Polymer nanocarrier system for endosome escape and timed release of siRNA with complete gene silencing and cell death in cancer cells

An influenza virus-inspired polymer mimic nanocarrier was used to deliver siRNA for specific and near complete gene knockdown of an osteoscarcom cell line (U-2SO). The polymer was synthesized by single-electron transfer living radical polymerization (SET-LRP) at room temperature to avoid complexities of transfer to monomer or polymer. It was the only LRP method that allowed good block copolymer formation with a narrow molecular weight distribution. At nitrogen to phosphorus (N/P) ratios of equal to or greater than 20 (greater than a polymer concentration of 13.8 μg/mL) with polo-like kinase 1 (PLK1) siRNA gave specific and near complete (>98%) cell death. The polymer further degrades to a benign polymer that showed no toxicity even at polymer concentrations of 200 μg/mL (or N/P ratio of 300), suggesting that our polymer nanocarrier can be used as a very effective siRNA delivery system and in a multiple dose administration. This work demonstrates that with a well-designed delivery device, siRNA can specifically kill cells without the inclusion of an additional clinically used highly toxic cochemotherapeutic agent. Our work also showed that this excellent delivery is sensitive for the study of off-target knockdown of siRNA.

On natures of sub-gap photoelectric and optical spectra in nitrogen-contaminated nanocrystalline diamond

Experimentally observed optical and photoelectrical spectra of nitrogen-contaminated (unintentionally doped) nano-crystalline CVD diamond films are simulated using semi-empirical adiabatic General Skettrup Model (GSM), which presumes dominant contributions of defect states from sp 3-coordinated intra-granular carbon atoms to intra-band single electron spectrum N(E) of the material. This picture disagrees with a common viewpoint that the N(E) spectrum of the gap states in diamond powders and polycrystalline CVD films mainly originates from π and π* bonds of sp2-coordinated carbon atoms, which are distributed nearly uniformly over outer surfaces and/or interfaces of the diamond grains. The GSM predicts as well strong effect of granular morphology on the density of intra-band defect states in polycrystalline diamonds.

Kinetic analysis of nitroxide radical coupling reactions mediated by CuBr

In a previous paper, we described the room temperature rapid, selective, reversible, and near quantitative Cu-activated nitroxide radical coupling (NRC) technique to prepare 3-arm polystyrene stars. In this work, we evaluated the Cu-activation mechanism, either conventional atom transfer or single electron transfer (SET), through kinetic simulations. Simulation data showed that one can describe the system by either activation mechanism. We also found through simulations that bimolecular radical termination, regardless of activation mechanism, was extremely low and could be considered negligible in an NRC reaction. Experiments were carried out to form 2- and 3-arm PSTY stars using two ligands, PMDETA and Me6TREN, in a range of solvent conditions by varying the ratio of DMSO to toluene, and over a wide temperature range. The rate of 2- or 3-arm star formation was governed by the choice of solvent and ligand. The combination of Me6TREN and toluene/DMSO showed a relatively temperature independent rate, and remarkably reached near quantitative yields for 2-arm star formation after only 1 min at 25 °C.

Ultrafast and reversible multiblock formation by the SET-Nitroxide radical coupling reaction

The single electron transfer-nitroxide radical coupling (SET-NRC) reaction has been used to produce multiblock polymers with high molecular weights in under 3 min at 50◦C by coupling a difunctional telechelic polystyrene (Br-PSTY-Br)with a dinitroxide. The well known combination of dimethyl sulfoxide as solvent and Me6TREN as ligand facilitated the in situ disproportionation of CuIBr to the highly active nascent Cu0 species. This SET reaction allowed polymeric radicals to be rapidly formed from their corresponding halide end-groups. Trapping of these carbon-centred radicals at close to diffusion controlled rates by dinitroxides resulted in high-molecular-weight multiblock polymers. Our results showed that the disproportionation of CuI was critical in obtaining these ultrafast reactions, and confirmed that activation was primarily through Cu0. We took advantage of the reversibility of the NRC reaction at elevated temperatures to decouple the multiblock back to the original PSTY building block through capping the chain-ends with mono-functional nitroxides. These alkoxyamine end-groups were further exchanged with an alkyne mono-functional nitroxide (TEMPO–≡) and ‘clicked’ by a CuI-catalyzed azide/alkyne cycloaddition (CuAAC) reaction with N3–PSTY–N3 to reform the multiblocks. This final ‘click’ reaction, even after the consecutive decoupling and nitroxide-exchange reactions, still produced high molecular-weight multiblocks efficiently. These SET-NRC reactions would have ideal applications in re-usable plastics and possibly as self-healing materials.

