2D Radiative Processes Near Cloud Edges

Because of the importance and complexity of dynamical, microphysical, and radiative processes taking place near cloud edges, the transition zone between clouds and cloud free air has been the subject of intense research both in the ASR program and in the wider community. One challenge in this research is that the one-dimensional (1D) radiative models widely used in both remote sensing and dynamical simulations become less accurate near cloud edges: The large horizontal gradients in particle concentrations imply that accurate radiative calculations need to consider multi-dimensional radiative interactions among areas that have widely different optical properties. This study examines the way the importance of multidimensional shortwave radiative interactions changes as we approach cloud edges. For this, the study relies on radiative simulations performed for a multiyear dataset of clouds observed over the NSA, SGP, and TWP sites. This dataset is based on Microbase cloud profiles as well as wind measurements and ARM cloud classification products. The study analyzes the way the difference between 1D and 2D simulation results increases near cloud edges. It considers both monochromatic radiances and broadband radiative heating, and it also examines the influence of factors such as cloud type and height, and solar elevation. The results provide insights into the workings of radiative processes and may help better interpret radiance measurements and better estimate the radiative impacts of this critical region

Observation-Based Study on Aerosol Optical Depth and Particle Size in Partly Cloudy Regions

This study seeks to help better understand aerosol-cloud interactions by examining statistical relationships between aerosol properties and nearby low-altitude cloudiness using satellite data. The analysis of a global dataset of MODIS (Moderate Resolution Imaging Spectroradiometer) observations reveals that the positive correlation between cloudiness and aerosol optical depth (AOD) reported in earlier studies is strong throughout the globe and during both winter and summer. Typically, AOD is 30-50 higher on cloudier-than-average days than on less cloudy days. A combination of satellite observations and MERRA-2 global reanalysis data reveals that the correlation between cloud cover and AOD is strong for all aerosol types considered: sulfate, dust, carbon, and sea salt. The observations also indicate that in the presence of nearby clouds, aerosol size distributions tend to shift toward smaller particles over large regions of the Earth. This is consistent with a greater cloud-related increase in the AOD of fine mode than of coarse mode particles. The greater increase in fine mode AOD implies that the cloudiness-AOD correlation does not come predominantly from cloud detection uncertainties. Additionally, the results show that aerosol particle size increases near clouds even in regions where it decreases with increasing cloudiness. This suggests that the decrease with cloudiness comes mainly from changes in large-scale environment, rather than from clouds increasing the number or the size of fine mode aerosols. Finally, combining different aerosol retrieval algorithms demonstrated that quality assessment flags based on local variability can help identifying when the observed aerosol populations are affected by surrounding clouds

Taking the Pulse of PyroCumulus Clouds

Forest fires can burn large areas, but can also inject smoke into the upper troposphere/lower stratosphere (UT/LS), where stakes are even higher for climate, because emissions tend to have a longer lifetime, and can produce significant regional and even global climate effects, as is the case with some volcanoes. Large forest fires are now believed to be more common in summer, especially in the boreal regions, where pyrocumulus (pyroCu), and occasionally pyrocumuionimbus (pyroCb) clouds are formed, which can transport emissions into the UT/LS. A major difficulty in developing realistic fire plume models is the lack of observational data within fire plumes that resolves structure at a few 100 m scales, which can be used to validate these models. Here, we report detailed airborne radiation measurements within strong pyroCu taken over boreal forest fires in Saskatchewan, Canada during the Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) summer field campaign in 2008. We find that the angular distribution of radiance within the pyroCu is closely related to the diffusion domain in water clouds and can be described by very similar simple cosine functions. We demonstrate with Monte Carlo simulations that radiation transport in pyroCu is inherently a 3D phenomenon and must account for particle absorption. However, the simple cosine function promises to offer an easy solution for climate models. The presence of a prominent smoke core, defined by strong extinction in the UV, VIS and NIR, suggests that the core might be an important pathway for emission transport to the upper troposphere and lower stratosphere. We speculate that this plume injection core is generated and sustained by complex processes not yet well understood, but not necessarily related directly to the intense fires that originally initiated the plume rise

