Modelling delta-notch perturbations during zebrafish somitogenesis

The discovery over the last 15 years of molecular clocks and gradients in the pre-somitic mesoderm of numerous vertebrate species has added significant weight to Cooke and Zeeman's ‘clock and wavefront’ model of somitogenesis, in which a travelling wavefront determines the spatial position of somite formation and the somitogenesis clock controls periodicity (Cooke and Zeeman, 1976). However, recent high-throughput measurements of spatiotemporal patterns of gene expression in different zebrafish mutant backgrounds allow further quantitative evaluation of the clock and wavefront hypothesis. In this study we describe how our recently proposed model, in which oscillator coupling drives the propagation of an emergent wavefront, can be used to provide mechanistic and testable explanations for the following observed phenomena in zebrafish embryos: (a) the variation in somite measurements across a number of zebrafish mutants; (b) the delayed formation of somites and the formation of ‘salt and pepper’ patterns of gene expression upon disruption of oscillator coupling; and (c) spatial correlations in the ‘salt and pepper’ patterns in Delta-Notch mutants. In light of our results, we propose a number of plausible experiments that could be used to further test the model

BIOFUELS, CLIMATE POLICY, AND WATER MANAGEMENT: ASSESSING POLICY-INDUCED SHIFTS ON AGRICULTURE’S EXTENSIVE AND INTENSIVE MARGINS

Biofuel expansion efforts and climate mitigation policy could fundamentally alter land management trends in U.S. agriculture and forestry (AF) by mandating biofuel feedstock production and providing incentives for greenhouse gas (GHG) emissions reduction and carbon sequestration from terrestrial sources. Research has shown that biofuel expansion can alter commodity markets, induce agricultural land expansion, and intensify production. Meanwhile, GHG mitigation efforts could limit agricultural expansion, reduce current cultivation, and lower management intensity by incentivizing GHG emissions reduction and carbon sequestration within AF. To date, little work has attempted to quantify biofuel and climate policy-induced shifts together along the extensive and intensive agricultural production margins within a systems-based framework, though such shifts could have resounding implications on agricultural water consumption and quality. This study uses a comprehensive and detailed economic model of the U.S. AF sectors to simulate land management responses to biofuel expansion and GHG policies. While bioenergy production and altered AF management practices are found to significantly reduce GHG emissions, additional water consumption and nutrient use are possible policy outcomes. Specifically, we find that policies that influence shifts to the extensive margin will increase aggregate water use and nutrient application, but lead to lower intensity per-unit area. Conversely, when combined with biofuel mandates climate mitigation incentives lower agricultural land expansion, but lead to higher levels of management intensity. Somewhat contrary to expectations, GHG mitigation incentives cause water and nutrient use intensity to grow at an increasing rate due to the greater level of land use competition. Additionally, important regional trends emerge, as water use and quality concerns grow with the CO2 price in areas with limited GHG mitigation possibilities. This suggests that “water leakage” is possible whereby emissions reduction activities decrease output in one region and stimulate management intensity elsewhere. The potential indirect consequences of combined biofuel and climate mitigation incentives on water resource systems warrant further attention in policy design and future research.Greenhouse gas mitigation, biofuels, water resource management, Environmental Economics and Policy, Production Economics, Resource /Energy Economics and Policy,

Outflows at the Edges of an Active Region in a Coronal Hole: A Signature of Active Region Expansion?

Outflows of plasma at the edges of active regions surrounded by quiet Sun are now a common observation with the Hinode satellite. While there is observational evidence to suggest that the outflows are originating in the magnetic field surrounding the active regions, there is no conclusive evidence that reveals how they are driven. Motivated by observations of outflows at the periphery of a mature active region embedded in a coronal hole, we have used a three-dimensional simulation to emulate the active region's development in order to investigate the origin and driver of these outflows. We find outflows are accelerated from a site in the coronal hole magnetic field immediately surrounding the active region and are channelled along the coronal hole field as they rise through the atmosphere. The plasma is accelerated simply as a result of the active region expanding horizontally as it develops. Many of the characteristics of the outflows generated in the simulation are consistent with those of observed outflows: velocities up to 45 km per sec, properties akin to the coronal hole, proximity to the active region's draining loops, expansion with height, and projection over monopolar photospheric magnetic concentrations. Although the horizontal expansion occurs as a consequence of the active region's development in the simulation, expansion is also a general feature of established active regions. Hence, it is entirely possible and plausible that the expansion acceleration mechanism displayed in the simulation is occurring in active regions on the Sun and, in addition to reconnection, is driving the outflows observed at their edges.Comment: 19 pages, 9 figure

