Single-particle tracking uncovers dynamics of glutamate-induced retrograde transport of NF-κB p65 in living neurons

Retrograde transport of NF-κB from the synapse to the nucleus in neurons is mediated by the dynein/dynactin motor complex and can be triggered by synaptic activation. The calibre of axons is highly variable ranging down to 100 nm, aggravating the investigation of transport processes in neurites of living neurons using conventional light microscopy. In this study we quantified for the first time the transport of the NF-κB subunit p65 using high-density single-particle tracking in combination with photoactivatable fluorescent proteins in living mouse hippocampal neurons. We detected an increase of the mean diffusion coefficient (Dmean) in neurites from 0.12 ± 0.05 µm2/s to 0.61 ± 0.03 µm2/s after stimulation with glutamate. We further observed that the relative amount of retrogradely transported p65 molecules is increased after stimulation. Glutamate treatment resulted in an increase of the mean retrograde velocity from 10.9 ± 1.9 to 15 ± 4.9 µm/s, whereas a velocity increase from 9 ± 1.3 to 14 ± 3 µm/s was observed for anterogradely transported p65. This study demonstrates for the first time that glutamate stimulation leads to an increased mobility of single NF-κB p65 molecules in neurites of living hippocampal neurons.

Using laboratory and field measurements to constrain a single habit shortwave optical parameterization for cirrus

A single habit parameterization for the shortwave optical properties of cirrus is presented. The parameterization utilizes a hollow particle geometry, with stepped internal cavities as identified in laboratory and field studies. This particular habit was chosen as both experimental and theoretical results show that the particle exhibits lower asymmetry parameters when compared to solid crystals of the same aspect ratio. The aspect ratio of the particle was varied as a function of maximum dimension, D, in order to adhere to the same physical relationships assumed in the microphysical scheme in a configuration of the Met Office atmosphere-only global model, concerning particle mass, size and effective density. Single scattering properties were then computed using T-Matrix, Ray Tracing with Diffraction on Facets (RTDF) and Ray Tracing (RT) for small, medium, and large size parameters respectively. The scattering properties were integrated over 28 particle size distributions as used in the microphysical scheme. The fits were then parameterized as simple functions of Ice Water Content (IWC) for 6 shortwave bands. The parameterization was implemented into the GA6 configuration of the Met Office Unified Model along with the current operational long-wave parameterization. The GA6 configuration is used to simulate the annual twenty-year short-wave (SW) fluxes at top-of-atmosphere (TOA) and also the temperature and humidity structure of the atmosphere. The parameterization presented here is compared against the current operational model and a more recent habit mixture model.

Black carbon measurements in the boundary layer over western and northern Europe

Europe is a densely populated region that is a significant global source of black carbon (BC) aerosol, but there is a lack of information regarding the physical properties and spatial/vertical distribution of rBC in the region. We present the first aircraft observations of sub-micron refractory BC (rBC) aerosol concentrations and physical properties measured by a single particle soot photometer (SP2) in the lower troposphere over Europe. The observations spanned a region roughly bounded by 50° to 60° N and from 15° W to 30° E. The measurements, made between April and September 2008, showed that average rBC mass concentrations ranged from about 300 ng m−3 near urban areas to approximately 50 ng m−3 in remote continental regions, lower than previous surface-based measurements. rBC represented between 0.5 and 3% of the sub-micron aerosol mass. Black carbon mass size distributions were log-normally distributed and peaked at approximately 180 nm, but shifted to smaller diameters (~160 nm) near source regions. rBC was correlated with carbon monoxide (CO) but had different ratios to CO depending on location and air mass. Light absorption coefficients were measured by particle soot absorption photometers on two separate aircraft and showed similar geographic patterns to rBC mass measured by the SP2. We summarize the rBC and light absorption measurements as a function of longitude and air mass age and also provide profiles of rBC mass concentrations and size distribution statistics. Our results will help evaluate model-predicted regional rBC concentrations and properties and determine regional and global climate impacts from rBC due to atmospheric heating and surface dimming.

Variation of the mixing state of Saharan dust particles with atmospheric transport

Mineral dust is an important aerosol species in the Earth’s atmosphere and has a major source within North Africa, of which the Sahara forms the major part. Aerosol Time of Flight Mass Spectrometry (ATOFMS) is first used to determine the mixing state of dust particles collected from the land surface in the Saharan region, showing low abundance of species such as nitrate and sulphate internally mixed with the dust mineral matrix. These data are then compared with the ATOFMS single particle mass spectra of Saharan dust particles detected in the marine atmosphere in the vicinity of the Cape Verde islands, which are further compared with those from particles with longer atmospheric residence sampled at a coastal station at Mace Head, Ireland. Saharan dust particles collected near the Cape Verde Islands showed increased internally mixed nitrate but no sulphate, whilst Saharan dust particles collected on the coast of Ireland showed a very high degree of internally mixed secondary species including nitrate, sulphate and methanesulphonate. This uptake of secondary species will change the pH and hygroscopic properties of the aerosol dust and thus can influence the budgets of other reactive gases, as well as influencing the radiative properties of the particles and the availability of metals for dissolution.

