An Advanced, Three-Dimensional Plotting Library for Astronomy

We present a new, three-dimensional (3D) plotting library with advanced features, and support for standard and enhanced display devices. The library - S2PLOT - is written in C and can be used by C, C++ and FORTRAN programs on GNU/Linux and Apple/OSX systems. S2PLOT draws objects in a 3D (x,y,z) Cartesian space and the user interactively controls how this space is rendered at run time. With a PGPLOT inspired interface, S2PLOT provides astronomers with elegant techniques for displaying and exploring 3D data sets directly from their program code, and the potential to use stereoscopic and dome display devices. The S2PLOT architecture supports dynamic geometry and can be used to plot time-evolving data sets, such as might be produced by simulation codes. In this paper, we introduce S2PLOT to the astronomical community, describe its potential applications, and present some example uses of the library.Comment: 12 pages, 10 eps figures (higher resolution versions available from http://astronomy.swin.edu.au/s2plot/paperfigures). The S2PLOT library is available for download from http://astronomy.swin.edu.au/s2plo

Using a Web-Archiving Service - How to ensure your cited web-references remain available and valid

In today’s electronic information age, academic authors increasingly cite online resources such as blog posts, news articles, online policies and reports in their scholarly publications. Citing such webpages, or their URLs, poses long-term accessibility concern due to the ephemeral nature of the Internet: webpages can (and do!) change or disappear1 over time. When looking up cited web references, readers of scholarly publications might thus find content that is different from what author/s originally referenced; this is referred to as ‘content drift’. Other times, readers are faced with a ‘404 Page Not Found’ message, a phenomenon known as ‘link rot’2. A recent Canadian study3 for example found a 23% link rot when examining 11,437 links in 664 doctoral dissertations from 2011-2015. Older publications are likely to face even higher rates of invalid links. Luckily, there are a few things you can do to make your cited web references more stable. The most common method is to use a web archiving service. Using a web archiving service means your web references and links are more likely to connect the reader to the content accessed at the time of writing/citing. In other words, references are less likely to “rot” or “drift” over time. As citing authors, we have limited influence on preserving web content that we don’t own. We are generally at the mercy of the information custodians who tend to adjust, move or delete their web content to keep their site(s) current and interesting. All we can do to keep web content that we don’t own but want to cite intact so that our readers can still access it in years to come is to create a “representative memento" of the online material as it was at the time of citing. This can be achieved by submitting the URL of the webpage we want to cite to a web archiving service which will generate a static (‘cached’) copy of it and allocate it a new, unique and permanent link, also called ‘persistent identifier’. We can then use this new link to the archived webpage rather than the ephemeral link to the original webpage for our citation purposes. There are a range of web archives available. This guide contains a list of trusted web archiving services

Spatial ecology of a range-expanding bumble bee pollinator

Molecular methods have greatly increased our understanding of the previously cryptic spatial ecology of bumble bees (Bombus spp.), with knowledge of the spatial ecology of these bees being central to conserving their essential pollination services. Bombus hypnorum, the Tree Bumble Bee, is unusual in that it has recently rapidly expanded its range, having colonized much of the UK mainland since 2001. However, the spatial ecology of B. hypnorum has not previously been investigated. To address this issue, and to investigate whether specific features of the spatial ecology of B. hypnorum are associated with its rapid range expansion, we used 14 microsatellite markers to estimate worker foraging distance, nest density, between‐year lineage survival rate and isolation by distance in a representative UK B. hypnorum population. After assigning workers to colonies based on full or half sibship, we estimated the mean colony‐specific worker foraging distance as 103.6 m, considerably less than values reported from most other bumble bee populations. Estimated nest density was notably high (2.56 and 0.72 colonies ha−1 in 2014 and 2015, respectively), estimated between‐year lineage survival rate was 0.07, and there was no evidence of fine‐scale isolation by distance. In addition, genotyping stored sperm dissected from sampled queens confirmed polyandry in this population (mean minimum mating frequency of 1.7 males per queen). Overall, our findings establish critical spatial ecological parameters and the mating system of this unusual bumble bee population and suggest that short worker foraging distances and high nest densities are associated with its rapid range expansion

MicroRNAs Associated with Caste Determination and Differentiation in a Primitively Eusocial Insect

