WHY STUDY SEEDS

Seeds are one of the most important sources of food for human and animal consumption. Over half of the calories consumed by humans world wide is obtained from either seeds or seed by-products (e.g., rice, wheat, maize, soybean). In addition, most major crop plants are generated directly from seeds.

Seeds contain a complex collection of cells, tissues, and organs with distinct origins and developmental fates that ensure the survival of higher plants. The major events that occur during seed development are shown schematically in the figures on this web page. Seed development begins with a unique double fertilization process. One sperm cell unites with the diploid central cell of the embryo sac, giving rise to a triploid endosperm tissue that nourishes the embryo during the early stages of seed development. The other sperm cell unites with the egg cell giving rise to the zygote that initiates embryo formation. At maturity, a seed contains a fully differentiated embryo that contains one or two cotyledons and an axis. The cotyledons accumulate storage reserves that are used after germination by the developing seedling. The axis contains meristematic tissues that will give rise to the stem, roots, and leaves of the plant following germination. By contrast, the endosperm is either fully absorbed by the embryo during seed development (e.g., Arabidopsis) or is consumed during germination and supports growth of the seedling until photosynthesis begins (e.g., maize). Proteins, oils, and starches that are stored in the endosperm and cotyledons are the major sources of food provided by seeds for human and animal consumption.

Little is known about the processes that regulate the complex events that are required to coordinate both endosperm and embryo formation during seed development. That is, the genes and regulatory networks that control seed development are not well understood. Because seeds are an important source of human nutrition, Bob Goldberg's laboratory hopes to identify all of the genes required to "make a seed." He wants to use this information to engineer crops to produce more seeds and/or bigger seeds and, ultimately, increase the human food supply. Undergraduates who participate in the HC70AL Gene Discovery are helping to facilitate this goal by using functional genomics to identify genes that play a major role in controlling seed development.

THE WEEKLY LAB MEETING AND ETHICS DISCUSSION

Undergraduates Discussing and Presenting Research Data During the Weekly Lab Meeting

DISTRIBUTION OF STUDENTS THAT HAVE TAKEN THE HC70AL GENE DISCOVERY LABORATORY

One of the unique aspects of HC70AL is the breadth of undergraduate majors and levels represented by students in the class. Freshman work side-by-side with seniors, and life science students that will become molecular biology, microbiology, and biochemistry majors team up with philosophy, business, and communication majors, among others, in carrying out their experiments. Kyoto University students also participate in HC70AL, providing an novel cross-cultural laboratory experience for everyone involved. During the past three years, 34 students took HC70AL, representing 15 different majors. Approximately 30 of the students were undeclared, 35 of the students were non-science students, and the remainder entering life science students who had declared a major but were just beginning the core curriculum required of all life science students at UCLA. The pie charts shown on this page summarize the HC70AL student population overt he past three years.

GENE DISCOVERY LABORATORY QUESTIONS, APPROACHES, AND RESULTS

Research carried out in Bob Goldberg's laboratory has identified transcription factor genes that may play an important role in seed development. Two approaches have been taken. First, a unique plant with "giant" embryos, the Scarlet Runner Bean (Phaseolus coccineus), has been used as a "genomics engine" to uncover genes that are active in both the embryo-proper and suspensor regions of plant embryos shortly after fertilization. Scarlet Runner Bean embryos are ~100 times larger than those in Arabidopsis, and, unlike most plant embryos, can be hand-dissected at very early stages of embryo development. Bob Goldberg's laboratory has microdissected embryo-proper and suspensor regions from these embryos, and generated over 20,000 ESTs that have provided unique insights into the genes that are active at the earliest stages of seed development. Using the Scarlet Runner Bean EST database as a guide, HC70AL undergraduates have used bioinformatics and reverse genetics to identify knock outs in Arabidopsis orthologs of transcription factor genes that are active in the embryo proper and/or the suspensor. Second, a large number of whole-genome GeneChip microarray experiments have been carried out in Bob Goldberg's laboratory to identify transcription factor genes that are active at specific stages of Arabidopsis seed development (see figure on this web page). HC70AL undergraduates have used reverse genetics to obtain knock outs in seed-stage-specific transcription factor genes identified in the GeneChip microarray experiments. In both approaches, HC70AL undergraduates used Arabidopsis knock-out lines generated by Agrobacterium T-DNA mutagenesis at the either the Salk Institute (click here to link to Salk website) or the University of Wisconsin (click here to link to the Wisconsin web site). A summary of the experiments carried out by both non-science and entering life science students in the HC70AL Gene Discovery Laboratory is presented in the figure shown on this web page. During the past three years, approximately 50 knock-outs in Arabidopsis transcription factor genes have been identified and studied by undergraduates who had never worked in a lab or held a pipette prior to taking the HC70A and HC70AL courses created by Bob Goldberg's HHMI Program.

