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

Thin-film elemental analyses for precise characterization of minerals

The Analytical Electron Microscope (AEM), with which secondary X-ray emission from a thin (<150nm), electron-transparent material is measured, has rapidly become a versatile instrument for qualitative and quantitative elemental analyses of many materials, including minerals. With due regard for sources of error in experimental procedures, it is possible to obtain high spatial resolution (~20nm diameter) and precise elemental analyses (~3% to 5% relative) from many silicate minerals. In addition, by utilizing the orientational dependence of X-ray emission for certain multi-substituted crystal structures, site occupancies for individual elements within a unit cell can be determined though with lower spatial resolution. The relative ease with which many of these compositional data may be obtained depends in part on the nature of the sample, but, in general, is comparable to other solid state analytical techniques such as X-ray diffraction and electron microprobe analysis. However, the improvement in spatial resolution obtained with the AEM (up to two orders of magnitude in analysis diameter) significantly enhances interpretation of fine-grained assemblages in many terrestrial or extraterrestrial rocks.

Targeted flight opportunities with large area collectors

A major factor in the stratospheric collection process is the relative density of particles at the collection altitude. With current aircraft-borne collector plate geometries, one potential extraterrestrial particle of about 10 micron diameter is collected approximately every hour. However, a new design for the collector plate, termed the Large Area Collector (LAC), allows a factor of 10 improvement in collection efficiency over current conventional geometry. The implementation of LAC design on future stratospheric collection flights will provide many opportunities for additional data on both terrestrial and extraterrestrial phenomena. With the improvement in collection efficiency, LAC's may provide a suitable number of potential extraterrestrial particles in one short flight of between 4 and 8 hours duration. Alternatively, total collection periods of approximately 40 hours enhance the probability that rare particles can be retrieved from the stratosphere. This latter approach is of great value for the cosmochemist who may wish to perform sophisticated analyses on interplanetary dust greater than a picogram. The former approach, involving short duration flights, may also provide invaluable data on the source of many extraterrestrial particles. The time dependence of particle entry to the collection altitude is an important parameter which may be correlated with specific global events (e.g., meteoroid streams) provided the collection time is known to an accuracy of 2 hours.

Expander graph based key distribution mechanisms in wireless sensor networks

Secure communications between large number of sensor nodes that are randomly scattered over a hostile territory, necessitate efficient key distribution schemes. However, due to limited resources at sensor nodes such schemes cannot be based on post deployment computations. Instead, pairwise (symmetric) keys are required to be pre-distributed by assigning a list of keys, (a.k.a. key-chain), to each sensor node. If a pair of nodes does not have a common key after deployment then they must find a key-path with secured links. The objective is to minimize the keychain size while (i) maximizing pairwise key sharing probability and resilience, and (ii) minimizing average key-path length. This paper presents a deterministic key distribution scheme based on Expander Graphs. It shows how to map the parameters (e.g., degree, expansion, and diameter) of a Ramanujan Expander Graph to the desired properties of a key distribution scheme for a physical network topology.

Transmission X-ray microscopy : a new tool in clay mineral floccules characterization

Effective flocculation and dewatering of mineral processing streams containing clays are microstructure dependent in clay-water systems. Initial clay flocculation is crucial in the design and for the development of a new methodology of gas exploitation. Microstructural engineering of clay aggregates using covalent cations and Keggin macromolecules have been monitored using the new state of the art Transmission X-ray Microscope (TXM) with 60 nm tomography resolution installed in a Taiwanese synchrotron. The 3-D reconstructions from TXM images show complex aggregation structures in montmorillonite aqueous suspensions after treatment with Na+, Ca2+ and Al13 Keggin macromolecules. Na-montmorillonite displays elongated, parallel, well-orientated and closed-void cellular networks, 0.5–3 μm in diameter. After treatment by covalent cations, the coagulated structure displays much smaller, randomly orientated and openly connected cells, 300–600 nm in diameter. The average distances measured between montmorillonite sheets was around 450 nm, which is less than half of the cell dimension measured in Na-montmorillonite. The most dramatic structural changes were observed after treatment by Al13 Keggin; aggregates then became arranged in compacted domains of a 300 nm average diameter composed of thick face-to-face oriented sheets, which forms porous aggregates with larger intra-aggregate open and connected voids.