In eusocial Hymenoptera (ants, bees and wasps), queen and worker adult castes typically arise via environmental influences. A fundamental challenge is to understand how a single genome can thereby produce alternative phenotypes. A powerful approach is to compare the molecular basis of caste determination and differentiation along the evolutionary trajectory between primitively and advanced eusocial species, which have, respectively, relatively undifferentiated and strongly differentiated adult castes. In the advanced eusocial honeybee, Apis mellifera, studies suggest that microRNAs (miRNAs) play an important role in the molecular basis of caste determination and differentiation. To investigate how miRNAs affect caste in eusocial evolution, we used deep sequencing and Northern blots to isolate caste-associated miRNAs in the primitively eusocial bumblebee Bombus terrestris. We found that the miRNAs Bte-miR-6001-5p and -3p are more highly expressed in queen- than in worker-destined late-instar larvae. These are the first caste-associated miRNAs from outside advanced eusocial Hymenoptera, so providing evidence for caste-associated miRNAs occurring relatively early in eusocial evolution. Moreover, we found little evidence that miRNAs previously shown to be associated with caste in A. mellifera were differentially expressed across caste pathways in B. terrestris, suggesting that, in eusocial evolution, the caste-associated role of individual miRNAs is not conserved

Pathways for nutrient loss to water with emphasis on phosphorus

Teagasc wishes to acknowledge the support of the Environmental Research Technological Development and Innovation (ERTDI) Programme under the Productive Sector Operational Programme which was financed by the Irish Government under the National Development Plan 2000-2006.End of project reportThe main objective of this project was to study phosphorus (P) loss from agricultural land under a range of conditions in Ireland, to quantify the main factors influencing losses and make recommendations on ways to reduce these losses. This report is a synthesis of the main conclusions and recommendations from the results of the studies. The final reports from the individual sub-projects in this project are available from the EPA (www.epa.ie).Environmental Protection Agenc

Costs of reproduction are present but latent in eusocial bumblebee queens

Background: The standard evolutionary theory of ageing proposes that ageing occurs because of a trade-off between reproduction and longevity. Eusocial insect queens exhibit positive fecundity-longevity associations and so have been suggested to be counter-examples through not expressing costs of reproduction and through remodelling conserved genetic and endocrine networks regulating ageing and reproduction. If so, eusocial evolution from solitary ancestors with negative fecundity-longevity associations must have involved a stage at which costs of reproduction were suppressed and fecundity and longevity became positively associated. Using the bumblebee (Bombus terrestris), we experimentally tested whether queens in annual eusocial insects at an intermediate level of eusocial complexity experience costs of reproduction, and, using mRNA-seq, the extent to which they exhibit a remodelling of relevant genetic and endocrine networks. Specifically, we tested whether costs of reproduction are present but latent, or whether a remodelling of relevant genetic and endocrine networks has already occurred allowing queens to reproduce without costs. Results: We experimentally increased queens’ costs of reproduction by removing their eggs, which caused queens to increase their egg-laying rate. Treatment queens had significantly reduced longevity relative to control queens whose egg-laying rate was not increased. Reduced longevity in treatment queens was not caused by increased worker-to-queen aggression or by increased overall activity in queens. In addition, treatment and control queens differed in age-related gene expression based on mRNA-seq in both their overall expression profiles and the expression of ageing-related genes. Remarkably, these differences appeared to occur principally with respect to relative age, not chronological age. Conclusions: This study represents the first simultaneously phenotypic and transcriptomic experimental test for a longevity cost of reproduction in eusocial insect queens. The results support the occurrence of costs of reproduction in annual eusocial insects of intermediate social complexity and suggest that reproductive costs are present but latent in queens of such species, i.e. that these queens exhibit condition-dependent positive fecundity-longevity associations. They also raise the possibility that a partial remodelling of genetic and endocrine networks underpinning ageing may have occurred in intermediately eusocial species such that, in unmanipulated conditions, age-related gene expression depends more on chronological than relative age

Developmental diet alters the fecundity-longevity relationship and age-related gene expression in Drosophila melanogaster

