Polarimetric remote sensing in oxygen A and B bands: sensitivity study and information content analysis for vertical profile of aerosols

Theoretical analysis is conducted to reveal the information content of aerosol vertical profile in space-borne measurements of the backscattered radiance and degree of linear polarization (DOLP) in oxygen (O2) A and B bands. Assuming a quasi-Gaussian shape for aerosol vertical profile characterized by peak height H and half width y (at half maximum), the Unified Linearized Vector Radiative Transfer Model (UNL-VRTM) is used to simulate the Stokes fourvector elements of upwelling radiation at the top of atmosphere (TOA) and their Jacobians with respect to H and y. Calculations for different aerosol types and different combinations of H and values show that the wide range of gas absorption optical depth in O2 A and B band enables the sensitivity of backscattered DOLP and radiance at TOA to the aerosol layer at different altitudes. Quantitatively, DOLP in O2 A and B bands is found to be more sensitive to H and y than radiance, especially over the bright surfaces (with large visible reflectance). In many O2 absorption wavelengths, the degree of freedom of signal (DFS) for retrieving H (or y) generally increases with H (and y) and can be close to unity in many cases, assuming that the composite uncertainty from surface and aerosol scattering properties as well as measurements is less than 5%. Further analysis demonstrates that DFS needed for simultaneous retrieval of H and y can be obtained from a combined use of DOLP measurements at ~10–100 O2 A and B absorption wavelengths (or channels), depending on the specific values of H. The higher the aerosol layer, the fewer number of channels for DOLP measurements in O2 A and B bands are needed for characterizing H and . Future hyperspectral measurements of DOLP in O2 A and B bands are needed to continue studying their potential and their combination with radiance and DOLP in atmospheric window channels for retrieving the vertical profiles of aerosols, especially highly scattering aerosols, over land

Formation of stable homodimer via the C-terminal α-helical domain of coronavirus nonstructural protein 9 is critical for its function in viral replication

AbstractCoronaviruses devote more than three quarters of their coding capacity to encode two large polyproteins (1a and 1ab polyproteins), which are proteolytically processed into 15–16 mature, nonstructural replicase proteins (nsp1 to 16). These cleavage products are believed to play essential roles in replication of the giant RNA genome of ∼30 kb and transcription of a nested set of 5 to 9 subgenomic RNA species by a unique discontinuous transcription mechanism. In this report, one of these replicase proteins, nsp9 of the coronavirus infectious bronchitis virus (IBV) is systematically studied using both biochemical and reverse genetic approaches. The results showed that substitution mutation of a conserved Gly (G98) residue in the C-terminal α-helix domain with an Asp greatly destabilized the IBV nsp9 homodimer and abolished its RNA-binding activity. Introduction of the same mutation into an infectious IBV clone system showed that the mutation totally abolishes the transcription of subgenomic RNA and no infectious virus could be recovered. Mutation of a semi-conserved Ile (I95) residue in the same region showed moderately destabilizing effect on the IBV nsp9 homodimer but minimal effect on its RNA-binding activity. Introduction of the mutation into the IBV infectious clone system showed recovery of a mutant virus with severe growth defects, supporting that dimerization is critical for the function of this replicase protein. Meanwhile, mutations of some positively charged residues in the β-barrel regions of the IBV nsp9 protein significantly reduced its RNA-binding activity, but with no obvious effect on dimerization of the protein. Introduction of these mutations into the viral genome showed only mild to moderate effects on the growth and infectivity of the rescued mutant viruses

Polarimetric remote sensing in oxygen A and B bands: sensitivity study and information content analysis for vertical profile of aerosols