Click here for the knock-out results obtained by each HC70AL student or click on the image below.

Click on image to enlarge

Click here for the HC70AL Gene Discovery Laboratory syllabus, and a detailed summary of experiments, approaches, and questions addressed each week of the ten-week quarter.

Click here to search the Goldberg Lab Scarlet Runner Bean EST database

Click here to search the Goldberg Lab Arabidopsis GeneChip database

UNDERGRADUATE RESEARCH TOOLS DEVELOPED FOR THE GENE DISCOVERY LABORATORY

Gene Discovery Laboratory Lab Manual

A comprehensive set of experiments and protocols was written for undergraduate laboratories using genomics to study the function and activity of plant genes. This lab manual was designed to be used by both non-science and science majors. The Gene Discovery Lab Manual introduces students to basic molecular biology techniques and contains week-by-week experiments that allow undergraduates to use reverse genetics to identify T-DNA knock outs in Arabidopsis genes, describe the expression pattern of wild-type and mutant Arabidopsis genes, amplify and clone Arabidopsis gene promoters, and use microscopy to study wild-type and mutant seeds phenotypes. Detailed protocols are provided for DNA sequencing, PCR, RT-PCR, bioinformatics to characterize gene structure and T-DNA insert sites, planting seeds and growing Arabidopsis plants, isolating DNA and RNA, and using Nomarski optics to study seed and embryo phenotypes, among others.

Click here to download the HC70AL Gene Discovery Lab Manual (PDF size: 9 Mb)

Interactive Lab Webbook

An web-based interactive laboratory webbook was created that allows students and instructors real-time viewing of all experiments and results obtained in the Gene Discovery Laboratory. Students use the webbook to organize, summarize, and post their research results. In addition, protocols can be uploaded to the webbook and linked to each experiment. The webbook uses a relational data base and is designed to be used in any undergraduate laboratory course or research laboratory.

Click here to browse the webbook and view how this interactive web laboratory book is used to manage experiments and results

Click here to download the webbook program (un-compress the ZIP file using Winzip (Windows) or Stuffit Expander (Mac)).

GENE DISCOVERY LABORATORY FINAL SYMPOSIUM AND LAB COAT CEREMONY

At the end of the quarter, undergraduates give PowerPoint presentations of their research results at the final class symposium. Groups of students present an overview of seed development and the features of each transcription factor family investigated during the quarter, providing an introduction and background information for the symposium. Each student then gives a ten minute talk on their specific research results. At the end of the symposium Bob Goldberg presents a cake to the class decorated with a relevant design, and presents each student with a lab coat embroidered with their name, class year, and Goldberg Laboratory in honor of their hard work and participation in the gene Discovery Laboratory.

Click here to download a sample PowerPoint presentation from a non-science student

Click here to download a sample PowerPoint presentation from an entering life science student

If the video does not play, please download Quicktime 7 by clicking here for Mac or here for Windows.

If the video does not play, please download Quicktime 7 by clicking here for Mac or here for Windows.

Undergraduates enjoy the weekly lab dinner with professor Bob Goldberg and peer research mentors