© 2004 by The International Union of Biochemistry and Molecular Biology BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION

Printed in U.S.A. Vol. 32, No. 2, pp. 101–107, 2004

Laboratory Exercises

Outcomes of a Research-driven Laboratory and Literature

Course Designed to Enhance Undergraduate Contributions to
Original Research*
Received for publication, June 17, 2003, and in revised form, September 23, 2003

Madeline E. Rasche‡
From the Microbiology and Cell Science Department, University of Florida, Gainesville, Florida 32611-0700

This work describes outcomes of a research-driven advanced microbiology laboratory and literature
research course intended to enhance undergraduate preparation for and contributions to original research.
The laboratory section was designed to teach fundamental biochemistry and molecular biology techniques
in the context of an original research project. Site-directed mutants of a gene of interest were constructed,
and the effects of mutations on the resulting enzymes were analyzed. Students were also introduced to the
literature surrounding their project, electronic literature databases, and preparation of computer-gener-
ated slides for oral presentations. Student progress was evaluated through a laboratory report written as
scientific manuscript, an oral presentation, a 10-page written review, and an essay examination. In the
semester following the laboratory course, four of the 14 undergraduates joined the host laboratory to
continue their projects as individual undergraduate researchers. Quantifiable outcomes of the course and
subsequent undergraduate research included i) production of eight new site-directed mutants and prelim-
inary characterization of the corresponding enzymes, ii) training of four individual undergraduate research-
ers prior to joining the laboratory, iii) publication of a manuscript with results from two undergraduate
researchers, and iv) presentation of two posters with undergraduate co-authors at a national meeting. This
research-driven approach may be applicable to enhance undergraduate contributions to other original
research projects that have defined goals achievable within the timeframe of a single semester.
Keywords: Microbiology, laboratory course, undergraduate research.

FACILITATING UNDERGRADUATE RESEARCH PRODUCTIVITY
Active participation in undergraduate research plays a
valuable role in enhancing the educational experience of
undergraduate science majors. In addition to providing
training in practical laboratory techniques, undergraduate
research can facilitate the development of higher thinking
skills, expose students to the excitement of scientific dis-
covery, and contribute to preparation for careers in scien-
tific research [1– 4]. Indeed, increased participation in dis-
covery-driven research and literature colloquia comprise
two of the specific recommendations made by the Na-
tional Research Council to improve undergraduate training
for future biological research scientists [5]. In addition,
undergraduate research is strongly recommended as part
of the core curriculum for a biochemistry and molecular
biology major [6].
Faculty at primarily undergraduate institutions and early
career faculty have been noted as individuals with strong
* This work was supported by National Science Foundation
Grant MCB-9876212 and by the Florida Agricultural Experiment
Station. This manuscript is Florida Agricultural Experiment Station
Journal No. R-09890.
‡ To whom correspondence should be addressed: Microbiol-
ogy and Cell Science Department, University of Florida, P.O. Box
110700, Gainesville, FL 32611-0700. E-mail: mrasche@ufl.edu.
This paper is available on line at http://www.bambed.org
potential to provide research opportunities for undergrad-
uates [5]. However, in these laboratories, conscientious
promotion of undergraduate research can require consid-
erable commitments of time, energy, and dedication, par-
ticularly if graduate students and postdoctoral associates
are unavailable to assist in the mentoring process [7, 8].
Because acquiring laboratory skills can require a semester
or longer, undergraduates who begin research in their
senior year may have little time to aggressively pursue
experiments that lead to publishable results.
Inquiry-based courses have been designed that enable
students to obtain a short research experience while learn-
ing laboratory techniques and pursuing open-ended re-
search questions. For example, Boomer et al. [9, 10] de-
veloped a laboratory course in which students use 16S
rRNA sequencing to characterize novel bacteria isolated
from hot springs at Yellowstone National Park. Other ap-
proaches have ranged from reserving several laboratory
periods for student-designed experiments [11–14] to chal-
lenging students to implement their own semester-long
research projects [15–17].