Controlled electronic transport in single-walled carbon nanotube networks : selecting electron hopping and chemical doping mechanisms

The electronic transport in both intrinsic and acid-treated single-walled carbon nanotube networks containing more than 90% semiconducting nanotubes is investigated using temperature-dependent resistance measurements. The semiconducting behavior observed in the intrinsic network is attributed to the three-dimensional electron hopping mechanism. In contrast, the chemical doping mechanism in the acid-treated network is found to be responsible for the revealed metal-like linear resistivity dependence in a broad temperature range. This effective method to control the electrical conductivity of single-walled carbon nanotube networks is promising for future nanoscale electronics, thermometry, and bolometry. © 2010 American Institute of Physics.

Nanoparticle manipulation in plasma-assisted nanofabrication of electron field emitters based on single crystalline carbon nanotip patterns

Nanoparticle manipulation by various plasma forces in near-substrate areas of the Integrated Plasma-Aided Nanofabrication Facility (IPANF) is investigated. In the IPANF, high-density plasmas of low-temperature rf glow discharges are sustained. The model near-substrate area includes a variable-length pre-sheath, where a negatively charged nanoparticle is accelerated, and a self-consistent collisionless sheath with a repulsive electrostatic potential. Conditions enabling the nanoparticle to overcome the repulsive barrier and deposit onto the substrate are investigated numerically and experimentally. Under certain conditions the momentum gained by the nanoparticle in the pre-sheath area appears to be sufficient for the driving ion drag force to outbalance the repulsive electrostatic and thermophoretic forces. Numerical results are applied for the explanation of size-selective nanoparticle deposition in the Ar+H2+CH4 plasma-assisted chemical vapor deposition of various carbon nanostructure patterns for electron field emitters and are cross-referenced by the field emission scanning electron microscopy. It is shown that the nanoparticles can be efficiently manipulated by the temperature gradient-controlled thermophoretic force. Experimentally, the temperature gradients in the near-substrate areas are measured in situ by means of the temperature gradient probe and related to the nanofilm fabrication conditions. The results are relevant to plasma-assisted synthesis of numerous nanofilms employing structural incorporation of the plasma-grown nanoparticles, including but not limited to nanofabrication of ordered single-crystalline carbon nanotip arrays for electron field emission applications.

Poly(3-hexyl-thiophene) coil-wrapped single wall carbon nanotube investigated by scanning tunneling spectroscopy

Scanning Tunneling Spectroscopy was performed on a (15,0) single wall carbon nanotube partially wrapped by Poly(3-hexyl-thiophene). On the bare nanotube section, the local density of states is in good agreement with the theoretical model based on local density approximation and remarkably is not perturbed by the polymer wrapping. On the coiled section, a rectifying current-voltage characteristic has been observed along with the charge transfer from the polymer to the nanotube. The electron transfer from Poly(3-hexyl-thiophene) to metallic nanotube was previously theoretically proposed and contributes to the presence of the Schottky barrier at the interface responsible for the rectifying behavior.

SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Single crystal Raman spectroscopy of selected arsenite, antimonite and hydroxyantimonate minerals

This thesis concentrates on the characterisation of selected arsenite, antimonite, and hydroxyantimonate minerals based on their vibrational spectra. A number of natural arsenite and antimonite minerals were studied by single crystal Raman spectroscopy in order to determine the contribution of bridging and terminal oxygen atoms to the vibrational spectra. A series of natural hydrated antimonate minerals was also compared and contrasted using single crystal Raman spectroscopy to determine the contribution of the isolated antimonate ion. The single crystal data allows each band in the spectrum to be assigned to a symmetry species. The contribution of bridging and terminal oxygen atoms in the case of the arsenite and antimonite minerals was determined by factor group analysis, the results of which are correlated with the observed symmetry species. In certain cases, synthetic analogues of a mineral and/or synthetic compounds isostructural or related to the mineral of interest were also prepared. These synthetic compounds are studied by non-oriented Raman spectroscopy to further aid band assignments of the minerals of interest. Other characterisation techniques include IR spectroscopy, SEM and XRD. From the single crystal data, it was found that good separation between different symmetry species is observed for the minerals studied.

