs for functional and structural studies. Like bacteria, they are straightforward to manipulate genetically, are well characterized, can be easily cultured, and can be grown inexpensively in large quantities. The advantage of yeast compared to bacteria is that they have protein-processing and posttranslational modification mechanisms related to those found in mammalian cells. The recombinant rabbit muscle Ca(2+)-ATPase (adenosine triphosphatase), the first heterologously expressed mammalian MP for which the crystal structure was resolved, has been produced in S. cerevisiae. In this chapter, the focus is on expression of recombinant human integral MPs in a functional state at the plasma membrane of the yeast S. cerevisiae. Optimization of yeast culture and of MP preparations is detailed for two human receptors of the Hedgehog pathway: Patched and Smoothened.
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The time-course of visual categorizations: you spot the animal faster than the bird.
PLoS ONE
PUBLISHED: 04-15-2009
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Since the pioneering study by Rosch and colleagues in the 70s, it is commonly agreed that basic level perceptual categories (dog, chair...) are accessed faster than superordinate ones (animal, furniture...). Nevertheless, the speed at which objects presented in natural images can be processed in a rapid go/no-go visual superordinate categorization task has challenged this "basic level advantage".
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Rapid visual categorization of natural scene contexts with equalized amplitude spectrum and increasing phase noise.
J Vis
PUBLISHED: 03-11-2009
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This study aimed to determine the extent to which rapid visual context categorization relies on global scene statistics, such as diagnostic amplitude spectrum information. We measured performance in a Natural vs. Man-made context categorization task using a set of achromatic photographs of natural scenes equalized in average luminance, global contrast, and spectral energy. Results suggest that the visual system might use amplitude spectrum characteristics of the scenes to speed up context categorization processes. In a second experiment, we measured performance impairments with a parametric degradation of phase information applied to power spectrum averaged scenes. Results showed that performance accuracy was virtually unaffected up to 50% of phase blurring, but then rapidly fell to chance level following a sharp sigmoid curve. Response time analysis showed that subjects tended to make their fastest responses based on the presence of diagnostic man-made information; if no man-made characteristics enable to reach rapidly a decision threshold, because of a natural scene display or a high level of noise, the alternative decision for a natural response became increasingly favored. This two-phase strategy could maximize categorization performance if the diagnostic features of man-made environments tolerate higher levels of noise than natural features, as proposed recently.
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Functional studies of membrane-bound and purified human Hedgehog receptor Patched expressed in yeast.
Biochim. Biophys. Acta
PUBLISHED: 01-27-2009
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The Sonic Hedgehog (Shh) signalling pathway plays an important role both in embryonic development and in adult stem cell function. Inappropriate regulation of this pathway is often due to dysfunction between two membrane receptors Patched (Ptc) and Smoothened (Smo), which lead to birth defects, cancer or neurodegenerative diseases. However, little is known about Ptc, the receptor of the Shh protein, and the way Ptc regulates Smo, the receptor responsible for the transduction of the signal. To develop structure-function studies of these receptors, we expressed human Ptc (hPtc) in the yeast Saccharomyces cerevisiae. We demonstrated that hPtc expressed in a yeast membrane fraction is able to interact with its purified ligand Shh, indicating that hPtc is produced in yeast in its native conformational state. Using Surface Plasmon Resonance technology, we showed that fluorinated surfactants preserve the ability of hPtc to interact with its ligand after purification. This is the first report on the heterologous expression and the purification of a native and stable conformation of the human receptor Ptc. This work will allow the scale-up of hPtc production enabling its biochemical characterization, allowing the development of new therapeutic approaches against diseases induced by Shh signalling dysfunction.
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Animal detection precedes access to scene category.
PLoS ONE
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The processes underlying object recognition are fundamental for the understanding of visual perception. Humans can recognize many objects rapidly even in complex scenes, a task that still presents major challenges for computer vision systems. A common experimental demonstration of this ability is the rapid animal detection protocol, where human participants earliest responses to report the presence/absence of animals in natural scenes are observed at 250-270 ms latencies. One of the hypotheses to account for such speed is that people would not actually recognize an animal per se, but rather base their decision on global scene statistics. These global statistics (also referred to as spatial envelope or gist) have been shown to be computationally easy to process and could thus be used as a proxy for coarse object recognition. Here, using a saccadic choice task, which allows us to investigate a previously inaccessible temporal window of visual processing, we showed that animal - but not vehicle - detection clearly precedes scene categorization. This asynchrony is in addition validated by a late contextual modulation of animal detection, starting simultaneously with the availability of scene category. Interestingly, the advantage for animal over scene categorization is in opposition to the results of simulations using standard computational models. Taken together, these results challenge the idea that rapid animal detection might be based on early access of global scene statistics, and rather suggests a process based on the extraction of specific local complex features that might be hardwired in the visual system.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.