Engineering Pt in ceria for a maximum metal-support interaction in catalysis

Conventional supported metal catalysts are metal nanoparticles deposited on high surface area oxide supports with a poorly defined metal−support interface. Typically, the traditionally prepared Pt/ceria catalyzes both methanation (H2/CO to CH4) and water−gas shift (CO/H2O to CO2/H2) reactions. By using simple nanochemistry techniques, we show for the first time that Pt or PtAu metal can be created inside each CeO2 particle with tailored dimensions. The encapsulated metal is shown to interact with the thin CeO2 overlayer in each single particle in an optimum geometry to create a unique interface, giving high activity and excellent selectivity for the water−gas shift reaction, but is totally inert for methanation. Thus, this work clearly demonstrates the significance of nanoengineering of a single catalyst particle by a bottom-up construction approach in modern catalyst design which could enable exploitation of catalyst site differentiation, leading to new catalytic properties.

Stirring and mixing in two-dimensional divergent flow

While stirring and mixing properties in the stratosphere are reasonably well understood in the context of balanced (slow) dynamics, as is evidenced in numerous studies of chaotic advection, the strongly enhanced presence of high-frequency gravity waves in the mesosphere gives rise to a significant unbalanced (fast) component to the flow. The present investigation analyses result from two idealized shallow-water numerical simulations representative of stratospheric and mesospheric dynamics on a quasi-horizontal isentropic surface. A generalization of the Hua–Klein Eulerian diagnostic to divergent flow reveals that velocity gradients are strongly influenced by the unbalanced component of the flow. The Lagrangian diagnostic of patchiness nevertheless demonstrates the persistence of coherent features in the zonal component of the flow, in contrast to the destruction of coherent features in the meridional component. Single-particle statistics demonstrate t2 scaling for both the stratospheric and mesospheric regimes in the case of zonal dispersion, and distinctive scaling laws for the two regimes in the case of meridional dispersion. This is in contrast to two-particle statistics, which in the mesospheric (unbalanced) regime demonstrate a more rapid approach to Richardson’s t3 law in the case of zonal dispersion and is evidence of enhanced meridional dispersion.

Retrieval of effective ice crystal size in the infrared: sensitivity study and global measurements from TIROS-N Operational Vertical Sounder

The difference between cirrus emissivities at 8 and 11 μm is sensitive to the mean effective ice crystal size of the cirrus cloud, De. By using single scattering properties of ice crystals shaped as planar polycrystals, diameters of up to about 70 μm can be retrieved, instead of up to 45 μm assuming spheres or hexagonal columns. The method described in this article is used for a global determination of mean effective ice crystal sizes of cirrus clouds from TOVS satellite observations. A sensitivity study of the De retrieval to uncertainties in hypotheses on ice crystal shape, size distributions, and temperature profiles, as well as in vertical and horizontal cloud heterogeneities shows that uncertainties can be as large as 30%. However, the TOVS data set is one of few data sets which provides global and long-term coverage. Having analyzed the years 1987–1991, it was found that measured effective ice crystal diameters De are stable from year to year. For 1990 a global median De of 53.5 μm was determined. Averages distinguishing ocean/land, season, and latitude lie between 23 μm in winter over Northern Hemisphere midlatitude land and 64 μm in the tropics. In general, larger Des are found in regions with higher atmospheric water vapor and for cirrus with a smaller effective emissivity.

Purification and electron cryomicroscopy of coronavirus particles

Intact, enveloped coronavirus particles vary widely in size and contour, and are thus refractory to study by traditional structural means such as X-ray crystallography. Electron microscopy (EM) overcomes some problems associated with particle variability and has been an important tool for investigating coronavirus ultrastructure. However, EM sample preparation requires that the specimen be dried onto a carbon support film before imaging, collapsing internal particle structure in the case of coronaviruses. Moreover, conventional EM achieves image contrast by immersing the specimen briefly in heavy-metal-containing stain, which reveals some features while obscuring others. Electron cryomicroscopy (cryo-EM) instead employs a porous support film, to which the specimen is adsorbed and flash-frozen. Specimens preserved in vitreous ice over holes in the support film can then be imaged without additional staining. Cryo-EM, coupled with single-particle image analysis techniques, makes it possible to examine the size, structure and arrangement of coronavirus structural components in fully hydrated, native virions. Two virus purification procedures are described.