The current work investigates the possibility that inquiry-
based laboratory courses can further enhance undergrad-
uate research contributions by serving as a springboard
for research projects that individual undergraduates can
later pursue in the host laboratory. With prior training, the
101
102
Summary of the syllabi for “Advanced Microbiology Laboratory with Research Emphasis” (MCB 4034L) and
“Literature Research in Microbiology” (MCB 4934L)
Week Scheduled laboratory activities
1 Laboratory safety, notebooks; preparation
of plates, buffers, medium; use of pH
meter; sterilization and pipetting
techniques
2 Growth of E. coli cells; plasmid
purification
3 Preparation of competent cells; primer
design for site-directed mutagenesis
(SDM)
4 SDM reaction using a thermocycler
5 DpnI digest of SDM products;
transformation of competent cells
6 Streaking for pure colonies; restriction
digest of mutated plasmids; agarose
gel electrophoresis
Break Summer break: sequencing of plasmids
7 Transformation into expression cells;
induced expression of altered genes
8 No laboratory activities planned
9 Cell breakage using French Press; 65 °C
heat treatment of cell-free extract;
protein concentration measurements;
SDS-PAGE gel of cells and fractions;
enzyme assay, part 1
10 Enzyme assay, part 2; protein purification,
hydroxyapatite column; enzyme assay
of fractions, part 1
11 Enzyme assay of fractions, part 2; gel
electrophoresis of fractions; begin
ELISA experiment
12 Complete ELISA experiment; laboratory
reports due
BAMBED, Vol. 32, No. 2, pp. 101–107, 2004
TABLE I
Actual laboratory activities
As scheduled
As scheduled
As scheduled
As scheduled
As scheduled
Trouble-shooting of SDM reaction
Trouble-shooting of SDM reaction
Streaking for pure colonies; restriction
digest of mutated plasmids;
agarose gel electrophoresis
Sequencing of plasmids
Transformation into expression cells;
induced expression of altered
genes
Cell breakage using French Press
65 °C heat treatment of cell-free
extract; protein concentration
measurements; SDS-PAGE gel of
cells; enzyme assay, part 1
Enzyme assay, part 2; SDS-PAGE gel
of soluble fraction; begin ELISA
experiment
As scheduled
Literature research activities
Literature searches and electronic (Web)
databases; literature presentation no. 1
by instructor: introduction to the research
problem
Plasmid purification
Literature presentation no. 2 by instructor;
guest lecture on primer design
Student presentations; turn in research
topic and main references
Student presentations; BLAST searches
Student presentations; turn in brief outline
and complete bibliography
Student presentations; turn in detailed
outline of paper
Student presentations
Student presentations; research papers
due
Student presentations
Final exam

selected undergraduates are better positioned to posi-
tively impact the research program of their chosen labo-
ratory. At the same time, the laboratory benefits from the
opportunity to select trained undergraduates from among
students demonstrating strong ability, perseverance, and
research interest. Here we describe the outcomes of a
formal research-driven laboratory course in which funda-
mental biochemistry and molecular biology techniques
were taught in the context of an original site-directed
mutagenesis project. Four students subsequently joined
the laboratory as undergraduate researchers and within
two semesters contributed as co-authors to one peer-
reviewed publication [18] and two posters presented at a
national meeting. Similar research-driven courses may be
applicable to enhance undergraduate preparation for and
contributions to other research projects that have defined
goals achievable within a single semester.
COURSE STRUCTURE AND GOALS
Course Structure—The University of Florida is a land-
grant research university with 45,000 students and over
1,000 undergraduate microbiology majors. “Advanced Mi-
crobiology Laboratory with Research Emphasis” (one 3-h
laboratory per week) and “Literature Research in Microbi-
ology” (one 1-h colloquium per week) were offered as
co-requisite courses during the Summer of 2002 to teach
biochemistry and molecular biology techniques to under-
graduate microbiology majors expressing strong interest
in scientific research. The course was limited to 16 partic-
ipants, and students were selected based on research
interest and the grade of an A or B⫹ in the upper division
introductory microbiology course. The grade requirement
was waived for two students who demonstrated an excep-
tionally strong desire to obtain research experience. Four-
teen microbiology undergraduates and two chemical en-
gineering graduate students participated in the laboratory
section.
The original course syllabi, along with the modifications
implemented during the semester, are presented in Table
I. Laboratory techniques included sterile microbiological
technique, microbial cell growth, plasmid purification, po-
lymerase chain reaction, site-directed mutagenesis, mi-
crobial transformation, expression of recombinant DNA,
agarose and polyacrylamide gel electrophoresis, enzy-
matic assays, and enzyme-linked immunosorbent assays
(ELISA). Critical analysis of data, experimental design,
notebook documentation, and a formal laboratory report
were emphasized in preparation for undergraduate and
graduate research. In the literature colloquium, students
researched, discussed, and critically analyzed recent sci-
entific literature in molecular microbiology. Students were
introduced to literature search engines and internet-based
bioinformatics tools, a computer program for slide prepa-
ration, and presentation of research articles. Students

considering graduate school were encouraged to choose
articles that explored their specific fields of interest.
