School of Agriculture, Food and Ecosystem Sciences - Research Publications
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ItemNo Preview AvailableTesting the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptome(EDP SCIENCES S A, 2006)Despite growing evidence of rapid evolution in protein coding genes, the contribution of positive selection to intra- and interspecific differences in protein coding regions of the genome is unclear. We attempted to see if genes coding for secreted proteins and genes with narrow expression, specifically those preferentially expressed in the mammary gland, have diverged at a faster rate between domestic cattle (Bos taurus) and humans (Homo sapiens) than other genes and whether positive selection is responsible. Using a large data set, we identified groups of genes based on secretion and expression patterns and compared them for the rate of nonsynonymous (dN) and synonymous (dS) substitutions per site and the number of radical (Dr) and conservative (Dc) amino acid substitutions. We found evidence of rapid evolution in genes with narrow expression, especially for those expressed in the liver and mammary gland and for genes coding for secreted proteins. We compared common human polymorphism data with human-cattle divergence and found that genes with high evolutionary rates in human-cattle divergence also had a large number of common human polymorphisms. This argues against positive selection causing rapid divergence in these groups of genes. In most cases dN/dS ratios were lower in human-cattle divergence than in common human polymorphism presumably due to differences in the effectiveness of purifying selection between long-term divergence and short-term polymorphism.
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ItemNo Preview AvailableRiparian tree water use by eucalyptus coolabah in the Lake Eyre Basin(Conference Organising Committee, 2006)The Lake Eyre Basin (LEB) is characterised by enormous stream flow variability, low rainfall, saline groundwater and at times saline surface water; conditions that demand flexible tree water use strategies in the riparian zone. In the lower reaches of the Diamantina River, the water sources and extraction patterns of Eucalyptus coolabah were examined using isotope data from xylem, soil water, groundwater and surface water. Additionally, soil chloride and matric potential data were used to infer zones of water availability for root uptake. It was found that despite their elevated salinity, groundwater and soil water formed a large proportion of the transpiration flux, with little contribution from standing pools of surface water. At two sites located on the dry floodplain, the data indicated E. coolabah relied substantially on groundwater with a salinity exceeding 30,000 mgL-1Cl. However, some dilution with fresher soil water was evident at most sites, highlighting the importance of flooding in replenishing soil water. Water extraction primarily occurred in the unsaturated zone where a compromise between salinity and source reliability was required. However, E. coolabah was found to have higher salinity tolerances than previously reported for Eucalyptus species.
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ItemGene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks(BMC, 2006-03-03)BACKGROUND: Genes and proteins are organized into functional modular networks in which the network context of a gene or protein has implications for cellular function. Highly connected hub proteins, largely responsible for maintaining network connectivity, have been found to be much more likely to be essential for yeast survival. RESULTS: Here we investigate the properties of weighted gene co-expression networks formed from multiple microarray datasets. The constructed networks approximate scale-free topology, but this is not universal across all datasets. We show strong positive correlations between gene connectivity within the whole network and gene essentiality as well as gene sequence conservation. We demonstrate the preservation of a modular structure of the networks formed, and demonstrate that, within some of these modules, it is possible to observe a strong correlation between connectivity and essentiality or between connectivity and conservation within the modules particularly within modules containing larger numbers of essential genes. CONCLUSION: Application of these techniques can allow a finer scale prediction of relative gene importance for a particular process within a group of similarly expressed genes.
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ItemAlf Leslie: the skeptical forest economist(Ian Ferguson, 2006)This book reflects a critical review and synthesis of economic and related literature pertaining to forestry and forest management by a long-time forester, teacher of forest economics, UN administrator, and forest policy advisor and consultant to many governments, agencies and companies. To quote the author 'After playing around in the field of forest economics for the best part of sixty years, I wanted to sort out my ideas on the subject'.
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ItemMicrowave Treatment Accelerates Solar Timber Drying(American Society of Agricultural and Biological Engineers, 2006)
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ItemExtraordinary drought of 2003 overrules ozone impact on adult beech trees (Fagus sylvatica)(Springer, 2006)The extraordinary drought during the summer of 2003 in Central Europe allowed to examine responses of adult beech trees (Fagus sylvatica) to co-occurring stress by soil moisture deficit and elevated O3 levels under forest conditions in southern Germany. The study comprised tree exposure to the ambient O3 regime at the site and to a twice-ambient O3 regime as released into the canopy through a free-air O3 fumigation system. Annual courses of photosynthesis (Amax), stomatal conductance (gs), electron transport rate (ETR) and chlorophyll levels were compared between 2003 and 2004, the latter year representing the humid long-term climate at the site. ETR, Amax and gs were lowered during 2003 by drought rather than ozone, whereas chlorophyll levels did not differ between the years. Radial stem increment was reduced in 2003 by drought but fully recovered during the subsequent, humid year. Comparison of AOT40, an O3 exposure-based risk index of O3 stress, and cumulative ozone uptake (COU) yielded a linear relationship throughout humid growth conditions, but a changing slope during 2003. Our findings support the hypothesis that drought protects plants from O3 injury by stomatal closure, which restricts O3 influx into leaves and decouples COU from high external ozone levels. High AOT40 erroneously suggested high O3 risk under drought. Enhanced ozone levels did not aggravate drought effects in leaves and stem.
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