The genome organization and affinities of an Australian isolate of carrot mottle umbravirus

The genomic sequence of an Australian isolate of carrot mottle umbravirus (CMoV-A) was determined from cDNA generated from dsRNA. This provides the first data on the genome organization and phylogeny of an umbravirus. The 4201-nucleotide genome contains four major open reading frames (ORFs). Analysis suggests that ORF2 encodes an RNA-dependent RNA polymerase, that ORF4 encodes a movement protein, and that the virus has no coat protein gene. The functions of ORFs 1 and 3 remain unknown. ORF2 is probably translated following ribosomal frameshifting. ORFs 3 and 4 are probably translated from a subgenomic mRNA. Sequence comparisons showed CMoV-A to be closely related to pea enation mosaic RNA2 NA2), but also to have affinities with the Bromoviridae. These findings shed light on the relationships between the luteoviruses, PEMV, and the umbraviruses and on the relationships between the carmo-like viruses and the Bromoviridae.

Structural analysis of dihydrofolate reductases enables rationalization of antifolate binding affinities and suggests repurposing possibilities

Antifolates are competitive inhibitors of dihydrofolate reductase ( DHFR), a conserved enzyme that is central to metabolism and widely targeted in pathogenic diseases, cancer and autoimmune disorders. Although most clinically used antifolates are known to be target specific, some display a fair degree of cross-reactivity with DHFRs from other species. A method that enables identification of determinants of affinity and specificity in target DHFRs from different species and provides guidelines for the design of antifolates is currently lacking. To address this, we first captured the potential druggable space of a DHFR in a substructure called the `supersite' and classified supersites of DHFRs from 56 species into 16 `site-types' based on pairwise structural similarity. Analysis of supersites across these site-types revealed that DHFRs exhibit varying extents of dissimilarity at structurally equivalent positions in and around the binding site. We were able to explain the pattern of affinities towards chemically diverse antifolates exhibited by DHFRs of different site-types based on these structural differences. We then generated an antifolate-DHFR network by mapping known high-affinity antifolates to their respective supersites and used this to identify antifolates that can be repurposed based on similarity between supersites or antifolates. Thus, we identified 177 human-specific and 458 pathogen-specific antifolates, a large number of which are supported by available experimental data. Thus, in the light of the clinical importance of DHFR, we present a novel approach to identifying differences in the druggable space of DHFRs that can be utilized for rational design of antifolates.

The coupling of St. John, US Virgin Islands Marine Protected Areas based on reef fish habitat affinities and movements across management boundaries [Poster]

NOAA's Biogeograpy Branch, the National Park Service (NPS), US Geological Survey, and the University of the Virgin Islands (UVI) are using acoustice telemetry to quantify spatial patterns and habitat affinities of reef fishes in the US Virgin Islands (USVI). The objective of the study is to define the movements of reef fishes among habitats within and between the Virgin Islands Coral Reef Nationla Monument (VICRNM), adjacent to Virgin Islands National Park (VIIS), and USVI Territorial waters. In order to better understand species habitat utilization patterns and movement of fishes among management regimes and areas open to fishing around St. John, we deployed an array of hydroacoutstic receivers and acoustically tagged reef fishes. A total of 150 fishes, representing 18 species and 10 families were acoustically tagged along the south shore of St. John from July 2006 to June 2008. Thirty six receivers with a detection range of approximately 300m each were deployed in shallow nearshore bays and across the shelf to depths of approximately 30m. Receivers were located within reefs and adjacent to reefs in seagrass, algal beds, or sand habitats. Example results include the movement of lane snappers and blue striped grunts that demonstrated diel movement from reef habitats during daytime hours to offshore seagrass beds at night. Fish associated with reefs that did not have adjacent seagrass beds made more extensive movements than those fishes associated with reefs that had adjacent seagrass habitats. The array comprised of both nearshore and cross shelf location of receives provides information on fine to broad scale fish movement patterns across habitats and among management units to examine the strength of ecological connectivity between management areas and habitats. For more information go to: http://ccma.nos.noaa.gov/ecosystems/ coralreef/acoustic_tracking.html

Electron affinities and ionization potentials of 4d and 5d transition metal atoms by CCSD(T), MP2 and density functional theory

The electron affinities and ionization potentials of 4d and 5d transition metal atoms were studied by CCSD(T), MP2 and density functional methods. The calculated results indicate that density functional method B3LYP has the best overall performance in predicting both electron affinity and ionization potential. SVWN gives largest IP and EA for 4d and 5d atoms. For the two basis sets used in this study, LANL2DZ and SDD, the performance of B3LYP/SDD combination is better than B3LYP/LANL2DZ, in particular for electron affinity calculation.

