SWIRP (Submm-Wave and Long Wave InfraRed Polarimeter); Development and Characterization of a Sub-Mm Polarimeter for Ice Cloud Investigations

A major source of uncertainty in climate models is the presence, shape and distribution of ice particles in the uppermost layers of the clouds. The effects of this component are poorly constrained, turning ice particles into an almost-free variable in many climate models.NASA-GSFC is developing a new instrument aimed at measuring the size and shape of ice particles. The instrument consists of two sub-mm polarimeters (at 220 and 670 GHz) coupled with a long-wave infrared polarimeter at 10 micron. Each polarimeter has identical V-pol and H-pol channels; the axes of polarization are defined geometrically by the orientation of the waveguide elements, and the purity has been measured in the lab. The instrument is configured as a conical scanner, suitable for deployment as a payload on a small satellite or on a high-altitude sub-orbital platform. From a 400 km orbit, the instrument has a 3dB spatial resolution of 20 (10) km at 220 (670) GHz and a swath of 600 km over 180 degrees of view.The BAPTA (Bearing And Power Transfer Assembly) carries heritage from the SSMIS design, now in its 22nd year of on-orbit operation, but with a much reduced SWaP (Size Weight and Power) footprint, suitable for a small satellite.The main components of the instrument have been fabricated and are undergoing final testing prior to their integration as a single unit. The sub-mm channels have dedicated secondary reflectors which illuminate a shared primary reflector. The receiving units are placed behind the focal point of the optical arrangement, so that all beams equally illuminate the primary reflector and are almost co-located on the ground (within a single 220 GHz footprint). Primary and secondary beam patterns have been measured and verified to match the as-designed expectations. A Zytex (TM) window is deployed to protect the secondary reflectors and the feed horns from debris and other contaminants, and to reduce the heat load from the active (hot) IR calibration unit. The insertion loss of Zytex has been measured and is accounted in the calibration equation of the sub-mm channels.The radiometric performance of the sub-mm receivers has been characterized in the lab and under operational conditions of temperature and pressure.This paper discusses the design constraints on the sub-mm components, details of the scientific goals and their flowdown, and describes the characterization of the polarimeters. Options to optimize the layout and distribution of the masses within the assembly, with the goal of making the instrument even more compact and fully-compatible with cubesat-class satellites will be presented

Land cover classification using multi-temporal MERIS vegetation indices

The spectral, spatial, and temporal resolutions of Envisat's Medium Resolution Imaging Spectrometer (MERIS) data are attractive for regional- to global-scale land cover mapping. Moreover, two novel and operational vegetation indices derived from MERIS data have considerable potential as discriminating variables in land cover classification. Here, the potential of these two vegetation indices (the MERIS global vegetation index (MGVI), MERIS terrestrial chlorophyll index (MTCI)) was evaluated for mapping eleven broad land cover classes in Wisconsin. Data acquired in the high and low chlorophyll seasons were used to increase inter-class separability. The two vegetation indices provided a higher degree of inter-class separability than data acquired in many of the individual MERIS spectral wavebands. The most accurate landcover map (73.2%) was derived from a classification of vegetation index-derived data with a support vector machine (SVM), and was more accurate than the corresponding map derived from a classification using the data acquired in the original spectral wavebands

Mapping the Structure and Function of the E1 and E2 Glycoproteins in Alphaviruses

The 9 Å resolution cryo-electron microscopy map of Sindbis virus presented here provides structural information on the polypeptide topology of the E2 protein, on the interactions between the E1 and E2 glycoproteins in the formation of a heterodimer, on the difference in conformation of the two types of trimeric spikes, on the interaction between the transmembrane helices of the E1 and E2 proteins, and on the conformational changes that occur when fusing with a host cell. The positions of various markers on the E2 protein established the approximate topology of the E2 structure. The largest conformational differences between the icosahedral surface spikes at icosahedral 3-fold and quasi-3-fold positions are associated with the monomers closest to the 5-fold axes. The long E2 monomers, containing the cell receptor recognition motif at their extremities, are shown to rotate by about 180^o and to move away from the center of the spikes during fusion

Measurements and Modeling of Near-Surface Radio Propagation in Glacial Ice and Implications for Neutrino Experiments