A complete atomistic model of molten polyethylene from neutron scattering data: a new methodology for polymer structure

A new approach to the study of the local organization in amorphous polymer materials is presented. The method couples neutron diffraction experiments that explore the structure on the spatial scale 1–20 Å with the reverse Monte Carlo fitting procedure to predict structures that accurately represent the experimental scattering results over the whole momentum transfer range explored. Molecular mechanics and molecular dynamics techniques are also used to produce atomistic models independently from any experimental input, thereby providing a test of the viability of the reverse Monte Carlo method in generating realistic models for amorphous polymeric systems. An analysis of the obtained models in terms of single chain properties and of orientational correlations between chain segments is presented. We show the viability of the method with data from molten polyethylene. The analysis derives a model with average C-C and C-H bond lengths of 1.55 Å and 1.1 Å respectively, average backbone valence angle of 112, a torsional angle distribution characterized by a fraction of trans conformers of 0.67 and, finally, a weak interchain orientational correlation at around 4 Å.

The effect of the tensor force on the predicted stability of superheavy nuclei

The effect of the tensor component of the Skyrme effective nucleon-nucleon interaction on the single-particle structure in superheavy elements is studied. A selection of the available Skyrme forces has been chosen and their predictions for the proton and neutron shell closures investigated. The inclusion of the tensor term with realistic coupling strength parameters leads to a small increase in the spin-orbit splitting between the proton 2f7/2 and 2f5/2 partners, opening the Z=114 shell gap over a wide range of nuclei. The Z=126 shell gap, predicted by these models in the absence of the tensor term, is found to be stongly dependent on neutron number with a Z=138 gap opening for large neutron numbers, having a consequent implication for the synthesis of neutron-rich superheavy elements. The predicted neutron shell structures remain largely unchanged by inclusion of the tensor component.

TNF-α influences the lateral dynamics of TNF receptor I in living cells

In mammalian cells, inflammation is mainly mediated by the binding of tumor necrosis factor alpha to tumor necrosis factor receptor 1. In this study, we investigated lateral dynamics of TNF-R1 before and after ligand binding using high-density single-particle tracking in combination with photoactivated localization microscopy. Our single-molecule data indicates the presence of tumor necrosis factor receptor 1 with different mobilities in the plasma membrane, suggesting different molecular organizations. Cholesterol depletion led to a decrease of slow receptor species and a strong increase in the average diffusion coefficient. Moreover, as a consequence of tumor necrosis factor-alpha treatment, the mean diffusion coefficient moderately increased while its distribution narrowed. Based on our observation, we propose a refined mechanism on the structural arrangement and activation of tumor necrosis factor receptor 1 in the plasma membrane.

Single amino acid substitutions in puroindoline-b mutants influence lipid binding properties

External reflectance Fourier transform infrared (ER-FTIR) spectroscopy and surface pressure measurements have been used to characterize the interaction of wild-type puroindoline-b (Pin-b) and two mutant forms featuring single residue substitutions-namely, Gly-46 to Ser-46 (Pin-bH) and Trp-44 to Arg-44 (Pin-bS)-with condensed-phase monolayers of zwitterionic (L-alpha-dipalmitoylphosphatidylcholine, DPPC) and anionic (L-alpha-dipalmitoylphosphatidyl-dl-glycerol, DPPG) phospholipids. The interaction with anionic DPPG monolayers, monitored by surface pressure isotherms, was influenced significantly by mutations in Pin-b (p < 0.05); wild-type Pin-b showed the highest surface pressure change of 10.6 +/- 1.0 mN m(-1), followed by Pin-bH (7.9 +/- 1.6 mN m(-1)) and Pin-bS (6.3 +/- 1.0 mN m(-1)), and the surface pressure isotherm kinetics were also different in each case. Integrated Amide I peak areas from corresponding ER-FTIR spectra confirmed the differences in adsorption kinetics, but also showed that differences in adsorbed amount were less significant, suggesting that mutations influence the degree of penetration into DPPG films. All Pin-b types showed evidence of interaction with DPPC films, detected as changes in surface pressure (5.6 +/- 1.1 mN m(-1)); however, no protein peaks were detected in the ER-FTIR spectra, which indicated that the interaction was via penetration with limited adsorption at the lipid/water interface. The expression of Pin-b mutants is linked to wheat endosperm hardness; therefore, the data presented here suggest that the lipid binding properties may be pivotal within the mechanism for this quality trait. In addition, the data suggest antimicrobial activities of Pin-b mutants would be lower than those of the wild-type Pin-b, because of decreased selectivity toward anionic phospholipids.

