Similar T-cell immune responses induced by group M consensus env immunogens with wild-type or minimum consensus variable regions.

Consensus HIV-1 genes can decrease the genetic distances between candidate immunogens and field virus strains. To ensure the functionality and optimal presentation of immunologic epitopes, we generated two group-M consensus env genes that contain variable regions either from a wild-type B/C recombinant virus isolate (CON6) or minimal consensus elements (CON-S) in the V1, V2, V4, and V5 regions. C57BL/6 and BALB/c mice were primed twice with CON6, CON-S, and subtype control (92UG37_A and HXB2/Bal_B) DNA and boosted with recombinant vaccinia virus (rVV). Mean antibody titers against 92UG37_A, 89.6_B, 96ZM651_C, CON6, and CON-S Env protein were determined. Both CON6 and CON-S induced higher mean antibody titers against several of the proteins, as compared with the subtype controls. However, no significant differences were found in mean antibody titers in animals immunized with CON6 or CON-S. Cellular immune responses were measured by using five complete Env overlapping peptide sets: subtype A (92UG37_A), subtype B (MN_B, 89.6_B and SF162_B), and subtype C (Chn19_C). The intensity of the induced cellular responses was measured by using pooled Env peptides; T-cell epitopes were identified by using matrix peptide pools and individual peptides. No significant differences in T-cell immune-response intensities were noted between CON6 and CON-S immunized BALB/c and C57BL/6 mice. In BALB/c mice, 10 and eight nonoverlapping T-cell epitopes were identified in CON6 and CON-S, whereas eight epitopes were identified in 92UG37_A and HXB2/BAL_B. In C57BL/6 mice, nine and six nonoverlapping T-cell epitopes were identified after immunization with CON6 and CON-S, respectively, whereas only four and three were identified in 92UG37_A and HXB2/BAL_B, respectively. When combined together from both mouse strains, 18 epitopes were identified. The group M artificial consensus env genes, CON6 and CON-S, were equally immunogenic in breadth and intensity for inducing humoral and cellular immune responses.

Thermodynamic analysis of ligand-induced changes in protein thermal unfolding applied to high-throughput determination of ligand affinities with extrinsic fluorescent dyes.

The quantification of protein-ligand interactions is essential for systems biology, drug discovery, and bioengineering. Ligand-induced changes in protein thermal stability provide a general, quantifiable signature of binding and may be monitored with dyes such as Sypro Orange (SO), which increase their fluorescence emission intensities upon interaction with the unfolded protein. This method is an experimentally straightforward, economical, and high-throughput approach for observing thermal melts using commonly available real-time polymerase chain reaction instrumentation. However, quantitative analysis requires careful consideration of the dye-mediated reporting mechanism and the underlying thermodynamic model. We determine affinity constants by analysis of ligand-mediated shifts in melting-temperature midpoint values. Ligand affinity is determined in a ligand titration series from shifts in free energies of stability at a common reference temperature. Thermodynamic parameters are obtained by fitting the inverse first derivative of the experimental signal reporting on thermal denaturation with equations that incorporate linear or nonlinear baseline models. We apply these methods to fit protein melts monitored with SO that exhibit prominent nonlinear post-transition baselines. SO can perturb the equilibria on which it is reporting. We analyze cases in which the ligand binds to both the native and denatured state or to the native state only and cases in which protein:ligand stoichiometry needs to treated explicitly.

Using fractal downscaling of satellite precipitation products for hydrometeorological applications