Measurement of inositol 1,4,5-trisphosphate in living cells using an improved set of resonance energy transfer-based biosensors

Improved versions of inositol-1,4,5-trisphosphate (InsP3) sensors were created to follow intracellular InsP3 changes in single living cells and in cell populations. Similar to previous InsP3 sensors the new sensors are based on the ligand binding domain of the human type-I InsP3 receptor (InsP3R-LBD), but contain a mutation of either R265K or R269K to lower their InsP3 binding affinity. Tagging the InsP3R-LBD with N-terminal Cerulean and C-terminal Venus allowed measurement of Ins P3 in single-cell FRET experiments. Replacing Cerulean with a Luciferase enzyme allowed experiments in multi-cell format by measuring the change in the BRET signal upon stimulation. These sensors faithfully followed the agonist-induced increase in InsP3 concentration in HEK 293T cells expressing the Gq-coupled AT1 angiotensin receptor detecting a response to agonist concentration as low as 10 pmol/L. Compared to the wild type InsP3 sensor, the mutant sensors showed an improved off-rate, enabling a more rapid and complete return of the signal to the resting value of InsP3 after termination of M3 muscarinic receptor stimulation by atropine. For parallel measurements of intracellular InsP3 and Ca2+ levels in BRET experiments, the Cameleon D3 Ca2+ sensor was modified by replacing its CFP with luciferase. In these experiments depletion of plasma membrane PtdIns(4,5)P2 resulted in the fall of InsP3 level, followed by the decrease of the Ca2+-signal evoked by the stimulation of the AT1 receptor. In contrast, when type-III PI 4-kinases were inhibited with a high concentration of wortmannin or a more specific inhibitor, A1, the decrease of the Ca2+-signal preceded the fall of InsP3 level indicating an InsP3-, independent, direct regulation of capacitative Ca2+ influx by plasma membrane inositol lipids. Taken together, our results indicate that the improved InsP3 sensor can be used to monitor both the increase and decrease of InsP3 levels in live cells suitable for high-throughput BRET applications. © 2015, Public Library of Science. All rights reserved

Cloud Droplet Size and Liquid Water Path Retrievals From Zenith Radiance Measurements: Examples From the Atmospheric Radiation Measurement Program and the Aerosol Robotic Network

The ground-based Atmospheric Radiation Measurement Program (ARM) and NASA Aerosol Robotic Network (AERONET) routinely monitor clouds using zenith radiances at visible and near-infrared wavelengths. Using the transmittance calculated from such measurements, we have developed a new retrieval method for cloud effective droplet size and conducted extensive tests for non-precipitating liquid water clouds. The underlying principle is to combine a water-absorbing wavelength (i.e. 1640 nm) with a nonwater-absorbing wavelength for acquiring information on cloud droplet size and optical depth. For simulated stratocumulus clouds with liquid water path less than 300 g/sq m and horizontal resolution of 201m, the retrieval method underestimates the mean effective radius by 0.8 m, with a root-mean-squared error of 1.7 m and a relative deviation of 13 %. For actual observations with a liquid water path less than 450 gm.2 at the ARM Oklahoma site during 2007-2008, our 1.5 min-averaged retrievals are generally larger by around 1 m than those from combined ground-based cloud radar and microwave radiometer at a 5min temporal resolution. We also compared our retrievals to those from combined shortwave flux and microwave observations for relatively homogeneous clouds, showing that the bias between these two retrieval sets is negligible, but the error of 2.6 m and the relative deviation of 22% are larger than those found in our simulation case. Finally, the transmittance-based cloud effective droplet radii agree to better than 11% with satellite observations and have a negative bias of 1 m. Overall, the retrieval method provides reasonable cloud effective radius estimates, which can enhance the cloud products of both ARM and AERONET

Characterizing Structural Transitions Using Localized Free Energy Landscape Analysis

Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes.Molecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined) base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom.The calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5' and 3' directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins

A generalized conformational energy function of DNA derived from molecular dynamics simulations