Near infrared (NIR) absorption spectra correlates with subchondral bone micro-CT parameters in osteoarthritic rat models

Determining the properties and integrity of subchondral bone in the developmental stages of osteoarthritis, especially in a form that can facilitate real-time characterization for diagnostic and decision-making purposes, is still a matter for research and development. This paper presents relationships between near infrared absorption spectra and properties of subchondral bone obtained from 3 models of osteoarthritic degeneration induced in laboratory rats via: (i) menisectomy (MSX); (ii) anterior cruciate ligament transaction (ACL); and (iii) intra-articular injection of mono-ido-acetate (1 mg) (MIA), in the right knee joint, with 12 rats per model group (N = 36). After 8 weeks, the animals were sacrificed and knee joints were collected. A custom-made diffuse reflectance NIR probe of diameter 5 mm was placed on the tibial surface and spectral data were acquired from each specimen in the wavenumber range 4000–12 500 cm− 1. After spectral acquisition, micro computed tomography (micro-CT) was performed on the samples and subchondral bone parameters namely: bone volume (BV) and bone mineral density (BMD) were extracted from the micro-CT data. Statistical correlation was then conducted between these parameters and regions of the near infrared spectra using multivariate techniques including principal component analysis (PCA), discriminant analysis (DA), and partial least squares (PLS) regression. Statistically significant linear correlations were found between the near infrared absorption spectra and subchondral bone BMD (R2 = 98.84%) and BV (R2 = 97.87%). In conclusion, near infrared spectroscopic probing can be used to detect, qualify and quantify changes in the composition of the subchondral bone, and could potentially assist in distinguishing healthy from OA bone as demonstrated with our laboratory rat models.

Assessment of neuroretinal function in a group of functional amblyopes with documented LGN deficits

Purpose In this study we examine neuroretinal function in five amblyopes, who had been shown in previous functional MRI (fMRI) studies to have compromised function of the lateral geniculate nucleus (LGN), to determine if the fMRI deficit in amblyopia may have its origin at the retinal level. Methods We used slow flash multifocal ERG (mfERG) and compared averaged five ring responses of the amblyopic and fellow eyes across a 35 deg field. Central responses were also assessed over a field which was about 6.3 deg in diameter. We measured central retinal thickness using optical coherence tomography. Central fields were measured using the MP1-Microperimeter which also assesses ocular fixation during perimetry. MfERG data were compared with fMRI results from a previous study. Results Amblyopic eyes had reduced response density amplitudes (first major negative to first positive (N1-P1) responses) for the central and paracentral retina (up to 18 deg diameter) but not for the mid-periphery (from 18 to 35 deg). Retinal thickness was within normal limits for all eyes, and not different between amblyopic and fellow eyes. Fixation was maintained within the central 4° more than 80% of the time by four of the five participants; fixation assessed using bivariate contour ellipse areas (BCEA) gave rankings similar to those of the MP-1 system. There was no significant relationship between BCEA and mfERG response for either amblyopic or fellow eye. There was no significant relationship between the central mfERG eye response difference and the selective blood oxygen level dependent (BOLD) LGN eye response difference previously seen in these participants. Conclusions Retinal responses in amblyopes can be reduced within the central field without an obvious anatomical basis. Additionally, this retinal deficit may not be the reason why the LGN BOLD (blood oxygen level dependent) responses are reduced for amblyopic eye stimulation.

An in-vitro 3-D cell culture model for studying pathomechanisms in AMD

Purpose To develop a novel 3-D cell culture model with the view to studying the pathomechanisms underlying the development of age-related macular degeneration (AMD). Our central hypothesis is that the silk structural protein fibroin used in conjunction with cultured human cells can be used to mimic the structural relationships between the RPE and choriocapillaris in health and disease. Methods Co-cultures of human RPE cells (ARPE-19 cells grown in Miller’s medium) and microvascular endothelial cells (HMEC-1 cells grown in endothelial culture medium) were established on opposing sides of a synthetic Bruch’s membrane (3 microns thick) constructed from B mori silk fibroin. Cell attachment was facilitated by pre-coating the fibroin membrane with vitronectin (for ARPE-19 cells) and gelatin (for HMEC-1 cells) respectively. The effects of tropoelastin on attachment of ARPE-19 cells was also examined. Barrier function was examined by measurement of trans-epithelial resistance (TER) using a voltohmmeter (EVOM-2). The phagocytic activity of the synthetic RPE was tested using vitronectin-coated microspheres (2 micron diameter FluoSpheres). In some cultures, membrane defects were created by puncturing within a 24 G needle. The architecture of the synthetic tissue before and after wounding was examined by confocal microscopy after staining for ZO-1 and F-actin. Results The RPE layer of the 3D model developed a cobblestoned morphology (validated by staining for ZO-1 and F-actin), displayed barrier function (validated by measurement of TER) and demonstrated cytoplasmic uptake of vitronectin-coated microspheres. Attachment of ARPE-19 cells to fibroin was unaffected by tropoelastin. Microvascular endothelial cells attached well to the gelatin-coated surface of the fibroin membrane and remained physically separated from the overlaying RPE layer. The fibroin membranes were amenable to puncturing without collapse thus providing the opportunity to study transmembrane migration of the endothelial cells. Conclusions Synthetic Bruch’s membranes constructed from silk fibroin, vitronectin and gelatin, support the co-cultivation of RPE cells and microvascular endothelial cells. The resulting RPE layer displays functions similar to that of native RPE and the entire tri-layered structure displays potential to be used as an in vitro model of choroidal neovascularization.