The standard evolutionary theory of aging predicts a negative relationship (trade-off) between fecundity and longevity. However, in principle, the fecundity-longevity relationship can become positive in populations in which individuals have unequal resources. Positive fecundity-longevity relationships also occur in queens of eusocial insects such as ants and bees. Developmental diet is likely to be central to determining trade-offs as it affects key fitness traits, but its exact role remains uncertain. For example, in Drosophila melanogaster, changes in adult diet can affect fecundity, longevity, and gene expression throughout life, but it is unknown how changes in developmental (larval) diet affect fecundity-longevity relationships and gene expression in adults. Using D. melanogaster, we tested the hypothesis that varying developmental diet alters the directionality of fecundity-longevity relationships in adults, and characterised associated gene expression changes. We reared larvae on low (20%), medium (100%), and high (120%) yeast diets, and transferred adult females to a common diet. We measured fecundity and longevity of individual adult females and profiled gene expression changes with age. Adult females raised on different larval diets exhibited fecundity-longevity relationships that varied from significantly positive to significantly negative, despite minimal differences in mean life-time fertility or longevity. Treatments also differed in age-related gene expression, including for aging-related genes. Hence the sign of fecundity-longevity relationships in adult insects can be altered and even reversed by changes in larval diet quality. By extension, larval diet differences may represent a key mechanistic factor underpinning positive fecundity-longevity relationships observed in species such as eusocial insects

From Molecular Cores to Planet-forming Disks: An SIRTF Legacy Program

Crucial steps in the formation of stars and planets can be studied only at mid‐ to far‐infrared wavelengths, where the Space Infrared Telescope (SIRTF) provides an unprecedented improvement in sensitivity. We will use all three SIRTF instruments (Infrared Array Camera [IRAC], Multiband Imaging Photometer for SIRTF [MIPS], and Infrared Spectrograph [IRS]) to observe sources that span the evolutionary sequence from molecular cores to protoplanetary disks, encompassing a wide range of cloud masses, stellar masses, and star‐forming environments. In addition to targeting about 150 known compact cores, we will survey with IRAC and MIPS (3.6–70 μm) the entire areas of five of the nearest large molecular clouds for new candidate protostars and substellar objects as faint as 0.001 solar luminosities. We will also observe with IRAC and MIPS about 190 systems likely to be in the early stages of planetary system formation (ages up to about 10 Myr), probing the evolution of the circumstellar dust, the raw material for planetary cores. Candidate planet‐forming disks as small as 0.1 lunar masses will be detectable. Spectroscopy with IRS of new objects found in the surveys and of a select group of known objects will add vital information on the changing chemical and physical conditions in the disks and envelopes. The resulting data products will include catalogs of thousands of previously unknown sources, multiwavelength maps of about 20 deg^2 of molecular clouds, photometry of about 190 known young stars, spectra of at least 170 sources, ancillary data from ground‐based telescopes, and new tools for analysis and modeling. These products will constitute the foundations for many follow‐up studies with ground‐based telescopes, as well as with SIRTF itself and other space missions such as SIM, JWST, Herschel, and TPF/Darwin

Study protocol: a randomised controlled trial investigating the effect of exercise training on peripheral blood gene expression in patients with stable angina

Background: Exercise training has been shown to reduce angina and promote collateral vessel development in patients with coronary artery disease. However, the mechanism whereby exercise exerts these beneficial effects is unclear. There has been increasing interest in the use of whole genome peripheral blood gene expression in a wide range of conditions to attempt to identify both novel mechanisms of disease and transcriptional biomarkers. This protocol describes a study in which we will assess the effect of a structured exercise programme on peripheral blood gene expression in patients with stable angina, and correlate this with changes in angina level, anxiety, depression, and exercise capacity. Methods/Design: Sixty patients with stable angina will be recruited and randomised 1: 1 to exercise training or conventional care. Patients randomised to exercise training will attend an exercise physiology laboratory up to three times weekly for supervised aerobic interval training sessions of one hour in total duration. Patients will undergo assessments of angina, anxiety, depression, and peripheral blood gene expression at baseline, after six and twelve weeks of training, and twelve weeks after formal exercise training ceases. Discussion: This study will provide comprehensive data on the effect of exercise training on peripheral blood gene expression in patients with angina. By correlating this with improvement in angina status we will identify candidate peripheral blood transcriptional markers predictive of improvements in angina level in response to exercise training