Coral Reefs, Fisheries, and Food Security: Integrated Approaches to Addressing Multiple Challenges in the Coral Triangle

The Coral Triangle is the most biologically and economically valuable marine ecosystem on the planet. Covering just three percent of the globe, the region represents more than half of the world's reefs and boasts 76 percent of its known coral species. Sustaining more than 130 million people who rely directly on the marine ecosystems for their livelihoods and food, the marine habitats of the Coral Triangle contribute billions of dollars each year toward the economies of the region.Although the environmental imperative for preserving this area of incredible value and biodiversity is obvious, the growing pressures and threats from widespread poverty, rapid development, and global demands continue to place enormous strain on the natural marine resources of the Coral Triangle

On the hierarchical classification of G Protein-Coupled Receptors

Motivation: G protein-coupled receptors (GPCRs) play an important role in many physiological systems by transducing an extracellular signal into an intracellular response. Over 50% of all marketed drugs are targeted towards a GPCR. There is considerable interest in developing an algorithm that could effectively predict the function of a GPCR from its primary sequence. Such an algorithm is useful not only in identifying novel GPCR sequences but in characterizing the interrelationships between known GPCRs. Results: An alignment-free approach to GPCR classification has been developed using techniques drawn from data mining and proteochemometrics. A dataset of over 8000 sequences was constructed to train the algorithm. This represents one of the largest GPCR datasets currently available. A predictive algorithm was developed based upon the simplest reasonable numerical representation of the protein's physicochemical properties. A selective top-down approach was developed, which used a hierarchical classifier to assign sequences to subdivisions within the GPCR hierarchy. The predictive performance of the algorithm was assessed against several standard data mining classifiers and further validated against Support Vector Machine-based GPCR prediction servers. The selective top-down approach achieves significantly higher accuracy than standard data mining methods in almost all cases

The Ratio of Ortho- to Para-H2 in Photodissociation Regions

We discuss the ratio of ortho- to para-H2 in photodissociation regions (PDRs). We draw attention to an apparent confusion in the literature between the ortho-to-para ratio of molecules in FUV-pumped vibrationally excited states, and the H2 ortho-to-para abundance ratio. These ratios are not the same because the process of FUV-pumping of fluorescent H2 emission in PDRs occurs via optically thick absorption lines. Thus, gas with an equilibrium ratio of ortho- to para-H2 equal to 3 will yield FUV-pumped vibrationally excited ortho-to-para ratios smaller than 3, because the ortho-H2 pumping rates are preferentially reduced by optical depth effects. Indeed, if the ortho and para pumping lines are on the ``square root'' part of the curve-of-growth, then the expected ratio of ortho and para vibrational line strengths is the square root of 3, ~ 1.7, close to the typically observed value. Thus, contrary to what has sometimes been stated in the literature, most previous measurements of the ratio of ortho- to para-H2 in vibrationally excited states are entirely consistent with a total ortho-to-para ratio of 3, the equilibrium value for temperatures greater than 200 K. We present an analysis and several detailed models which illustrate the relationship between the total ratios of ortho- to para-H2 and the vibrationally excited ortho-to-para ratios in PDRs. Recent Infrared Space Observatory (ISO) measurements of pure rotational and vibrational H2 emissions from the PDR in the star-forming region S140 provide strong observational support for our conclusions.Comment: 23 pages (including 5 figures), LaTeX, uses aaspp4.sty, accepted for publication in Ap

SiO line emission from C-type shock waves : interstellar jets and outflows

We study the production of SiO in the gas phase of molecular outflows, through the sputtering of Si--bearing material in refractory grain cores, which are taken to be olivine; we calculate also the rotational line spectrum of the SiO. The sputtering is driven by neutral particle impact on charged grains, in steady--state C-type shock waves, at the speed of ambipolar diffusion. The emission of the SiO molecule is calculated by means of an LVG code. A grid of models has been generated. We compare our results with those of an earlier study (Schilke et al. 1997). Improvements in the treatment of the coupling between the charged grains and the neutral fluid lead to narrower shock waves and lower fractions of Si being released into the gas phase. More realistic assumptions concerning the initial fractional abundance of O2 lead to SiO formation being delayed, so that it occurs in the cool, dense postshock flow. Good agreement is obtained with recent observations of SiO line intensities in the L1157 and L1448 molecular outflows. The inferred temperature, opacity, and SiO column density in the emission region differ significantly from those estimated by means of LVG `slab' models. The fractional abundance of SiO is deduced. Observed line profiles are wider than predicted and imply multiple, unresolved shock regions within the beam.Comment: 1 tex doc, 19 figure

