Study of resonance light scattering for remote optical probing

Enhanced scattering and fluorescence processes in the visible and UV were investigated which will enable improved remote measurements of gas properties. The theoretical relationship between scattering and fluorescence from an isolated molecule in the approach to resonance is examined through analysis of the time dependence of re-emitted light following excitation of pulsed incident light. Quantitative estimates are developed for the relative and absolute intensities of fluorescence and resonance scattering. New results are obtained for depolarization of scattering excited by light at wavelengths within a dissociative continuum. The experimental work was performed in two separate facilities. One of these utilizes argon and krypton lasers, single moded by a tilted etalon, and a 3/4 meter double monochromator. This facility was used to determine properties of the re-emission from NO2, I2 and O3 excited by visible light. The second facility involves a narrow-line dye laser, and a 3/4 meter single monochromator. The dye laser produces pulsed light with 5 nsec pulse duration and 0.005 nm spectral width

Redefining the expressed prototype SICAvar gene involved in Plasmodium knowlesi antigenic variation

<p>Abstract</p> <p>Background</p> <p>The <it>SICAvar </it>gene family, expressed at the surface of infected erythrocytes, is critical for antigenic variation in <it>Plasmodium knowlesi</it>. When this family was discovered, a prototypic <it>SICAvar </it>gene was characterized and defined by a 10-exon structure. The predicted 205-kDa protein lacked a convincing signal peptide, but included a series of variable cysteine-rich modules, a transmembrane domain encoded by the penultimate exon, and a cytoplasmic domain encoded by the final highly conserved exon. The <it>205 SICAvar </it>gene and its family with up to 108 possible family members, was identified prior to the sequencing of the <it>P. knowlesi </it>genome. However, in the published <it>P. knowlesi </it>database this gene remains disjointed in five fragments. This study addresses a number of structural and functional questions that are critical for understanding <it>SICAvar </it>gene expression.</p> <p>Methods</p> <p>Database mining, bioinformatics, and traditional genomic and post-genomic experimental methods including proteomic technologies are used here to confirm the genomic context and expressed structure of the prototype <it>205 SICAvar </it>gene.</p> <p><b>Results</b></p> <p>This study reveals that the <it>205 SICAvar </it>gene reported previously to have a 10-exon expressed gene structure has, in fact, 12 exons, with an unusually large and repeat-laden intron separating two newly defined upstream exons and the <it>bona fide </it>5'UTR from the remainder of the gene sequence. The initial exon encodes a PEXEL motif, which may function to localize the SICA protein in the infected erythrocyte membrane. This newly defined start of the 205 <it>SICAvar </it>sequence is positioned on chromosome 5, over 340 kb upstream from the rest of the telomerically positioned <it>SICAvar </it>gene sequence in the published genome assembly. This study, however, verifies the continuity of these sequences, a 9.5 kb transcript, and provides evidence that the 205 <it>SICAvar </it>gene is located centrally on chromosome 5.</p> <p>Conclusion</p> <p>The prototype <it>205 SICAvar </it>gene has been redefined to have a 12-exon structure. These data are important because they 1) address questions raised in the <it>P. knowlesi </it>genome database regarding <it>SICAvar </it>gene fragments, numbers and structures, 2) show that this prototype gene encodes a PEXEL motif, 3) emphasize the need for further refinement of the <it>P. knowlesi </it>genome data, and 4) retrospectively, provide evidence for recombination within centrally located <it>SICAvar </it>sequences.</p

Performance modeling of ultraviolet Raman lidar systems for daytime profiling of atmospheric water vapor

We describe preliminary results from a comprehensive computer model developed to guide optimization of a Raman lidar system for measuring daytime profiles of atmospheric water vapor, emphasizing an ultraviolet, solar-blind approach

Phenex: Ontological Annotation of Phenotypic Diversity

Phenex is a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic variation using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Despite the centrality of the phenotype to so much of biology, traditions for communicating information about phenotypes are idiosyncratic to different disciplines. Phenotypes seem to elude standardized descriptions due to the variety of traits that compose them and the difficulty of capturing the complex forms and subtle differences among organisms that we can readily observe. Consequently, phenotypes are refractory to attempts at data integration that would allow computational analyses across studies and study systems. Phenex addresses this problem by allowing scientists to employ standard ontologies and syntax to link computable phenotype annotations to evolutionary character matrices, as well as to link taxa and specimens to ontological identifiers. Ontologies have become a foundational technology for establishing shared semantics, and, more generally, for capturing and computing with biological knowledge

apex: phylogenetics with multiple genes.

Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria and eukaryotes. While such data may sometimes be treated as a single locus, in practice, a number of biological and statistical phenomena can lead to phylogenetic incongruence. In such cases, different loci should, at least as a preliminary step, be examined and analysed separately. The r software has become a popular platform for phylogenetics, with several packages implementing distance-based, parsimony and likelihood-based phylogenetic reconstruction, and an even greater number of packages implementing phylogenetic comparative methods. Unfortunately, basic data structures and tools for analysing multiple genes have so far been lacking, thereby limiting potential for investigating phylogenetic incongruence. In this study, we introduce the new r package apex to fill this gap. apex implements new object classes, which extend existing standards for storing DNA and amino acid sequences, and provides a number of convenient tools for handling, visualizing and analysing these data. In this study, we introduce the main features of the package and illustrate its functionalities through the analysis of a simple data set

Preclinical assessment of the receptor-binding domain of Plasmodium vivax duffy-binding protein as a vaccine candidate in rhesus macaques

The receptor-binding domain of Plasmodium vivax Duffy-binding protein, region II (PvRII), is an attractive candidate for a vaccine against P. vivax malaria. Here, we have studied the safety and immunogenicity of recombinant PvRII in Macaca mulatta (rhesus monkeys). Recombinant PvRII with a C-terminal 6-histidine tag was expressed in E. coli, recovered from inclusion bodies, refolded into its functional conformation, purified to homogeneity and formulated with three adjuvants, namely, Alhydrogel, Montanide ISA 720 and the GSK proprietary Adjuvant System AS02A for use in immunogenicity studies. All the PvRII vaccine formulations tested were safe and highly immunogenic. The overall magnitude of the antibody response was significantly higher for both Montanide ISA 720 and AS02A formulations in comparison with Alhydrogel. Furthermore, there was a significant correlation between antibody recognition titers by ELISA and binding inhibition titers in in vitro binding assays. The PvRII vaccine formulations also induced IFN-γ recall responses that were identified using ex vivo ELISPOT assays. These results provide support for further clinical development of a vaccine for P. vivax malaria based on recombinant PvRII