Intracule functional models. IV. Basis set effects

We have calculated position and dot intracules for a series of atomic and molecular systems, starting from an unrestricted Hartree-Fock wave function, expanded using the STO-3G, 6-31G, 6-311G, 6-311++G, 6-311++G(d,p), 6-311++G(3d,3p), and 6-311++G(3df,3pd) basis sets as well as the nonpolarized part of Dunning's cc-pV5Z basis. We find that the basis set effects on the intracules are small and that correlation energies from the dot intracule ansatz are remarkably insensitive to the basis set quality. Mean absolute errors in correlation energies across the G1 data set agree to within 2 mE(h) for all basis sets tested.P.M.W.G. thanks the APAC Merit Allocation Scheme for a generous grant of supercomputer resources and the Australian Research Council Grant Nos. DP0664466 and DP0771978 for funding

Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease

<p>Abstract</p> <p>Background</p> <p>Systems biology holds promise as a new approach to drug target identification and drug discovery against neglected tropical diseases. Genome-scale metabolic reconstructions, assembled from annotated genomes and a vast array of bioinformatics/biochemical resources, provide a framework for the interrogation of human pathogens and serve as a platform for generation of future experimental hypotheses. In this article, with the application of selection criteria for both <it>Leishmania major </it>targets (e.g. <it>in silico </it>gene lethality) and drugs (e.g. toxicity), a method (MetDP) to rationally focus on a subset of low-toxic Food and Drug Administration (FDA)-approved drugs is introduced.</p> <p>Results</p> <p>This metabolic network-driven approach identified 15 <it>L. major </it>genes as high-priority targets, 8 high-priority synthetic lethal targets, and 254 FDA-approved drugs. Results were compared to previous literature findings and existing high-throughput screens. Halofantrine, an antimalarial agent that was prioritized using MetDP, showed noticeable antileishmanial activity when experimentally evaluated <it>in vitro </it>against <it>L. major </it>promastigotes. Furthermore, synthetic lethality predictions also aided in the prediction of superadditive drug combinations. For proof-of-concept, double-drug combinations were evaluated <it>in vitro </it>against <it>L. major </it>and four combinations involving the drug disulfiram that showed superadditivity are presented.</p> <p>Conclusions</p> <p>A direct metabolic network-driven method that incorporates single gene essentiality and synthetic lethality predictions is proposed that generates a set of high-priority <it>L. major </it>targets, which are in turn associated with a select number of FDA-approved drugs that are candidate antileishmanials. Additionally, selection of high-priority double-drug combinations might provide for an attractive and alternative avenue for drug discovery against leishmaniasis.</p

Evidence for a pervasive 'idling-mode' activity template in flying and pedestrian insects

Understanding the complex movement patterns of animals in natural environments is a key objective of ‘movement ecology’. Complexity results from behavioural responses to external stimuli but can also arise spontaneously in their absence. Drawing on theoretical arguments about decision-making circuitry, we predict that the spontaneous patterns will be scale-free and universal, being independent of taxon and mode of locomotion. To test this hypothesis, we examined the activity patterns of the European honeybee, and multiple species of noctuid moth, tethered to flight mills and exposed to minimal external cues. We also reanalysed pre-existing data for Drosophila flies walking in featureless environments. Across these species, we found evidence of common scale-invariant properties in their movement patterns; pause and movement durations were typically power law distributed over a range of scales and characterized by exponents close to 3/2. Our analyses are suggestive of the presence of a pervasive scale-invariant template for locomotion which, when acted on by environmental cues, produces the movements with characteristic scales observed in nature. Our results indicate that scale-finite complexity as embodied, for instance, in correlated random walk models, may be the result of environmental cues overriding innate behaviour, and that scale-free movements may be intrinsic and not limited to ‘blind’ foragers as previously thought

Using Photometrically-Derived Properties of Young Stars to Refine TESS's Transiting Young Planet Survey Completeness

The demographics of young exoplanets can shed light onto their formation and evolution processes. Exoplanet properties are derived from the properties of their host stars. As such, it is important to accurately characterize the host stars since any systematic biases in their derivation can negatively impact the derivation of planetary properties. Here, we present a uniform catalog of photometrically-derived stellar effective temperatures, luminosities, radii, and masses for 4,865 young (<1 Gyr) stars in 31 nearby clusters and moving groups within 200 pc. We compared our photometrically-derived properties to a subset of those derived from spectra, and found them to be in good agreement. We also investigated the effect of stellar properties on the detection efficiency of transiting short-period young planets with TESS as calculated in Fernandes et al. 2022, and found an overall increase in the detection efficiency when the new photometrically derived properties were taken into account. Most notably, there is a 1.5 times increase in the detection efficiencies for sub-Neptunes/Neptunes (1.8-6 Re) implying that, for our sample of young stars, better characterization of host star properties can lead to the recovery of more small transiting planets. Our homogeneously derived catalog of updated stellar properties, along with a larger unbiased stellar sample and more detections of young planets, will be a crucial input to the accurate estimation of the occurrence rates of young short-period planets.Comment: 16 pages, 5 Figures, 3 Tables. Revised and resubmitted to AJ after a favorable referee report. Co-First Author

