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James R.A.,CSIRO | Sirault X.R.R.,High Resolution Plant Phenomics Center
Methods in Molecular Biology

The recent advances made in the use of infrared thermal imaging (thermography) as a non-invasive, high-throughput technique for the screening of salinity tolerance in plants is reviewed. Taking wheat seedlings as an example, the methods and protocols used to impose a homogeneous salt stress to a large number of genotypes, as well as capturing infrared images of these genotypes and automatically processing the images are described in detail in this chapter. We also present the source code of the Matlab program applied to automatically identify plants and batch process IR images. © 2012 Springer Science+Business Media, LLC. Source

Pengelly J.J.L.,Australian National University | Tan J.,National University of Singapore | Furbank R.T.,High Resolution Plant Phenomics Center | von Caemmerer S.,Australian National University
Plant Physiology

An antisense construct targeting the C4 isoform of NADP-malic enzyme (ME), the primary enzyme decarboxylating malate in bundle sheath cells to supply CO2 to Rubisco, was used to transform the dicot Flaveria bidentis. Transgenic plants (a-NADP-ME) exhibited a 34% to 75% reduction in NADP-ME activity relative to the wild type with no visible growth phenotype. We characterized the effect of reducing NADP-ME on photosynthesis by measuring in vitro photosynthetic enzyme activity, gas exchange, and real-time carbon isotope discrimination (Δ). In α-NADP-ME plants with less than 40% of wild-type NADP-ME activity, CO2 assimilation rates at high intercellular CO2 were significantly reduced, whereas the in vitro activities of both phosphoenolpyruvate carboxylase and Rubisco were increased. Δ measured concurrently with gas exchange in these plants showed a lower Δ and thus a lower calculated leakiness of CO2 (the ratio of CO2 leak rate from the bundle sheath to the rate of CO2 supply). Comparative measurements on antisense Rubisco small subunit F. bidentis plants showed the opposite effect of increased Δ and leakiness. We use these measurements to estimate the C4 cycle rate, bundle sheath leak rate, and bundle sheath CO2 concentration. The comparison of a-NADP-ME and antisense Rubisco small subunit demonstrates that the coordination of the C3 and C4 cycles that exist during environmental perturbations by light and CO2 can be disrupted through transgenic manipulations. Furthermore, our results suggest that the efficiency of the C4 pathway could potentially be improved through a reduction in C4 cycle activity or increased C3 cycle activity. © 2012 American Society of Plant Biologists. All Rights Reserved. Source

Li Y.-F.,Monash University | Kennedy G.,University of Queensland | Kennedy G.,High Resolution Plant Phenomics Center | Ngoran F.,University of Queensland | And 2 more authors.
Future Generation Computer Systems

Data management has become a critical challenge faced by a wide array of scientific disciplines in which the provision of sound data management is pivotal to the achievements and impact of research projects. Massive and rapidly expanding amounts of data combined with data models that evolve over time contribute to making data management an increasingly challenging task that warrants a new approach. In this paper we present an ontology-centric architecture for data management systems that is extensible and domain independent. In this architecture, the behaviors of domain concepts and objects are captured entirely by ontological entities, around which all data management tasks are carried out. The open and semantic nature of ontology languages also makes this architecture amenable to greater data reuse and interoperability. To evaluate the proposed architecture, we have applied it to the challenge of managing phenomics data. © 2012 Elsevier B.V. All rights reserved. Source

Munns R.,CSIRO | James R.A.,CSIRO | Sirault X.R.R.,CSIRO | Sirault X.R.R.,High Resolution Plant Phenomics Center | And 3 more authors.
Journal of Experimental Botany

This review considers stomatal conductance as an indicator of genotypic differences in the growth response to water stress. The benefits of using stomatal conductance are compared with photosynthetic rate and other indicators of genetic variation in water stress tolerance, along with the use of modern phenomics technologies. Various treatments for screening for genetic diversity in response to water deficit in controlled environments are considered. There is no perfect medium: there are pitfalls in using soil in pots, and in using hydroponics with ionic and non-ionic osmotica. Use of mixed salts or NaCl is recommended over non-ionic osmotica. Developments in infrared thermography provide new and feasible screening methods for detecting genetic variation in the stomatal response to water deficit in controlled environments and in the field. © 2010 The Author. Source

Pengelly J.J.L.,Australian National University | Kwasny S.,High Resolution Plant Phenomics Center | Bala S.,Australian National University | Evans J.R.,Australian National University | And 5 more authors.
Plant Physiology

The husk surrounding the ear of corn/maize (Zea mays) has widely spaced veins with a number of interveinal mesophyll (M) cells and has been described as operating a partial C3 photosynthetic pathway, in contrast to its leaves, which use the C4photosynthetic pathway. Here, we characterized photosynthesis in maize husk and leaf by measuring combined gas exchange and carbon isotope discrimination, the oxygen dependence of the CO2compensation point, and photosynthetic enzyme activity and localization together with anatomy. The CO2 assimilation rate in the husk was less than that in the leaves and did not saturate at high CO2, indicating CO2 diffusion limitations. However, maximal photosynthetic rates were similar between the leaf and husk when expressed on a chlorophyll basis. The CO2compensation points of the husk were high compared with the leaf but did not vary with oxygen concentration. This and the low carbon isotope discrimination measured concurrently with gas exchange in the husk and leaf suggested C4-like photosynthesis in the husk. However, both Rubisco activity and the ratio of phosphoenolpyruvate carboxylase to Rubisco activity were reduced in the husk. Immunolocalization studies showed that phosphoenolpyruvate carboxylase is specifically localized in the layer of Mcells surrounding the bundle sheath cells, while Rubisco and glycine decarboxylase were enriched in bundle sheath cells but also present in M cells. We conclude that maize husk operates C4 photosynthesis dispersed around the widely spaced veins (analogous to leaves) in a diffusion-limited manner due to low M surface area exposed to intercellular air space, with the functional role of Rubisco and glycine decarboxylase in distant M yet to be explained. © 2011 American Society of Plant Biologists. Source

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