Evolution of transcriptional networks in yeast: Alternative teams of transcriptional factors for different species

Background: The diversity in eukaryotic life reflects a diversity in regulatory pathways. Nocedal and Johnson argue that the rewiring of gene regulatory networks is a major force for the diversity of life, that changes in regulation can create new species. Results: We have created a method (based on our new "ping-pong algorithm) for detecting more complicated rewirings, where several transcription factors can substitute for one or more transcription factors in the regulation of a family of co-regulated genes. An example is illustrative. A rewiring has been reported by Hogues et al. that RAP1 in Saccharomyces cerevisiae substitutes for TBF1/CBF1 in Candida albicans for ribosomal RP genes. There one transcription factor substitutes for another on some collection of genes. Such a substitution is referred to as a "rewiring". We agree with this finding of rewiring as far as it goes but the situation is more complicated. Many transcription factors can regulate a gene and our algorithm finds that in this example a "team" (or collection) of three transcription factors including RAP1 substitutes for TBF1 for 19 genes. The switch occurs for a branch of the phylogenetic tree containing 10 species (including Saccharomyces cerevisiae), while the remaining 13 species (Candida albicans) are regulated by TBF1. Conclusions: To gain insight into more general evolutionary mechanisms, we have created a mathematical algorithm that finds such general switching events and we prove that it converges. Of course any such computational discovery should be validated in the biological tests. For each branch of the phylogenetic tree and each gene module, our algorithm finds a sub-group of co-regulated genes and a team of transcription factors that substitutes for another team of transcription factors. In most cases the signal will be small but in some cases we find a strong signal of switching. We report our findings for 23 Ascomycota fungi species. © 2016 The Author(s)

Turbulence transition and the edge of chaos in pipe flow

The linear stability of pipe flow implies that only perturbations of sufficient strength will trigger the transition to turbulence. In order to determine this threshold in perturbation amplitude we study the \emph{edge of chaos} which separates perturbations that decay towards the laminar profile and perturbations that trigger turbulence. Using the lifetime as an indicator and methods developed in (Skufca et al, Phys. Rev. Lett. {\bf 96}, 174101 (2006)) we show that superimposed on an overall $1/\Re$-scaling predicted and studied previously there are small, non-monotonic variations reflecting folds in the edge of chaos. By tracing the motion in the edge we find that it is formed by the stable manifold of a unique flow field that is dominated by a pair of downstream vortices, asymmetrically placed towards the wall. The flow field that generates the edge of chaos shows intrinsic chaotic dynamics.Comment: 4 pages, 5 figure

The HII Region KR 140: Spontaneous Formation of a High Mass Star

We have used a multiwavelength data set from the Canadian Galactic Plane Survey (CGPS) to study the Galactic HII region KR 140, both on the scale of the nebula itself and in the context of the star forming activity in the nearby W3/W4/W5 complex of molecular clouds and HII regions. From both radio and infrared data we have found a covering factor of about 0.5 for KR 140 and we interpret the nebula as a bowl-shaped region viewed close to face on. Extinction measurements place the region on the near side of its parent molecular cloud. The nebula is kept ionized by one O8.5 V(e) star, VES 735, which is less than a few million years old. CO data show that VES 735 has disrupted much of the original molecular cloud for which the estimated mass and density are about 5000 $M_{\odot}$ and 100 cm$^{-3}$, respectively. KR 140 is isolated from the nearest star forming activity, in W3. Our data suggest that KR 140 is an example of spontaneous (i.e., non-triggered) formation of, unusually, a high mass star.Comment: 46 pages; includes 15 figures; accepted by the Ap

Engaging and empowering first-year students through curriculum design: perspectives from the literature

