User:LauraHoopes

Laura Hoopes hopes to discover the elixir of youth before too long, or it will be too late. She encourages any and all communications from GCAT users and friends.

Laura L. Mays Hoopes is the Halstead-Bent Professor of Biology and Molecular Biology at Pomona College in Claremont, CA. She was lucky to get in on the ground floor of GCAT and has used GCAT chips each year of her Genetic Regulation of Eukaryotes class since the laboratory was added in year 2 of the course. In that first year, her class got to be the first undergraduate students to have their data posted on the Stanford Microarray Database, and although the data were not so good, the thrill remained! The summer following that class, LH worked hard on microarrays with Judy Campbell's laboratory group at Caltech, but in year 2 the problems getting good student data persisted. She then got a Wig Grant from the Curriculum Committee to go and visit the important microarray laboratories at Stanford (Barbara Dunn, who was associated with Pat Brown and David Botstein), and at Institute for Systems Biology (Krassen Dimitrov, director of the microarray core facility), contacts suggested by Malcolm Campbell. This trip finally got LH connected with great techniques, and subsequent classes have always had data to analyze, not just gone through the procedure. She also began to work with GCAT to set up a series of workshops so best practices could be discovered and disseminated to faculty using microarrays with undergraduates. In 2004, LH learned to do quantitative reverse transcription PCR on the real time PCR machine, and her research students and technician and she found that the results of many carefully performed microarrays on yeast aging samples, even those with nice looking quality control results in GenePix, were not able to be confirmed by RT PCR. That was not as surprizing as it might have been, since the statistical collaborators on the project Johanna Hardin and her student Alison Wise, had found that using different tests for significant genes had brought out quite different gene lists from the data. The lab then started using a mRNA amplification strategy that LH had seen used at Stanford and ISB when visiting, and found that results from that method did correspond well with the RT PCR results. The summer, 2005 results using this method gave quite similar gene lists from ANOVA, SAM, and PAM. The course lab tried the mRNA amplification method for the first time in 2005, and used RT PCR for the third year. The 2005 lab was the first whose quantitative PCR results were similar to the microarray results, at least in direction of changes.