Spatial patterns of aerobic and anaerobic mineralization rates and oxygen penetration dynamics in coral reef sediments

Oxygen consumption rates (OCR), aerobic mineralization and sulfate reduction rates (SRR) were studied in the permeable carbonate reef sediments of Heron Reef, Australia. We selected 4 stations with different hydrodynamic regimes for this study. In situ oxygen penetration into the sediments was measured with an autonomous microsensor profiler. Areal OCR were quantified from the measured oxygen penetration depth and volumetric OCR. Oxygen penetration and dynamics (median penetration depths at the 4 stations ranged between 0.3 and 2.2 cm), OCR (median 57 to 196 mmol C m(-2) d(-1)), aerobic mineralization (median 24 to 176 mmol C m(-2) d(-1)) and SRR (median 9 to 42 mmol C m(-2) d(-1)) were highly variable between sites. The supply of oxygen by pore water advection was a major cause for high mineralization rates by stimulating aerobic mineralization at all sites. However, estimated bottom water filtration rates could not explain the differences in volumetric OCR and SRR between the 4 stations. This suggests that local mineralization rates are additionally controlled by factors other than current driven pore water advection, e.g. by the distribution of the benthic fauna or by local differences in labile organic carbon supply from sources such as benthic photosynthesis. Carbon mineralization rates were among the highest reported for coral reef sediments, stressing the role of these sediments in the functioning of the reef ecosystem.

Transcriptional network dynamics in macrophage activation

Transcriptional regulatory networks govern cell differentiation and the cellular response to external stimuli. However, mammalian model systems have not yet been accessible for network analysis. Here, we present a genome-wide network analysis of the transcriptional regulation underlying the mouse macrophage response to bacterial lipopolysaccharide (LPS). Key to uncovering the network structure is our combination of time-series cap analysis of gene expression with in silico prediction of transcription factor binding sites. By integrating microarray and qPCR time-series expression data with a promoter analysis, we find dynamic subnetworks that describe how signaling pathways change dynamically during the progress of the macrophage LPS response, thus defining regulatory modules characteristic of the inflammatory response. In particular, our integrative analysis enabled us to suggest novel roles for the transcription factors ATF-3 and NRF-2 during the inflammatory response. We believe that our system approach presented here is applicable to understanding cellular differentiation in higher eukaryotes. (c) 2006 Elsevier Inc. All rights reserved.

Using computational fluid dynamics in combating erosion-corrosion

Computational fluid dynamics was used to search for the links between the observed pattern of attack seen in a bauxite refinery's heat exchanger headers and the hydrodynamics inside the header. Validation of the computational fluid dynamics results was done by comparing then with flow parameters measured in a 1:5 scale model of the first pass header in the laboratory. Computational fluid dynamics simulations were used to establish hydrodynamic similarity between the 1:5 scale and full scale models of the first pass header. It was found that the erosion-corrosion damage seen at the tubesheet of the first pass header was a consequence of increased levels of turbulence at the tubesheet caused by a rapidly turning flow. A prismatic flow corrections device introduced in the past helped in rectifying the problem at the tubesheet but exaggerated the erosion-corrosion problem at the first pass header shell. A number of alternative flow correction devices were tested using computational fluid dynamics. Axial ribbing in the first pass header and an inlet flow diffuser have shown the best performance and were recommended for implementation. Computational fluid dynamics simulations have revealed a smooth orderly low turbulence flow pattern in the second, third and fourth pass as well as the exit headers where no erosion-corrosion was seen in practice. This study has confirmed that near-wall turbulence intensity, which can be successfully predicted by using computational fluid dynamics, is a good hydrodynamic predictor of erosion-corrosion damage in complex geometries. (c) 2006 Published by Elsevier Ltd.

Evolving noisy oscillatory dynamics in genetic regulatory networks

We introduce a genetic programming (GP) approach for evolving genetic networks that demonstrate desired dynamics when simulated as a discrete stochastic process. Our representation of genetic networks is based on a biochemical reaction model including key elements such as transcription, translation and post-translational modifications. The stochastic, reaction-based GP system is similar but not identical with algorithmic chemistries. We evolved genetic networks with noisy oscillatory dynamics. The results show the practicality of evolving particular dynamics in gene regulatory networks when modelled with intrinsic noise.

Organic Matter Dynamics in the Wet Tropics Under Different Sugarcane Residue Management Regimes

Retention of sugarcane leaves and tops on the soil surface after harvesting has almost completely replaced pre- and post-harvest burning of crop residues in the Australian sugar industry. Since its introduction around 25 years ago, residue retention has increased soil organic matter to improve soil fertility as well as improve harvest flexibility and reduce erosion. However, in the wet tropics residue retention also poses potential problems of prolonged waterlogging, and late-season release of nitrogen which can reduce sugar content of the crop. The objective of this project is to examine the management of sugarcane residues in the wet tropics using a systems approach. Subsidiary objectives are (a) to improve understanding of nitrogen cycling in Australian sugarcane soils in the wet tropics, and (b) to identify ways to manage crop residues to retain their advantages and limit their disadvantages. Project objectives will be addressed using several approaches. Historic farm production data recorded by sugar mills in the wet tropics will be analysed to determine the effect of residue burning or retention on crop yield and sugar content. The impact of climate on soil processes will be highlighed by development of an index of nitrogen mineralisation using the Agricultural Production Systems Simulator (APSIM) model. Increased understanding of nitrogen cycling in Australian sugarcane soils and management of crop residues will be gained through a field experiment recently established in the Australian wet tropics. From this experiment the decomposition and nitrogen dynamics of residues placed on the soil surface and incorporated will be compared. The effect of differences in temperature, soil water content and pH will be further examined on these soils under glasshouse conditions. Preliminary results show a high ammonium to nitrate ratio in tropics soils, which may be due to low rates of nitrification that increase the retention of nitrogen in a form (ammonium) that is less subject to leaching. Further results will be presented at Congress.