Probing biomolecular interaction forces using an anharmonic acoustic technique for selective detection of bacterial spores

Receptor-based detection of pathogens often suffers from non-specific interactions, and as most detection techniques cannot distinguish between affinities of interactions, false positive responses remain a plaguing reality. Here, we report an anharmonic acoustic based method of detection that addresses the inherent weakness of current ligand dependant assays. Spores of Bacillus subtilis (Bacillus anthracis simulant) were immobilized on a thickness-shear mode AT-cut quartz crystal functionalized with anti-spore antibody and the sensor was driven by a pure sinusoidal oscillation at increasing amplitude. Biomolecular interaction forces between the coupled spores and the accelerating surface caused a nonlinear modulation of the acoustic response of the crystal. In particular, the deviation in the third harmonic of the transduced electrical response versus oscillation amplitude of the sensor (signal) was found to be significant. Signals from the specifically-bound spores were clearly distinguishable in shape from those of the physisorbed streptavidin-coated polystyrene microbeads. The analytical model presented here enables estimation of the biomolecular interaction forces from the measured response. Thus, probing biomolecular interaction forces using the described technique can quantitatively detect pathogens and distinguish specific from non-specific interactions, with potential applicability to rapid point-of-care detection. This also serves as a potential tool for rapid force-spectroscopy, affinity-based biomolecular screening and mapping of molecular interaction networks. © 2011 Elsevier B.V.

Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication

Background: Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection. Results: Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process. Conclusion: How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experiencedsub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.

Photo-assisted hydrosilylation of silicon nanoparticles: Dependence of particle size on grafting chemistry

Silicon nanoparticles between 2.5 nm and 30 nm in diameter were functionalized by means of photoassisted hydrosilylation reactions in the aerosol phase with terminal alkenes of varying chain length. Using infrared spectroscopy and nuclear magnetic resonance, the chemical composition of the alkyl layer was determined for each combination of particle size and alkyl chain length. The spectroscopic techniques were used to determine that smaller particles functionalized with short chains in the aerosol phase tend to attach to the interior (β) alkenyl carbon atom, whereas particles >10 nm in diameter exhibit attachment primarily with the exterior (α) alkenyl carbon atom, regardless of chain length. © 2011 American Chemical Society.

Channel selective tunnelling through a nanographene assembly.

We report selective tunnelling through a nanographene intermolecular tunnel junction achieved via scanning tunnelling microscope tip functionalization with hexa-peri-hexabenzocoronene (HBC) molecules. This leads to an offset in the alignment between the energy levels of the tip and the molecular assembly, resulting in the imaging of a variety of distinct charge density patterns in the HBC assembly, not attainable using a bare metallic tip. Different tunnelling channels can be selected by the application of an electric field in the tunnelling junction, which changes the condition of the HBC on the tip. Density functional theory-based calculations relate the imaged HBC patterns to the calculated molecular orbitals at certain energy levels. These patterns bear a close resemblance to the π-orbital states of the HBC molecule calculated at the relevant energy levels, mainly below the Fermi energy of HBC. This correlation demonstrates the ability of an HBC functionalized tip as regards accessing an energy range that is restricted to the usual operating bias range around the Fermi energy with a normal metallic tip at room temperature. Apart from relating to molecular orbitals, some patterns could also be described in association with the Clar aromatic sextet formula. Our observations may help pave the way towards the possibility of controlling charge transport between organic interfaces.

Dispersion of carbon nanotubes: Mixing, sonication, stabilization, and composite properties

Advances in functionality and reliability of carbon nanotube (CNT) composite materials require careful formulation of processing methods to ultimately realize the desired properties. To date, controlled dispersion of CNTs in a solution or a composite matrix remains a challenge, due to the strong van der Waals binding energies associated with the CNT aggregates. There is also insufficiently defined correlation between the microstructure and the physical properties of the composite. Here, we offer a review of the dispersion processes of pristine (non-covalently functionalized) CNTs in a solvent or a polymer solution. We summarize and adapt relevant theoretical analysis to guide the dispersion design and selection, from the processes of mixing/sonication, to the application of surfactants for stabilization, to the final testing of composite properties. The same approaches are expected to be also applicable to the fabrication of other composite materials involving homogeneously dispersed nanoparticles. © 2012 by the authors; licensee MDPI, Basel, Switzerland.

