Computational challenges of systems biology

Progress in the study of biological systems such as the heart, brain, and liver will require computer scientists to work closely with life scientists and mathematicians. Computer science will play a key role in shaping the new discipline of systems biology and addressing the significant computational challenges it poses

Large amounts of optically-obscured star formation in the host galaxies of some type-2 quasars

We present Hubble Space Telescope images, and spectral energy distributions from optical to infrared wavelengths for a sample of six 0.3<z<0.8 type-2 quasars selected in the mid-infrared using data from the Spitzer Space Telescope. All the host galaxies show some signs of disturbance. Most seem to possess dusty, star-forming disks. The disk inclination, estimated from the axial ratio of the hosts, correlates with the depth of the silicate feature in the mid-infrared spectra, implying that at least some of the reddening towards the AGN arises in the host galaxy. The star formation rates in these objects, as inferred from the strengths of the PAH features and far-infrared continuum, range from 3-90 Msun/yr, but are mostly much larger than those inferred from the [OII]3727 emission line luminosity, due to obscuration. Taken together with studies of type-2 quasar hosts from samples selected in the optical and X-ray, this is consistent with previous suggestions that two types of extinction processes operate within the type-2 quasar population, namely a component due to the dusty torus in the immediate environment of the AGN, and a more extended component due to a dusty, star forming disk.Comment: 5 pages, 3 figures. Accepted by ApJ Letter

Prostaglandin E2 enhances alveolar bone formation in the rat mandible

Prostaglandin E-2 (PGE(2)) induces bone formation in stress-bearing bones. The mandible, a stress-bearing bone, is loaded daily during mastication. The aim of this study was to determine if PGE(2) delivered locally to the mandible over 20 days enhances alveolar bone deposition. In 18 Lewis rats, controlled-release pellets containing PGE2 were implanted on the buccal aspect on the left-hand side of the mandible, mesial to the root of the first molar. Controlled-release pellets locally delivered 0.1, 0.05, or 0.025 mg/day of PGE2. The right side of the mandible was used as a matched control for each animal. Six sham-treated animals were implanted with a placebo pellet. On days 7 and 19, animals were injected with the bone markers tetracycline and calcein, respectively. On day 21, animals were sacrificed and undecalcified tissues obtained for morphometrical analysis. Morphometrical measurements were analyzed by paired t test to determine differences between the matched samples and one-way ANOVA to compare the different treatment groups. A significant increase in alveolar bone area was observed in mandibles treated with 0.1 and 0.05 mg/day when compared with matched controls and the placebo group. This was accompanied by a significant increase in alveolar bone height and width. The proportions of double-labeled surface (dLS), the mineral apposition rate (MAR), and bone formation rate (BFR) were significantly increased in mandibles treated with the two higher doses of PGE(2). The proportion of resorptive surface (RS) was significantly reduced in these two groups. It is concluded that PGE2 induces alveolar bone formation in the mandible when locally delivered at a dose of 0.1 or 0.05 mg/day for 20 days. (C) 2004 Elsevier Inc. All rights reserved

Effect of the Synthetic Bile Salt Analog CamSA on the Hamster Model of Clostridium difficile Infection

Clostridium difficile infection (CDI) is the leading cause of antibiotic-associated diarrhea and has gained worldwide notoriety due to emerging hypervirulent strains and the high incidence of recurrence. We previously reported protection of mice from CDI using the antigerminant bile salt analog CamSA. Here we describe the effects of CamSA in the hamster model of CDI. CamSA treatment of hamsters showed no toxicity and did not affect the richness or diversity of gut microbiota; however, minor changes in community composition were observed. Treatment of C. difficile-challenged hamsters with CamSA doubled the mean time to death, compared to control hamsters. However, CamSA alone was insufficient to prevent CDI in hamsters. CamSA in conjunction with suboptimal concentrations of vancomycin led to complete protection from CDI in 70% of animals. Protected animals remained disease-free at least 30 days postchallenge and showed no signs of colonic tissue damage. In a delayed-treatment model of hamster CDI, CamSA was unable to prevent infection signs and death. These data support a putative model in which CamSA reduces the number of germinating C. difficile spores but does not keep all of the spores from germinating. Vancomycin halts division of any vegetative cells that are able to grow from spores that escape CamSA

A SQUAMOSA MADS-box gene involved in the regulation of anthocyanin accumulation in bilberry fruits

