Genetic lesions within the 3a gene of SARS-CoV

A series of frameshift mutations within the 3a gene has been observed in culture-derived severe acute respiratory syndrome coronavirus (SARS-CoV). We report here that viral RNA from clinical samples obtained from SARS-CoV infected patients also contains a heterogeneous population of wild-type and mutant 3a transcripts.Web of Scienc

A Novel Severe Acute Respiratory Syndrome Coronavirus Protein, U274, is transported to the Cell Surface and undergoes Endocytosis

The severe acute respiratory syndrome coronavirus (SARS-CoV) genome contains open reading frames (ORFs) that encode for several genes that are homologous to proteins found in all known coronaviruses. These are the replicase gene 1a/1b and the four structural proteins, nucleocapsid (N), spike (S), membrane (M), and envelope (E), and these proteins are expected to be essential for the replication of the virus. In addition, this genome also contains nine other potential ORFs varying in length from 39 to 274 amino acids. The largest among these is the first ORF of the second longest subgenomic RNA, and this protein (termed U274 in the present study) consists of 274 amino acids and contains three putative transmembrane domains. Using antibody specific for the C terminus of U274, we show U274 to be expressed in SARS-CoV-infected Vero E6 cells and, in addition to the full-length protein, two other processed forms were also detected. By indirect immunofluorescence, U274 was localized to the perinuclear region, as well as to the plasma membrane, in both transfected and infected cells. Using an N terminus myc-tagged U274, the topology of U274 and its expression on the cell surface were confirmed. Deletion of a cytoplasmic domain of U274, which contains Yxx and diacidic motifs, abolished its transport to the cell surface. In addition, U274 expressed on the cell surface can internalize antibodies from the culture medium into the cells. Coimmunoprecipitation experiments also showed that U274 could interact specifically with the M, E, and S structural proteins, as well as with U122, another protein that is unique to SARS-CoV.Web of Scienc

Cellular Characterization of SARS Coronavirus Nucleocapsid

The Severe and Acute Respiratory Syndrome coronavirus (SARS CoV) is a newly-emerged virus that caused an outbreak of atypical pneumonia in the winter of 2002-2003. Polyclonal antibodies raised against the nucleocapsid (N) of the SARS CoV showed the localization of N to the cytoplasm and the nucleolus in virus-infected and N-expressing Vero E6 cells. Like other coronavirus N proteins, the SARS N is probably a phosphoprotein. N protein expressed in mammalian cells is apparently able to “spread” to neighboring cells. For N to spread to neighboring cells, it must be exported out of the expressing cells. This is shown by the immunoprecipitation of N from the culture medium of a stable cell line expressing myc-N. Deletion studies showed that the 27 kD C-terminal domain of N (C1/2) is the minimal region of N that can spread to other cells. The nucleolar localization and spreading of N are artefacts of fixation, reminiscent of other protein-transduction domain (PTD)-containing proteinsWeb of Scienc

A general T-matrix approach applied to two-body and three-body problems in cold atomic gases

We propose a systematic T-matrix approach to solve few-body problems with s-wave contact interactions in ultracold atomic gases. The problem is generally reduced to a matrix equation expanded by a set of orthogonal molecular states, describing external center-of-mass motions of pairs of interacting particles; while each matrix element is guaranteed to be finite by a proper renormalization for internal relative motions. This approach is able to incorporate various scattering problems and the calculations of related physical quantities in a single framework, and also provides a physically transparent way to understand the mechanism of resonance scattering. For applications, we study two-body effective scattering in 2D-3D mixed dimensions, where the resonance position and width are determined with high precision from only a few number of matrix elements. We also study three fermions in a (rotating) harmonic trap, where exotic scattering properties in terms of mass ratios and angular momenta are uniquely identified in the framework of T-matrix.Comment: 14 pages, 4 figure

Complementarity and the uncertainty relations

We formulate a general complementarity relation starting from any Hermitian operator with discrete non-degenerate eigenvalues. We then elucidate the relationship between quantum complementarity and the Heisenberg-Robertson's uncertainty relation. We show that they are intimately connected. Finally we exemplify the general theory with some specific suggested experiments.Comment: 9 pages, 4 figures, REVTeX, uses epsf.sty and multicol.st

Severe acute respiratory syndrome coronavirus protein 7a interacts with hSGT

Severe acute respiratory syndrome coronavirus (SARS-CoV) 7a is an accessory protein with no known homologues. In this study, we report the interaction of a SARS-CoV 7a and small glutamine-rich tetratricopeptide repeat-containing protein (SGT). SARS-CoV 7a and human SGT interaction was identified using a two-hybrid system screen and confirmed with interaction screens in cell culture and cellular co-localization studies. The SGT domain of interaction was mapped by deletion mutant analysis and results indicated that tetratricopeptide repeat 2 (aa 125-158) was essential for interaction. We also showed that 7a interacted with SARS-CoV structural proteins M (membrane) and E (envelope), which have been shown to be essential for virus-like particle formation. Taken together, our results coupled with data from studies of the interaction between SGT and HIV-1 vpu indicated that SGT could be involved in the life-cycle, possibly assembly of SARS-CoV.IS

Over-expression of severe acute respiratory syndrome coronavirus 3b protein induces both apoptosis and necrosis in Vero E6 cells

The genome of the severe acute respiratory syndrome coronavirus encodes for eight accessory viral proteins with no known homologues in other coronaviruses. One of these is the 3b protein, which is encoded by the second open reading frame in subgenomic RNA 3 and contains 154 amino acids. Here, a detailed time-course study was performed to compare the apoptosis and necrosis profiles induced by full-length 3b, a 3b mutant that was deleted by 30 amino acids from the C terminus (3b 124-154) and the classical apoptosis inducer, Bax. Our results showed that Vero E6 cells transfected with a construct for expressing 3b underwent necrosis as early as 6 h after transfection and underwent simultaneous necrosis and apoptosis at later time-points. At all the time-points analysed, the apoptosis induced by the expression of 3b was less than the level induced by Bax but the level of necrosis was comparable. The 3b 124-154 mutant behaves in a similar manner indicating that the localization of the 3b protein does not seems to be important for the cell-death pathways since full-length 3b is localized predominantly to the nucleolus, while the mutant is found to be concentrated in the peri-nuclear regions. To our knowledge, this is the first report of the induction of necrosis by a SARS-CoV protein.IS

Direct measurement of optical quasidistribution functions: multimode theory and homodyne tests of Bell's inequalities

We develop a multimode theory of direct homodyne measurements of quantum optical quasidistribution functions. We demonstrate that unbalanced homodyning with appropriately shaped auxiliary coherent fields allows one to sample point-by-point different phase space representations of the electromagnetic field. Our analysis includes practical factors that are likely to affect the outcome of a realistic experiment, such as non-unit detection efficiency, imperfect mode matching, and dark counts. We apply the developed theory to discuss feasibility of observing a loophole-free violation of Bell's inequalities by measuring joint two-mode quasidistribution functions under locality conditions by photon counting. We determine the range of parameters of the experimental setup that enable violation of Bell's inequalities for two states exhibiting entanglement in the Fock basis: a one-photon Fock state divided by a 50:50 beam splitter, and a two-mode squeezed vacuum state produced in the process of non-degenerate parametric down-conversion.Comment: 18 pages, 7 figure