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2005/2006 Lab Members
2005-2006 Lab members and their projects
Graduate Students:
- Mike Fischer:
Characterizing Chlamydomonas reinhardtii 5'-3' exoribonuclease genes (CrXrn's). Genomic evidence indicates that C. reinhardtii has up to four nuclear CrXrn genes. Mike's RT-PCR and sequencing data indicate that the CrXrn1 gene generates two distinct mRNAs (CrXrn1a and CrXrn1b) via alternative splicing of an exon near the 5' end of the coding region. The CrXrn1b mRNA has a second translation start site that results in the addition of 40 extra amino acides at the N-terminus of the CrXrn1b protein. This N-terminal extension has strong sequence and structural similarities to C. reinhardtii chloroplast targeting sequences. Mike will use GFP fusions to test the cellular location (nucleus, cytosol, chloroplast, or mitochondria) of CrXrn1a and CrXrn1b proteins, the latter may be targetted to the chloroplast where it could regulate chloroplast mRNA stability. He is also characterizing the CrXrn2 gene and its expressed mRNA in order to predict the encoded CrXrn2 protein, thought to be either cyostolic or nuclear localized.
- Kyle Upchurch:
Characterization of Chlamydomonas reinhardtii 5'-3' exoribonuclease proteins (CrXrn's) and sub-cellular location using cell fractionation and immunoblotting methods. Kyle has generated an anti-CrXrn antibody using a synthetic peptide from a highly conserved region among all Xrn proteins and preliminary evidence indicates that this cross-reacts with an approximately 200-kDa protein, the expected size of the CrXrn1 protein. Molecular evidence indicates that a 5'-3' exoribonucleolytic activity exists in the chloroplasts of Chlamydomonas and is involved in degrading chloroplasts mRNAs that encode photosynthetic chloroplast proteins.
Jacob Tatay:
Jacob is adapting computer algarithms that uses an "oligo-search method" to analyze chloroplast and mitochondrial genomic sequence data for conserved small RNA sequences in the mRNA 5' untranslated regions (UTRs) that may function to control RNA stability and/or translation. This oligo-search strategy is being combined with our microarray data on non-photosynthetic mcd1 mutants using a Self-Organizing Tree Algarith (SOTA) to correlate expression with conserved small RNA sequences. These bioinformatic approaches complement the molecular biology projects in the lab, and Jacob is also investigating the known RNA stability sequence, termed element I, at the 5' end of the petD mRNA that exists in a small stem-loop structure. Jacob is using site-directed mutagenesis and chloroplast transformation to test the importance of each nt in element I and RNA structure.
Jennifer Lavender:
Jennifer is a new graduate studeent to the lab, having completed her Molecular Biology and Bioinformatics (MBB) undergradaute degree at UW-Parkside. She will be studying an RNA 5' UTR sequence conserved among a small set of C. reinhardtii chloroplast genes. This small sequence was identified by Jacob Tatay, graduate student in the lab, using a genomic sequence analysis computer appliation he modified. Jennifer will test the functionality of this small sequence in vivo using reporter genes transformed into C. reinhardtii chloroplasts. The function of this sequence is not known, but it could affect RNA stability, processing and/or translation.
Undergraduate Students:
- Theresa Dailey:
Theresa is a Biological Sciences undergraduate student who is continuing work that was started by a Research Experience For Undergraduates (REU) student, Rachel Jarrard. Theresa's and Mike Fischer (graduate student) have developed RT-PCR primers that amplify both alternative spliced variants (CrXrn1a and CrXrn1b) in C. reinhardtii. These nucleus-encoded mRNAs are predicted to encode type I 5'-3' exoribonucleases. The CrXrn1b mRNA has one in-frame start site that adds 40 extra amino acids to the N-terminus. This N-terminal extension has sequences and structures consistent with known chloroplast targeting transit peptides. One possibility is that the CrXrn1b protein is targeted to chloroplast, where it could perform the previously published 5'-3' exoribonucease activity that degrades petD, psbD and psbB mRNAs. Theresa is studying possible regulation of this alternative splicing that appears to changes from little CrXrn1b mRNA at early stagese in a liquid culture to roughly equal amounts of the two spliced alternates in an older liquid culture (7 day old). These preliminary data indicate that this might be a regulated process.
Former lab members:
- Brian Erickson, MAMB graduate student
- José Henriquez, Biological Sciences undergraduate
- Rachel Jarrad, REU summer 2004
- Jamie Jaskolski, Biological Sciences undergraduate
- Nathaniel Jeanson, Molecular Biology and Bioinformatics undergraduate
- Lynn Kramzar, Molecular Biology undergraduate and MAMB graduate student
- Angela Leis, Molecular Biology undergraduate
- Toby Mueller, MAMB graduate student
- Aaron Naatz, REU summer 2002
- Kate Schassberger, Biological Sciences undergraduate
Interested in Joining the Higgs Lab?
If you are interested in doing molecular genetic research in my lab contact me by phone (262-595-2786), e-mail (higgs@uwp.edu), or stop in for a visit (Greenquist 301). If you are a prospective student interested in the Molecular Biology and Bioinformatics program, or the Masters in Applied Molecular Biology contact the Department of Biological Sciences at UW-Parkside (262-595-2744) for information.
UW-Parkside Home Page
Questions, comments or suggestions should be e-mailed to David Higgs (higgs@uwp.edu)
