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Article

Ariana L. Boltax†,‡

Stephanie Armanious†

Melissa S.

Kosinski-Collins†*

Jason K. Pontrello‡*

From the †Department of Biology, Brandeis University, Waltham,Massachusetts 02454, ‡Department of Chemistry, BrandeisUniversity, Waltham, Massachusetts 02454

Abstract

Modern research often requires collaboration of experts in

fields, such as math, chemistry, biology, physics, and com-

puter science to develop unique solutions to common

problems. Traditional introductory undergraduate labora-

tory curricula in the sciences often do not emphasize con-

nections possible between the various disciplines. We

designed an interdisciplinary, medically relevant, project

intended to help students see connections between chem-

istry and biology. Second term organic chemistry labora-

tory students designed and synthesized potential polymer

inhibitors or inducers of polyglutamine protein aggrega-

tion. The use of novel target compounds added the uncer-

tainty of scientific research to the project. Biology

laboratory students then tested the novel potential pharma-

ceuticals in Huntington’s disease model assays, using in

vitro polyglutamine peptide aggregation and in vivo lethal-

ity studies in Drosophila. Students read articles from the

primary literature describing the system from both chemi-

cal and biological perspectives. Assessment revealed that

students emerged from both courses with a deeper under-

standing of the interdisciplinary nature of biology and

chemistry and a heightened interest in basic research. The

design of this collaborative project for introductory biology

and organic chemistry labs demonstrated how the local

interests and expertise at a university can be drawn from

to create an effective way to integrate these introductory

courses. Rather than simply presenting a series of experi-

ments to be replicated, we hope that our efforts will inspire

other scientists to think about how some aspect of authen-

tic work can be brought into their own courses, and we

also welcome additional collaborations to extend the scope

of the scientific exploration. VC 2015 by the International

Union of Biochemistry and Molecular Biology, 43(4):233–

244, 2015.

Keywords: curriculum design and development; integration of

courses; integration of research into undergraduate courses;

laboratory exercises; learning and curriculum design;

neurodegenerative diseases

IntroductionLaboratory components have long been integral to intro-ductory courses in the basic sciences (biology, chemistry,and physics). Traditionally, labs have been designed to

complement the lecture portion of the course, illustratingtopics, and concepts in lecture that are specific only to thesingle discipline. Students develop basic technical skills toprepare them for more advanced courses and laboratoryresearch through use of highly standardized experimentswith known outcomes [1]. Unfortunately, these types ofexperiments too often fall short of engaging students andfail to stress the underlying importance of current interdis-ciplinary research [2, 3].

In 2003, the National Research Council published areport emphasizing the importance of engaging students inthe scientific process and in the elements of scientific dis-covery early in their scientific careers [4]. Undergraduatecourses focused on a project- or inquiry-based laboratoryresearch project in biology increase student engagement,promote understanding of the scientific process, cultivatecritical thinking skills and help retain students in Science,Technology, Engineering, and Math (STEM) careers [5–10].

ws Additional Supporting Information may be found in the online

version of this article.

Melissa S. Kosinski-Collins and Jason K. Pontrello contributed equallyto this work.*Address for correspondence to: Department of Biology, Brandeis Uni-versity, Waltham, Massachusetts 02454, USA. E-mail: [email protected] or Department of Chemistry, Brandeis University, Waltham,Massachusetts 02454, USA. E-mail: [email protected] 29 January 2015; Accepted 25 March 2015DOI 10.1002/bmb.20871Published online 3 July 2015 in Wiley Online Library(wileyonlinelibrary.com)

Connecting Biology and Organic Chemistry

Introductory Laboratory Courses Through a

Collaborative Research Projectws

Biochemistry and Molecular Biology Education 233

Similarly, work to integrate project-based labs into chemis-try laboratory courses has been well documented [11–16].Assessment and impact of undergraduate courses in whichresearch experiences have been incorporated has beenreviewed [17].

If introductory biology laboratory courses are meant toprepare students for potential STEM careers, experiencesshould reflect trends and techniques in current researchinitiatives [4]. Labs that demonstrate interdisciplinaryapproaches to scientific problems may serve to introducestudents to the nature of current scientific research, pro-vide an opportunity to work on a single project from theperspectives of different subjects, and demonstrate theresult of successful collaboration [17–19]. Some examplesexist of “integrated laboratory” programs designed tobridge chemistry courses with other courses as diverse asart, geology, ecology, or cellular biology [20–28], yet pro-grams are not always designed to integrate multiple fea-tures of authentic scientific research into introductory labo-ratory courses.

