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image from chloroplast 2010 database

Image of a chloroplast 2010 databaseAs the site of photosynthesis, the chloroplast is the defining organelle of green plants and may be thought of as the world’s life-support system. We have chosen it for functional genomics studies because it produces many molecules important to agriculture and human health yet is similar in complexity to a bacterial cell.

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Recent publications from the project:

Savage, L.J., K.M. Imre, D.A. Hall and R.L. Last. 2013. Analysis of essential Arabidopsis Nuclear Genes Ecoding Plastid-Targeted Proteins. PLoSONE 8(9): e73291. doi 10.1371/journal.pone.0073291

Bell, S.M., L.D. Burgoon and R.L. Last. 2012. MIPHENO: Data normalization for high throughput metabolite analysis. BMC Bioinformatics. Published 13 January; doi:10.1186/1471-2105-13-10

Gu, L., A.D. Jones and R.L. Last. 2012. Rapid LC−MS/MS Profiling of protein amino acids and metabolically related compounds for large-scale assessment of metabolic phenotypes. Amino Acid Analysis Handbook in Methods in Molecular Biology. M.A. Alterman and P. Hunziker, eds. Humana Press, NY. 828:1-11. DOI: 10.1007/978-1-61779-445-2_1

Yang, Y., T.L. Sage, Y. Liu, T.R. Ahmad, W.F. Marshall, S.-H. Shiu, J.E. Froehlich, K.M. Imre and K.W. Osteryoung, 2011. Clumped chloroplasts 1 is required for plastid separation in Arabidopsis. Proc. Natl. Acad. USA 108:18530-18535. To read the paper click here.

Lu, Y., D.A. Hall, R.L. Last. 2011. A small zinc finger thylakoid protein plays a role in maintenance of photosystem II in Arabidopsis thaliana. Plant Cell 23: 1861-1875.
To read the paper click here.

Previous papers

(updated 12/13)

The Chloroplast Function Database at RIKEN in Japan contains phenotypic screening data for chloroplast targeted protein mutants that is highly complementary to our project.

To take advantage of updated in silico and experimental analysis we have expanded the universe of genes that are being included in our analysis. These genes are from stromal proteomics data from Klaas van Wijk at Cornell University and annotation made available from the SubCellular Proteomic Database (SUBA) at the Plant Energy Biology Centre of Excellence in Australia.

The gene list can be found elsewhere on this website.

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Past research news


Photograph of an Arabidopsis plant for Chloroplast 2010 database

520 homozygous mutant lines sent to ABRC
Our Plastid Network Genes project (NSF MCB-1119778) donated 520 newly homozygosed insertion mutant lines to the ABRC at Ohio State University. For a list of donated lines, click here.

Large-scale phenomics data from the project for >5,200 mutants are freely available. Please click here and establish a user account to access the data using our data analysis tools.

Protocols that we use for this project are accessible through this website. For more information click here.

Genotyping information for nearly 12,000 t-DNA lines is available online. The most up to date information can be found here.

An earlier version, with approximately 9.000 lines can be found by looking at Supplemental Table 1, Ajjawi et al. 2010.

Summer Internships:
This project supports students participating in the Plant Genomics @ Michigan State University Summer Research Experiences for Undergraduates Program. For information click here.

Past News

Chloroplast Phenomics' is a collaborative Arabidopsis functional genomics project funded by National Science Foundation grants to Michigan State University and Western Michigan University.  Did you find a bug or an error? Please let us know.