Structural polymorphism of the HIV-1 leader region explored by computational methods

Experimental studies revealed that the elements of the human immunodeficiency virus type 1 (HIV-1) 5′-untranslated leader region (5′-UTR) can fold in vitro into two alternative conformations, branched (BMH) and ‘linearized’ (LDI) and switch between them to achieve different functionality. In this study we computationally explored in detail, with our massively parallel genetic algorithm (MPGAfold), the propensity of 13 HIV-1 5′-UTRs to fold into the BMH and the LDI conformation types. Besides the BMH conformations these results predict the existence of two functionally equivalent types of LDI conformations. One is similar to what has been shown in vitro to exist in HIV-1 LAI, the other is a novel conformation exemplified by HIV-1 MAL long-distance interactions. These novel MPGAfold results are further corroborated by a consensus probability matrix algorithm applied to a set of 155 HIV-1 sequences. We also have determined in detail the impact of various strain mutations, domain sizes and folds of elongating sequences simulating folding during transcription on HIV-1 RNA secondary structure folding dynamics

Journalists and Safety Training: Experiences and Opinions

Over the last generation, safety trainings (sometimes known as Hostile Environment and First Aid Training or HEFAT) have been widely embraced by the news industry as a means of preparing journalists to cover conflict, crisis and other potentially dangerous assignments. Yet the effectiveness, relevance and usefulness of such trainings – both generally and in terms of specific content and approaches – have not been independently assessed. For this reason, the Dart Center for Journalism and Trauma, a project of the Graduate School of Journalism at Columbia University, surveyed a wide range of journalists around the world about the safety trainings they attended, the skills they acquired and the gaps between these trainings and their professional needs on the ground. From October 2016 to February 2017, 247 journalists completed the survey, which was conducted by the Dart Center’s research lab housed at The University of Tulsa Department of Psychology. This report, prepared by an interdisciplinary team of researchers in psychology, occupational safety and journalism practice, details the survey results. We make no attempt to evaluate particular commercial or nonprofit safety training providers. Instead, this report examines the various approaches to journalism safety training; how journalists assess their training experiences; and the systematic gaps and other issues suggested by their assessments

CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments

We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual information of two alignment positions as well as the position-specific fraction of gaps. The nucleotide composition of both single columns and column pairs is visualized with the help of color-coded 3D bars labeled with letters. The server generates both VRML and JVX output that can be viewed with a VRML viewer or the JavaView applet, respectively. We show that combining these different features of an alignment into one 3D representation is helpful in identifying correlations between bases and potential RNA and DNA base pairs. Significant known correlations between the tRNA 3′ anticodon cardinal nucleotide and the extended anticodon were observed, as were correlations within the amino acid acceptor stem and between the cardinal nucleotide and the acceptor stem. The online server can be accessed using the URL

Coarse Graining RNA Nanostructures for Molecular Dynamics Simulations

A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for the systems of thousands of nucleotides, a time scale of microseconds (i.e. by three orders of magnitude longer than in the full atomistic modelling) and thus to enable simulations of large RNA polymers in the context of bionanotechnology. We find that the 3-beads-per-nucleotide models, described by a set of just a few universal parameters, are able to describe different RNA conformations and are comparable in structural precision to the models where detailed values of the backbone P-C4' dihedrals taken from a reference structure are included. These findings are discussed in the context of the RNA conformation classes

RADAR: a web server for RNA data analysis and research

RADAR is a web server that provides a multitude of functionality for RNA data analysis and research. It can align structure-annotated RNA sequences so that both sequence and structure information are taken into consideration during the alignment process. This server is capable of performing pairwise structure alignment, multiple structure alignment, database search and clustering. In addition, RADAR provides two salient features: (i) constrained alignment of RNA secondary structures, and (ii) prediction of the consensus structure for a set of RNA sequences. RADAR will be able to assist scientists in performing many important RNA mining operations, including the understanding of the functionality of RNA sequences, the detection of RNA structural motifs and the clustering of RNA molecules, among others. The web server together with a software package for download is freely accessible at http://datalab.njit.edu/biodata/rna/RSmatch/server.htm and http://www.ccrnp.ncifcrf.gov/~bshapiro

Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization

Thermodynamic processes with free energy parameters are often used in algorithms that solve the free energy minimization problem to predict secondary structures of single RNA sequences. While results from these algorithms are promising, an observation is that single sequence-based methods have moderate accuracy and more information is needed to improve on RNA secondary structure prediction, such as covariance scores obtained from multiple sequence alignments. We present in this paper a new approach to predicting the consensus secondary structure of a set of aligned RNA sequences via pseudo-energy minimization. Our tool, called RSpredict, takes into account sequence covariation and employs effective heuristics for accuracy improvement. RSpredict accepts, as input data, a multiple sequence alignment in FASTA or ClustalW format and outputs the consensus secondary structure of the input sequences in both the Vienna style Dot Bracket format and the Connectivity Table format. Our method was compared with some widely used tools including KNetFold, Pfold and RNAalifold. A comprehensive test on different datasets including Rfam sequence alignments and a multiple sequence alignment obtained from our study on the Drosophila X chromosome reveals that RSpredict is competitive with the existing tools on the tested datasets. RSpredict is freely available online as a web server and also as a jar file for download at http://datalab.njit.edu/biology/RSpredict

Lattice dynamics reveals a local symmetry breaking in the emergent dipole phase of PbTe

Local symmetry breaking in complex materials is emerging as an important contributor to materials properties but is inherently difficult to study. Here we follow up an earlier structural observation of such a local symmetry broken phase in the technologically important compound PbTe with a study of the lattice dynamics using inelastic neutron scattering (INS). We show that the lattice dynamics are responsive to the local symmetry broken phase, giving key insights in the behavior of PbTe, but also revealing INS as a powerful tool for studying local structure. The new result is the observation of the unexpected appearance on warming of a new zone center phonon branch in PbTe. In a harmonic solid the number of phonon branches is strictly determined by the contents and symmetry of the unit cell. The appearance of the new mode indicates a crossover to a dynamic lower symmetry structure with increasing temperature. No structural transition is seen crystallographically but the appearance of the new mode in inelastic neutron scattering coincides with the observation of local Pb off-centering dipoles observed in the local structure. The observation resembles relaxor ferroelectricity but since there are no inhomogeneous dopants in pure PbTe this anomalous behavior is an intrinsic response of the system. We call such an appearance of dipoles out of a non-dipolar ground-state "emphanisis" meaning the appearance out of nothing. It cannot be explained within the framework of conventional phase transition theories such as soft-mode theory and challenges our basic understanding of the physics of materials

EC11-101 Spring Seed Guide

Welcome to the 2011 Spring Seed Guide. Corn, soybean, sorghum, and alfalfa are included in this seed guide. This circular is a progress report of variety trials conducted by personnel of the Agronomy Department, West Central, and Northeast Extension Centers, and their associated agricultural laboratories and the associates of the University of Wyoming at SAREC