Spectroscopic characteristics and cellular compatibility of protein wrapped single wall carbon nanotubes

Non-covalent functionalization of CoMoCAT single-wall carbon nanotubes (SWNTs) by bovine serum albumin (BSA) was achieved. Photoluminescence spectra for the functionalized nanotubes showed good dispersion by BSA functionalization. Raman spectra were taken for the sonicated SWNT-BSA solution to establish the signal versus concentration correlation. Cellular uptake of functionalized carbon nanotubes by mouse macrophage (RAW264.7) was then investigated using Raman spectroscopy. For a seeding density of 50% confluence in a culture solution containing 10 μg/ml of BSA-SWNTs, uptake of 200 μg/ml by the macrophages was recorded after 23hr incubation, indicating an active uptake of SWNTs. © 2012 IEEE.

Optimized vertical carbon nanotube forests for multiplex surface-enhanced raman scattering detection

The highly sensitive and molecule-specific technique of surface-enhanced Raman spectroscopy (SERS) generates high signal enhancements via localized optical fields on nanoscale metallic materials, which can be tuned by manipulation of the surface roughness and architecture on the submicrometer level. We investigate gold-functionalized vertically aligned carbon nanotube forests (VACNTs) as low-cost straightforward SERS nanoplatforms. We find that their SERS enhancements depend on their diameter and density, which are systematically optimized for their performance. Modeling of the VACNT-based SERS substrates confirms consistent dependence on structural parameters as observed experimentally. The created nanostructures span over large substrate areas, are readily configurable, and yield uniform and reproducible SERS enhancement factors. Further fabricated micropatterned VACNTs platforms are shown to deliver multiplexed SERS detection. The unique properties of CNTs, which can be synergistically utilized in VACNT-based substrates and patterned arrays, can thus provide new generation platforms for SERS detection. © 2012 American Chemical Society.

Hierarchical carbon nanowire microarchitectures made by plasma-assisted pyrolysis of photoresist

We present a new approach for the fabrication and integration of vertically aligned forests of amorphous carbon nanowires (CNWs), using only standard lithography, oxygen plasma treatment, and thermal processing. The simplicity and scalability of this process, as well as the hierarchical organization of CNWs, provides a potential alternative to the use of carbon nanotubes and graphene for applications in microsystems and high surface area materials. The CNWs are highly branched at the nanoscale, and novel hierarchical microstructures with CNWs connected to a solid amorphous core are made by controlling the plasma treatment time. By multilayer processing we demonstrate deterministic joining of CNW micropillars into 3D sensing networks. Finally we show that these networks can be chemically functionalized and used for measurement of DNA binding with increased sensitivity. © 2011 American Chemical Society.

Self-assembled multilayer graphene oxide membrane and carbon nanotubes synthesized using a rare form of natural graphite