The objective of spatial downscaling strategies is to increase the information content of coarse datasets at smaller scales. In the case of quantitative precipitation estimation (QPE) for hydrological applications, the goal is to close the scale gap between the spatial resolution of coarse datasets (e.g., gridded satellite precipitation products at resolution L × L) and the high resolution (l × l; L»l) necessary to capture the spatial features that determine spatial variability of water flows and water stores in the landscape. In essence, the downscaling process consists of weaving subgrid-scale heterogeneity over a desired range of wavelengths in the original field. The defining question is, which properties, statistical and otherwise, of the target field (the known observable at the desired spatial resolution) should be matched, with the caveat that downscaling methods be as a general as possible and therefore ideally without case-specific constraints and/or calibration requirements? Here, the attention is focused on two simple fractal downscaling methods using iterated functions systems (IFS) and fractal Brownian surfaces (FBS) that meet this requirement. The two methods were applied to disaggregate spatially 27 summertime convective storms in the central United States during 2007 at three consecutive times (1800, 2100, and 0000 UTC, thus 81 fields overall) from the Tropical Rainfall Measuring Mission (TRMM) version 6 (V6) 3B42 precipitation product (~25-km grid spacing) to the same resolution as the NCEP stage IV products (~4-km grid spacing). Results from bilinear interpolation are used as the control. A fundamental distinction between IFS and FBS is that the latter implies a distribution of downscaled fields and thus an ensemble solution, whereas the former provides a single solution. The downscaling effectiveness is assessed using fractal measures (the spectral exponent β, fractal dimension D, Hurst coefficient H, and roughness amplitude R) and traditional operational scores statistics scores [false alarm rate (FR), probability of detection (PD), threat score (TS), and Heidke skill score (HSS)], as well as bias and the root-mean-square error (RMSE). The results show that both IFS and FBS fractal interpolation perform well with regard to operational skill scores, and they meet the additional requirement of generating structurally consistent fields. Furthermore, confidence intervals can be directly generated from the FBS ensemble. The results were used to diagnose errors relevant for hydrometeorological applications, in particular a spatial displacement with characteristic length of at least 50 km (2500 km2) in the location of peak rainfall intensities for the cases studied. © 2010 American Meteorological Society.

Bunching-induced optical nonlinearity and instability in cold atoms [Invited].

We report a new nonlinear optical process that occurs in a cloud of cold atoms at low-light-levels when the incident optical fields simultaneously polarize, cool, and spatially-organize the atoms. We observe an extremely large effective fifth-order nonlinear susceptibility of χ(⁵) = 7.6 × 10⁻¹⁵ (m/V)⁴, which results in efficient Bragg scattering via six-wave mixing, slow group velocities (∼ c/10⁵), and enhanced atomic coherence times (> 100 μs). In addition, this process is particularly sensitive to the atomic temperatures, and provides a new tool for in-situ monitoring of the atomic momentum distribution in an optical lattice. For sufficiently large light-matter couplings, we observe an optical instability for intensities as low as ∼ 1 mW/cm² in which new, intense beams of light are generated and result in the formation of controllable transverse optical patterns.

Variability of particulate matter concentrations along roads and motorways determined by a moving measurement unit

The spatial variability of aerosol number and mass along roads was determined in different regions (urban, rural and coastal-marine) of the Netherlands. A condensation particle counter (CPC) and an optical aerosol spectrometer (LAS-X) were installed in a van along with a global positioning system (GPS). Concentrations were measured with high-time resolutions while driving allowing investigations not possible with stationary equipment. In particular, this approach proves to be useful to identify those locations where numbers and mass attain high levels ('hot spots'). In general, concentrations of number and mass of particulate matter increase along with the degree of urbanisation, with number concentration being the more sensitive indicator. The lowest particle numbers and PM1-concentrations are encountered in a coastal and rural area: <5000cm-3 and 6μgm-3, respectively. The presence of sea-salt material along the North-Sea coast enhances PM>1-concentrations compared to inland levels. High-particle numbers are encountered on motorways correlating with traffic intensity; the largest average number concentration is measured on the ring motorway around Amsterdam: about 160000cm-3 (traffic intensity 100000vehday-1). Peak values occur in tunnels where numbers exceed 106cm-3. Enhanced PM1 levels (i.e. larger than 9μgm-3) exist on motorways, major traffic roads and in tunnels. The concentrations of PM>1 appear rather uniformly distributed (below 6μgm-3 for most observations). On the urban scale, (large) spatial variations in concentration can be explained by varying intensities of traffic and driving patterns. The highest particle numbers are measured while being in traffic congestions or when behind a heavy diesel-driven vehicle (up to 600×103cm-3). Relatively high numbers are observed during the passages of crossings and, at a decreasing rate, on main roads with much traffic, quiet streets and residential areas with limited traffic. The number concentration exhibits a larger variability than mass: the mass concentration on city roads with much traffic is 12% higher than in a residential area at the edge of the same city while the number of particles changes by a factor of two (due to the presence of the ultrafine particles (aerodynamic diameter <100nm). It is further indicated that people residing at some 100m downwind a major traffic source are exposed to (still) 40% more particles than those living in the urban background areas. © 2004 Elsevier Ltd. All rights reserved.