In the interest of engaging students as well as demon-strating the interdisciplinary nature of current biology andbiology research, specifically in the area of chemical biol-ogy, we developed a collaborative project for introductoryorganic chemistry and biology laboratory courses that (1)employed basic technical skills traditionally taught in intro-ductory laboratory courses, with potential to expand tomore sophisticated skills, (2) required expertise from bothbiology and chemistry, (3) illustrated an “interesting” appli-cation of the scientific efforts, (4) required students to ana-lyze and interpret original scientific data, and (5) intro-duced students to the world of scientific research atBrandeis University.

Connecting Courses Through aCommon Research HypothesisIn creating our collaborative laboratory design, we believedthat a research project addressing a neurodegenerative dis-ease involving protein aggregation [29] (such as Hunting-ton’s, Alzheimer’s, Parkinson’s, etc.) would be of significantinterest to many of our students, given that approximately70% of students enrolled in introductory biology andorganic chemistry plan to pursue careers in the alliedhealth professions. Huntington’s disease is associated witha genetic defect in the huntingtin protein that produces anextended polyglutamine (polyQ) sequence at the terminusof the protein. Although the mechanism of the disease isnot well understood, statistical correlations have revealedthat individuals with a protein containing over 36 gluta-mine repeats at the N-terminus will develop symptoms ofHuntington’s disease at some point in their life, with theage of onset and severity of the disease associated with thelength of the polyQ repeat [30]. Since postmortem patients

with full symptomatic Huntington’s are found to have largeamounts of amyloid inclusion in their brain tissue [31], pro-tein aggregation has been attributed to onset of the disease.However, the consequence of protein aggregation has beendebated, with some studies even suggesting potential bene-fits of aggregates [32–34]. Although the exact role of hun-tingtin aggregation in the progression of the disease isunknown, the aggregation has traditionally been viewed asdetrimental to neuronal function. Research efforts havefocused on development of inhibitors of aggregation withnumerous examples of small molecules reported to disruptpolyQ-associated protein aggregation [35–37].

With the goal of controlling huntingtin protein aggrega-tion, we designed a series of compounds with the intent ofeither inducing or inhibiting aggregation of the polyQ pro-tein. Our strategy was based on the so-called “polar zipperhypothesis” [38, 39] which suggests that glutamine residuesof the polyQ tail form an extensive network of hydrogenbonds, causing protein aggregation and precipitation. Wehypothesized that targeting the polyQ tail with designedmolecules would allow for manipulation of the proteinaggregation state.

Our work targeted the polyQ sequence of huntingtinprotein with synthetic multivalent ligands. Multivalentligands consist of a structure (natural or synthetic)repeated multiple times on a “scaffold” (which could benatural or synthetic) as shown in Fig. 1. For example, apeptide consisting of amino acids is a natural polymer“scaffold” for amino acid side chain functionality. Chemicalsynthesis allowed appendage of multiple copies of ligandson a single synthetic scaffold, resulting in a linear“multivalent display” as shown in Fig. 1. A multivalentligand is defined as a structure that can create multiplerecognition events simultaneously with another entity,where valency refers to the number of ligands [40]. Poly-meric scaffold synthesis also allowed variation in averagepolymer length. By controlling the length of the scaffold,the length of the multivalent ligand display was thus con-trolled. We utilized multivalent ligands of varying valency,hypothesizing that “short” multivalent ligands would onlybe able to bind a single huntingtin protein polyQ target,resulting in disruption of protein aggregation by a mecha-nism of competitive inhibition (Fig. 1). Conversely, we

We hypothesized that “short” multivalent ligands

would function to inhibit protein aggregation,

while “longer” multivalent ligands would bind

multiple copies of the target protein, inducing

protein aggregation. [Color figure can be viewed

in the online issue, which is available at wileyon-

linelibrary.com.]

FIG 1

Biochemistry andMolecular Biology Education

234 Interdisciplinary Organic Chemistry and Biology Laboratory

http://wileyonlinelibrary.com


hypothesized that “longer” multivalent ligands, able to bindpolyQ regions on multiple protein targets, would bring pro-teins together, inducing aggregation (Fig. 1).

Here we describe the design and implementation of acollaborative research project that connects introductorybiology and organic chemistry laboratory courses througha common hypothesis about huntingtin protein aggregation.In the organic lab, students synthesized multivalent ligandswith potential to inhibit or promote polyQ aggregation. Inthe biology lab, the students tested the compounds using invivo and in vitro models of polyQ aggregation.