Hydrothermal synthesis of single crystallin strontium titanate nanocubes

Strontium titanate nanocubes with an average edge length of 150mm have been successfully synthesized from a simple hydrothermal system. Characterization techniques such as X-ray powder diffraction analysis, scanning electron microscopy and energy-dispersive analysis of X-rays were used to investigate the products. The results showed that as-prepared powders are pure SrTiO3 with cubic shape, which consists with the growth habit of its intrinsic crystal structure. These uniform nanocubes with high crystallinity will exhibit superior physical properties in the practical applications. Furthermore, during the experimental process, it has been found that the dilute acid washing process is very important to obtain high pure SrTiO3.

Automatic particle picking of biological molecules imaged by electron microscopy

One of the next great challenges of cell biology is the determination of the enormous number of protein structures encoded in genomes. In recent years, advances in electron cryo-microscopy and high-resolution single particle analysis have developed to the point where they now provide a methodology for high resolution structure determination. Using this approach, images of randomly oriented single particles are aligned computationally to reconstruct 3-D structures of proteins and even whole viruses. One of the limiting factors in obtaining high-resolution reconstructions is obtaining a large enough representative dataset ($>100,000$ particles). Traditionally particles have been manually picked which is an extremely labour intensive process. The problem is made especially difficult by the low signal-to-noise ratio of the images. This paper describes the development of automatic particle picking software, which has been tested with both negatively stained and cryo-electron micrographs. This algorithm has been shown to be capable of selecting most of the particles, with few false positives. Further work will involve extending the software to detect differently shaped and oriented particles.

An investigation into factors affecting electron density calibration for a megavoltage cone-beam CT system

There is a growing interest in the use of megavoltage cone-beam computed tomography (MV CBCT) data for radiotherapy treatment planning. To calculate accurate dose distributions, knowledge of the electron density (ED) of the tissues being irradiated is required. In the case of MV CBCT, it is necessary to determine a calibration-relating CT number to ED, utilizing the photon beam produced for MV CBCT. A number of different parameters can affect this calibration. This study was undertaken on the Siemens MV CBCT system, MVision, to evaluate the effect of the following parameters on the reconstructed CT pixel value to ED calibration: the number of monitor units (MUs) used (5, 8, 15 and 60 MUs), the image reconstruction filter (head and neck, and pelvis), reconstruction matrix size (256 by 256 and 512 by 512), and the addition of extra solid water surrounding the ED phantom. A Gammex electron density CT phantom containing EDs from 0.292 to 1.707 was imaged under each of these conditions. The linear relationship between MV CBCT pixel value and ED was demonstrated for all MU settings and over the range of EDs. Changes in MU number did not dramatically alter the MV CBCT ED calibration. The use of different reconstruction filters was found to affect the MV CBCT ED calibration, as was the addition of solid water surrounding the phantom. Dose distributions from treatment plans calculated with simulated image data from a 15 MU head and neck reconstruction filter MV CBCT image and a MV CBCT ED calibration curve from the image data parameters and a 15 MU pelvis reconstruction filter showed small and clinically insignificant differences. Thus, the use of a single MV CBCT ED calibration curve is unlikely to result in any clinical differences. However, to ensure minimal uncertainties in dose reporting, MV CBCT ED calibration measurements could be carried out using parameter-specific calibration measurements.

Electron petrography of fine-grained matrix in the Karoonda C4 carbonaceous chondrite

