Innate Intracellular Antiviral Responses Restrict the Amplification of Defective Virus Genomes of Parainfluenza Virus 5.

During the replication of parainfluenza virus 5 (PIV5), copyback defective virus genomes (DVGs) are erroneously produced and are packaged into "infectious" virus particles. Copyback DVGs are the primary inducers of innate intracellular responses, including the interferon (IFN) response. While DVGs can interfere with the replication of nondefective (ND) virus genomes and activate the IFN-induction cascade before ND PIV5 can block the production of IFN, we demonstrate that the converse is also true, i.e., high levels of ND virus can block the ability of DVGs to activate the IFN-induction cascade. By following the replication and amplification of DVGs in A549 cells that are deficient in a variety of innate intracellular antiviral responses, we show that DVGs induce an uncharacterized IFN-independent innate response(s) that limits their replication. High-throughput sequencing was used to characterize the molecular structure of copyback DVGs. While there appears to be no sequence-specific break or rejoining points for the generation of copyback DVGs, our findings suggest there are region, size, and/or structural preferences selected for during for their amplification.IMPORTANCE Copyback defective virus genomes (DVGs) are powerful inducers of innate immune responses both in vitro and in vivo They impact the outcome of natural infections, may help drive virus-host coevolution, and promote virus persistence. Due to their potent interfering and immunostimulatory properties, DVGs may also be used therapeutically as antivirals and vaccine adjuvants. However, little is known of the host cell restrictions which limit their amplification. We show here that the generation of copyback DVGs readily occurs during parainfluenza virus 5 (PIV5) replication, but that their subsequent amplification is restricted by the induction of innate intracellular responses. Molecular characterization of PIV5 copyback DVGs suggests that while there are no genome sequence-specific breaks or rejoin points for the generation of copyback DVGs, genome region, size, and structural preferences are selected for during their evolution and amplification

Early Triassic disaster and opportunistic foraminifers in South China

Survival and recovery are important dynamic processes of biotic evolution during major geological transitions. Disaster and opportunistic taxa are two significant groups that dominate the ecosystem in the aftermath of mass extinction events. Disaster taxa appear immediately after such crises whilst opportunists pre-date the crisis but also bloom in the aftermath. This paper documents three disaster foraminiferal species and seven opportunistic foraminiferal species from Lower Triassic successions of South China. They are characterized by extreme high abundance and low diversity and occurred occasionally in Griesbachian, Smithian and Spathian strata. The characteristics (small size, simple morphology) and stratigraphic ranges of these groups suggest that r-selection is a commonly used strategy for survivors to cope with either harsh post-extinction conditions and/or environments lacking incumbents

Fractal geometry of rocks

The analysis of small- and ultra-small-angle neutron scattering data for sedimentary rocks shows that the pore-rock fabric interface is a surface fractal (Ds = 2.82) over 3 orders of magnitude of the length scale and 10 orders of magnitude in intensity. The fractal dimension and scatterer size obtained from scanning electron microscopy image processing are consistent with neutron scattering data

Progressive environmental deterioration in northwestern Pangea leading to the latest Permian extinction

Stratigraphic records from northwestern Pangea provide unique insight into global processes that occurred during the latest Permian extinction (LPE). We examined a detailed geochemical record of the Festningen section, Spitsbergen. A stepwise extinction is noted as: starting with (1) loss of carbonate shelly macrofauna, followed by (2) loss of siliceous sponges in conjunction with an abrupt change in ichnofabrics as well as dramatic change in the terrestrial environment, and (3) final loss of all trace fossils. We interpret loss of carbonate producers as related to shoaling of the lysocline in higher latitudes, in relationship to building atmospheric CO2. The loss of siliceous sponges is coincident with the global LPE event and is related to onset of high loading rates of toxic metals (Hg, As, Co) that we suggest are derived from Siberian Trap eruptions. The final extinction stage is coincident with redox-sen- sitive trace metal and other proxy data that suggest onset of anoxia after the other extinction events. These results show a remarkable record of progressive environmental deterioration in northwestern Pangea during the extinction crises

