Sanjeena Subedi

Genome-wide expression profiling of maize in response to individual and combined water and nitrogen stresses

BackgroundWater and nitrogen are two of the most critical inputs required to achieve the high yield potential of modern corn varieties. Under most agricultural settings however they are often scarce and costly. Fortunately, tremendous progress has been made in the past decades in terms of modeling to assist growers in the decision making process and many tools are now available to achieve more sustainable practices both environmentally and economically. Nevertheless large gaps remain between our empirical knowledge of the physiological changes observed in the field in response to nitrogen and water stresses, and our limited understanding of the molecular processes leading to those changes.ResultsThis work examines in particular the impact of simultaneous stresses on the transcriptome. In a greenhouse setting, corn plants were grown under tightly controlled nitrogen and water conditions, allowing sampling of various tissues and stress combinations. A microarray profiling experiment was performed using this material and showed that the concomitant presence of nitrogen and water limitation affects gene expression to an extent much larger than anticipated. A clustering analysis also revealed how the interaction between the two stresses shapes the patterns of gene expression over various levels of water stresses and recovery.ConclusionsOverall, this study suggests that the molecular signature of a specific combination of stresses on the transcriptome might be as unique as the impact of individual stresses, and hence underlines the difficulty to extrapolate conclusions obtained from the study of individual stress responses to more complex settings.

Model-based classification via mixtures of multivariate t-distributions

A novel model-based classification technique is introduced based on mixtures of multivariate t-distributions. A family of four mixture models is defined by constraining, or not, the covariance matrices and the degrees of freedom to be equal across mixture components. Parameters for each of the resulting four models are estimated using a multicycle expectation-conditional maximization algorithm, where convergence is determined using a criterion based on the Aitken acceleration. A straightforward, but very effective, technique for the initialization of the unknown component memberships is introduced and compared with a popular, more sophisticated, initialization procedure. This novel four-member family is applied to real and simulated data, where it gives good classification performance, even when compared with more established techniques.

Identification of Multiple Phosphorylation Sites on Maize Endosperm Starch Branching Enzyme IIb, a Key Enzyme in Amylopectin Biosynthesis

Background: Starch is the major component of cereal yield, yet the biochemical regulation of its synthesis is poorly understood. Results: Starch branching enzyme IIb is phosphorylated at three sites by two Ca2+-dependent protein kinases. Conclusion: Two phosphorylation sites represent a general mechanism of control in plants, the third is cereal specific. Significance: Identification of post-translational regulatory mechanism offers possibilities for targeted manipulation of starch. Starch branching enzyme IIb (SBEIIb) plays a crucial role in amylopectin biosynthesis in maize endosperm by defining the structural and functional properties of storage starch and is regulated by protein phosphorylation. Native and recombinant maize SBEIIb were used as substrates for amyloplast protein kinases to identify phosphorylation sites on the protein. A multidisciplinary approach involving bioinformatics, site-directed mutagenesis, and mass spectrometry identified three phosphorylation sites at Ser residues: Ser649, Ser286, and Ser297. Two Ca2+-dependent protein kinase activities were partially purified from amyloplasts, termed K1, responsible for Ser649 and Ser286 phosphorylation, and K2, responsible for Ser649 and Ser297 phosphorylation. The Ser286 and Ser297 phosphorylation sites are conserved in all plant branching enzymes and are located at opposite openings of the 8-stranded parallel β-barrel of the active site, which is involved with substrate binding and catalysis. Molecular dynamics simulation analysis indicates that phospho-Ser297 forms a stable salt bridge with Arg665, part of a conserved Cys-containing domain in plant branching enzymes. Ser649 conservation appears confined to the enzyme in cereals and is not universal, and is presumably associated with functions specific to seed storage. The implications of SBEIIb phosphorylation are considered in terms of the role of the enzyme and the importance of starch biosynthesis for yield and biotechnological application.

Clustering and classification via cluster-weighted factor analyzers

In model-based clustering and classification, the cluster-weighted model is a convenient approach when the random vector of interest is constituted by a response variable

Cluster-weighted \(t\)-factor analyzers for robust model-based clustering and dimension reduction

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Nitrogen limitation and high density responses in rice suggest a role for ethylene under high density stress

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Marine fish oil is more potent than plant based n-3 polyunsaturated fatty acids in the prevention of mammary tumours

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