The fabrication of flexible multilayer graphene oxide (GO) membrane and carbon nanotubes (CNTs) using a rare form of high-purity natural graphite, vein graphite, is reported for the first time. Graphite oxide is synthesized using vein graphite following Hummer's method. By facilitating functionalized graphene sheets in graphite oxide to self-assemble, a multilayer GO membrane is fabricated. Electric arc discharge is used to synthesis CNTs from vein graphite. Both multilayer GO membrane and CNTs are investigated using microscopy and spectroscopy experiments, i.e., scanning electron microscopy (SEM), atomic force microscopy (AFM), high-resolution transmission electron microscopy (HRTEM), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), thermogravimetric analysis (TGA), core level photoelectron spectroscopy, and C K-edge X-ray absorption spectroscopy (NEXAFS), to characterize their structural and topographical properties. Characterization of vein graphite using different techniques reveals that it has a large number of crystallites, hence the large number of graphene sheets per crystallite, preferentially oriented along the (002) plane. NEXAFS and core level spectra confirm that vein graphite is highly crystalline and pure. Fourier transform infrared (FT-IR) and C 1s core level spectra show that oxygen functionalities (-C-OH, -CO,-C-O-C-) are introduced into the basal plane of graphite following chemical oxidation. Carbon nanotubes are produced from vein graphite through arc discharge without the use of any catalyst. HRTEM confirm that multiwalled carbon nanotube (MWNTs) are produced with the presence of some structure in the central pipe. A small percentage of single-walled nanotubes (SWNTs) are also produced simultaneously with MWNTs. Spectroscopic and microscopic data are further discussed here with a view to using vein graphite as the source material for the synthesis of carbon nanomaterials. © 2013 American Chemical Society.

Spectroscopic characterization of protein-wrapped single-wall carbon nanotubes and quantification of their cellular uptake in multiple cell generations

We study the spectral characteristics of bovine serum albumin (BSA) protein conjugated single-wall carbon nanotubes (SWNTs), and quantify their uptake by macrophages. The binding of BSA onto the SWNT surface is found to change the protein structure and to increase the doping of the nanotubes. The G-band Raman intensity follows a well-defined power law for SWNT concentrations of up to 33 μg ml-1 in aqueous solutions. Subsequently, in vitro experiments demonstrate that incubation of BSA-SWNT complexes with macrophages affects neither the cellular growth nor the cellular viability over multiple cell generations. Using wide spot Raman spectroscopy as a fast, non-destructive method for statistical quantification, we observe that macrophages effectively uptake BSA-SWNT complexes, with the average number of nanotubes internalized per cell remaining relatively constant over consecutive cell generations. The number of internalized SWNTs is found to be ∼30 × 106 SWNTs/cell for a 60 mm-2 seeding density and ∼100 × 10 6 SWNTs/cell for a 200 mm-2 seeding density. Our results show that BSA-functionalized SWNTs are an efficient molecular transport system with low cytotoxicity maintained over multiple cell generations. © 2013 IOP Publishing Ltd.

Differentiated adipose-derived stem cells act synergistically with RGD-modified surfaces to improve neurite outgrowth in a co-culture model.

Peripheral nerve damage is a problem encountered after trauma and during surgery and the development of synthetic polymer conduits may offer a promising alternative to autografts. In order to improve the performance of the polymer to be used for nerve conduits, poly-ε-caprolactone (PCL) films were chemically functionalized with RGD moieties, using a chemical reaction previously developed. In vitro cultures of dissociated dorsal root ganglion (DRG) neurons provide a valid model to study different factors affecting axonal growth. In this work, DRG neurons were cultured on RGD-functionalized PCL films. Adult adipose-derived stem cells differentiated to Schwann cells (dASCs) were initially cultured on the functionalized PCL films, resulting in improved attachment and proliferation. dASCs were also co-cultured with DRG neurons on treated and untreated PCL to assess stimulation by dASCs on neurite outgrowth. Neuron response was generally poor on untreated PCL films, but long neurites were observed in the presence of dASCs or RGD moieties. A combination of the two factors enhanced even further neurite outgrowth, acting synergistically. Finally, in order to better understand the extracellular matrix (ECM)-cell interaction, a β1 integrin blocking experiment was carried out. Neurite outgrowth was not affected by the specific antibody blocking, showing that β1 integrin function can be compensated by other molecules present on the cell membrane. Copyright © 2013 John Wiley & Sons, Ltd.