Student progress in the laboratory was evaluated based
on a laboratory report written as a scientific manuscript,
notebook entries, a quiz, and an informal ELISA report.
Progress in the literature colloquium was evaluated based
on a 20-min oral presentation, class participation, a 10-
page review written as a grant proposal or Annual Review
article, and an essay examination.
Goal of the Undergraduate Research Project—The over-
all goal of the research was to use site-directed mutagen-
esis to identify amino acids important for the activity of
ribofuranosylaminobenzene 5⬘-phosphate (RFAP)1 syn-
thase) from Methanothermobacter thermautotrophicus
[18]. This enzyme catalyzes the first step in the biosynthe-
sis of methanopterin [19, 20], a folate analog originally
discovered in methane-producing archaea [21]. The pro-
ject had two specific objectives: i) to construct new site-
directed mutants of the RFAP synthase gene and ii) to
characterize the effects of the mutations on enzyme activ-
ity. Students worked in pairs, and each pair was respon-
sible for characterizing one altered protein.
Site-directed Mutagenesis—Alignment of the amino
acid sequences of RFAP synthases from nine prokaryotes
[20, 22, 23] revealed four strictly conserved arginines, two
conserved histidines, and two conserved aspartic acids.
To determine if these charged residues play important
roles in enzyme activity, each pair of students designed a
set of oligonucleotide primers to change one residue to
alanine. The oligonucleotides were purchased from Geno-
Mechanix (Gainesville, FL) or Sigma-Genosys (St. Louis,
MO). The template for site-directed mutagenesis was the
plasmid pED2 (provided by Matthew Bechard), which con-
tains the RFAP synthase gene (MTH0830) inserted into the
NdeI and BamHI sites of the plasmid pET41a (Novagen,
Madison, WI) [18]. Site-directed mutagenesis was first at-
tempted using the QuikChange kit from Stratagene (La
Jolla, CA) according to the manufacturer’s instructions,
but no transformants were obtained. Ultimately, transfor-
mants were produced using a high efficiency kit
(QuikChange XL; Stratagene). Mutagenesis to alanine
codons and the fidelity of the remaining nucleotides were
verified by dideoxy sequencing [24].
The mutated plasmids were transformed into competent
Escherichia coli DH5-␣ cells containing the plasmid pG-
Tf2 (HSP Research Institute, Osaka, Japan), which en-
codes genes for a chaperone to assist in protein folding
[25]. To express genes altered by site-directed mutagen-
esis, cells were grown in Luria-Bertani-kanamycin-chlor-
amphenicol medium, and expression was induced with
tetracycline and isopropylthiogalactoside (Inalco, San Luis
Obispo, CA) exactly as described by Bechard et al. [18].
The RFAP synthase activity of the cell-free extract was
measured as described [18, 20]. The solubility of the al-
tered proteins was evaluated by SDS-PAGE and Coomas-
sie staining [26].
1
The abbreviations used are: RFAP, ribofuranosylaminoben-
zene 5⬘-phosphate; ELISA, enzyme-linked immunosorbent assay.
103
COURSE OUTCOMES AND UNDERGRADUATE
RESEARCH CONTRIBUTIONS
Laboratory Course—The educational feature that distin-
guishes the research-driven section of “Advanced Micro-
biology Laboratory” from the regular (nonresearch) section
offered at the University of Florida is that students in the
research-driven course contribute actively and directly to
an original research project while learning the same labo-
ratory techniques. Students are also challenged to engage
higher thinking skills in order to critically analyze experi-
mental data, formulate testable hypotheses, and design
new experimental protocols.
For the course described here, students worked in pairs
to create site-directed mutants of RFAP synthase and
characterize the activity of the altered enzymes. The eight
amino acid targets were chosen because of strict conser-
vation in RFAP synthase homologs [20], but the effects of
altering the amino acids were unknown to the instructor
and students at the start of the course. Given the uncertain
nature of the results, it was anticipated that flexibility
would be required in the laboratory schedule. Indeed, al-
though the activities of the first 4 weeks proceeded as
scheduled, during the fifth week, technical obstacles were
encountered, requiring changes to the original syllabus
(Table I). During the first 4 weeks, students grew the E. coli
strain carrying the plasmid with the wild-type gene [18, 20],
isolated the plasmid, designed mutagenic oligonucleotide
primers, and prepared site-directed mutagenesis reac-
tions using the QuikChange kit (Stratagene). After treating
the products with DpnI to degrade the methylated tem-
plate strands, students transformed competent cells from
the kit with a portion of the remaining DNA. The control
mutagenesis reaction contained a known template (the
␤-galactosidase gene inactivated by a point mutation) with
primers to correct the mutation.
