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Research ArticleResearch Article
Open Access

Systems Biology Approach in Chlamydomonas Reveals Connections between Copper Nutrition and Multiple Metabolic Steps

Madeli Castruita, David Casero, Steven J. Karpowicz, Janette Kropat, Astrid Vieler, Scott I. Hsieh, Weihong Yan, Shawn Cokus, Joseph A. Loo, Christoph Benning, Matteo Pellegrini and Sabeeha S. Merchant
The Plant Cell April 2011, tpc.111.084400; DOI: https://doi.org/10.1105/tpc.111.084400
Madeli Castruita
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David Casero
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Steven J. Karpowicz
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Janette Kropat
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Astrid Vieler
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Scott I. Hsieh
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Weihong Yan
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Shawn Cokus
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Joseph A. Loo
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Christoph Benning
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Matteo Pellegrini
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Sabeeha S. Merchant
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  • For correspondence: sabeeha@chem.ucla.edu

Author Profile

Madeli Castruita and David Casero

Madeli Castruita

bio pic

Current Position: Postdoctoral Research Assistant, Chemistry and Biochemistry Department, University of California, Los Angeles.

Education: Ph.D., Princeton University.

Non-scientific Interests: Soccer, Traveling, and Cooking

Though I initially worked in organometallic chemistry researching the properties and material potential of several compounds, I also learned about their impact on biochemistry and their environmental fate. As a result, I switched my focus to biological oceanography for my Ph.D., working on the mechanism of iron homeostasis in marine cyanobacteria. Numerous field studies have demonstrated that primary production by phytoplankton in the high-nitrate, low-chlorophyll regions of the ocean are limited by iron bioavailability. My thesis addressed the question of iron storage, which is made critical by the episodic nature of iron inputs to many regions of the oceans. Continuing on the interaction between trace metal and mineral deficiency, I began a post-doc at UCLA studying copper-deficiency, which, for example, has been linked to birth defects and cardiovascular disease in humans. My primary goal has been to study copper nutrition in Chlamydomonas reinhardtii, and we have implemented a novel next-generation sequencing technique (RNA-Seq) to study the changes in gene expression as cells acclimate to various stages in copper nutrition at a whole system level. Besides direct targets of copper-deficiency signaling, we identified a small set of differentially expressed genes, which we suggest are specific but indirect targets that overlap very well with the anaerobic response of Chlamydomonas. This suggests that a copper protein may be involved in sensing O2 levels.

David Casero

bio pic

Current Position: Postdoctoral fellow, Department of Molecular, Cell and Developmental Biology, University of California Los Angeles (UCLA).

Education: B.S. (1998) in Theoretical Physics and Ph.D. (2007) in Applied Mathematics, Complutense University of Madrid (Spain).

Non-scientific Interests: Contemporary art.

Soon after I graduated in Theoretical Physics, my first research mentor, Antonio Brù, encouraged me to learn how to apply mathematical and computational techniques to the understanding of biological problems. Fortunately, I didn't lose contact with multidisciplinary projects during my Ph.D., which was focused on theoretical problems in materials science. Both my Ph.D. advisor, Juan José López Velázquez, and one of my mentors, Miguel Angel Herrero, were actively working on the mathematical formulation of a number of relevant biological processes. It was in this context that I decided to dedicate my postdoctoral research to computational biology. In 2007, I joined Matteo Pellegrini's group at UCLA to work on a project that was focused on the development of computational models for transcriptional regulation. And then came next-generation sequencing (NGS). This technology has revolutionized both the experimental and computational approaches employed for the understanding of DNA modifications, structure, transcription and its regulation. My efforts in this field are mostly devoted to the development of computational methods that exploit the high amount of information resulting from the new sequencing technologies. Built upon our synergistic collaboration with Sabeeha Merchant's group, I am involved in a number of community projects where we apply NGS methodology in the fields of next-generation biofuels and trace metals metabolism. I have tried to focus my work on methods for the production of accurate datasets and structural annotations of interest to the plant biology community, and I hope these efforts will pave the way for the discovery of new and exciting biology.

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