Exercise elicits phase shifts and acute alterations of melatonin that vary with circadian phase

To examine the immediate phase-shifting effects of high-intensity exercise of a practical duration (1 h) on human circadian phase, five groups of healthy men 20-30 yr of age participated in studies involving no exercise or exposure to morning, afternoon, evening, or nocturnal exercise. Except during scheduled sleep/dark and exercise periods, subjects remained under modified constant routine conditions allowing a sleep period and including constant posture, knowledge of clock time, and exposure to dim light intensities averaging (±SD) 42 ± 19 lx. The nocturnal onset of plasma melatonin secretion was used as a marker of circadian phase. A phase response curve was used to summarize the phase-shifting effects of exercise as a function of the timing of exercise. A significant effect of time of day on circadian phase shifts was observed (P < 0.004). Over the interval from the melatonin onset before exercise to the first onset after exercise, circadian phase was significantly advanced in the evening exercise group by 30 ± 15 min (SE) compared with the phase delays observed in the no-exercise group (-25 ± 14 min, P < 0.05). Phase shifts in response to evening exercise exposure were attenuated on the second day after exercise exposure and no longer significantly different from phase shifts observed in the absence of exercise. Unanticipated transient elevations of melatonin levels were observed in response to nocturnal exercise and in some evening exercise subjects. Taken together with the results from previous studies in humans and diurnal rodents, the current results suggest that 1) a longer duration of exercise exposure and/or repeated daily exposure to exercise may be necessary for reliable phase-shifting of the human circadian system and that 2) early evening exercise of high intensity may induce phase advances relevant for nonphotic entrainment of the human circadian system.

Contenido de carbono orgánico y biomasa microbiana en un suelo sometido a distintas intensidades de cultivo

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Interactions between multiple large macrofauna species and nematode communities — Mechanisms for indirect impacts of trawling disturbance

Highlights •We exposed meiofauna to 7 different large macrofauna species at high and low densities. •Macrofauna presence altered nematode community structure and reduced their abundance. •Macrofauna species had similar effects by reducing the few dominant nematode species. •Meio–macrofauna resource competition and spatial segregation are the main drivers. •Trawling effects on macrofauna affect nematode communities indirectly. Diverse assemblages of infauna in sediments provide important physical and biogeochemical services, but are under increasing pressure by anthropogenic activities, such as benthic trawling. It is known that trawling disturbance has a substantial effect on the larger benthic fauna, with reductions in density and diversity, and changes in community structure, benthic biomass, production, and bioturbation and biogeochemical processes. Largely unknown, however, are the mechanisms by which the trawling impacts on the large benthic macro- and megafauna may influence the smaller meiofauna. To investigate this, a mesocosm experiment was conducted whereby benthic nematode communities from a non-trawled area were exposed to three different densities (absent, low, normal) of 7 large (> 10 mm) naturally co-occurring, bioturbating species which are potentially vulnerable to trawling disturbance. The results showed that total abundances of nematodes were lower if these large macrofauna species were present, but no clear nematode abundance effects could be assigned to the macrofauna density differences. Nematode community structure changed in response to macrofauna presence and density, mainly as a result of the reduced abundance of a few dominant nematode species. Any detectable effects seemed similar for nearly all macrofauna species treatments, supporting the idea that there may be a general indirect, macrofauna-mediated trawling impact on nematode communities. Explanations for these results may be, firstly, competition for food resources, resulting in spatial segregation of the meio- and macrobenthic components. Secondly, different densities of large macrofauna organisms may affect the nematode community structure through different intensities of bioturbatory disturbance or resource competition. These results suggest that removal or reduced densities of larger macrofauna species as a result of trawling disturbance may lead to increased nematode abundance and hints at the validity of interference competition between large macrofauna organisms and the smaller meiofauna, and the energy equivalence hypothesis, where a trade-off is observed between groups of organisms that are dependent on a common source of energy.