During the fifth week, the students were disappointed to
find that no colonies appeared on the kanamycin plates,
indicating that some aspect of the RFAP synthase mu-
tagenesis reaction was unsuccessful. This was unex-
pected because the same kit had been used previously by
the host laboratory to create a site-directed mutation in the
RFAP synthase gene from a different organism. In addi-
tion, the control mutagenesis reaction worked, based on
the appearance of numerous blue colonies on Luria-Ber-
tani-ampicillin plates containing 5-bromo-4-chloro-3-indo-
lyl-beta-D-galactopyranoside (X-gal; Sigma, St. Louis, MO)
Overcoming Research Obstacles—The negative result
provided a fortuitous opportunity for the students to pro-
pose explanations for the problem and design experiments
to test their hypotheses. Each student submitted proposed
modifications to the protocol, and the suggestions were
collated (Table II). After verifying the efficacy of the plates,
competent cells, and heat-shock protocol, the students
tested the next six hypotheses by systematically incorpo-
rating procedural modifications to maximize the DNA
product yield (Table II). Unfortunately, none of the changes
resulted in the production of colonies, and many of the
students became discouraged. Students were then given
the option to continue pursuing their own mutagenesis
project, or switch to an uncharacterized site-directed mu-
tant created previously by a graduate student.
104 BAMBED, Vol. 32, No. 2, pp. 101–107, 2004
TABLE II
Student suggestions to resolve problems with site-directed mutagenesis
Student suggestions Experiment or result
1 Check kanamycin plates Known kanamycin-resistant cells grew on plates
2 Check cell competence Commercial competent cells could be transformed with control DNA
from the kit
3 Check heat shock step of transformation Careful heat shock did not produce colonies
4 Use different amounts of template Four different template concentrations within the recommended range
were tested
5 Produce more mutated DNA The number of cycles was increased
6 Increase extension time The extension time was increased to 12.5 or 14 min
7 Use more DNA for the transformation Cells were transformed with either 1 or 5 ␮l of DNA
8 Use lower kanamycin concentration New plates contained the lowest recommended kanamycin
concentration
9 Incubate plates for longer than 16 h Plates were observed for up to 1 wk
10 Use more efficient competent cells Ultracompetent XL cells (Stratagene) were used; transformants were
found for five groups
11 Change primer supplier Two of the eight primer sets were ordered from a different supplier;
no observable difference
12 Remove DpnI and other contaminants before DpnI was removed using PCR clean up kit; transformants obtained for
transformation groups 6 and 7
13 Remove DpnI and add dimethyl sulfoxide to site-directed Transformation obtained for group 8
mutagenesis reaction
14 During transformation, incubate cells without shaking Not tested
15 Redesign primers Not tested

TABLE III
Properties of RFAP synthase proteins altered by site-directed mutagenesis
Construction of Activity in Solubility
Variant
Forward sequence of the mutagenic primera site-directed cell-free extracts after cell
protein
mutant at 70 °Cb breakagec
R12A 5⬘-GATCATAAACACACCATCCGCGCTCCACCTGACCCTC ⫹ ⫺ ⫹
R26A 5⬘-CTCAACGGTGAGAGGGGCGCACTTGACGGTGGAGTTGG ⫹ ⫺ ⫹
R134A 5⬘-CGCACACATTGTGGGAGCGGGAGGAACCTCAGGTATAG ⫹ ⫹ ⫹
R180A 5⬘-CACCACCACCTGTAATTGCAGCGTATGATTTTCCTGAGGAATGG ⫹ ⫹ ⫹
H14A 5⬘-CACACCATCCAGACTCGCGCTGACCCTCATAGACCTC ⫹ ⫺ NDd
H98A 5⬘-GAAGCATGTTCCCTGCCGCGTCAGGTCTGGGTTCAGG ⫹ ⫺ ⫺
D19A 5⬘-CCACCTGACCCTCATAGCGCTCAACGGTGAGAGGG ⫹ ⫺ ND
D153A 5⬘-GGAGGATTCATAGTGGCGGCAGGCCACAGCAGCAG ⫹ ⫺ ND
a
In this protocol, the reverse primer was the exact complement of the forward primer. The position of the alanine codon is underlined.