Temporal summation of intrinsically photosensitive retinal ganglion cell (ipRGC) contributions to the human pupil.

Purpose: IpRGCs mediate non-image forming functions including photoentrainment and the pupil light reflex (PLR). Temporal summation increases visual sensitivity and decreases temporal resolution for image forming vision, but the summation properties of nonimage forming vision are unknown. We investigated the temporal summation of inner (ipRGC) and outer (rod/cone) retinal inputs to the PLR. Method: The consensual PLR of the left eye was measured in six participants with normal vision using a Maxwellian view infrared pupillometer. Temporal summation was investigated using a double-pulse protocol (100 ms stimulus pairs; 0–1024 ms inter-stimulus interval, ISI) presented to the dilated fellow right eye (Tropicamide 1%). Stimulus lights (blue λmax = 460 nm; red λmax = 638 nm) biased activity to inneror outer retinal inputs to non-image forming vision. Temporal summation was measured suprathreshold (15.2 log photons.cm−2.s−1 at the cornea) and subthreshold (11.4 log photons.cm−2.s−1 at the cornea). Results: RM-ANOVAs showed the suprathreshold and subthreshold 6 second post illumination pupil response (PIPR: expressed as percentage baseline diameter) did not significantly vary for red or blue stimuli (p > .05). The PIPR for a subthreshold red 16 ms double-pulse control condition did not significantly differ with ISI (p > .05). The maximum constriction amplitude for red and blue 100 ms double- pulse stimuli did not significantly vary with ISI (p > .05). Conclusion: The non-significant changes in suprathreshold PIPR and subthreshold maximum pupil constriction indicate that inner retinal ipRGC inputs and outer retinal photoreceptor inputs to the PLR do not show temporal summation. The results suggest a fundamental difference between the temporal summation characteristics of image forming and non-image forming vision.

Fast scanning electron microscope (FSEM)

High magnification and large depth of field with a temporal resolution of less than 100 microseconds are possible using the present invention which combines a linear electron beam produced by a tungsten filament from an SX-40A Scanning Electron Microscope (SEM), a magnetic deflection coil with lower inductance resulting from reducing the number of turns of the saddle-coil wires, while increasing the diameter of the wires, a fast scintillator, photomultiplier tube, photomultiplier tube base, and signal amplifiers and a high speed data acquisition system which allows for a scan rate of 381 frames per second and 256.times.128 pixel density in the SEM image at a data acquisition rate of 25 MHz. The data acquisition and scan position are fully coordinated. A digitizer and a digital waveform generator which generates the sweep signals to the scan coils run off the same clock to acquire the signal in real-time.

Enhanced photocatalytic activity of titanium oxide nanotubes after heating treatment

Titanium oxide nanotubes were obtained by an electrochemical anodization method. Scanning electron microscope results demonstrate that the diameter of the tubes is about 120 nm and the length of the tubes is around 13 μm. Transmission electron microscope results indicate that the nanotubes are assembled by numerous nanoparticles and tube-like structure remains well after heat treatment at 400-600 °C. The photocatalysis performance of the nanotubes was evaluated in terms of the decomposition rate of methyl orange under UV irradiation. The results show that the photocatalytic activity was enhanced through the heating treatment of the nanotubes, and the nanotubes heated at 600 °C exhibits the best photocatalytic activity. X-ray diffraction patterns indicate that there is no phase transformation during the heat treatment. Therefore, the enhanced activity can be attributed to the improvement of nanotubes crystallinity, which may provide more insights about the effect of the crystallinity on the photocatalytic performance.

Combustion products of bulk aluminum rods burning in high pressure oxygen

Characterization of the combustion products released during the burning of commonly used engineering metallic materials may aid in material selection and risk assessment for the design of oxygen systems. The characterization of combustion products in regards to size distribution and morphology gives useful information for systems addressing fire detection. Aluminum rods (3.2-mm diameter cylinders) were vertically mounted inside a combustion chamber and ignited in pressurized oxygen by resistively heating an aluminum/palladium igniter wire attached to the bottom of the test sample. This paper describes the experimental work conducted to establish the particle size distribution and morphology of the resultant combustion products collected after the burning was completed and subsequently analyzed. In general, the combustion products consisted of a re-solidified oxidized slag and many small hollow spheres of size ranging from about 500 nm to 1000 µm in diameter, surfaced with quenched dendritic and grain-like structures. The combustion products were characterized using optical and scanning electron microscopy.