We present measurements of radio transmission in the $\sim$100 MHz range through a $\sim100$ m deep region below the surface of the ice at Summit Station, Greenland, called the firn. In the firn, the index of refraction changes due to the transition from snow at the surface to glacial ice below, affecting the propagation of radio signals in that region. We compare our observations to a finite-difference time-domain (FDTD) electromagnetic wave simulation, which supports the existence of three classes of propagation: a bulk propagation ray-bending mode that leads to so-called "shadowed" regions for certain geometries of transmission, a surface-wave mode induced by the ice/air interface, and an arbitrary-depth horizontal propagation mode that requires perturbations from a smooth density gradient. In the non-shadowed region, our measurements are consistent with the bulk propagation ray-bending mode both in timing and in amplitude. We also observe signals in the shadowed region, in conflict with a bulk-propagation-only ray-bending model, but consistent with FDTD simulations using a variety of firn models for Summit Station. The amplitude and timing of our measurements in all geometries are consistent with the predictions from FDTD simulations. In the shadowed region, the amplitude of the observed signals is consistent with a best-fit coupling fraction value of $2.4$% (0.06% in power) or less to a surface or horizontal propagation mode from the bulk propagation mode. The relative amplitude of observable signals in the two regions is important for experiments that aim to detect radio emission from astrophysical high-energy neutrinos interacting in glacial ice, which rely on a radio propagation model to inform simulations and perform event reconstruction.Comment: 14 pages, 13 figures, version accepted to PR

Visualization of membrane protein domains by cryo-electron microscopy of dengue virus

Improved technology for reconstructing cryo-electron microscopy (cryo-EM) images has now made it possible to determine secondary structural features of membrane proteins in enveloped viruses. The structure of mature dengue virus particles was determined to a resolution of 9.5 Å by cryo-EM and image reconstruction techniques, establishing the secondary structural disposition of the 180 envelope (E) and 180 membrane (M) proteins in the lipid envelope. The ɑ-helical 'stem' regions of the E molecules, as well as part of the N-terminal section of the M proteins, are buried in the outer leaflet of the viral membrane. The 'anchor' regions of E and the M proteins each form antiparallel E-E and M-M transmembrane alpha-helices, leaving their C termini on the exterior of the viral membrane, consistent with the predicted topology of the unprocessed polyprotein. This is one of only a few determinations of the disposition of transmembrane proteins in situ and shows that the nucleocapsid core and envelope proteins do not have a direct interaction in the mature virus

Structure of Dengue Virus: Implications for Flavivirus Organization, Maturation, and Fusion

The first structure of a flavivirus has been determined by using a combination of cryoelectron microscopy and fitting of the known structure of glycoprotein E into the electron density map. The virus core, within a lipid bilayer, has a less-ordered structure than the external, icosahedral scaffold of 90 glycoprotein E dimers. The three E monomers per icosahedral asymmetric unit do not have quasiequivalent symmetric environments. Difference maps indicate the location of the small membrane protein M relative to the overlaying scaffold of E dimers. The structure suggests that flaviviruses, and by analogy also alphaviruses, employ a fusion mechanism in which the distal barrels of domain II of the glycoprotein E are inserted into the cellular membrane

Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate

Hen egg-white lysozyme (HEWL) was the first enzyme to have its three-dimensional structure determined by X-ray diffraction techniques(1). A catalytic mechanism, featuring a long-lived oxo-carbenium-ion intermediate, was proposed on the basis of model-building studies(2). The `Phillips' mechanism is widely held as the paradigm for the catalytic mechanism of beta -glycosidases that cleave glycosidic linkages with net retention of configuration of the anomeric centre. Studies with other retaining beta -glycosidases, however, provide strong evidence pointing to a common mechanism for these enzymes that involves a covalent glycosyl-enzyme intermediate, as previously postulated(3). Here we show, in three different cases using electrospray ionization mass spectrometry, a catalytically competent covalent glycosyl-enzyme intermediate during the catalytic cycle of HEWL. We also show the three-dimensional structure of this intermediate as determined by Xray diffraction. We formulate a general catalytic mechanism for all retaining beta -glycosidases that includes substrate distortion, formation of a covalent intermediate, and the electrophilic migration of C1 along the reaction coordinate