Handbook of nanoindentation with biological applications

Nanoindentation is ideal for the characterization of inhomogeneous biological materials. However, the use of nanoindentation techniques in biological systems is associated with some distinctively different techniques and challenges. For example, engineering materials used in the microelectronics industry (e.g. ceramics and metals) for which the technique was developed, are relatively stiff and exhibit time-independent mechanical responses. Biological materials, on the other hand, exhibit time-dependent behavior, and can span a range of stiffness regimes from moduli of Pa to GPa - eight to nine orders of magnitude. As such, there are differences in the selection of instrumentation, tip geometry, and data analysis in comparison with the "black box" nanoindentation techniques as sold by commercial manufacturers. The use of scanning probe equipment (atomic force miscroscopy) is also common for small-scale indentation of soft materials in biology. The book is broadly divided into two parts. The first part presents the "basic science" of nanoindentation including the background of contact mechanics underlying indentation technique, and the instrumentation used to gather mechanical data. Both the mechanics background and the instrumentation overview provide perspectives that are optimized for biological applications, including discussions on hydrated materials and adaptations for low-stiffness materials. The second part of the book covers the applications of nanoindentation technique in biological materials. Included in the coverage are mineralized and nonmineralized tissues, wood and plant tissues, tissue-engineering substitute materials, cells and membranes, and cutting-edge applications at molecular level including the use of functionalized tips to probe specific molecular interactions (e.g. the ligand-receptor binding). The book concludes with a concise summary and an insightful forecast of the future highlighting the current challenges. © 2011 by Pan Stanford Publishing Pte. Ltd. All rights reserved.

Controlled amine functionality in self-assembled monolayers via the hidden amine route: chemical and electronic tunability.

A synthetic strategy for fabricating a dense amine functionalized self-assembled monolayer (SAM) on hydroxylated surfaces is presented. The assembly steps are monitored by X-ray photoelectron spectroscopy, Fourier transform infrared- attenuated total reflection, atomic force microscopy, variable angle spectroscopic ellipsometry, UV-vis surface spectroscopy, contact angle wettability, and contact potential difference measurements. The method applies alkylbromide-trichlorosilane for the fabrication of the SAM followed by surface transformation of the bromine moiety to amine by a two-step procedure: S(N)2 reaction that introduces the hidden amine, phthalimide, followed by the removal of the protecting group and exposing the free amine. The use of phthalimide moiety in the process enabled monitoring the substitution reaction rate on the surface (by absorption spectroscopy) and showed first-order kinetics. The simplicity of the process, nonharsh reagents, and short reaction time allow the use of such SAMs in molecular nanoelectronics applications, where complete control of the used SAM is needed. The different molecular dipole of each step of the process, which is verified by DFT calculations, supports the use of these SAMs as means to tune the electronic properties of semiconductors and for better synergism between SAMs and standard microelectronics processes and devices.

Low-cost PCB-integrated polymer waveguide sensor for gas detection

An optical waveguide sensor formed directly on low-cost PCB substrates is presented for the first time. The device integrates polymer waveguides functionalized with chemical dyes, photonic and electronic components and allows multiple-gas detection. © OSA/CLEO 2011.

Reusable, robust, and accurate laser-generated photonic nanosensor.

Developing noninvasive and accurate diagnostics that are easily manufactured, robust, and reusable will provide monitoring of high-risk individuals in any clinical or point-of-care environment. We have developed a clinically relevant optical glucose nanosensor that can be reused at least 400 times without a compromise in accuracy. The use of a single 6 ns laser (λ = 532 nm, 200 mJ) pulse rapidly produced off-axis Bragg diffraction gratings consisting of ordered silver nanoparticles embedded within a phenylboronic acid-functionalized hydrogel. This sensor exhibited reversible large wavelength shifts and diffracted the spectrum of narrow-band light over the wavelength range λpeak ≈ 510-1100 nm. The experimental sensitivity of the sensor permits diagnosis of glucosuria in the urine samples of diabetic patients with an improved performance compared to commercial high-throughput urinalysis devices. The sensor response was achieved within 5 min, reset to baseline in ∼10 s. It is anticipated that this sensing platform will have implications for the development of reusable, equipment-free colorimetric point-of-care diagnostic devices for diabetes screening.