Double ionization of atomic negative ions in an intense laser field

In recent years there have been many studies of multiple ionization of closed shell rare gas atoms by intense laser fields. Until now no similar work has been done in the study of more diverse targets such as negative ions where low binding energies and strong electron correlations could yield distinctive behaviour. We present the first results of ionization of more than one electron from a range of atomic negative ions by intense laser pulses. Although these pulses are long by modern standards, and tend to produce sequential ionization in atoms, the positive ion yields from the negative ions do not depend predictably on the ionization potentials. This suggests that there may, intriguingly, be an alternative mechanism enhancing double ionization at low intensities.

Wavelet phase coherence analysis: Application to a quiet-sun magnetic element

A new application of wavelet analysis is presented that utilizes the inherent phase information residing within the complex Morlet transform. The technique is applied to a weak solar magnetic network region, and the temporal variation of phase difference between TRACE 1700 Angstrom and SOHO/SUMER C II 1037 Angstrom intensities is shown. We present, for the first time in an astrophysical setting, the application of wavelet phase coherence, including a comparison between two methods of testing real wavelet phase coherence against that of noise. The example highlights the advantage of wavelet analysis over more classical techniques, such as Fourier analysis, and the effectiveness of the former to identify wave packets of similar frequencies but with differing phase relations is emphasized. Using cotemporal, ground-based Advanced Stokes Polarimeter measurements, changes in the observed phase differences are shown to result from alterations in the magnetic topology.

A comparison of theoretical MgVI emission line strengths with active-region observations from serts

R-matrix calculations of electron impact excitation rates in N-like Mg vi are used to derive theoretical electron-density-sensitive emission line ratios involving 2s(2)2p(3)-2s2p(4) transitions in the 269-403 Angstrom wavelength range. A comparison of these with observations of a solar active region, obtained during the 1989 flight of the Solar EUV Rocket Telescope and Spectrograph (SERTS), reveals good agreement between theory and observation for the 2s(2)2p(3) S-4-2s2p(4) P-4 transitions at 399.28, 400.67, and 403.30 Angstrom, and the 2s(2)2p(3) P-2-2s2p(4) D-2 lines at 387.77 and 387.97 Angstrom. However, intensities for the other lines attributed to Mg vi in this spectrum by various authors do not match the present theoretical predictions. We argue that these discrepancies are not due to errors in the adopted atomic data, as previously suggested, but rather to observational uncertainties or mis-identifications. Some of the features previously identified as Mg vi lines in the SERTS spectrum, such as 291.36 and 293.15 Angstrom, are judged to be noise, while others (including 349.16 Angstrom) appear to be blended.

Improved data for solar flare X-ray spectral analysis

The inclusion of collisional rates for He-like Fe and Ca ions is discussed with reference to the analysis of solar flare Fe XXV and Ca XIX line emission, particularly from the Yohkoh Bragg Crystal Spectrometer (BCS). The new data are a slight improvement on calculations presently used in the BCS analysis software in that the discrepancy in the Fe XXV y and z line intensities (observed larger than predicted) is reduced. Values of electron temperature from satellite-to-resonance line ratios are slightly reduced (by up to 1 MK) for a given observed ratio. The new atomic data will be incorporated in the Yohkoh BCS databases. The data should also be of interest for the analysis of high-resolution, non-solar spectra expected from the Constellation-X and Astro-E space missions. A comparison is made of a tokamak S XV spectrum with a synthetic spectrum using atomic data in the existing software and the agreement is found to be good, so validating these data for particularly high-n satellite wavelengths close to the S XV resonance line. An error in a data file used for analyzing BCS Fe XXVI spectra is corrected, so permitting analysis of these spectra.