Investigation of the airborne submicrometer particles emitted by dredging vessels using a plume capture method

This paper presents a method for investigating ship emissions, the plume capture and analysis system (PCAS), and its application in measuring airborne pollutant emission factors (EFs) and particle size distributions. The current investigation was conducted in situ, aboard two dredgers (Amity: a cutter suction dredger and Brisbane: a hopper suction dredger) but the PCAS is also capable of performing such measurements remotely at a distant point within the plume. EFs were measured relative to the fuel consumption using the fuel combustion derived plume CO2. All plume measurements were corrected by subtracting background concentrations sampled regularly from upwind of the stacks. Each measurement typically took 6 minutes to complete and during one day, 40 to 50 measurements were possible. The relationship between the EFs and plume sample dilution was examined to determine the plume dilution range over which the technique could deliver consistent results when measuring EFs for particle number (PN), NOx, SO2, and PM2.5 within a targeted dilution factor range of 50-1000 suitable for remote sampling. The EFs for NOx, SO2, and PM2.5 were found to be independent of dilution, for dilution factors within that range. The EF measurement for PN was corrected for coagulation losses by applying a time dependant particle loss correction to the particle number concentration data. For the Amity, the EF ranges were PN: 2.2 - 9.6 × 1015 (kg-fuel)-1; NOx: 35-72 g(NO2).(kg-fuel)-1, SO2 0.6 - 1.1 g(SO2).(kg-fuel)-1and PM2.5: 0.7 – 6.1 g(PM2.5).(kg-fuel)-1. For the Brisbane they were PN: 1.0 – 1.5 x 1016 (kg-fuel)-1, NOx: 3.4 – 8.0 g(NO2).(kg-fuel)-1, SO2: 1.3 – 1.7 g(SO2).(kg-fuel)-1 and PM2.5: 1.2 – 5.6 g(PM2.5).(kg-fuel)-1. The results are discussed in terms of the operating conditions of the vessels’ engines. Particle number emission factors as a function of size as well as the count median diameter (CMD), and geometric standard deviation of the size distributions are provided. The size distributions were found to be consistently uni-modal in the range below 500 nm, and this mode was within the accumulation mode range for both vessels. The representative CMDs for the various activities performed by the dredgers ranged from 94-131 nm in the case of the Amity, and 58-80 nm for the Brisbane. A strong inverse relationship between CMD and EF(PN) was observed.

Utility of an alternative bicycle commute route of lower proximity to motorised traffic in decreasing exposure to ultra-fine particles, respiratory symptoms and airway inflammation - a structured exposure experiment

Background: Bicycle commuting in an urban environment of high air pollution is known as a potential health risk, especially for susceptible individuals. While risk management strategies aimed to reduce motorised traffic emissions exposure have been suggested, limited studies have assessed the utility of such strategies in real-world circumstances. Objectives: The potential of reducing exposure to ultrafine particles (UFP; < 0.1 µm) during bicycle commuting by lowering interaction with motorised traffic was investigated with real-time air pollution and acute inflammatory measurements in healthy individuals using their typical, and an alternative to their typical, bicycle commute route. Methods: Thirty-five healthy adults (mean ± SD: age = 39 ± 11 yr; 29% female) each completed two return trips of their typical route (HIGH) and a pre-determined altered route of lower interaction with motorised traffic (LOW; determined by the proportion of on-road cycle paths). Particle number concentration (PNC) and diameter (PD) were monitored in real-time in-commute. Acute inflammatory indices of respiratory symptom incidence, lung function and spontaneous sputum (for inflammatory cell analyses) were collected immediately pre-commute, and one and three hours post-commute. Results: LOW resulted in a significant reduction in mean PNC (1.91 x e4 ± 0.93 x e4 ppcc vs. 2.95 x e4 ± 1.50 x e4 ppcc; p ≤ 0.001). Besides incidence of in-commute offensive odour detection (42 vs. 56 %; p = 0.019), incidence of dust and soot observation (33 vs. 47 %; p = 0.038) and nasopharyngeal irritation (31 vs. 41 %; p = 0.007), acute inflammatory indices were not significantly associated to in-commute PNC, nor were these indices reduced with LOW compared to HIGH. Conclusions: Exposure to PNC, and the incidence of offensive odour and nasopharyngeal irritation, can be significantly reduced when utilising a strategy of lowering interaction with motorised traffic whilst bicycle commuting, which may bring important benefits for both healthy and susceptible individuals.