There is an increasing value being placed on engaging and empowering first-year students and first-year curriculum design is a key driver and opportunity to ensure early enculturation into successful learning at university. This paper summarises the literature on first-year curriculum design linked to student engagement and empowerment. We present conceptualisations of ‘curriculum’ and examples from first-year curriculum design. We also note the limited literature where students have been involved in designing first-year curricula. The results of the literature review suggest that key characteristics of engaging first-year curricula include active learning, timely feedback, relevance and challenge. The literature also points to the importance of identifying students' abilities on entry to university as well as being clear about desired graduate attributes and developmental goals. Acknowledging realities and constraints, we present a framework for the first-year curriculum design process based on the literature

HST/WFPC2 and VLT/ISAAC observations of PROPLYDS in the giant HII region NGC 3603

We report the discovery of three proplyd-like structures in the giant HII region NGC 3603. The emission nebulae are clearly resolved in narrow-band and broad-band HST/WFPC2 observations in the optical and broad-band VLT/ISAAC observations in the near-infrared. All three nebulae are tadpole shaped, with the bright ionization front at the head facing the central cluster and a fainter ionization front around the tail pointing away from the cluster. Typical sizes are 6,000 A.U. x 20,000 A.U. The nebulae share the overall morphology of the proplyds (``PROto PLanetarY DiskS'') in Orion, but are 20 to 30 times larger in size. Additional faint filaments located between the nebulae and the central ionizing cluster can be interpreted as bow shocks resulting from the interaction of the fast winds from the high-mass stars in the cluster with the evaporation flow from the proplyds. The striking similarity of the tadpole shaped emission nebulae in NGC 3603 to the proplyds in Orion suggests that the physical structure of both types of objects might be the same. We present 2D radiation hydrodynamical simulations of an externally illuminated star-disk-envelope system, which was still in its main accretion phase when first exposed to ionizing radiation from the central cluster. The simulations reproduce the overall morphology of the proplyds in NGC 3603 very well, but also indicate that mass-loss rates of up to 10^-5 Mo/yr are required in order to explain the size of the proplyds. (abbreviated)Comment: 10 pages, 4 Postscript figures, uses emulateapj.sty and psfig.tex. Astronomical Journal, in press (January 2000 issue

A Keck High Resolution Spectroscopic Study of the Orion Nebula Proplyds

We present the results of spectroscopy of four bright proplyds in the Orion Nebula obtained at a velocity resolution of 6 km/s. After careful isolation of the proplyd spectra from the confusing nebular radiation, the emission line profiles are compared with those predicted by realistic dynamic/photoionization models of the objects. The spectral line widths show a clear correlation with ionization potential, which is consistent with the free expansion of a transonic, ionization-stratified, photoevaporating flow. Fitting models of such a flow simultaneously to our spectra and HST emission line imaging provides direct measurements of the proplyd size, ionized density and outflow velocity. These measurements confirm that the ionization front in the proplyds is approximately D-critical and provide the most accurate and robust estimate to date of the proplyd mass loss rate. Values of 0.7E-6 to 1.5E-6 Msun/year are found for our spectroscopic sample, although extrapolating our results to a larger sample of proplyds implies that 0.4E-6 Msun/year is more typical of the proplyds as a whole. In view of the reported limits on the masses of the circumstellar disks within the proplyds, the length of time that they can have been exposed to ionizing radiation should not greatly exceed 10,000 years - a factor of 30 less than the mean age of the proplyd stars. We review the various mechanisms that have been proposed to explain this situation, and conclude that none can plausibly work unless the disk masses are revised upwards by a substantial amount.Comment: 23 pages, 8 figures, uses emulateapj.sty, accepted for publication in The Astronomical Journal (scheduled November 1999

Pan-European grading scales: lessons from national systems and the ECTS

This article assesses the impact of the Bologna Process on the grading schemes of EU member countries. In light of some problems regarding the implementation of the European Credit Transfer system (ECTS), the author proposes further reforms and offers some elements of a unified grading system for European higher education. The author explores the variation among Europe’s grading systems and the resulting lessons learned are shared here. Lastly, this article also argues that principles of justice and fairness, deemed central to academic freedom, are best upheld by the use of a unified grading system at national and European levels