The clockfront and wavefront model revisited

The currently accepted interpretation of the clock and wavefront model of somitogenesis is that a posteriorly moving molecular gradient sequentially slows the rate of clock oscillations, resulting in a spatial readout of temporal oscillations. However, while molecular components of the clocks and wavefronts have now been identified in the pre-somitic mesoderm (PSM), there is not yet conclusive evidence demonstrating that the observed molecular wavefronts act to slow clock oscillations. Here we present an alternative formulation of the clock and wavefront model in which oscillator coupling, already known to play a key role in oscillator synchronisation, plays a fundamentally important role in the slowing of oscillations along the anterior–posterior (AP) axis. Our model has three parameters which can be determined, in any given species, by the measurement of three quantities: the clock period in the posterior PSM, somite length and the length of the PSM. A travelling wavefront, which slows oscillations along the AP axis, is an emergent feature of the model. Using the model we predict: (a) the distance between moving stripes of gene expression; (b) the number of moving stripes of gene expression and (c) the oscillator period profile along the AP axis. Predictions regarding the stripe data are verified using existing zebrafish data. We simulate a range of experimental perturbations and demonstrate how the model can be used to unambiguously define a reference frame along the AP axis. Comparing data from zebrafish, chick, mouse and snake, we demonstrate that: (a) variation in patterning profiles is accounted for by a single nondimensional parameter; the ratio of coupling strengths; and (b) the period profile along the AP axis is conserved across species. Thus the model is consistent with the idea that, although the genes involved in pattern propagation in the PSM vary, there is a conserved patterning mechanism across species

Turing Patterns and Biological Explanation

Turing patterns are a class of minimal mathematical models that have been used to discover and conceptualize certain abstract features of early biological development. This paper examines a range of these minimal models in order to articulate and elaborate a philosophical analysis of their epistemic uses. It is argued that minimal mathematical models aid in structuring the epistemic practices of biology by providing precise descriptions of the quantitative relations between various features of the complex systems, generating novel predictions that can be compared with experimental data, promoting theory exploration, and acting as constitutive parts of empirically adequate explanations of naturally occurring phenomena, such as biological pattern formation. Focusing on the roles that minimal model explanations play in science motivates the adoption of a broader diachronic view of scientific explanation

A modified Oster-Murray-Harris mechanical model of morphogenesis

There are two main modeling paradigms for biological pattern formation in developmental biology: chemical prepattern models and cell aggregation models. This paper focuses on an example of a cell aggregation model, the mechanical model developed by Oster, Murray, and Harris [Development, 78 (1983), pp. 83--125]. We revisit the Oster--Murray--Harris model and find that, due to the infinitesimal displacement assumption made in the original version of this model, there is a restriction on the types of boundary conditions that can be prescribed. We derive a modified form of the model which relaxes the infinitesimal displacement assumption. We analyze the dynamics of this model using linear and multiscale nonlinear analysis and show that it has the same linear behavior as the original Oster--Murray--Harris model. Nonlinear analysis, however, predicts that the modified model will allow for a wider range of parameters where the solution evolves to a bounded steady state. The results from both analyses are verified through numerical simulations of the full nonlinear model in one and two dimensions. The increased range of boundary conditions that are well-posed, as well as a wider range of parameters that yield bounded steady states, renders the modified model more applicable to, and more robust for, comparisons with experiments

BIOFUELS, CLIMATE POLICY, AND WATER MANAGEMENT: ASSESSING POLICY-INDUCED SHIFTS ON AGRICULTURE’S EXTENSIVE AND INTENSIVE MARGINS