Multiwavelength observations of the M15 intermediate-velocity cloud

We present Westerbork Synthesis Radio Telescope HI images, Lovell telescope multibeam H I wide-field mapping, William Herschel Telescope long-slit echelle Ca II observations, Wisconsin Halpha Mapper (WHAM) facility images, and IRAS ISSA 60- and 100-mum co-added images towards the intermediate- velocity cloud (IVC) at + 70 km s(-1), located in the general direction of the M15 globular cluster. When combined with previously published Arecibo data, the H I gas in the IVC is found to be clumpy, with a peak H I column density of similar to1.5 x 10(20) cm(-2), inferred volume density (assuming spherical symmetry) of similar to24 cm(-3)/D (kpc) and a maximum brightness temperature at a resolution of 81 x 14 arcsec(2) of 14 K. The major axis of this part of the IVC lies approximately parallel to the Galactic plane, as does the low- velocity H I gas and IRAS emission. The H I gas in the cloud is warm, with a minimum value of the full width at half-maximum velocity width of 5 km s(-1) corresponding to a kinetic temperature, in the absence of turbulence, of similar to540 K. From the H I data, there are indications of two-component velocity structure. Similarly, the Ca II spectra, of resolution 7 km s(-1), also show tentative evidence of velocity structure, perhaps indicative of cloudlets. Assuming that there are no unresolved narrow-velocity components, the mean values of log(10)[N(Ca II K) cm(2)] similar to 12.0 and Ca II/H I similar to2 5 x 10(-8) are typical of observations of high Galactic latitude clouds. This compares with a value of Ca II/H I>10(-6) for IVC absorption towards HD 203664, a halo star of distance 3 kpc, some 3.degrees1 from the main M15 IVC condensation. The main IVC condensation is detected by WHAM in Halpha with central local-standard-of-rest velocities of similar to60-70 km s(-1), and intensities uncorrected for Galactic extinction of up to 1.3 R, indicating that the gas is partially ionized. The FWHM values of the Halpha IVC component, at a resolution of 1degrees, exceed 30 km s(-1). This is some 10 km s(-1) larger than the corresponding H I value at a similar resolution, and indicates that the two components may not be mixed. However, the spatial and velocity coincidence of the Halpha and H I peaks in emission towards the main IVC component is qualitatively good. If the Halpha emission is caused solely by photoionization, the Lyman continuum flux towards the main IVC condensation is similar to2.7 x 10(6) photon cm(-2) s(-1). There is not a corresponding IVC Halpha detection towards the halo star HD 203664 at velocities exceeding similar to60 km s(- 1). Finally, both the 60- and 100-mum IRAS images show spatial coincidence, over a 0.675 x 0 625 deg(2) field, with both low- and intermediate-velocity H I gas (previously observed with the Arecibo telescope), indicating that the IVC may contain dust. Both the Halpha and tentative IRAS detections discriminate this IVC from high-velocity clouds, although the H I properties do not. When combined with the H I and optical results, these data point to a Galactic origin for at least parts of this IVC.

Dynamic tunnelling ionization of H-+(2) in intense fields

Intense-field ionization of the hydrogen molecular ion by linearly polarized light is modelled by direct solution of the fixed-nuclei time-dependent Schrodinger equation and compared with recent experiments. Parallel transitions are calculated using algorithms which exploit massively parallel computers. We identify and calculate dynamic tunnelling ionization resonances that depend on laser wavelength and intensity, and molecular bond length. Results for lambda similar to 1064 nm are consistent with static tunnelling ionization. At shorter wavelengths lambda similar to 790 nm large dynamic corrections are observed. The results agree very well with recent experimental measurements of the ion spectra. Our results reproduce the single peak resonance and provide accurate ionization rate estimates at high intensities. At lower intensities our results confirm a double peak in the ionization rate as the bond length varies.

High-energy cutoff in the spectrum of strong-field nonsequential double ionization

Electron energy distributions of singly and doubly ionized helium in an intense 390 nm laser field have been measured at two intensities (0.8 PW/cm(2) and 1.1 PW/cm(2), where PW equivalent to 10(15) W/cm(2)). Numerical solutions of the full-dimensional time-dependent helium Schrodinger equation show excellent agreement with the experimental measurements. The high-energy portion of the two-electron energy distributions reveals an unexpected 5U(p) cutoff for the double ionization (DI) process and leads to a proposed model for DI below the quasiclassical threshold.