Ammonium ocean following the end-Permian mass extinction

The aftermath of end-Permian mass extinction was marked by a ~5 million year interval of poorly-understood, extreme environments that likely hindered biotic recovery. Contemporary nitrogen isotope variations are considered, using a new conceptual model, to support a scenario that shows intensive nitrate-removal processes gradually depleted the global oceanic nitrate inventory during long-lasting oceanic anoxia. Enhanced nitrogen fixation shifted the oceanic nitrogenous nutrient (nutrient-N) inventory to an ammonium dominated state. Ammonium is toxic to animals and higher plants but fertilizes algae and bacteria. This change in ocean chemistry could account for the intense and unexplained losses of nektonic taxa and the proliferation of microbial blooms in the Early Triassic. The transition from a nitrate ocean to an ammonium ocean was accompanied by a decrease in respiration efficiency of organisms and a shrinking oceanic nutrient-N inventory, ultimately leading to generally low productivity in the Early Triassic oceans. These unappreciated nutrient changes during episodes of prolonged ocean anoxia may be the key life-limiting factor at such times

The use of small angle neutron scattering with contrast matching and variable adsorbate partial pressures in the study of porosity in activated carbons

The porosity of a typical activated carbon is investigated with small angle neutron scattering (SANS), using the contrast matching technique, by changing the hydrogen/deuterium content of the absorbed liquid (toluene) to extract the carbon density at different scattering vector (Q) values and by measuring the p/p0 dependence of the SANS, using fully deuterated toluene. The contrast matching data shows that the apparent density is Q-dependent, either because of pores opening near the carbon surface during the activation processor or changes in D-toluene density in nanoscale pores. For each p/p0 value, evaluation of the Porod Invariant yields the fraction of empty pores. Hence, comparison with the adsorption isotherm shows that the fully dry powder undergoes densification when liquid is added. An algebraic function is developed to fit the SANS signal at each p/p0 value hence yielding the effective Kelvin radii of the liquid surfaces as a function of p/p0. These values, when compared with the Kelvin Equation, show that the resultant surface tension value is accurate for the larger pores but tends to increase for small (nanoscale) pores. The resultant pore size distribution is less model-dependent than for the traditional methods of analyzing the adsorption isotherms

SAXS and SANS studies of surfactants and reverse micelles in supercritical CO{sub 2}

Surfactants promise to extend the applicability of supercritical CO{sub 2} (SC-CO{sub 2}) to processing of insoluble materials such as polymers and aqueous systems. In this short paper the authors summarize the techniques for studying surfactants and reverse micelles in SC-CO{sub 2} using SAXS and SANS; they will describe the scattering instruments and the pressure cells for conducting these studies; they will describe the types of measurement that yield the desired characterizations; they will describe the methods of data analysis and interpretation; and they will provide illustrative results from this laboratory. Industry seeks to replace common organic solvents now used in many reaction and separation processes; SC-CO{sub 2} is a potential solvent substitute widely favored by both government and industry. The currently available surfactants are limited in number and performance. In ongoing work the authors are coupling their SAXS and SANS scattering studies with complementary molecular simulations in efforts to understand, at a molecular level, what surfactant characteristics lead to improved performance. They hope that superior surfactants for use in SC-CO{sub 2} can be designed and synthesized based on this new level of understanding

Small angle neutron scattering studies of critical phenomena in a three-component microemulsion

Critical density fluctuations of a ``water-in-oil`` microemulsion consisting of water, benzene, and BHDC (benzyldimethyl-n-hexadecyl ammonium chloride) were observed near the phase boundary by SANS. Observed profiles were well described by product of a form factor of spherical droplets and a structure factor, consisting of a term describing the inter-droplet correlations and also an Ornstein- Zernike component describing the droplet density fluctuations. Allowance was also made fro droplet polydispersity,though the width of the distribution turned out to be very small (1-2%). Observed temperature dependence of osmotic compressibility was fitted using the crossover function proposed by Belyakov et al., and the Ginzburg numbers were obtained on the order of 10{sup -2}. This indicates that long range interdroplet forces are not significant in this system, which displays upper critical solution temperature behavior. In contrast, previous studies of systems displaying lower critical solution temperature behavior (e.g., water, n-decane, and dioctyl sulfosuccinate sodium salt) indicate that long range interactions appear to dominate the phase separation behavior