Biofuel expansion efforts and climate mitigation policy could fundamentally alter land management trends in U.S. agriculture and forestry (AF) by mandating biofuel feedstock production and providing incentives for greenhouse gas (GHG) emissions reduction and carbon sequestration from terrestrial sources. Research has shown that biofuel expansion can alter commodity markets, induce agricultural land expansion, and intensify production. Meanwhile, GHG mitigation efforts could limit agricultural expansion, reduce current cultivation, and lower management intensity by incentivizing GHG emissions reduction and carbon sequestration within AF. To date, little work has attempted to quantify biofuel and climate policy-induced shifts together along the extensive and intensive agricultural production margins within a systems-based framework, though such shifts could have resounding implications on agricultural water consumption and quality. This study uses a comprehensive and detailed economic model of the U.S. AF sectors to simulate land management responses to biofuel expansion and GHG policies. While bioenergy production and altered AF management practices are found to significantly reduce GHG emissions, additional water consumption and nutrient use are possible policy outcomes. Specifically, we find that policies that influence shifts to the extensive margin will increase aggregate water use and nutrient application, but lead to lower intensity per-unit area. Conversely, when combined with biofuel mandates climate mitigation incentives lower agricultural land expansion, but lead to higher levels of management intensity. Somewhat contrary to expectations, GHG mitigation incentives cause water and nutrient use intensity to grow at an increasing rate due to the greater level of land use competition. Additionally, important regional trends emerge, as water use and quality concerns grow with the CO2 price in areas with limited GHG mitigation possibilities. This suggests that “water leakage” is possible whereby emissions reduction activities decrease output in one region and stimulate management intensity elsewhere. The potential indirect consequences of combined biofuel and climate mitigation incentives on water resource systems warrant further attention in policy design and future research

Red Quasars and Quasar Evolution: the Case of BALQSO FIRST J155633.8+351758

We present the first near-IR spectroscopy of the z=1.5 radio-loud BALQSO FIRST J155633.8+351758. Both the Balmer decrement and the slope of the rest-frame UV-optical continuum independently suggest a modest amount of extinction along the line of sight to the BLR (E(B-V)~0.5 for SMC-type screen extinction at the QSO redshift). The implied gas column density along the line of sight is much less than is implied by the weak X-ray flux of the object, suggesting that either the BLR and BAL region have a low dust-to-gas ratio, or that the rest-frame optical light encounters significantly lower mean column density lines of sight than the X-ray emission. From the rest-frame UV-optical spectrum, we are able to constrain the stellar mass content of the system. Comparing the maximal stellar mass with the black hole mass estimated from the bolometric luminosity of the QSO, we find that the ratio of the black hole to stellar mass may be comparable to the Magorrian value, which would imply that the Magorrian relation is already in place at z=1.5. However, multiple factors favor a much larger black hole to stellar mass ratio. This would imply that if the Magorrian relation characterizes the late history of QSOs, and the situation observed for F1556+3517 is typical of the early evolutionary history of QSOs, central black hole masses develop more rapidly than bulge masses. [ABRIDGED]Comment: 23 pages, 4 embedded postscript figures; Accepted for publication in The Astronomical Journal, December 200

The Nineteenth Century Oboe Concertino: An Overview of its Structure with Two Performance Guides

Music written for oboe and orchestra in the nineteenth century falls into three categories: Classical Concerto, Opera Fantasy, and Concertino. The classical, or standard, three movement, sonata-ritornello format was only sparingly used. Instead, composers chose more the experimental forms of the Opera Fantasy and Concertino. The Opera Fantasy was used as a way for oboe players to play popular opera arias of the time, while showcasing their virtuosity and expression. It is in the Concertino where composers expanded the oboe repertoire to its highest form in the nineteenth century, experimenting with structure, and using the oboe to the height of its expressive powers. In addition to discussion on the Concertino in general, performance guides have been provided for two concertinos, Concertino for Oboe and Winds, by Carl Maria von Weber and Concertino for Oboe and Orchestra, Op. 18, by August Klughardt. Information is provided regarding composer biography, compositional/historical perspective, technical and stylistic considerations, and structure. By examining the two very different pieces, one from the beginning of the nineteenth century and one from the end, the evolution of the Concertino can be seen, as well as gaining an understanding of the wide variety of repertoire written for the oboe in the nineteenth century