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Addendum to STANDARDS DOCUMENT: BIOLOGY - Level 14-16

Addendum to the level 14 standards that extended them through level 16.
Barbara Baumstark (Georgia State University)
- March 2000


        During the last half of the 20th century, scientific advances have caused the information base in biology to increase at an unprecedented rate. As a consequence, no student can be expected to become an "expert" in all areas of the biological sciences during four years of undergraduate education. An academic program that attempts to give equal priority indiscriminately to all biology subject matter will be forced to limit itself to a surface level treatment of the field. On the other hand, a program that balances general content knowledge with an in-depth investigation of specialized topics gives students the opportunity to ask questions, evaluate alternative scientific theories, and take an active role in deciding the direction their education will take. This approach not only teaches students fundamental biological concepts but also enables them to acquire the skills necessary to continue their exploration into the field of biology long after they complete their undergraduate education.

        Ideally, biology instruction at the introductory level (Level 14) provides students with a general body of scientific knowledge that serves as a foundation for further study in the field, along with the basic skills to use this knowledge in experimental situations. Then, as students progress to more advanced levels of study, they use this broad knowledge base to develop a deeper understanding of selected biological concepts. As their understanding of these concepts matures, students usually discover that their interests become focused in areas of increasing specialization. Thus, for most undergraduate majors, education in biology proceeds in three stages: 1) an introductory stage, where they learn general biological concepts; 2) an intermediate stage, where they are exposed to several broad-based "subdisciplines" that serve as a foundation for subsequent specialization; and 3) an advanced stage, where they use the information they have accumulated to delve more deeply into a few limited areas which excite their curiosity.

        Immediately following the completion of Level 14 course work, undergraduate majors begin to receive more intensive instruction in several broad-based "biology subdisciplines." The material learned at this intermediate stage of their programs can then serve as the foundation for subsequent specialization. Subdisciplines may include (but need not be limited to):

        animal/plant biology
        biochemistry cell/molecular biology
        genetics
        microbiology

        Students can gain content knowledge related to these subdisciplines in a variety of ways. For example, a single "gateway" series may cover all or a subset of topics in an integrated fashion. Alternatively, individual courses may be designed around a single subdiscipline. It is important to note that at any given undergraduate institution, variations in faculty research and instructional interests (which will influence the types of advanced courses available for undergraduates) may cause some subdisciplines to receive more emphasis than others.

        As students progress to increasingly advanced levels, they find that their studies become focused into more specialized areas of concentration, especially as they identify specific topics that are of particular interest to them. Undergraduate biology majors can usually tailor their curriculum to fit their chosen area(s) of concentration by selecting from a variety of advanced elective courses. Depending on the courses they choose, two students may acquire distinctly different specialized content knowledge by the time they complete their Level 16 course work. However, as long as they have mastered fundamental biological concepts, developed critical thinking skills, and acquired proficiency in a research setting, each will graduate with the expertise necessary to become successful biologists, regardless of the area of specialization they ultimately choose.

Standards for Level 16 performance

        A top priority of any curriculum designed to meet Level 16 Standards, regardless of content material, is to ensure that students are provided with experiences that hone their skills in using,
generating, and evaluating scientific information. Students should demonstrate the ability to:
  • form hypotheses, design experiments, collect data, and evaluate results
  • read and comprehend the current scientific literature
  • place reports of new discoveries into the context of previous scientific progress, and develop an understanding of the impact of these discoveries on society.

        On the following pages is an example of a standards-based undergraduate experience at Georgia State University. In this example, it is assumed that the student gradually develops an interest in molecular genetics, which ultimately becomes the preferred area of focus.


---SAMPLE---



A STANDARDS-BASED UNDERGRADUATE EXPERIENCE


IN MOLECULAR GENETICS



        In the sample outlined on the following pages, it is assumed that the student either entered the program with an interest in molecular genetics or became interested in exploring this field after the experiences of his/her Level 14 course work. As the student progresses through intermediate and ultimately advanced level biology course work, he or she can select increasing numbers of elective courses that expand and extend their expertise in this field.

Introductory Stage (Level 14):

        The student will meet Standards 1-5 as outlined in the Standards Document (8/98; revised 8/99). A course or set of courses will give students the basic content knowledge outlined in Standard 5. In addition, the students will be given experience in conducting laboratory experiments and using appropriate technology. They will be made aware of the historical context in which scientific advances are made, as well as the impact of these advances on society. Students will also be receiving instruction in fundamental concepts of chemistry, mathematics and other fields related to biology.

Intermediate Stage (Level 16):

A. The student will acquire a firm foundation of content knowledge in:

Genetics: Mendelian genetics; genetic linkage; chromosome mapping; chromosome structure; population genetics; quantitative genetics; regulation of gene
expression, recombinant DNA technology.

Microbiology: structural characteristics of microbes; microbial metabolism; classification (bacteria, fungi, and viruses); mechanisms of pathogenesis; epidemiology; host defense mechanisms.