University and Profile of CoursesBrandeis University is a private, liberal arts, and researchuniversity. Each year, about 200–250 students take intro-ductory biology and organic chemistry laboratory courses,with a majority of students enrolling in both courses simul-taneously. The laboratory courses are structured similarly,including one 80-min laboratory lecture and one 4-h labo-ratory period each week. Graduate and undergraduateTeaching Assistants (TAs) supervise small groups of stu-dents (up to 10 in organic chemistry and up to 24 in biol-ogy) in laboratory each week. Although most students areco-enrolled in both of these laboratory courses, traditionalversions of the curricula were completely isolated from oneanother and taught as disparate disciplinary content.

Research Contributions from OrganicChemistry LaboratoryProject Design—Expansion of Typical OrganicTopics and Use of Scientific LiteratureWe designed our multivalent ligands using a synthetic poly-mer scaffold amenable to display multiple copies of a tar-geting ligand, allowing control over the valency by usingsynthetic polymer scaffolds of different average length. Dueto time constraints, we synthesized the polymer scaffoldsourselves, using Ring-Opening Metathesis Polymerization(ROMP) of strained norbornene olefin monomer displayinga reactive N-hydroxysuccinimide (NHS) ester functionalityas shown in Fig. 2 [41, 42]. By varying the monomer to ini-tiator ratio in the polymerization reaction, we were able togenerate polymers of varying average length (n). Studentsthen reacted the synthetic polymer scaffolds with differenttargeting ligands containing a nucleophilic amine func-tional group, resulting in multivalent displays of varyinglength, dependent on the length of the original polymerscaffold (Fig. 2). Based on the polar zipper hypothesis, wesought to incorporate the carboxamide functionality of theglutamine amino acid sidechain into the synthetic polymerscaffold, resulting in a multivalent display anticipated totarget polyQ sequences. Because of reports that peptidesrich in tryptophan were able to disrupt polyglutamine

oligomerization [43–45], we also sought to explore incorpo-ration of this amino acid into our multivalent displays, aswell as a variety of other ligands.

Students were introduced to primary scientific litera-ture through formal handouts (see Supporting Information),laboratory lectures, and assigned readings related to Hun-tington’s disease research and the chemistry utilized in theresearch project [36, 41]. As part of a Final Report due atthe end of the course, each student wrote a properly for-matted scientific procedure for preparing their compoundand also answered specific questions designed to introducethem to the science behind the research project and to leadthem through the assigned literature readings (see Sup-porting Information). At the end of the course, studentgroups delivered formal presentations of the assigned read-ings and discussed their synthetic results.

Our synthetic strategy resulted in both advantages andchallenges. We expanded the scope of the typical secondsemester organic lab, allowing additional links to class-room learning through the research project. For example,the ligand conjugation reaction is an acyl substitution, areaction of great importance in the second semesterorganic chemistry lecture course. Since the activated NHSester reacts selectively with amine-bearing nucleophiles inthe presence of other less nucleophilic groups, such asalcohols and carboxylic acids, instructors could discuss apractical example of chemoselectivity. The generation of apolymer multivalent ligand that was not soluble in com-monly used organic solvents prevented purification by typi-cal silica chromatography, extractions, or recrystallization.This provided an opportunity to introduce size exclusionchromatography into the laboratory course using watereluent to separate polymer product from small moleculereagents and byproducts. The polymer products were ana-lyzed using 1H-nuclear magnetic resonance (1H-NMR) spec-troscopy, a technique typically taught in the second semes-ter organic chemistry laboratory course for analysis ofsmall molecule structures. Using NMR to analyze popula-tions of similar polymeric structures provided an extensionof this important technique (Fig. 3 and Supporting Informa-tion). Although students did not perform the polymeriza-tion, use of ROMP and a ruthenium-based metathesis cata-lyst provided an opportunity to incorporate organometallicchemistry into the course through this Nobel prize-winningreaction [46]. Finally, this project allowed students to learn

Synthetic multivalent ligands produced by react-

ing ligands with an amine nucleophile and N-

hydroxysuccinimide (NHS) ester-substituted poly-

mer scaffolds of varying average length (n).

FIG 2

Boltax et al. 235

an advanced application of reaction molecular stoichiome-try, providing new educational challenges for a topic thatmay become routine (see Supporting Information for Stoi-chiometry Handout).