Bayesian Classification and Regression Trees for Predicting Incidence of Cryptosporidiosis

Background Classification and regression tree (CART) models are tree-based exploratory data analysis methods which have been shown to be very useful in identifying and estimating complex hierarchical relationships in ecological and medical contexts. In this paper, a Bayesian CART model is described and applied to the problem of modelling the cryptosporidiosis infection in Queensland, Australia. Methodology/Principal Findings We compared the results of a Bayesian CART model with those obtained using a Bayesian spatial conditional autoregressive (CAR) model. Overall, the analyses indicated that the nature and magnitude of the effect estimates were similar for the two methods in this study, but the CART model more easily accommodated higher order interaction effects. Conclusions/Significance A Bayesian CART model for identification and estimation of the spatial distribution of disease risk is useful in monitoring and assessment of infectious diseases prevention and control

Structural Studies of West Nile Virus in Complex with Neutralizing Antibodies.

West Nile virus (WNV) is a positive strand RNA virus in the family Flaviviridae, which includes members such as dengue, Japanese encephalitis, tick-borne encephalitis, yellow fever and Hepatitis C. As with other members of the genus, it is arthropod transmitted and has recently established itself as an endemic virus in the United States. Although most infections are asymptomatic, clinical manifestations of WNV include encephalitis and death. We have been interested in investigating the nature of the immune response with particular emphasis on the role of antibodies in reducing the level of infection. We have used a combination of techniques, but primarily structure, as a tool to probe the nature of antibody-mediated virus neutralization. Our results suggest that neutralization of virus particles is more complex than originally envisioned, with multiple mechanisms utilized. Using a combination of X-ray crystallography and cryo-electron microscopy, several virus-antibody complexes have been determined at pseudo-atomic resolution. These studies suggest the following: 1) flavivirus particles exhibit dynamic motions or breathing that transiently expose cryptic epitopes; 2) although there are 180 potential binding sites for each monoclonal antibody the quasi-equivalent nature of the virion usually permits only a subset of sites to be utilized; 3) the availability of these sites, the epitope itself, and the avidity of antibody directly influence the mechanism of neutralization; and 4) particles thought to be incapable of infecting cells, so-called immature viruses, may play a critical role in immune surveillance and reactivity. The structure of the flavivirus virion and complexes of monoclonal antibodies will be presented along with data to support mechanisms antibody-mediated flavivirus neutralizatio

Expression of Distal-less, dachshund, and optomotor blind in Neanthes arenaceodentata (Annelida, Nereididae) does not support homology of appendage-forming mechanisms across the Bilateria

The similarity in the genetic regulation of arthropod and vertebrate appendage formation has been interpreted as the product of a plesiomorphic gene network that was primitively involved in bilaterian appendage development and co-opted to build appendages (in modern phyla) that are not historically related as structures. Data from lophotrochozoans are needed to clarify the pervasiveness of plesiomorphic appendage forming mechanisms. We assayed the expression of three arthropod and vertebrate limb gene orthologs, Distal-less (Dll), dachshund (dac), and optomotor blind (omb), in direct-developing juveniles of the polychaete Neanthes arenaceodentata. Parapodial Dll expression marks premorphogenetic notopodia and neuropodia, becoming restricted to the bases of notopodial cirri and to ventral portions of neuropodia. In outgrowing cephalic appendages, Dll activity is primarily restricted to proximal domains. Dll expression is also prominent in the brain. dac expression occurs in the brain, nerve cord ganglia, a pair of pharyngeal ganglia, presumed interneurons linking a pair of segmental nerves, and in newly differentiating mesoderm. Domains of omb expression include the brain, nerve cord ganglia, one pair of anterior cirri, presumed precursors of dorsal musculature, and the same pharyngeal ganglia and presumed interneurons that express dac. Contrary to their roles in outgrowing arthropod and vertebrate appendages, Dll, dac, and omb lack comparable expression in Neanthes appendages, implying independent evolution of annelid appendage development. We infer that parapodia and arthropodia are not structurally or mechanistically homologous (but their primordia might be), that Dll’s ancestral bilaterian function was in sensory and central nervous system differentiation, and that locomotory appendages possibly evolved from sensory outgrowths