b
For RFAP synthase activity, cell extracts (160 ␮l) were incubated for 1 h at 70 °C in the presence of 50 mM tris(hydroxymethyl)methyl-2-
aminoethanesulfonic acid, pH 6.8, 8 mM MgCl2, 2 mM dithiothreitol, 4 mM p-aminobenzoic acid, and 8.3 mM phosphoribosylpyrophosphate in
a final volume of 220 ␮l. RFAP was converted to the pink azo-dye derivative as described by Bechard et al. [18]. ⫹, RFAP synthase activity
was detected after 1 h. In the students’ assays, the absorbance reading of final reaction was beyond the detection limit of the spectropho-
tometer, indicating a specific activity of greater than 0.09 nmol/min/mg protein. This was comparable to the wild-type specific activity of 0.10
nmol/min/mg protein. ⫺, no activity was detected. The detection limit was 0.3 nmol of RFAP.
c
For solubility, ⫹ indicates the protein was detectable by SDS-PAGE in the soluble fraction.
d
ND, not determined.

Although no classes were scheduled for the next week,
six persistent undergraduates volunteered to conduct ad-
ditional experiments to overcome the technical obstacles.
The students proposed that either the kit was inefficient for
the relatively large template or contaminants in the primers
were interfering with the mutagenesis reaction. A kit con-
taining more efficient competent cells was purchased
(QuikChange XL; Stratagene), and primers were obtained
from a different company (Sigma-Genosys). Using the
more efficient competent cells, the volunteers were suc-
cessful in obtaining colonies for five of the class’s eight
site-directed mutagenesis reactions. The source of the
primers did not influence the results.
One particularly determined student attempted to create
the remaining mutants by removing DpnI with a polymer-
ase chain reaction cleanup kit (Qiagen, Valencia, CA) prior
to transformation and by adding dimethyl sulfoxide to the
mutagenesis reaction. These modifications produced col-
onies for the last three groups. During week seven, the
students screened the colonies for plasmids with the de-
sired mutations. Sequencing showed 100% efficiency in
creating the site-directed mutants, indicating that the class
had achieved its first research objective by creating eight
novel site-directed mutants of the RFAP synthase gene.
Activity of the Altered Proteins—After overcoming the
initial research barrier, the students enthusiastically pur-
sued characterization of the altered proteins. E. coli cells
expressing the mutated genes were broken by French
pressure lysis and centrifuged to separate soluble proteins
(cell-free extract) from insoluble proteins. Students meas-
ured RFAP synthase activity and found that the cell-free
extracts of only two mutants (R134A and R180A) showed
detectable enzyme activity (Table III).
The inactivity of the remaining six variants could be
explained by i) lack of gene expression, ii) production of
insoluble, inactive protein, or iii) production of soluble pro-
tein that differed substantially in structure or function from
the wild-type enzyme. To determine if the genes had been

FIG. 1. SDS-PAGE gel of uninduced versus induced cells of
E. coli expressing an RFAP synthase variant. Uninduced cells
(collected prior to induction, lane 1) and cells induced for the
production of the chaperone and RFAP synthase variant (lane 2)
were boiled in the presence of reducing SDS-PAGE loading buffer
for 10 min. The samples were loaded onto a 12% acrylamide gel,
the proteins were separated, and the gel was stained with Coo-
massie blue. Each lane contains ⬃20 ␮g of protein. The arrow
indicates the position of the RFAP synthase variant, which has a
predicted molecular mass of 34 kDa. The two dark high molecular
mass bands in lane 2 represent the chaperone proteins induced
to assist in protein folding.
expressed, students analyzed the protein profiles of unin-
duced cells versus cells induced with isopropylthiogalac-
toside and tetracycline. In seven out of eight cases, the
intensity of a band corresponding to the molecular mass of
RFAP synthase (34 kDa) increased after induction (Fig. 1).
Although no difference in the intensity of the 34-kDa band
was evident for the R180A variant, RFAP synthase activity
was detected, indicating that soluble, active protein had
been produced. Thus, in all eight cases, the students
successfully induced cells to produce the RFAP synthase
variants.
Because of time limitations, the students were unable to
purify the proteins as planned. However, five groups used
SDS-PAGE to determine if the altered proteins were solu-
ble. Bands of the appropriate molecular masses were
found in the soluble fractions of four of the five variants
(Table III). Taken together, the students’ results indicated
that two of the amino acids tested (R134 and R180) could
be changed without loss of enzyme activity and were thus
nonessential for activity. However, alteration of six amino
acids (R12, R26, H14, H98, D19, and D153) produced
inactive proteins, indicating a possible role in the structure
or function of RFAP synthase. These results served as the
foundation for individual undergraduates to further analyze
the roles of four residues during the next two semesters.