Distribution of Introns in Fungal Histone Genes

Saccharomycotina and Taphrinomycotina lack intron in their histone genes, except for an intron in one of histone H4 genes of Yarrowia lipolytica. On the other hand, Basidiomycota and Perizomycotina have introns in their histone genes. We compared the distributions of 81, 47, 79, and 98 introns in the fungal histone H2A, H2B, H3, and H4 genes, respectively. Based on the multiple alignments of the amino acid sequences of histones, we identified 19, 13, 31, and 22 intron insertion sites in the histone H2A, H2B, H3, and H4 genes, respectively. Surprisingly only one hot spot of introns in the histone H2A gene is shared between Basidiomycota and Perizomycotina, suggesting that most of introns of Basidiomycota and Perizomycotina were acquired independently. Our findings suggest that the common ancestor of Ascomycota and Basidiomycota maybe had a few introns in the histone genes. In the course of fungal evolution, Saccharomycotina and Taphrinomycotina lost the histone introns; Basidiomycota and Perizomycotina acquired other introns independently. In addition, most of the introns have sequence similarity among introns of phylogenetically close species, strongly suggesting that horizontal intron transfer events between phylogenetically distant species have not occurred recently in the fungal histone genes

Stable isotope analysis provides new information on winter habitat use of declining avian migrants that is relevant to their conservation

Winter habitat use and the magnitude of migratory connectivity are important parameters when assessing drivers of the marked declines in avian migrants. Such information is unavailable for most species. We use a stable isotope approach to assess these factors for three declining African-Eurasian migrants whose winter ecology is poorly known: wood warbler Phylloscopus sibilatrix, house martin Delichon urbicum and common swift Apus apus. Spatially segregated breeding wood warbler populations (sampled across a 800 km transect), house martins and common swifts (sampled across a 3,500 km transect) exhibited statistically identical intra-specific carbon and nitrogen isotope ratios in winter grown feathers. Such patterns are compatible with a high degree of migratory connectivity, but could arise if species use isotopically similar resources at different locations. Wood warbler carbon isotope ratios are more depleted than typical for African-Eurasian migrants and are compatible with use of moist lowland forest. The very limited variance in these ratios indicates specialisation on isotopically restricted resources, which may drive the similarity in wood warbler populations' stable isotope ratios and increase susceptibility to environmental change within its wintering grounds. House martins were previously considered to primarily use moist montane forest during the winter, but this seems unlikely given the enriched nature of their carbon isotope ratios. House martins use a narrower isotopic range of resources than the common swift, indicative of increased specialisation or a relatively limited wintering range; both factors could increase house martins' vulnerability to environmental change. The marked variance in isotope ratios within each common swift population contributes to the lack of population specific signatures and indicates that the species is less vulnerable to environmental change in sub-Saharan Africa than our other focal species. Our findings demonstrate how stable isotope research can contribute to understanding avian migrants' winter ecology and conservation status

Historical Distribution and Molecular Diversity of Bacillus anthracis, Kazakhstan

This study provides useful baseline data for guiding future disease control programs

Batrachochytrium dendrobatidis Shows High Genetic Diversity and Ecological Niche Specificity among Haplotypes in the Maya Mountains of Belize

The amphibian pathogen Batrachochytrium dendrobatidis (Bd) has been implicated in amphibian declines around the globe. Although it has been found in most countries in Central America, its presence has never been assessed in Belize. We set out to determine the range, prevalence, and diversity of Bd using quantitative PCR (qPCR) and sequencing of a portion of the 5.8 s and ITS1-2 regions. Swabs were collected from 524 amphibians of at least 26 species in the protected areas of the Maya Mountains of Belize. We sequenced a subset of 72 samples that had tested positive for Bd by qPCR at least once; 30 samples were verified as Bd. Eight unique Bd haplotypes were identified in the Maya Mountains, five of which were previously undescribed. We identified unique ecological niches for the two most broadly distributed haplotypes. Combined with data showing differing virulence shown in different strains in other studies, the 5.8 s - ITS1-2 region diversity found in this study suggests that there may be substantial differences among populations or haplotypes. Future work should focus on whether specific haplotypes for other genomic regions and possibly pathogenicity can be associated with haplotypes at this locus, as well as the integration of molecular tools with other ecological tools to elucidate the ecology and pathogenicity of Bd