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Find video protocols related to scientific articles indexed in Pubmed.
Nanowire electrodes for high-density stimulation and measurement of neural circuits.
Front Neural Circuits
PUBLISHED: 02-24-2013
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Brain-machine interfaces (BMIs) that can precisely monitor and control neural activity will likely require new hardware with improved resolution and specificity. New nanofabricated electrodes with feature sizes and densities comparable to neural circuits may lead to such improvements. In this perspective, we review the recent development of vertical nanowire (NW) electrodes that could provide highly parallel single-cell recording and stimulation for future BMIs. We compare the advantages of these devices and discuss some of the technical challenges that must be overcome for this technology to become a platform for next-generation closed-loop BMIs.
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Direction-dependent optical modes in nanoscale silicon waveguides.
Opt Express
PUBLISHED: 09-22-2011
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We show that in high-index-contrast nanoscale waveguides counter propagating waves can posses distinct spatial near-field profiles. Using transmission-based near-field scanning optical microscopy (TraNSOM), we identify and map the unique near-field intensity distributions of these counter-propagating modes in a single-mode silicon waveguide. Based on this phenomenon, we design and simulate an integrated device 45 µm in length that selectively attenuates reflected light with an insertion loss of -3.6 dB and an extinction of greater than -20 dB.
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Systematic discovery of TLR signaling components delineates viral-sensing circuits.
Cell
PUBLISHED: 02-28-2011
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Deciphering the signaling networks that underlie normal and disease processes remains a major challenge. Here, we report the discovery of signaling components involved in the Toll-like receptor (TLR) response of immune dendritic cells (DCs), including a previously unkown pathway shared across mammalian antiviral responses. By combining transcriptional profiling, genetic and small-molecule perturbations, and phosphoproteomics, we uncover 35 signaling regulators, including 16 known regulators, involved in TLR signaling. In particular, we find that Polo-like kinases (Plk) 2 and 4 are essential components of antiviral pathways in vitro and in vivo and activate a signaling branch involving a dozen proteins, among which is Tnfaip2, a gene associated with autoimmune diseases but whose role was unknown. Our study illustrates the power of combining systematic measurements and perturbations to elucidate complex signaling circuits and discover potential therapeutic targets.
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Plasma free amino acid kinetics in rainbow trout (Oncorhynchus mykiss) using a bolus injection of 15N-labeled amino acids.
Amino Acids
PUBLISHED: 05-13-2010
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To gain insight into the metabolic design of the amino acid carrier systems in fish, we injected a bolus of (15)N amino acids into the dorsal aorta in mature rainbow trout (Oncorhynchus mykiss). The plasma kinetic parameters including concentration, pool size, rate of disappearance (R(d)), half-life and turnover rate were determined for 15 amino acids. When corrected for metabolic rate, the R(d) values obtained for trout for most amino acids were largely comparable to human values, with the exception of glutamine (which was lower) and threonine (which was higher). R(d) values ranged from 0.9 ?mol 100 g(-1) h(-1) (lysine) to 22.1 ?mol 100 g(-1) h(-1) (threonine) with most values falling between 2 and 6 ?mol 100 g(-1) h(-1). There was a significant correlation between R(d) and the molar proportion of amino acids in rainbow trout whole body protein hydrolysate. Other kinetic parameters did not correlate significantly with whole body amino acid composition. This indicates that an important design feature of the plasma-free amino acids system involves proportional delivery of amino acids to tissues for protein synthesis.
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Vertical silicon nanowires as a universal platform for delivering biomolecules into living cells.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 01-11-2010
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A generalized platform for introducing a diverse range of biomolecules into living cells in high-throughput could transform how complex cellular processes are probed and analyzed. Here, we demonstrate spatially localized, efficient, and universal delivery of biomolecules into immortalized and primary mammalian cells using surface-modified vertical silicon nanowires. The method relies on the ability of the silicon nanowires to penetrate a cells membrane and subsequently release surface-bound molecules directly into the cells cytosol, thus allowing highly efficient delivery of biomolecules without chemical modification or viral packaging. This modality enables one to assess the phenotypic consequences of introducing a broad range of biological effectors (DNAs, RNAs, peptides, proteins, and small molecules) into almost any cell type. We show that this platform can be used to guide neuronal progenitor growth with small molecules, knock down transcript levels by delivering siRNAs, inhibit apoptosis using peptides, and introduce targeted proteins to specific organelles. We further demonstrate codelivery of siRNAs and proteins on a single substrate in a microarray format, highlighting this technologys potential as a robust, monolithic platform for high-throughput, miniaturized bioassays.
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Silicon-waveguide-coupled high-Q chalcogenide microspheres.
Opt Express
PUBLISHED: 04-15-2009
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We fabricate high-Q arsenic triselenide glass microspheres through a three-step resistive heating process. We demonstrate quality factors greater than 2 x 10(6) at 1550 nm and achieve efficient coupling via a novel scheme utilizing index-engineered unclad silicon nanowires. We find that at powers above 1 mW the microspheres exhibit high thermal instability, which limits their application for resonator-enhanced nonlinear optical processes.
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Low loss etchless silicon photonic waveguides.