Literature Course—In the literature course, students
used electronic literature databases to identify original re-
search articles for a 10-page written review and 20-min
oral presentation. They were also introduced to the litera-
ture surrounding their project. The quality of the written
reviews met the expectations of the instructor, with an
average of grade of 92% and scores ranging from 70 to
100%. The quality of the oral presentations and subse-
quent discussions far exceeded the expectations of the
instructor (average grade of 94%). The question-and-an-
swer sessions at the end of each seminar were particularly
105
stimulating and dynamic, possibly because students were
graded on class participation.
The final examination consisted of answering four out of
six essay questions. The students demonstrated a reason-
able level of understanding of their own articles, papers
presented by their peers, and the theory behind the labo-
ratory techniques. However, it was clear that the students
had not mastered the background literature to the re-
search project. The raw average for the exam was 84%,
lower than anticipated by the instructor. Several students
noted informally that because only one examination was
offered, there was little incentive to study the material
during the semester. The results of a formal written survey
confirmed this sentiment. Therefore, quizzes and a second
examination will be added when the course is offered in
the future.
Student Feedback—Students evaluated the research-
driven “Advanced Microbiology Laboratory and Literature
Research” courses by responding to the standard teacher
evaluation given at the University of Florida. The overall
rating for the instructor in both the laboratory and literature
section was 4.75 out of 5.0 points. This score was higher
than the scores obtained by the same instructor for the
regular (nonresearch) section of “Advanced Microbiology
Laboratory” in previous semesters (4.52 and 4.09 points).
The overall course ratings for the laboratory and literature
sections were 4.86 and 5.0, respectively. In a separate
written survey, when asked for suggestions to improve the
course, seven out of eight respondents indicated that the
laboratory section should be expanded from one to two
afternoons per week to facilitate a more relaxed pace and
allow more time to overcome research obstacles.
Accomplishments of Individual Undergraduate Re-
searchers—Four students who showed perseverance in
resolving the site-directed mutagenesis problem were in-
vited to continue their projects as individual undergraduate
researchers in the host laboratory. The alanine mutants
constructed by all four students were soluble, but lacked
enzymatic activity. At the students’ suggestion, six addi-
tional conservative mutations were created, and, in agree-
ment with their hypothesis, conservative substitutions pro-
duced enzymes that retained partial activity. Initial
characterization of these altered proteins by two of the
undergraduates (Rosemarie Garcia and Dina Greene) was
included in a poster presented at the 2003 General Meet-
ing of the American Society for Microbiology. A third un-
dergraduate researcher (Courtney Malone) was the pre-
senting author on a different poster at the 2003 American
Society for Microbiology meeting and a co-author on the
manuscript submitted after the meeting. Finally, two of the
four undergraduates (Sonya Chhatwal and Rosemarie
Garcia) used the techniques learned in the course to assist
in purifying to homogeneity RFAP synthase from a differ-
ent organism, Archaeoglobus fulgidus. This work was pub-
lished with undergraduate co-authors in a peer-reviewed
journal [18].
DISCUSSION AND RECOMMENDATIONS
Undergraduate research can provide students with edu-
cational experiences beyond those offered in classrooms
and exercise-based laboratory courses [5]. Participants in
106
undergraduate research and research-driven laboratory
courses benefit from active rather than passive learning
environments [27] and experience both the uncertainty and
exhilaration of solving a research problem for which the
solution is unknown [11, 28]. Combined with a literature
colloquium, the research-driven laboratory can introduce
undergraduates to the expectations, challenges, and po-
tential rewards of graduate research [5].
The results presented here demonstrate that the ability
of undergraduates to contribute to original research can be
strongly enhanced by participation in an inquiry-based
laboratory course that provides the basis for individual
research projects. Within two semesters of participating in
the research-driven course, four senior undergraduates
contributed as co-authors to one published manuscript,
one submitted manuscript, and two posters at a national
meeting. A total of 14 new site-directed mutants of RFAP
synthase were constructed, and kinetic characterization of
the variants will form the basis for a future manuscript. By
comparison, in the 4 years prior to developing the re-
search-driven laboratory, only one out of 11 undergradu-
ates in the host laboratory had advanced a project far
enough to be included on a poster at a national meeting.
Increased undergraduate productivity is beneficial to
both the student and the host laboratory [1, 4, 10, 14, 29].