Cell/Molecular Biology: structure and function of organelles; the flow of genetic information (nuclear structure and communication with the cytoplasm); cell structure and
function (cytoskeleton and cell movement); the ER system and protein transport; mitochondria and bioenergetics), cell-cell communication; cell regulation (signaling
molecules and their receptors, the cell cycle, cancer).

Biochemistry: macromolecular structure and function; bioenergetics; biosynthetic and degradative processes, enzyme kinetics; acid/base chemistry; redox reactions; regulation of enzyme activity; regulation of gene expression.

B. The student will gain experience in designing experiments, collecting data, making appropriate calculations, and discussing results. Laboratory experiences will be focused in:

Genetics: genetic crosses, complementation analysis, mutagenesis (model systems could include Drosophila melanogaster, C. elegans, E. coli, etc.)

Microbiology: sterile technique, methods of microbe identification, measurement of growth patterns under varying environmental conditions, selection procedures for
isolation of mutants

Cell/Molecular Biology: cell fractionation techniques, macromolecular isolation techniques (particularly DNA and protein), basic recombinant DNA technology (transformation, gel electrophoresis, PCR amplification)


Advanced Stage (Level 16):

A. The student will acquire a subset of specialized information that complements and extends the fundamental principles of genetics and related fields that were learned at the intermediate level. Examples might include:

Advanced Genetics
Sample topics:
Mechanisms of genetic exchange
Control of gene expression in prokaryotes and eukaryotes
Developmental genetics
Epistatic mechanisms
Non-Mendelian genetic patterns
DNA topology and its effects on gene expression
Chromosome structure
Genome organization

Eukaryotic Molecular Genetics
Sample topics:
Non-Mendelian inheritance patterns
Chromosome structure (nucleosomes, centromeres, telomeres, repetitive sequences)
Gene structure (introns, pseudogenes)
Control of gene expression (transcription factors, enhancer elements, post-transcriptional processing, translational regulation)
Genetics of development
Molecular cloning techniques

Human Genetics
Sample topics:
Pedigree analysis
Simple and complex genetic disorders
Molecular techniques for diagnosis of genetic variation
Non-Mendelian patterns of inheritance
Genetics of behavior
Genetics of aging
Genetics and cancer
Gene therapy

Molecular Microbiology
Sample topics:
Genetic exchange in prokaryotes
Bacteriophage: mechanisms of infection and gene regulation
Molecular mechanisms of pathogenesis
Transcriptional and translational regulatory mechanisms
Membrane topology
Stress response patterns
Defense mechanisms: restriction/modification, colicin production

Immunology
Sample topics:
The nature of antibodies
Mechanisms of action by B and T cells
Lymphokines and cytokines
Genetics of antigen recognition
The complement system
Transplantation and tolerance
Regulation of the immune response

Virology
Sample topics:
Virion structure
Viral genetics
RNA viruses and DNA viruses
Retroviruses and HIV
Viral immunology
Viral pathogenesis
Viral epidemiology
New and emerging viruses
Viral diagnosis
Immunization and antiviral chemotherapy


B. The student will gain experience in laboratory techniques and will demonstrate the ability to 1) pose scientific questions, 2) generate hypotheses, 3) design experiments to test these hypotheses, 4) evaluate the results of these experiments, 5) identify sources of error and assess the limitations of the data, 6) revise or extend the original hypotheses, and 7) suggest additional experiments.


Samples of intermediate and advanced level laboratory exercises are given on the following pages.


SAMPLE LABORATORY EXPERIENCES FOR THE MOLECULAR GENETICS STUDENT.



Intermediate-Stage Experience

        Students are presented with a hypothetical scenario involving a problem that can be solved by DNA technology. They are given DNA samples from a crime scene and a group of suspects. They are then asked to use restriction enzyme analysis coupled with gel electrophoresis to characterize the DNA samples and determine whose DNA corresponds to the DNA at the crime scene.


Advanced-Stage Experiences



I. PROBLEM-BASED LABORATORY - students are asked to conduct an experiment that gives them results they do not initially expect. They must then revise their initial hypothesis to conform to their observations and test their revised hypothesis.

Reversion Analysis

        Students are given a mutant strain of E. coli that is lacZ- and trpE- (both are amber mutations) and are told to isolate Lac+ and/or Trp+ revertants.
A. Initial experimental design
1. Students devise growth media that will select for Trp+ [omitting tryptophan from the media; providing glucose as a carbon source], Lac+ [providing tryptophan but using including lactose as the sole carbon source] or Lac+Trp+ double mutants [omitting tryptophan and providing only
lactose as a carbon source].
B. Initial hypothesis
2. Students predict the frequency of reversion (Lac+Trp- or Lac-Trp+: about 10-
7; Lac+Trp+ double reversion: 10-7 x 10-7) = 10-14)
C. Results
Students discover that the frequency of double revertants (10-7-10-8) is nearly as high as the frequency of single revertants.
D. Revised hypothesis
Students generate a hypothesis to explain their observations. [Hypothesis: the fact that both original mutations are amber mutations raises the possibility that a single mutation in a tRNA gene can produce a translational suppressor that restores the Lac+ and Trp+ phenotypes
simultaneously.]
E. Predictions of revised hypothesis
1. Phenotypic double revertants should be able to support the growth of bacteriophage containing amber mutations in essential genes. Spot-test amber mutant phage on lawns
of revertant bacteria. Students devise appropriate controls.
2. Phenotypic double revertants retain the original lac- and trp- mutations. Conduct a bacterial mating with a strain that is defective at proA (a gene closely linked to lacZ). Select for Pro+ recombinants and test for the co-transfer of the lacZ- mutation.
F. Analysis of results, suggestions for further experiments