Theoretical analysis is conducted to reveal the information content of aerosol vertical profile in space-borne measurements of the backscattered radiance and degree of linear polarization (DOLP) in oxygen (O2) A and B bands. Assuming a quasi-Gaussian shape for aerosol vertical profile characterized by peak height H and half width y (at half maximum), the Unified Linearized Vector Radiative Transfer Model (UNL-VRTM) is used to simulate the Stokes fourvector elements of upwelling radiation at the top of atmosphere (TOA) and their Jacobians with respect to H and y. Calculations for different aerosol types and different combinations of H and values show that the wide range of gas absorption optical depth in O2 A and B band enables the sensitivity of backscattered DOLP and radiance at TOA to the aerosol layer at different altitudes. Quantitatively, DOLP in O2 A and B bands is found to be more sensitive to H and y than radiance, especially over the bright surfaces (with large visible reflectance). In many O2 absorption wavelengths, the degree of freedom of signal (DFS) for retrieving H (or y) generally increases with H (and y) and can be close to unity in many cases, assuming that the composite uncertainty from surface and aerosol scattering properties as well as measurements is less than 5%. Further analysis demonstrates that DFS needed for simultaneous retrieval of H and y can be obtained from a combined use of DOLP measurements at ~10–100 O2 A and B absorption wavelengths (or channels), depending on the specific values of H. The higher the aerosol layer, the fewer number of channels for DOLP measurements in O2 A and B bands are needed for characterizing H and . Future hyperspectral measurements of DOLP in O2 A and B bands are needed to continue studying their potential and their combination with radiance and DOLP in atmospheric window channels for retrieving the vertical profiles of aerosols, especially highly scattering aerosols, over land

An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells

AbstractGenetic manipulation of the RNA genomes by reverse genetics is a powerful tool to study the molecular biology and pathogenesis of RNA viruses. During construction of an infectious clone from a Vero cell-adapted coronavirus infectious bronchitis virus (IBV), we found that a G–C point mutation at nucleotide position 15526, causing Arg-to-Pro mutation at amino acid position 132 of the helicase protein, is lethal to the infectivity of IBV on Vero cells. When the in vitro-synthesized full-length transcripts containing this mutation were introduced into Vero cells, no infectious virus was rescued. Upon correction of the mutation, infectious virus was recovered. Further characterization of the in vitro-synthesized full-length transcripts containing the G15526C mutation demonstrated that this mutation may block the transcription of subgenomic RNAs. Substitution mutation of the Arg132 residue to a positively charged amino acid Lys affected neither the infectivity of the in vitro-synthesized transcripts nor the growth properties of the rescued virus. However, mutation of the Arg132 residue to Leu, a conserved residue in other coronaviruses at the same position, reduced the recovery rate of the in vitro-synthesized transcripts. The recovered mutant virus showed much smaller-sized plaques. On the contrary, a G–C and a G–A point mutations at nucleotide positions 4330 and 9230, respectively, causing Glu–Gln and Gly–Glu mutations in or near the catalytic centers of the papain-like (Nsp3) and 3C-like (Nsp5) proteinases, did not show detectable detrimental effect on the rescue of infectious viruses and the infectivity of the rescued viruses

A Fast Visible-Infrared Imaging Radiometer Suite Simulator for Cloudy Atmopheres

A fast instrument simulator is developed to simulate the observations made in cloudy atmospheres by the Visible Infrared Imaging Radiometer Suite (VIIRS). The correlated k-distribution (CKD) technique is used to compute the transmissivity of absorbing atmospheric gases. The bulk scattering properties of ice clouds used in this study are based on the ice model used for the MODIS Collection 6 ice cloud products. Two fast radiative transfer models based on pre-computed ice cloud look-up-tables are used for the VIIRS solar and infrared channels. The accuracy and efficiency of the fast simulator are quantify in comparison with a combination of the rigorous line-by-line (LBLRTM) and discrete ordinate radiative transfer (DISORT) models. Relative errors are less than 2 for simulated TOA reflectances for the solar channels and the brightness temperature differences for the infrared channels are less than 0.2 K. The simulator is over three orders of magnitude faster than the benchmark LBLRTM+DISORT model. Furthermore, the cloudy atmosphere reflectances and brightness temperatures from the fast VIIRS simulator compare favorably with those from VIIRS observations

Interaction of the Coronavirus Infectious Bronchitis Virus Membrane Protein with β-Actin and Its Implication in Virion Assembly and Budding