Chemical, physical and electrical properties of aged dodecylbenzene 2: thermal ageing of single isomers in air

The linear isomer of dodecylbenzene (DDB), 1-phenyldodecane, was aged at temperatures of 105 and 135 degrees C in air and the resultant products were analyzed using a range of analytical techniques. On ageing, the 1-phenyldodecane darkened, the acid number, dielectric loss and water content increased and significant oxidation peaks were detected in the infrared spectrum. When aged in the presence of copper, a characteristic peak at 680 nm was also detected by UV/visible spectroscopy but, compared with previous studies of a cable-grade DDB, the strength of this peak was much increased and no appreciable precipitate formation occurred. At the same time, very high values of dielectric loss were recorded. On ageing in the absence of copper, an unusually strong infrared carbonyl band was seen, which correlates well with the detection of dodecanophenone by gas chromatography / mass spectrometry and nuclear magnetic resonance spectroscopy. It was therefore concluded that the ageing process proceeds via the initial production of aromatic ketones, which may then be further oxidized to carboxylic acids. In the presence of copper, these oxidation products are present in lower quantities, most of these oxidation products being combined with the copper present in the oil to give copper carboxylates. The behavior is described in terms of a complex autoxidation mechanism, in which copper acts as both an oxidizing and a reducing agent, depending on its oxidation state and, in particular, promotes elimination via the oxidation of intermediate alkyl radical species to carbocations.

Sensitivity of direct radiative forcing by mineral dust to particle characteristics

Airborne dust affects the Earth's energy balance — an impact that is measured in terms of the implied change in net radiation (or radiative forcing, in W m-2) at the top of the atmosphere. There remains considerable uncertainty in the magnitude and sign of direct forcing by airborne dust under current climate. Much of this uncertainty stems from simplified assumptions about mineral dust-particle size, composition and shape, which are applied in remote sensing retrievals of dust characteristics and dust-cycle models. Improved estimates of direct radiative forcing by dust will require improved characterization of the spatial variability in particle characteristics to provide reliable information dust optical properties. This includes constraints on: (1) particle-size distribution, including discrimination of particle subpopulations and quantification of the amount of dust in the sub-10 µm to <0.1 µm mass fraction; (2) particle composition, specifically the abundance of iron oxides, and whether particles consist of single or multi-mineral grains; (3) particle shape, including degree of sphericity and surface roughness, as a function of size and mineralogy; and (4) the degree to which dust particles are aggregated together. The use of techniques that measure the size, composition and shape of individual particles will provide a better basis for optical modelling.

Optical properties of Saharan dust aerosol and contribution from the coarse mode as measured during the Fennec 2011 aircraft campaign

New in-situ aircraft measurements of Saharan dust originating from Mali, Mauritania and Algeria taken during the Fennec 2011 aircraft campaign over a remote part of the Sahara Desert are presented. Size distributions extending to 300 μm are shown, representing measurements extending further into the coarse mode than previously published for airborne Saharan dust. A significant coarse mode was present in the size distribution measurements with effective diameter (deff) from 2.3 to 19.4 μm and coarse mode volume median diameter (dvc) from 5.8 to 45.3 μm. The mean size distribution had a larger relative proportion of coarse mode particles than previous aircraft measurements. The largest particles (with deff >12 μm, or dvc >25 μm) were only encountered within 1 km of the ground. Number concentration, mass loading and extinction coefficient showed inverse relationships to dust age since uplift. Dust particle size showed a weak exponential relationship to dust age. Two cases of freshly uplifted dust showed quite different characteristics of size distribution and number concentration. Single Scattering Albed (SSA) values at 550 nm calculated from the measured size distributions revealed high absorption ranging from 0.70 to 0.97 depending on the refractive index. SSA was found to be strongly related to deff. New instrumentation revealed that direct measurements, behind Rosemount inlets, overestimate SSA by up to 0.11 when deff is greater than 2 μm. This is caused by aircraft inlet inefficiencies and sampling losses. Previous measurements of SSA from aircraft measurements may also have been overestimates for this reason. Radiative transfer calculations indicate that the range of SSAs during Fennec 2011 can lead to underestimates in shortwave atmospheric heating rates by 2.0 to 3.0 times if the coarse mode is neglected. This will have an impact on Saharan atmospheric dynamics and circulation,which should be taken into account by numerical weather prediction and climate models.