Because numerous students can be instructed at one time
and student commitment to the project can be evaluated,
this approach is particularly beneficial to faculty at primar-
ily undergraduate institutions and early career faculty who
depend heavily on the research productivity of undergrad-
uates. Establishing selection criteria for admission to the
course, such as research interest and minimum grades in
prerequisite courses, increases the probability of identify-
ing capable students motivated to pursue scientific re-
search. Observing the responses of students to the chal-
lenges and frustrations of original research can reveal the
individuals most compatible with the research program of
the host laboratory.
The research-driven approach is adaptable to a variety
of projects with defined goals that can be accomplished
within a single semester. Careful consideration must be
given to selecting research problems that have a reason-
ably high probability for success in the hands of under-
graduates. Successful projects are likely to involve
straightforward techniques that produce clear indicators of
success [27], meaningful research problems that can be
appreciated by the students [27], and potential for further
development by undergraduate or graduate researchers.
Screening-based problems related to the research of the
host laboratory are well suited for this purpose. When
designing a research-driven course, potential difficulties
should be anticipated and sufficient flexibility allowed in
the schedule to accommodate trouble-shooting experi-
ments. It is also recommended that instructors prepare
experimental resources to assist groups that may be un-
successful during the semester. For example, in the
course presented here, if the site-directed mutagenesis
reactions had failed, an uncharacterized mutant con-
structed previously by the host laboratory was available to
the students.
It is worthwhile to note that funding opportunities exist
BAMBED, Vol. 32, No. 2, pp. 101–107, 2004
to encourage research at primarily undergraduate institu-
tions, promote undergraduate research, integrate research
and education, and improve educational opportunities for
undergraduates [3, 30 –32]. Thus, the efforts of undergrad-
uates in a formal research-driven laboratory course can
increase undergraduate preparation for graduate research,
contribute to preliminary data for research projects and
grant proposals, and enhance the ability of undergraduate
researchers to contribute directly to the productivity of
their chosen laboratories.
Acknowledgments—I am grateful to Matthew Bechard for
teaching two of the lectures and for critical reading of the manu-
script, to Jack Shelton for sequencing the plasmids, and to
Beverley Driver for helpful comments. I gratefully acknowledge
the efforts of the students who participated in the “Advanced
Microbiology Laboratory” course (J. Akins, C. Capestany, A.
Casasus-Zambrana, S. Chen, S. Chhatwal, R. Garcia, D. Greene,
R. Hamilton, N. Hester, D. Kang, C. Malone, C. Pemble, M.
Reeves, N. Sanek, M. Worley, and A. Wright) and the additional
research contributions of S. Chhatwal, R. Garcia, D. Greene, and
C. Malone.
REFERENCES
[1] M. P. Doyle (2002) Academic excellence—The role of research,
J. Chem. Educ. 79, 1038 –1044.
[2] A. R. Hutchison, D. Atwood (2002) Research with first- and second-
year undergraduates: a new model for undergraduate inquiry at re-
search universities, J. Chem. Educ. 79, 125.
[3] R. L. Rawls (2002) An undergraduate champion. University of Arizo-
na’s Mike Doyle wants more undergraduates to do chemistry re-
search, Chem. Eng. News 80, 30 –31.
[4] T. J. Wenzel (2000) Undergraduate research: A capstone learning
experience, Anal. Chem. 15, 547A–549A.
[5] National Research Council of the National Academies (2002)
BIO2010: Transforming Undergraduate Education for Future Re-
search Biologists, National Academies Press, Washington, D.C.
[6] J. G. Voet, E. Bell, R. Boyer, J. Boyle, M. O’Leary, J. K. Zimmerman
(2003) Recommended curriculum for a program in biochemistry and
molecular biology, Biochem. Mol. Biol. Educ. 31, 161–162.
[7] K. M. Foos (1999) Scientific research on undergraduate teaching
campuses, J. College Sci. Teaching 28, 337–380.
[8] T. Longin (2001) Starting a research program at a PUI (primarily
undergraduate institution), Chemical Innovation 31, 3.
[9] S. M. Boomer, D. P. Lodge, B. E. Dutton (2002) Bacterial diversity
studies using the 16S rRNA gene provides a powerful research-based
curriculum for molecular biology laboratory, Microbiol. Educ. 3,
18 –25.
[10] S. M. Boomer, D. P. Lodge, B. E. Dutton, B. Pierson (2002) Molecular
characterization of novel red green nonsulfur bacteria from five dis-
tinct hot spring communities in Yellowstone National Park, Appl.
Environ. Microbiol. 68, 346 –355.