Anthocyanins are important health promoting phytochemicals that are abundant in many fleshy fruits. Bilberry (Vaccinium myrtillus L.) is one of the best sources of these compounds. Here we report on the expression pattern and functional analysis of a SQUAMOSA (SQUA) class MADS-box transcription factor, VmTDR4, associated with anthocyanin biosynthesis in bilberry. Levels of VmTDR4 expression were spatially and temporally linked with colour development and anthocyanin-related gene expression. Virus induced gene silencing (VIGS) was used to suppress VmTDR4 expression in bilberry resulting in substantial reduction in anthocyanin levels in fully ripe fruits. Chalcone synthase was used a positive control in the VIGS experiments. Additionally, in sectors of fruit tissue in which the expression of the VmTDR4 gene was silenced, the expression of R2R3 MYB family transcription factors related to the biosynthesis of flavonoids were also altered. We conclude that VmTDR4 plays an important role in the accumulation of anthocyanins during normal ripening in bilberry; probably through direct or indirect control of transcription factors belonging to the R2R3 MYB family

Floral temperature and optimal foraging: is heat a feasible floral reward for pollinators?

As well as nutritional rewards, some plants also reward ectothermic pollinators with warmth. Bumble bees have some control over their temperature, but have been shown to forage at warmer flowers when given a choice, suggesting that there is some advantage to them of foraging at warm flowers (such as reducing the energy required to raise their body to flight temperature before leaving the flower). We describe a model that considers how a heat reward affects the foraging behaviour in a thermogenic central-place forager (such as a bumble bee). We show that although the pollinator should spend a longer time on individual flowers if they are warm, the increase in total visit time is likely to be small. The pollinator's net rate of energy gain will be increased by landing on warmer flowers. Therefore, if a plant provides a heat reward, it could reduce the amount of nectar it produces, whilst still providing its pollinator with the same net rate of gain. We suggest how heat rewards may link with plant life history strategies

On the Monadic Second-Order Transduction Hierarchy

We compare classes of finite relational structures via monadic second-order transductions. More precisely, we study the preorder where we set C \subseteq K if, and only if, there exists a transduction {\tau} such that C\subseteq{\tau}(K). If we only consider classes of incidence structures we can completely describe the resulting hierarchy. It is linear of order type {\omega}+3. Each level can be characterised in terms of a suitable variant of tree-width. Canonical representatives of the various levels are: the class of all trees of height n, for each n \in N, of all paths, of all trees, and of all grids

Mass and Angular Momentum Transfer in the Massive Algol Binary RY Persei

We present an investigation of H-alpha emission line variations observed in the massive Algol binary, RY Per. We give new radial velocity data for the secondary based upon our optical spectra and for the primary based upon high dispersion UV spectra. We present revised orbital elements and an estimate of the primary's projected rotational velocity (which indicates that the primary is rotating 7 times faster than synchronous). We use a Doppler tomography algorithm to reconstruct the individual primary and secondary spectra in the region of H-alpha, and we subtract the latter from each of our observations to obtain profiles of the primary and its disk alone. Our H-alpha observations of RY Per show that the mass gaining primary is surrounded by a persistent but time variable accretion disk. The profile that is observed outside-of-eclipse has weak, double-peaked emission flanking a deep central absorption, and we find that these properties can be reproduced by a disk model that includes the absorption of photospheric light by the band of the disk seen in projection against the face of the star. We developed a new method to reconstruct the disk surface density distribution from the ensemble of H-alpha profiles observed around the orbit, and this method accounts for the effects of disk occultation by the stellar components, the obscuration of the primary by the disk, and flux contributions from optically thick disk elements. The resulting surface density distribution is elongated along the axis joining the stars, in the same way as seen in hydrodynamical simulations of gas flows that strike the mass gainer near trailing edge of the star. This type of gas stream configuration is optimal for the transfer of angular momentum, and we show that rapid rotation is found in other Algols that have passed through a similar stage.Comment: 39 pages, 12 figures, ApJ in press, 2004 June 20 issu

Testing Consumer Rationality using Perfect Graphs and Oriented Discs

Given a consumer data-set, the axioms of revealed preference proffer a binary test for rational behaviour. A natural (non-binary) measure of the degree of rationality exhibited by the consumer is the minimum number of data points whose removal induces a rationalisable data-set.We study the computational complexity of the resultant consumer rationality problem in this paper. This problem is, in the worst case, equivalent (in terms of approximation) to the directed feedback vertex set problem. Our main result is to obtain an exact threshold on the number of commodities that separates easy cases and hard cases. Specifically, for two-commodity markets the consumer rationality problem is polynomial time solvable; we prove this via a reduction to the vertex cover problem on perfect graphs. For three-commodity markets, however, the problem is NP-complete; we prove thisusing a reduction from planar 3-SAT that is based upon oriented-disc drawings