Processing and Transmission of Information

Contains reports on four research projects.National Aeronautics and Space Administration (Grant NGL 22-009-013)Joint Services Electronics Program (Contract DAAB07-71-C-0300

Proteomics in Vaccinology and Immunobiology: An Informatics Perspective of the Immunone

The postgenomic era, as manifest, inter alia, by proteomics, offers unparalleled opportunities for the efficient discovery of safe, efficacious, and novel subunit vaccines targeting a tranche of modern major diseases. A negative corollary of this opportunity is the risk of becoming overwhelmed by this embarrassment of riches. Informatics techniques, working to address issues of both data management and through prediction to shortcut the experimental process, can be of enormous benefit in leveraging the proteomic revolution.In this disquisition, we evaluate proteomic approaches to the discovery of subunit vaccines, focussing on viral, bacterial, fungal, and parasite systems. We also adumbrate the impact that proteomic analysis of host-pathogen interactions can have. Finally, we review relevant methods to the prediction of immunome, with special emphasis on quantitative methods, and the subcellular localization of proteins within bacteria

EpiJen:a server for multistep T cell epitope prediction

Background - The main processing pathway for MHC class I ligands involves degradation of proteins by the proteasome, followed by transport of products by the transporter associated with antigen processing (TAP) to the endoplasmic reticulum (ER), where peptides are bound by MHC class I molecules, and then presented on the cell surface by MHCs. The whole process is modeled here using an integrated approach, which we call EpiJen. EpiJen is based on quantitative matrices, derived by the additive method, and applied successively to select epitopes. EpiJen is available free online. Results - To identify epitopes, a source protein is passed through four steps: proteasome cleavage, TAP transport, MHC binding and epitope selection. At each stage, different proportions of non-epitopes are eliminated. The final set of peptides represents no more than 5% of the whole protein sequence and will contain 85% of the true epitopes, as indicated by external validation. Compared to other integrated methods (NetCTL, WAPP and SMM), EpiJen performs best, predicting 61 of the 99 HIV epitopes used in this study. Conclusion - EpiJen is a reliable multi-step algorithm for T cell epitope prediction, which belongs to the next generation of in silico T cell epitope identification methods. These methods aim to reduce subsequent experimental work by improving the success rate of epitope prediction

Efficient calculation of van der Waals dispersion coefficients with time-dependent density functional theory in real time: application to polycyclic aromatic hydrocarbons

The van der Waals dispersion coefficients of a set of polycyclic aromatic hydrocarbons, ranging in size from the single-cycle benzene to circumovalene (C66H20), are calculated with a real-time propagation approach to time-dependent density functional theory (TDDFT). In the non-retarded regime, the Casimir-Polder integral is employed to obtain C6, once the dynamic polarizabilities have been computed at imaginary frequencies with TDDFT. On the other hand, the numerical coefficient that characterizes the fully retarded regime is obtained from the static polarizabilities. This ab initio strategy has favorable scaling with the size of the system - as demonstrated by the size of the reported molecules - and can be easily extended to obtain higher order van der Waals coefficients.Comment: submitted to J. Chem. Phy

Formation of Hydrogen, Oxygen, and Hydrogen Peroxide in Electron Irradiated Crystalline Water Ice

Water ice is abundant both astrophysically, for example in molecular clouds, and in planetary systems. The Kuiper belt objects, many satellites of the outer solar system, the nuclei of comets and some planetary rings are all known to be water-rich. Processing of water ice by energetic particles and ultraviolet photons plays an important role in astrochemistry. To explore the detailed nature of this processing, we have conducted a systematic laboratory study of the irradiation of crystalline water ice in an ultrahigh vacuum setup by energetic electrons holding a linear energy transfer of 4.3 +/- 0.1 keV mm-1. The irradiated samples were monitored during the experiment both on line and in situ via mass spectrometry (gas phase) and Fourier transform infrared spectroscopy (solid state). We observed the production of hydrogen and oxygen, both molecular and atomic, and of hydrogen peroxide. The likely reaction mechanisms responsible for these species are discussed. Additional formation routes were derived from the sublimation profiles of molecular hydrogen (90-140 K), molecular oxygen (147 -151 K) and hydrogen peroxide (170 K). We also present evidence on the involvement of hydroxyl radicals and possibly oxygen atoms as building blocks to yield hydrogen peroxide at low temperatures (12 K) and via a diffusion-controlled mechanism in the warming up phase of the irradiated sample.Comment: ApJ, March 2006, v639 issue, 43 pages, 7 figure