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Davidson R.M.,Michigan State University | Gowda M.,Michigan State University | Gowda M.,Center for Cellular and Molecular Platforms | Moghe G.,Michigan State University | And 5 more authors.
Plant Journal | Year: 2012

The Poaceae family, also known as the grasses, includes agronomically important cereal crops such as rice, maize, sorghum, and wheat. Previous comparative studies have shown that much of the gene content is shared among the grasses; however, functional conservation of orthologous genes has yet to be explored. To gain an understanding of the genome-wide patterns of evolution of gene expression across reproductive tissues, we employed a sequence-based approach to compare analogous transcriptomes in species representing three Poaceae subgroups including the Pooideae (Brachypodium distachyon), the Panicoideae (sorghum), and the Ehrhartoideae (rice). Our transcriptome analyses reveal that only a fraction of orthologous genes exhibit conserved expression patterns. A high proportion of conserved orthologs include genes that are upregulated in physiologically similar tissues such as leaves, anther, pistil, and embryo, while orthologs that are highly expressed in seeds show the most diverged expression patterns. More generally, we show that evolution of gene expression profiles and coding sequences in the grasses may be linked. Genes that are highly and broadly expressed tend to be conserved at the coding sequence level while genes with narrow expression patterns show accelerated rates of sequence evolution. We further show that orthologs in syntenic genomic blocks are more likely to share correlated expression patterns compared with non-syntenic orthologs. These findings are important for agricultural improvement because sequence information is transferred from model species, such as Brachypodium, rice, and sorghum to crop plants without sequenced genomes. © 2012 The Authors.

Babu P.,Center for Cellular and Molecular Platforms
ACS Chemical Biology | Year: 2014

Glycans participate in many key cellular processes during development and in physiology and disease. In this review, the functional role of various glycans in the regeneration of neurons and body parts in adult metazoans is discussed. Understanding glycosylation may facilitate research in the field of stem cell biology and regenerative medicine. © 2013 American Chemical Society.

Rangiah K.,Center for Cellular and Molecular Platforms
Analytical Methods | Year: 2014

In recent years, the use of antipsychotics like olanzapine has increased leading to potentially serious adverse metabolic effects. A sensitive method to quantify olanzapine and its metabolites is therefore highly needed. A stable isotope dilution ultrahigh performance liquid chromatography-mass spectrometry/selected reaction monitoring based quantitative assay has been developed for the simultaneous estimation of olanzapine and its metabolites. This method includes the parent drug olanzapine, its metabolites (desmethyl olanzapine and olanzapine-N-oxide) and degradation derived piperazinium chloride, lactam and cyclic amine impurities. All analytes were well resolved and showed a linear relationship across a large dynamic range (0.017-1.25 ng mL-1) for all olanzapine metabolites except the lactam, in which the linear relationship was demonstrated at concentrations five times higher (0.085-6.25 ng mL-1). All analytes had regression coefficients higher than 0.998, accuracies between 92-113% and low coefficients of variation (0.94 to 9.3%). The recovery for all of the analytes from the sera matrix was 80 to 115%. This validated method is suitable for quantifying olanzapine and its metabolites from small volumes of sera samples with great sensitivity. © 2014 The Royal Society of Chemistry.

Dey G.,Stanford University | Gupta G.D.,Samuel Lunenfeld Research Institute | Ramalingam B.,Center for Cellular and Molecular Platforms | Sathe M.,Tata Institute of Fundamental Research | And 2 more authors.
PLoS ONE | Year: 2014

Any single-cell-resolved measurement generates a population distribution of phenotypes, characterized by a mean, a variance, and a shape. Here we show that changes in the shape of a phenotypic distribution can signal perturbations to cellular processes, providing a way to screen for underlying molecular machinery. We analyzed images of a Drosophila S2R+ cell line perturbed by RNA interference, and tracked 27 single-cell features which report on endocytic activity, and cell and nuclear morphology. In replicate measurements feature distributions had erratic means and variances, but reproducible shapes; RNAi down-regulation reliably induced shape deviations in at least one feature for 1072 out of 7131 genes surveyed, as revealed by a Kolmogorov-Smirnov-like statistic. We were able to use these shape deviations to identify a spectrum of genes that influenced cell morphology, nuclear morphology, and multiple pathways of endocytosis. By preserving single-cell data, our method was even able to detect effects invisible to a population-averaged analysis. These results demonstrate that cell-to-cell variability contains accessible and useful biological information, which can be exploited in existing cell-based assays. © 2014 Dey et al.

Neerathilingam M.,Center for Cellular and Molecular Platforms | Neerathilingam M.,University of Oxford | Bairy S.G.,Center for Cellular and Molecular Platforms | Mysore S.,Center for Cellular and Molecular Platforms
PLoS ONE | Year: 2016

Intrinsically disordered proteins (IDPs) play a major role in various cellular functions ranging from transcription to cell migration. Mutations/modifications in such IDPs are shown to be associated with various diseases. Current strategies to study the mode of action and regulatory mechanisms of disordered proteins at the structural level are time consuming and challenging. Therefore, using simple and swift strategies for identifying functionally important regions in unstructured segments and understanding their underlying mechanisms is critical for many applications. Here we propose a simple strategy that employs dissection of human paxillin (residues 1-313) that comprises intrinsically disordered regions, followed by its interaction study using FAT (Focal adhesion targeting domain of focal adhesion kinase) as its binding partner to retrace structural behavior. Our findings show that the paxillin interaction with FAT exhibits a masking and unmasking effect by a putative intra-molecular regulatory region. This phenomenon suggests how cancer associated mutations in paxillin affect its interactions with Focal Adhesion Kinase (FAK). The strategy could be used to decipher the mode of regulations and identify functionally relevant constructs for other studies. © 2016 Neerathilingam et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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