Rorty's Elective Affinities. The New Pragmatism and Postmodern Thought

The present book is devoted to "European connections of Richard Rorty's neopragmatism". The theme, chosen carefully and intentionally, is supposed to show the motivation behind the writing of the present work, as well as to show its intended extent. Let us consider briefly the first three parts of the theme, to enlighten a little our intentions. "European" is perhaps the most important description for it was precisely that thread that was most important to me, being the only context seriously taken into account, as I assumed right from the start that I would not be writing about rather more widely unknown to me - and much less fascinating (even to Rorty, the hero of the story) from my own, traditional, Continental philosophical perspective - American analytic philosophy. So accordingly I have almost totally skipped "American" connections (to use the distinction I need here) of Rorty's philosophy, that is to say, firstly, a years-long work within analytic philosophy, secondly struggles with it on its own grounds, and finally attempts to use classical American, mainly Deweyan, pragmatism for his own needs and numerous polemics associated with it - the questions that are far away from my interests and that arise limited interest among reading and writing philosophical audience in Poland, and perhaps also among Continental philosophers. It did not seem possible to me to write a book on Rorty in his American connections for they are insufficiently known to me, demanding knowledge of both post-war American analytic philosophy as well as pragmatism of its father-founders. I could see, setting to work on Richard Rorty, that a book on his American connections (leaving aside the issue that it would not be a philosophical problem but rather, let us say, the one of writing a monograph) written by a Polish philosopher in Poland and then in the USA was not a stimulating intellectual challenge but rather a thankless working task. Besides, having spent much time on Rorty's philosophy, writing extensively about him and translating his works, I already knew that the "Continental" context was extremely important to his neopragmatism, and that thinking about it could be relatively prolific (as opposed to the context potentially given by American philosophy).

Thermodynamic analysis of ligand-induced changes in protein thermal unfolding applied to high-throughput determination of ligand affinities with extrinsic fluorescent dyes.

The quantification of protein-ligand interactions is essential for systems biology, drug discovery, and bioengineering. Ligand-induced changes in protein thermal stability provide a general, quantifiable signature of binding and may be monitored with dyes such as Sypro Orange (SO), which increase their fluorescence emission intensities upon interaction with the unfolded protein. This method is an experimentally straightforward, economical, and high-throughput approach for observing thermal melts using commonly available real-time polymerase chain reaction instrumentation. However, quantitative analysis requires careful consideration of the dye-mediated reporting mechanism and the underlying thermodynamic model. We determine affinity constants by analysis of ligand-mediated shifts in melting-temperature midpoint values. Ligand affinity is determined in a ligand titration series from shifts in free energies of stability at a common reference temperature. Thermodynamic parameters are obtained by fitting the inverse first derivative of the experimental signal reporting on thermal denaturation with equations that incorporate linear or nonlinear baseline models. We apply these methods to fit protein melts monitored with SO that exhibit prominent nonlinear post-transition baselines. SO can perturb the equilibria on which it is reporting. We analyze cases in which the ligand binds to both the native and denatured state or to the native state only and cases in which protein:ligand stoichiometry needs to treated explicitly.

Conformational kinetics reveals affinities of protein conformational states.

Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination of their binding and conformational characteristics. However, many of these species are only transiently present and they have often been overlooked in mechanistic studies of reactions that couple binding to conformational change. We monitored the kinetics of ligand-induced conformational changes in a small protein using six different ligands. We analyzed the kinetic data to simultaneously determine both binding affinities for the conformational states and the rate constants of conformational change. The approach we used is sufficiently robust to determine the affinities of three conformational states and detect even modest differences in the protein's affinities for relatively similar ligands. Ligand binding favors higher-affinity conformational states by increasing forward conformational rate constants and/or decreasing reverse conformational rate constants. The amounts by which forward rate constants increase and reverse rate constants decrease are proportional to the ratio of affinities of the conformational states. We also show that both the affinity ratio and another parameter, which quantifies the changes in conformational rate constants upon ligand binding, are strong determinants of the mechanism (conformational selection and/or induced fit) of molecular recognition. Our results highlight the utility of analyzing the kinetics of conformational changes to determine affinities that cannot be determined from equilibrium experiments. Most importantly, they demonstrate an inextricable link between conformational dynamics and the binding affinities of conformational states.

The diet and landclass affinities of the Irish hare Lepus timidus hibernicus

The diet of the Irish hare Lepus timidus hibernicus was investigated in Northern Ireland. Faecal pellets were collected at regular intervals from three contrasting study sites and from a number of randomly selected sites from known land classes. Microhistological techniques were employed to analyse the pellets. Grass species occurred in high percentage frequencies in all samples of faecal pellets and a wide variety of plant species were represented (up to 26 species in one study site). In a stratified, random survey of the presence of hares, areas of lowland intensive agriculture had fewer positive records than expected. It is contended that L. t. hibernicus may not be able to sustain viable populations in areas of intensive agriculture, which are almost exclusively composed of ryegrass Lolium spp.