[11] T. W. Hanks, L. L. Wright (2002) Techniques in Chemistry: the cen-
terpiece of a research-oriented curriculum. J. Chem. Educ. 79, 1127.
[12] C. A. Heimbuck, N. W. Bower (2002) Teaching experimental design
using a GC-MS analysis of cocaine on money: A cross-disciplinary
laboratory, J. Chem. Educ. 79, 1254 –1256.
[13] J. Slezak (1999) Student-inspired undergraduate research, J. Chem.
Educ. 76, 1054 –1055.
[14] J. R. Vyvyan, D. L. Pavia, G. M. Lampman, G. S. Kriz (2002) Preparing
students for research: Synthesis of substituted chalcones as a com-
prehensive guided-inquiry experience, J. Chem. Educ. 79,
1119 –1121.
[15] R. V. Stahelin, R. E. Forslund, D. J. Wink, W. Cho (2003) Development
of a biochemistry laboratory course with a project-oriented goal,
Biochem. Mol. Biol. Educ. 31, 106 –112.
[16] A. R. Harker (1999) Full application of the scientific method in an
undergraduate teaching laboratory: A reality-based approach to ex-
periential student-directed instruction, J. College Science Teaching
28, 97–100.
[17] R. J. C McLean (1999) Original research projects—A major compo-
nent of an undergraduate microbiology course, J. College Sci. Teach-
ing 28, 38 – 40.
[18] M. E. Bechard, S. Chhatwal, R. E. Garcia, M. E. Rasche (2003)
Application of a colorimetric assay to identify putative ribofurano-
sylaminobenzene 5⬘-phosphate synthase genes expressed with ac-
tivity in Escherichia coli, Biological Procedures Online 5, 69 –77

(www.biologicalprocedures.com/bpo/general/home.htm).
[19] M. E. Rasche, R. H. White (1998) Mechanism for the enzymatic
formation of 4-(␤-D-ribofuranosyl)aminobenzene 5⬘-phosphate during
the biosynthesis of methanopterin, Biochemistry 37, 11343–51.
[20] J. W. Scott, M. E. Rasche (2002) Purification, overproduction, and
partial characterization of ␤-RFA-P synthase, a key enzyme in the
pathway of methanopterin biosynthesis. J. Bacteriol. 184,
4442– 4448.
[21] A. A. DiMarco, T. A. Bobik, R. S. Wolfe (1990) Unusual coenzymes of
methanogenesis, Annu. Rev. Biochem. 59, 355–94.
[22] S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, W. Miller, D. J.
Lipman (1997) Gapped BLAST and PSI-BLAST: A new generation of
protein database search programs, Nucleic Acids Res. 25,
3389 –3402.
[23] J. D Thompson, T. J. Gibson, F. Plewniak, F. Jeanmougin, D. G.
Higgins (1997) The ClustalX windows interface: Flexible strategies for
multiple sequence alignment aided by quality analysis tools, Nucleic
Acids Res. 24, 4876 – 4882.
[24] J. Sambrook, D. W. Russell (2001) Molecular Cloning: A Laboratory
Manual, 3rd Ed, Cold Spring Harbor Laboratory Press, Cold Spring
Harbor, NY.
107
[25] K. Nishihara, M. Kanemori, H. Yanagi, T. Yura (2000) Overexpression
of trigger factor prevents aggregation of recombinant proteins in
Escherichia coli, Appl. Environ. Microbiol. 66, 884 – 889.
[26] D. E. Garfin (1990) One-dimensional gel electrophoresis, Methods
Enzymol. 182, 425– 441.
[27] W. J. McKeachie (1994) in Project Methods and Independent Study
Teaching Tips: Strategies, Research, and Theory for College and
University Teachers (W. Cunningham, ed) 9th Ed., pp. 153–158, D. C.
Heath and Company, Lexington, MA.
[28] J. E. Heady (1993) Teaching embryology without lectures and without
traditional laboratories: An adventure in innovation, J. College Sci.
Teaching 23, 87–91.
[29] N. C. Craig (1999) The joys and trials of doing research with under-
graduates. J. Chem. Educ. 76, 595–597.
[30] S. Barkanic (2002) Fueling educational reform: The HHMI professors,
Cell Biology Educ. 1, 107–108.
[31] United States Department of Agriculture, Higher education challenge
grants program web site: www.reeusda.gov/1700/funding/rfahec.
htm.
[32] D. J. Wink (2000) Research opportunities for undergraduate institu-
tions at the NSF Web Site. J. Chem. Educ. 77, 1549.