II. OPEN-ENDED LABORATORY

        In an open-ended laboratory, the student designs and carries out a set of experiments in which the final answer is unknown. Gene cloning experiments and "mutant hunts" are two types of laboratory exercises that, if designed appropriately, can lead to the isolation of previously uncharacterized genes (and, in the best of circumstances, to a publishable piece of work). An example of each type of experiment is given below. In these cases, the bacteriophage P1 is used as a model system (just about
any organism can be used as long as it is easy to grow, makes lots of easily extractable DNA, and, in the case of the mutant hunt, exhibits an easily selectable mutant phenotype). P1 is well known as a generalized transducing phage; however, it also exhibits a complex but relatively unstudied mechanism for differentiating between lytic and lysogenic growth. The gene cloning experiment has the advantage of providing more in depth experience with cutting edge technology; however, it generally is more expensive
than a mutant hunt.

Gene Cloning:

Search for transcription initiation sites on the genome of bacteriophage P1.

A. Students digest P1 DNA with restriction enzymes that produce multiple small fragments. They then ligate the resulting fragments into a "promoter probe" vector (a plasmid that contains a promoter-less copy of lacZ (the gene for b-galactosidase).

B. Students transform their ligated samples into an E. coli lacZ- strain. They then plate the mixture on media containing X-gal, a lactose indicator dye that turns blue when
broken down by b-galactosidase, the lac Z gene product. Normally, lacZ- colonies are white, since the bacteria contain no enzyme to break down the indicator dye. Bacteria
that have picked up a recombinant plasmid coding for a P1 promoter will be able to express the lacZ gene, resulting in the cleavage of X-gal by b-galactosidase and the appearance of a colony that is blue in color.

C. Students pick blue colonies, purify the recombinant plasmid DNA and identify the size of the cloned fragment by restriction enzyme digestion and gel electrophoresis.

D. Depending on their findings, students will:
1. Test the strength of their promoters by conducting enzyme assays to
measure b-galactosidase activity
2. Conduct Southern hybridization experiments to localize their
promoter on a previously derived restriction map of P1.
3. PCR amplify their cloned fragment and determine the DNA sequence.
4. Subject the promoter to site-directed mutagenesis and assay for
alterations in b-galactosidase production


Mutant Hunt.


Isolation and characterization of regulatory mutants of bacteriophage P1.

        As a lysogenic phage, P1 is able to undergo two alternative modes of growth. If it enters the lytic mode of growth, it kills the infected cell, which then lyses and releases about 100 progeny phage. If it enters the lysogenic mode of growth, it does not kill the cell, but instead allows its genome to be maintained as a plasmid by the host for many generations in a quiescent state. The decision to let the cell live is mediated by several regulatory molecules, which repress the expression of proteins that would
normally cause the cell to die. The strain of P1 used in this experiment is wild-type for lysogeny and, as a consequence forms "turbid" plaques (composed of about 90% lysed bacteria and 10% surviving "lysogens"). The purpose of this exercise is to isolate regulatory mutants that are no longer able to enter lysogeny. These mutants are easy to detect because they produce "clear" plaques in which all infected cells are lysed. Using a purified lysate of P1 phage as their stock, students will:

A. perform serial dilutions to determine the titer and to look for "clear plaque" mutants.

B. calculate the numbers of clear mutants and divide by the total number of phage to determine the mutation frequency.

C. purify their clear mutant phage and grow up high-titer stocks.

D. test the mutant phage for virulence.

E. conduct complementation analysis against known clear plaque mutants to determine whether their phage contains a defect in a previously characterized regulatory gene. Subsequent experimental design will depend on the results of this test.

1. If the complementation test localizes the mutation to a previously characterized gene, mutant phage DNA will be isolated, the gene will be amplified by PCR, and the
mutation will be identified by DNA sequence analysis. The amplified DNA fragment containing the mutant gene will be cloned into a high-level expression plasmid and the mutant gene product will be isolated and characterized.

2. If the complementation tests are all "negative" (i.e., the mutation is not located in any previously characterized gene), or if the mutant is virulent (i.e., the mutation affects a
regulatory site rather than a gene product), the mutation will be localized by genetic mapping studies. A restriction fragment corresponding to that region of the P1 genome will be cloned into a multicopy vector and subjected to DNA sequence analysis.

        Because so little is known about the P1 genome, both the cloning experiment and the mutant hunt have a relatively high probability of turning up a promoter or regulatory gene that has never been reported before. Thus, each student can experience the excitement of searching for something that is yet to be discovered.