Proteins recognize DNA sequences by two different mechanisms. The first is direct readout, in which recognition is mediated by direct interactions between the protein and the DNA bases. The second is indirect readout, which is caused by the dependence of conformation and the deformability of the DNA structure on the sequence. Various energy functions have been proposed to evaluate the contribution of indirect readout to the free-energy changes in complex formations. We developed a new generalized energy function to estimate the dependence of the deformability of DNA on the sequence. This function was derived from molecular dynamics simulations previously conducted on B-DNA dodecamers, each of which had one possible tetramer sequence embedded at its center. By taking the logarithm of the probability distribution function (PDF) for the base-step parameters of the central base-pair step of the tetramer, its ability to distinguish the native sequence from random ones was superior to that with the previous method that approximated the energy function in harmonic form. From a comparison of the energy profiles calculated with these two methods, we found that the harmonic approximation caused significant errors in the conformational energies of the tetramers that adopted multiple stable conformations

Improved methodical approach for quantitative BRET analysis of G protein coupled receptor dimerization

G Protein Coupled Receptors (GPCR) can form dimers or higher ordered oligomers, the process of which can remarkably influence the physiological and pharmacological function of these receptors. Quantitative Bioluminescence Resonance Energy Transfer (qBRET) measurements are the gold standards to prove the direct physical interaction between the protomers of presumed GPCR dimers. For the correct interpretation of these experiments, the expression of the energy donor Renilla luciferase labeled receptor has to be maintained constant, which is hard to achieve in expression systems. To analyze the effects of non-constant donor expression on qBRET curves, we performed Monte Carlo simulations. Our results show that the decrease of donor expression can lead to saturation qBRET curves even if the interaction between donor and acceptor labeled receptors is non-specific leading to false interpretation of the dimerization state. We suggest here a new approach to the analysis of qBRET data, when the BRET ratio is plotted as a function of the acceptor labeled receptor expression at various donor receptor expression levels. With this method, we were able to distinguish between dimerization and non-specific interaction when the results of classical qBRET experiments were ambiguous. The simulation results were confirmed experimentally using rapamycin inducible heterodimerization system. We used this new method to investigate the dimerization of various GPCRs, and our data have confirmed the homodimerization of V2 vasopressin and CaSR calcium sensing receptors, whereas our data argue against the heterodimerization of these receptors with other studied GPCRs, including type I and II angiotensin, β2 adrenergic and CB1 cannabinoid receptors

PIP5KIβ Selectively Modulates Apical Endocytosis in Polarized Renal Epithelial Cells

Localized synthesis of phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] at clathrin coated pits (CCPs) is crucial for the recruitment of adaptors and other components of the internalization machinery, as well as for regulating actin dynamics during endocytosis. PtdIns(4,5)P2 is synthesized from phosphatidylinositol 4-phosphate by any of three phosphatidylinositol 5-kinase type I (PIP5KI) isoforms (α, β or γ). PIP5KIβ localizes almost exclusively to the apical surface in polarized mouse cortical collecting duct cells, whereas the other isoforms have a less polarized membrane distribution. We therefore investigated the role of PIP5KI isoforms in endocytosis at the apical and basolateral domains. Endocytosis at the apical surface is known to occur more slowly than at the basolateral surface. Apical endocytosis was selectively stimulated by overexpression of PIP5KIβ whereas the other isoforms had no effect on either apical or basolateral internalization. We found no difference in the affinity for PtdIns(4,5)P2-containing liposomes of the PtdIns(4,5)P2 binding domains of epsin and Dab2, consistent with a generic effect of elevated PtdIns(4,5)P2 on apical endocytosis. Additionally, using apical total internal reflection fluorescence imaging and electron microscopy we found that cells overexpressing PIP5KIβ have fewer apical CCPs but more internalized coated structures than control cells, consistent with enhanced maturation of apical CCPs. Together, our results suggest that synthesis of PtdIns(4,5)P2 mediated by PIP5KIβ is rate limiting for apical but not basolateral endocytosis in polarized kidney cells. PtdIns(4,5)P2 may be required to overcome specific structural constraints that limit the efficiency of apical endocytosis. © 2013 Szalinski et al