First record of a chiton from the Palaeocene of Denmark (Polyplacophora : Leptochitonidae) and its phylogenetic affinities

Anew species of fossil polyplacophoran from the Danian (Lower Palaeocene) of Denmark is described from over 450 individual disarticulated plates. The polyplacophorans originate from the 'nose-chalk' in the classical Danish locality of Fakse Quarry, an unconsolidated coral limestone in which aragonitic mollusc shells are preserved through transformation into calcite. In plate architecture and sculpture, the new Danish material is similar to Recent Leptochiton spp., but differs in its underdeveloped apophyses and high dorsal elevation (height/width ca. 0.54). Cladistic analysis of 55 original shell characters coded for more than loo Recent and fossil species in the order Lepiclopleurida shows very high resolution of interspecific relationships, but does not consistently recover traditional genera or subgenera. Inter-relationships within the suborder Lepidopleurina are of particular interest as it is often considered the most 'basal' neoloricate lineage. In a local context, the presence of chitons in the faunal assemblage of Fakse contributes evidence of shallow depositional depth for at least some elements of this Palaeocene seabed, a well-studied formation of azooxanthellic coral limestones. This new record for Denmark represents a well-dated and ecologically well-understood fossil chiton with potential value for understanding the radiation of the Neotoricata.

'What ever happened to breakdancing?' : transnational b-boy/b-girl networks, underground video magazines and imagined affinities

In 1997, Paul Gilroy was able to write: "I have been asking myself, whatever happened to breakdancing" (21), a form of vernacular dance associated with urban youth that emerged in the 1970s. However, in the last decade, breakdancing has experienced a massive renaissance in movies (You Got Served), commercials ("Gotta Have My Pops!") and documentaries (the acclaimed Freshest Kids). In this thesis, 1 explore the historical development of global b-boy/bgirl culture through a qualitative study involving dancers and their modes of communication. Widespread circulation of breakdancing images peaked in the mid-1980s, and subsequently b-boy/b-girl culture largely disappeared from the mediated landscape. The dance did not reemerge into the mainstream of North American popular culture until the late 1990s. 1 argue that the development of major transnational networks between b-boys and b-girls during the 1990s was a key factor in the return of 'b-boying/b-girling' (known formerly as breakdancing). Street dancers toured, traveled and competed internationally throughout this decade. They also began to create 'underground' video documentaries and travel video 'magazines.' These video artefacts circulated extensively around the globe through alternative distribution channels (including the backpacks of traveling dancers). 1 argue that underground video artefacts helped to produce 'imagined affinities' between dancers in various nations. Imagined affinities are identifications expressed by a cultural producer who shares an embodied activity with other practitioners through either mediated texts or travels through new places. These 'imagined affinities' helped to sustain b-boy/b-girl culture by generating visual/audio representations of popularity for the dance movement across geographical regions.

Inhibition of coxsackie B virus infection by soluble forms of its receptors: Binding affinities, altered particle formation, and competition with cellular receptors

We previously reported that soluble decay-accelerating factor (DAF) and coxsackievirus-adenovirus receptor (CAR) blocked coxsackievirus 133 (CVB3) myocarditis in mice, but only soluble CAR blocked CVB3-mediated pancreatitis. Here, we report that the in vitro mechanisms of viral inhibition by these soluble receptors also differ. Soluble DAF inhibited virus infection through the formation of reversible complexes with CVB3, while binding of soluble CAR to CVB induced the formation of altered (A) particles with a resultant irreversible loss of infectivity. A-particle formation was characterized by loss of VP4 from the virions and required incubation of CVB3-CAR complexes at 37 degrees C. Dimeric soluble DAF (DAF-Fc) was found to be 125-fold-more effective at inhibiting CVB3 than monomeric DAF, which corresponded to a 100-fold increase in binding affinity as determined by surface plasmon resonance analysis. Soluble CAR and soluble dimeric CAR (CAR-Fc) bound to CVB3 with 5,000- and 10,000-fold-higher affinities than the equivalent forms of DAF. While DAF-Fc was 125-fold-more effective at inhibiting virus than monomeric DAF, complement regulation by DAF-Fc was decreased 4 fold. Therefore, while the virus binding was a cooperative event, complement regulation was hindered by the molecular orientation of DAF-Fc, indicating that the regions responsible for complement regulation and virus binding do not completely overlap. Relative contributions of CVB binding affinity, receptor binding footprint on the virus capsid, and induction of capsid conformation alterations for the ability of cellular DAF and CAR to act as receptors are discussed.