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PBIO(BIOL) 3660L Plant Biology Intensive Lab
THE PLANT BIOLOGY DEPARTMENT AT THE UNIVERSITY OF GEORGIA
PLANT BIOLOGY INTENSIVE LAB
DESCRIPTION OF THE COURSE


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THE OFFICIAL COURSE DESCRIPTION

Plant biologists are expected to move from one discipline to another in pursuit of answers to large fundamental questions; the brilliant among us are creating new disciplines in doing so. Students have to be curious, adventurous, and persistent to discover at the University more than a passing knowledge of the questions and research methods in this new biology; most are way behind upon graduation. One attempt to help them along is this course, Intensive Plant Biology Laboratory.

I also often see students who are undecided about a profession. The reasonable first question I usually ask them is if they know if they are field, bench, or informatics biologist. The students have little practical experience in any of these areas and do not really know. The course is intended to give them some experience through doing something original. It recognizes that distinctions between these disciplines are increasingly artificial and intends to use long-term research projects to provide the framework to explore how each is done and integrated.

The course is really not that intensive. Its name is intended to attract Biology majors who satisfy a Laboratory Requirement with an Intensive Lab course or with two Lecture+Lab courses, or with Independent Research. They came, though probably because alternative courses are in short supply rather than the potential merits of this one.

The following is from the official description of the course as approved by the College and University Curriculum Committees. It was my vision of an ideal course and as such there are too many topics to cover even in passing in one semester.
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COURSE OBJECTIVES OR EXPECTED LEARNING OUTCOMES

The primary objective is to introduce students to the variety of research questions and methods that are used by plant biologists in an increasingly integrative discipline that expects its members to move seamlessly into whatever level of biology that becomes appropriate to the biological problem. To accomplish this goal, the course provides the student with hands-on experience with Field, Laboratory, and Informatics Research Methods, and with Scientific Writing, in the context of original research questions that require their integration. The secondary objective is that this training allow students to make more informed decisions about their educational and professional goals.

Additional learning outcomes include improving written and oral communication skills, learning about and applying ethical standards to individual and collaborative research and its publication.

Students will learn basic field, lab, and informatics skills through studies of Georgia plants in the context of addressing research problems with a plant community in a local habitat. Emphasis will be working in a natural habitat, experimental design, data collection and analysis, and use of local and international databases. Students will be encouraged to collaboratively identify their own research questions that can be addressed by the common techniques taught in the course. Students will collect plants, isolate their DNA, perform sequence and other analyses, and use bioinformatics methods to analyze the results. They will also learn taxonomic keying methods to identify plants based upon their morphological characters. The evolution of plants will be studied through molecular, biological, and taxonomic methods. Students will also learn the basic skills of writing a scientific paper, describing their individual and group contributions during the course.
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TOPICAL OUTLINE

Introduction to the Instructional and Research Objectives of the course
Review of Research Methods used in its Field, Laboratory, Data Reduction, and Informatics components
Introduction to Research Questions within which to organize the course
Basic Research Methods
    Good Practice in Research
    Safety and Good Practice in the field and the laboratory
    Keeping a Research Notebook
    Communicating results
    Concerns when doing Collaborative Research
    Ethical models for scientific research
Introduction to the Field Site
    Determining its geology, hydrology, habitat, community
    Discovering its history, past and potential land use
    Prior research on the site
    Potential for additional research
Field Research Methods
    Geographic Information System (GIS) and other Databases
    Global Positioning System and other spatial measurements
    Data Loggers, how to organize data
    Marking, documenting and collecting individuals and populations
    Experimental Design and execution, depending on question
    Floristic inventories
    For particular populations, measuring
        Genetic Structure
        Gene Flow
        Recruitment
    Restoration methods
    When to use DNA-based tools
    Others as suggested by students
Identifying Plants by Structure and Reproduction
    Plant structure used as characters in Taxonomy
    Recording morphological character states
    Dichotomous Keys, Floras, Web Resources
    Vouchers
Laboratory Research with DNA Sequences
    General Methods such as Experimental Design, making solutions
    Choosing DNA Sequences appropriate to the taxa of interest
    Designing Primers for PCR amplification of DNA
    Extraction of DNA
    PCR Amplification and external sequencing of the products
Informatics Methods
    Evaluating quality of sequences
    Annotation and submission of sequences to Public Databases
    Statistical Analysis of results
    Construction and use of a Site Database
    Working with Local and International Databases
    Computational analysis of DNA sequence leading to phylogeny reconstructions
    Developing a Public Information website for the course
Composition
    Elements of a scientific paper
    Preliminary and Final manuscripts
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GLENN GALAU, THE DEPARTMENT OF PLANT BIOLOGY, MILLER PLANT SCIENCES BUILDING, THE UNIVERSITY OF GEORGIA, ATHENS GA  30602-7271
PHONE 706 542 1859    FAX 706 542 1805
MODIFIED ON 13 FEBRUARY 2010. WEB DESIGN BY GLENN GALAU

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