Opt Express
PUBLISHED: 03-19-2009
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We demonstrate low loss silicon waveguides fabricated without any silicon etching. We define the waveguides by selective oxidation which produces ultra-smooth sidewalls with width variations of 0.3 nm. The waveguides have a propagation loss of 0.3 dB/cm at 1.55 microm. The waveguide geometry enables low bending loss of approximately 0.007 dB/bend for a 90 degrees bend with a 50 microm bending radius.
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Optical nonreciprocity in optomechanical structures.
Phys. Rev. Lett.
PUBLISHED: 02-25-2009
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We demonstrate that optomechanical devices can exhibit nonreciprocal behavior when the dominant light-matter interaction takes place via a linear momentum exchange between light and the mechanical structure. As an example, we propose a microscale optomechanical device that can exhibit a nonreciprocal behavior in a microphotonic platform operating at room temperature. We show that, depending on the direction of the incident light, the device switches between a high and low transparency state with more than a 20 dB extinction ratio.
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Stretchable photonic crystal cavity with wide frequency tunability.
Nano Lett.
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We report a new approach for realizing a flexible photonic crystal (PC) cavity that enables wide-range tuning of its resonance frequency. Our PC cavity consists of a regular array of silicon nanowires embedded in a polydimethylsiloxane (PDMS) matrix and exhibits a cavity resonance in the telecommunication band that can be reversibly tuned over 60 nm via mechanical stretching-a record for two-dimensional (2D) PC structures. These mechanically reconfigurable devices could find potential applications in integrated photonics, sensing in biological systems, and smart materials.
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Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia.
Nano Lett.
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A circuit level understanding of immune cells and hematological cancers has been severely impeded by a lack of techniques that enable intracellular perturbation without significantly altering cell viability and function. Here, we demonstrate that vertical silicon nanowires (NWs) enable gene-specific manipulation of diverse murine and human immune cells with negligible toxicity. To illustrate the power of the technique, we then apply NW-mediated gene silencing to investigate the role of the Wnt signaling pathway in chronic lymphocytic leukemia (CLL). Remarkably, CLL-B cells from different patients exhibit tremendous heterogeneity in their response to the knockdown of a single gene, LEF1. This functional heterogeneity defines three distinct patient groups not discernible by conventional CLL cytogenetic markers and provides a prognostic indicator for patients time to first therapy. Analyses of gene expression signatures associated with these functional patient subgroups reveal unique insights into the underlying molecular basis for disease heterogeneity. Overall, our findings suggest a functional classification that can potentially guide the selection of patient-specific therapies in CLL and highlight the opportunities for nanotechnology to drive biological inquiry.
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Characterization of Cupriavidus metallidurans CYP116B1--a thiocarbamate herbicide oxygenating P450-phthalate dioxygenase reductase fusion protein.
FEBS J.
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The novel cytochrome P450/redox partner fusion enzyme CYP116B1 from Cupriavidus?metallidurans was expressed in and purified from Escherichia coli. Isolated CYP116B1 exhibited a characteristic Fe(II)CO complex with Soret maximum at 449 nm. EPR and resonance Raman analyses indicated low-spin, cysteinate-coordinated ferric haem iron at both 10 K and ambient temperature, respectively, for oxidized CYP116B1. The EPR of reduced CYP116B1 demonstrated stoichiometric binding of a 2Fe-2S cluster in the reductase domain. FMN binding in the reductase domain was confirmed by flavin fluorescence studies. Steady-state reduction of cytochrome c and ferricyanide were supported by both NADPH/NADH, with NADPH used more efficiently (K(m[NADPH]) = 0.9 ± 0.5 ?M and K(m[NADH]) = 399.1 ± 52.1 ?M). Stopped-flow studies of NAD(P)H-dependent electron transfer to the reductase confirmed the preference for NADPH. The reduction potential of the P450 haem iron was -301 ± 7 mV, with retention of haem thiolate ligation in the ferrous enzyme. Redox potentials for the 2Fe-2S and FMN cofactors were more positive than that of the haem iron. Multi-angle laser light scattering demonstrated CYP116B1 to be monomeric. Type I (substrate-like) binding of selected unsaturated fatty acids (myristoleic, palmitoleic and arachidonic acids) was shown, but these substrates were not oxidized by CYP116B1. However, CYP116B1 catalysed hydroxylation (on propyl chains) of the herbicides S-ethyl dipropylthiocarbamate (EPTC) and S-propyl dipropylthiocarbamate (vernolate), and the subsequent N-dealkylation of vernolate. CYP116B1 thus has similar thiocarbamate-oxidizing catalytic properties to Rhodoccocus erythropolis CYP116A1, a P450 involved in the oxidative degradation of EPTC.
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Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits.
Nat Nanotechnol
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Deciphering the neuronal code--the rules by which neuronal circuits store and process information--is a major scientific challenge. Currently, these efforts are impeded by a lack of experimental tools that are sensitive enough to quantify the strength of individual synaptic connections and also scalable enough to simultaneously measure and control a large number of mammalian neurons with single-cell resolution. Here, we report a scalable intracellular electrode platform based on vertical nanowires that allows parallel electrical interfacing to multiple mammalian neurons. Specifically, we show that our vertical nanowire electrode arrays can intracellularly record and stimulate neuronal activity in dissociated cultures of rat cortical neurons and can also be used to map multiple individual synaptic connections. The scalability of this platform, combined with its compatibility with silicon nanofabrication techniques, provides a clear path towards simultaneous, high-fidelity interfacing with hundreds of individual neurons.
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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.

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.