Coronavirus M protein is an essential component of virion and plays pivotal roles in virion assembly, budding and maturation. The M protein is integrated into the viral envelope with three transmembrane domains flanked by a short amino-terminal ectodomain and a large carboxy-terminal endodomain. In this study, we showed co-purification of the M protein from coronavirus infectious bronchitis virus (IBV) with actin. To understand the cellular factors that may be involved in virion assembly, budding and maturation processes, IBV M was used as the bait in a yeast two-hybrid screen, resulting in the identification of β-actin as a potentially interacting partner. This interaction was subsequently confirmed by coimmunoprecipitation and immunofluorescence microscopy in mammalian cells, and mutation of amino acids A159 and K160 on the M protein abolished the interaction. Introduction of the A159-K160 mutation into an infectious IBV clone system blocks the infectivity of the clone, although viral RNA replication and subgenomic mRNA transcription were actively detected. Disruption of actin filaments with cell-permeable agent cytochalasin D at early stages of the infection cycle led to the detection of viral protein synthesis in infected cells but not release of virus particles to the cultured media. However, the same treatment at late stages of the infection cycle did not affect the release of virus particles to the media, suggesting that disruption of the actin filaments might block virion assembly and budding, but not release of the virus particles. This study reveals an essential function of actin in the replication cycle of coronavirus

Up-Regulation of Mcl-1 and Bak by Coronavirus Infection of Human, Avian and Animal Cells Modulates Apoptosis and Viral Replication

Virus-induced apoptosis and viral mechanisms that regulate this cell death program are key issues in understanding virus-host interactions and viral pathogenesis. Like many other human and animal viruses, coronavirus infection of mammalian cells induces apoptosis. In this study, the global gene expression profiles are first determined in IBV-infected Vero cells at 24 hours post-infection by Affymetrix array, using avian coronavirus infectious bronchitis virus (IBV) as a model system. It reveals an up-regulation at the transcriptional level of both pro-apoptotic Bak and pro-survival myeloid cell leukemia-1 (Mcl-1). These results were further confirmed both in vivo and in vitro, in IBV-infected embryonated chicken eggs, chicken fibroblast cells and mammalian cells at transcriptional and translational levels, respectively. Interestingly, the onset of apoptosis occurred earlier in IBV-infected mammalian cells silenced with short interfering RNA targeting Mcl-1 (siMcl-1), and was delayed in cells silenced with siBak. IBV progeny production and release were increased in infected Mcl-1 knockdown cells compared to similarly infected control cells, while the contrary was observed in infected Bak knockdown cells. Furthermore, IBV infection-induced up-regulation of GADD153 regulated the expression of Mcl-1. Inhibition of the mitogen-activated protein/extracellular signal-regulated kinase (MEK/ERK) and phosphoinositide 3-kinase (PI3K/Akt) signaling pathways by chemical inhibitors and knockdown of GADD153 by siRNA demonstrated the involvement of ER-stress response in regulation of IBV-induced Mcl-1 expression. These results illustrate the sophisticated regulatory strategies evolved by a coronavirus to modulate both virus-induced apoptosis and viral replication during its replication cycle

Upregulation of CHOP/GADD153 during coronavirus infectious bronchitis virus infection modulates apoptosis by restricting activation of the extracellular signal-regulated kinase pathway

Induction of the unfolded protein response (UPR) is an adaptive cellular response to endoplasmic reticulum (ER) stress that allows a cell to reestablish ER homeostasis. However, under severe and persistent ER stress, prolonged UPR may activate unique pathways that lead to cell death. In this study, we investigated the activation of the protein kinase R-like ER kinase (PERK) pathway of UPR in cells infected with the coronavirus infectious bronchitis virus (IBV) and its relationship with IBV-induced apoptosis. The results showed moderate induction of PERK phosphorylation in IBV-infected cells. Meanwhile, activating transcription factor 4 (ATF4) was upregulated at the protein level in the infected cells, resulting in the induction in trans of the transcription factor ATF3 and the proapoptotic growth arrest and DNA damage-inducible protein GADD153. Knockdown of PERK by small interfering RNA (siRNA) suppressed the activation of GADD153 and the IBV-induced apoptosis. Interestingly, knockdown of protein kinase R (PKR) by siRNA and inhibition of the PKR kinase activity by 2-aminopurine (2-AP) also reduced the IBV-induced upregulation of GADD153 and apoptosis induction. In GADD153-knockdown cells, IBV-induced apoptosis was suppressed and virus replication inhibited, revealing a key role of GADD153 in IBV-induced cell death and virus replication. Analysis of the pathways downstream of GADD153 revealed much more activation of the extracellular signal-related kinase (ERK) pathway in GADD153-knockdown cells during IBV infection, indicating that GADD153 may modulate apoptosis through suppression of the pathway. This study provides solid evidence that induction of GADD153 by PERK and PKR plays an important regulatory role in the apoptotic process triggered by IBV infection