Transfer RNA Mimicry in a New Group of Positive-Strand RNA Plant Viruses, the Furoviruses: Differential Aminoacylation between the RNA Components of One Genome

AbstractRecent sequencing of the genomes of several furoviruses—fungus-transmitted rod-shaped positive-strand plant viruses—has suggested the presence of tRNA-like structures (TLSs) at the 3′ ends of the genomic RNAs. We show here that the genomic RNAs of soil-borne wheat mosaic virus (SBWMV), beet soil-borne virus (BSBV), potato mop-top virus (PMTV), peanut clump virus (PCV), and Indian peanut clump virus (IPCV) all possess functional TLSs that are capable of high-efficiency valylation. While the SBWMV, BSBV, and PMTV TLSs are similar to those found in tymoviruses, the PCV and IPCV TLSs harbor an insertion of about 40 nucleotides between the two halves of the TLS. The valylated SBWMV and BSBV RNAs formed tight complexes with wheat germ EF-1α · GTP (Kd= 2 to 11 nM), whereas valylated PMTV, PCV, and IPCV RNAs bound EF-1α · GTP weakly (Kd≥ 50 nM). The TLS of PCV RNA2 differs from PCV RNA1 in lacking the major valine identity nucleotide in the anticodon and consequently is capable of only very inefficient valylation. This is the first case of differential aminoacylation between the RNA components of one genome

Effects of stellar outflows on interstellar sulfur oxide chemistry

Interferometer Maps with 2" to 6" resolution of a number of regions with active star formation (Orion A, W49, W51, SGRB2) show that the distribution of the molecule SO is very compact around stellar outflow sources. Both SO and SO2 were studied near three outflows, OrionA/IRc2 and two sources in W49. The two molecules have similar distributions and abundances. More than 95% of the emission comes from regions whose extents are only .05 to .2 pc., being larger around the more energetic sources. Their spectra are broad, 30 km/sec or more, suggesting that the oxide production is associated with the flows. The outflows are identified by water masers and by extended bipolar flows in SiO. Maps in other molecules, such as HCO+ and CS, which have similar collisional excitation requirements, have much greater spatial extent. Thus it appears that the SO and SO2 abundances are truly compact and are closely associated with the outflows

Physics development of web-based tools for use in hardware clusters doing lattice physics

Jefferson Lab and MIT are developing a set of web-based tools within the Lattice Hadron Physics Collaboration to allow lattice QCD theorists to treat the computational facilities located at the two sites as a single meta-facility. The prototype Lattice Portal provides researchers the ability to submit jobs to the cluster, browse data caches, and transfer files between cache and off-line storage. The user can view the configuration of the PBS servers and to monitor both the status of all batch queues as well as the jobs in each queue. Work is starting on expanding the present system to include job submissions at the meta-facility level (shared queue), as well as multi-site file transfers and enhanced policy-based data management capabilities

The galactic magnetic field in the quasar 3C216

Multifrequency polarimetric observations made with the Very Long Baseline Array of the quasar 3C216 reveal the presence of Faraday rotation measures (RMs) in excess of 2000 rad/m**2 in the source rest frame, in the arc of emission located at ~ 140 mas from the core. Rotation measures in the range -300 - +300 rad/m**2 are detected in the inner 5 mas (~30 parsecs). while the rotation measures near the core can be explained as due to a magnetic field in the narrow line region, we favor the interpretation for the high RM in the arc as due to a ``local'' Faraday screen, produced in a shock where the jet is deflected by the interstellar medium of the host galaxy. Our results indicate that a galacit magnetic field of the order of 50 microGauss on a scale greater than 100 pc must be present in the galactic medium.Comment: 23 pages, 3 tables, 11 figures. To appear on The Astronomical Journal, November 1999 Issu

Physicochemical analysis of rotavirus segment 11 supports a 'modified panhandle' structure and not the predicted alternative tRNA-like structure (TRLS)

.Rotaviruses are a major cause of acute gastroenteritis, which is often fatal in infants. The viral genome consists of 11 double-stranded RNA segments, but little is known about their cis-acting sequences and structural elements. Covariation studies and phylogenetic analysis exploring the potential structure of RNA11 of rotaviruses suggested that, besides the previously predicted "modified panhandle" structure, the 5' and 3' termini of one of the isoforms of the bovine rotavirus UKtc strain may interact to form a tRNA-like structure (TRLS). Such TRLSs have been identified in RNAs of plant viruses, where they are important for enhancing replication and packaging. However, using tRNA mimicry assays (in vitro aminoacylation and 3'- adenylation), we found no biochemical evidence for tRNA-like functions of RNA11. Capping, synthetic 3' adenylation and manipulation of divalent cation concentrations did not change this finding. NMR studies on a 5'- and 3'-deletion construct of RNA11 containing the putative intra-strand complementary sequences supported a predominant panhandle structure and did not conform to a cloverleaf fold despite the strong evidence for a predicted structure in this conserved region of the viral RNA. Additional viral or cellular factors may be needed to stabilise it into a form with tRNA-like properties

Configuring the HYSPLIT Model for National Weather Service Forecast Office and Spaceflight Meteorology Group Applications

The National Weather Service Forecast Office in Melbourne, FL (NWS MLB) is responsible for providing meteorological support to state and county emergency management agencies across East Central Florida in the event of incidents involving the significant release of harmful chemicals, radiation, and smoke from fires and/or toxic plumes into the atmosphere. NWS MLB uses the National Oceanic and Atmospheric Administration Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model to provide trajectory, concentration, and deposition guidance during such events. Accurate and timely guidance is critical for decision makers charged with protecting the health and well-being of populations at risk. Information that can describe the geographic extent of areas possibly affected by a hazardous release, as well as to indicate locations of primary concern, offer better opportunity for prompt and decisive action. In addition, forecasters at the NWS Spaceflight Meteorology Group (SMG) have expressed interest in using the HYSPLIT model to assist with Weather Flight Rules during Space Shuttle landing operations. In particular, SMG would provide low and mid-level HYSPLIT trajectory forecasts for cumulus clouds associated with smoke plumes, and high-level trajectory forecasts for thunderstorm anvils. Another potential benefit for both NWS MLB and SMG is using the HYSPLIT model concentration and deposition guidance in fog situations

Insight into nucleon structure from generalized parton distributions

The lowest three moments of generalized parton distributions are calculated in full QCD and provide new insight into the behavior of nucleon electromagnetic form factors, the origin of the nucleon spin, and the transverse structure of the nucleon.Comment: 3 pages, Lattice2003(Theoretical developments

Numerical modeling of quasiplanar giant water waves

In this work we present a further analytical development and a numerical implementation of the recently suggested theoretical model for highly nonlinear potential long-crested water waves, where weak three-dimensional effects are included as small corrections to exact two-dimensional equations written in the conformal variables [V.P. Ruban, Phys. Rev. E 71, 055303(R) (2005)]. Numerical experiments based on this theory describe the spontaneous formation of a single weakly three-dimensional large-amplitude wave (alternatively called freak, killer, rogue or giant wave) on the deep water.Comment: revtex4, 8 pages, 7 figure