The study of matrices of rare Type 4 carbonaceous chondrites can reveal important information on parent body rnetamorp~ic processes and provide a comparison with processes on parent bodies of ordinary chc-idrites. Reflectance spectra (Tholen, 1984) from the two largest asteroids in the asteroid belt, Ceres and Pallas, suggest that they may be metamorphosed carbonaceous chondrites. These two asteroids constitute - onethird of the mass in the asteroid belt implying that type 4-6 carbonaceous chondrites are poorly represented in the meteorite collection and may be of considerable importance. The matrix of the C4 chondrite Karoonda has been investigated using a JEOL 2000FX analytical electron microscope (AEM) with an attached Tracor-Northem TN5500 energy dispersive spectrometer (EDS). In previous studies (Scott and Taylor, 1985; Fitzgerald, 1979; Van Schmus, 1969), the petrography of the Karoonda matrix has been described as consisting largely of coarse-grained (50-200 urn in size) olivine and plagioclase (20-100 um in size), associated with micrometer sized magnetite and rare sulphides. AEM observations on matrix show that in addition to these large grains, there is a significant fraction (10 vol%) of interstitial fine grained phases « 5 urn). The mineralogy of these fine-grained phases differs in some respects from that of the coarser-grained matrix identified by optical and SEM techniques (Scott and Taylor, 1985; Fitzgerald, 1979; Van Schmus, 1969). I~ particular crystals of two compositionally distinct pyroxenes « 2 urn in size) have been identified which have not been previously observed in Karoonda by other analytical techniques. Thin film microanalyses (Mackinnon et al., 1986) of these two pyroxenes indicate compositions consistent with augite and low-Ca pyroxene (- Fs27). Fine-grained anhedral olivine « 2 urn size) is the most abundant phase with composition -Fa29' This composition is essentially indistinguishable from that determined for coarser-grained matrix olivines using an electron microprobe (Scott and Taylor, 1985; Fitzgerald, 1979; Van Schmus, 1969). All olivines are associated with subhedral magnetites « 1 urn size) which contain significant Cr (- 2%) and Al (- 1%) as was also noted for larger sized Karoonda magnetites by Delaney et al. (1985). It has recently been suggested (Burgess et al., 1987) on the basis of sulphur release profiles for S-isotope analyses of Karoonda that CaS04 (anhydrite) may be present. However, no sulphate phase has, as yet, been identified in the matrix of Karoonda. Low magnification contrast images suggest that Karoonda may have a significant porosity within the fine-grained matrix fraction. Most crystals are anhedral and do not show evidence for significant compaction. Individual grains often show single point contact with other grains which result in abundant intergranular voids. These voids frequently contain epoxy which was used as part of the specimen preparation procedure due to the friable nature of the bulk sample.

Structural dissection of Ebola virus and its assembly determinants using cryo-electron tomography

Ebola virus is a highly pathogenic filovirus causing severe hemorrhagic fever with high mortality rates. It assembles heterogenous, filamentous, enveloped virus particles containing a negative-sense, single-stranded RNA genome packaged within a helical nucleocapsid (NC). We have used cryo-electron microscopy and tomography to visualize Ebola virus particles, as well as Ebola virus-like particles, in three dimensions in a near-native state. The NC within the virion forms a left-handed helix with an inner nucleoprotein layer decorated with protruding arms composed of VP24 and VP35. A comparison with the closely related Marburg virus shows that the N-terminal region of nucleoprotein defines the inner diameter of the Ebola virus NC, whereas the RNA genome defines its length. Binding of the nucleoprotein to RNA can assemble a loosely coiled NC-like structure; the loose coil can be condensed by binding of the viral matrix protein VP40 to the C terminus of the nucleoprotein, and rigidified by binding of VP24 and VP35 to alternate copies of the nucleoprotein. Four proteins (NP, VP24, VP35, and VP40) are necessary and sufficient to mediate assembly of an NC with structure, symmetry, variability, and flexibility indistinguishable from that in Ebola virus particles released from infected cells. Together these data provide a structural and architectural description of Ebola virus and define the roles of viral proteins in its structure and assembly

Cryo-electron tomography of Marburg Virus particles and their morphogenesis within infected cells

Several major human pathogens, including the filoviruses, paramyxoviruses, and rhabdoviruses, package their single-stranded RNA genomes within helical nucleocapsids, which bud through the plasma membrane of the infected cell to release enveloped virions. The virions are often heterogeneous in shape, which makes it difficult to study their structure and assembly mechanisms. We have applied cryo-electron tomography and sub-tomogram averaging methods to derive structures of Marburg virus, a highly pathogenic filovirus, both after release and during assembly within infected cells. The data demonstrate the potential of cryo-electron tomography methods to derive detailed structural information for intermediate steps in biological pathways within intact cells. We describe the location and arrangement of the viral proteins within the virion. We show that the N-terminal domain of the nucleoprotein contains the minimal assembly determinants for a helical nucleocapsid with variable number of proteins per turn. Lobes protruding from alternate interfaces between each nucleoprotein are formed by the C-terminal domain of the nucleoprotein, together with viral proteins VP24 and VP35. Each nucleoprotein packages six RNA bases. The nucleocapsid interacts in an unusual, flexible "Velcro-like" manner with the viral matrix protein VP40. Determination of the structures of assembly intermediates showed that the nucleocapsid has a defined orientation during transport and budding. Together the data show striking architectural homology between the nucleocapsid helix of rhabdoviruses and filoviruses, but unexpected, fundamental differences in the mechanisms by which the nucleocapsids are then assembled together with matrix proteins and initiate membrane envelopment to release infectious virions, suggesting that the viruses have evolved different solutions to these conserved assembly steps.