Experiment Implementation and ResultsWe have run this version of the organic laboratory coursefive times since 2009, and with establishment of a stableproject design, we are excited to report our progress. Eachgroup of up to 10 students was divided into two “Research

Groups”, where student groups utilized the same labora-tory techniques, but synthesized unique compounds, result-ing in a total of 8 unique products in a normal section of40 students. The experiments were designed over four lab-oratory sessions, and were run in parallel with other workdone for the course (usually requiring less than 2 h to com-plete), utilizing the specific equipment and demonstratingthe teaching concepts listed in Fig. 4. Spanning two labora-tory sessions (weeks 1 and 2, Fig. 4), students conjugatedtheir ligands of interest to their polymer scaffold of defined

Example 1H-NMR spectrum of polymer product synthesized by students in Spring 2013. Integration of the polymer

alkene region (2H) vs. the aromatic region (5H for tryptophan) allows students to determine the mole fraction (v) of a

tryptophan ligand appended from the synthetic polymer scaffold, in this case vTrp 5 0.9.

Procedures completed, equipment used, and concepts taught are specified in the 4 weeks of the organic chemistry

course devoted to working on the project.

FIG 3

FIG 4



length. They completed calculations as indicated in a hand-out (see Supporting Information), performed a structuredpeer review at the start of lab, and after reaching a con-sensus regarding the necessary amounts of ligand solu-tions, students setup their reactions. During the third labo-ratory session of the project, students purified theirproducts using size-exclusion chromatography with watereluent, and they concentrated fractions using a SpeedVacconcentrator. In the fourth laboratory session, studentsweighed their concentrated fractions and dissolved thepolymer in d6-dimethylsulfoxide (DMSO) for NMR analysis.Following analysis, the solution was transferred to alabeled storage tube for biological evaluation. Class NMRdata were available through the course website, and inter-pretation of each group’s spectrum was part of the FinalReport (see Supporting Information).

Over the years, a variety of different ligands wereexplored in the conjugation reaction to polymer scaffold, allwith the intent of targeting the polyQ region of mutant hun-tingtin protein. Selected examples of compounds synthe-sized and characterized by students are shown in Fig. 5.We built on the data from previous semesters to refine andoptimize the conjugation protocol as well as the choice oftargeting ligands, and also explored more diverse function-ality, such as those introduced with different amino acids.In some cases, ligands utilized resulted in lack of recoveryof polymer product, likely due to poor solubility of theresulting polymer. This was especially evident in some ofthe longer polymer samples (n 5 100), and with some lesssoluble ligands investigated (Gln5). Frequently, solubilitywas addressed by heating and sonication to dissolve thepurified polymer product in the NMR solvent. However,with some ligands such as Gln5, longer polymers (n 5 100,250, 500) were not able to be redissolved. While frustratingfor students, exposure to “failed” experiments was critical

to an authentic research project. The specific ligandsselected had not previously been conjugated to these syn-thetic scaffolds, demonstrating that expected results werenot always obtained.

Research Contributions from BiologyLaboratoryProject Design—Extension of Typical LaboratoryExperimentsThe functionalities of the molecules were tested in both anin vitro and in vivo assay. The in vitro assay was added tothe fall semester introductory biology laboratory course(biochemistry/cell biology focus), while the in vivo experi-ment was incorporated into the spring semester bio course(genetics focus). All experiments were performed in paral-lel with other projects and required less than 2 h of eachlaboratory to complete.

The in vitro polyQ aggregation assay based on methodspreviously described used two polyQ peptides of the follow-ing sequence [47].

Poly(Q)35 [NH2-KKQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQKK-Acid]

Poly(Q)15 [NH2-KKQQQQQQQQQQQQQQQKK-acid]The peptides were dissolved in water at pH 3.0 and the

aggregation reaction was initiated by dilution in neutralwater with and without polymer present. Students deter-mined the concentration of polymer to use and whether ornot they would include a known inhibitor of polyQ aggrega-tion, Congo red. The initiation and extent of peptide aggre-gation was monitored using a right angle light scatteringassay for 3 weeks. The samples were tested every 24–48 hover the 21-day period. Although a scattering assay is notoften introduced in an introductory biology laboratory

Students in organic chemistry lab courses conjugated numerous ligands to polymer scaffolds as part of the research

project from Spring 2009 to 2013. Polymer lengths and ligand densities were varied as outlined above.FIG 5

Boltax et al. 237

course, it offered an unique opportunity to discuss dilution,concentration determination, and the effect of pH on bio-logical molecules.

To allow students to test the effect of the polymer onorganisms expressing polyQ proteins, we selected Drosoph-ila as our model system for the in vivo assay. The particu-lar fruit fly system allowed the instructor to introduce theconcepts of gene expression, cis/trans gene regulation, andcentral dogma within the laboratory. These concepts areall core tenets in introductory genetics and thus alignedwell with the learning objectives that are outlined in a tra-ditional curriculum (Fig. 6).

In groups of four, students crossed male flies express-ing elav–GAL4–GFP with three lines of female flies carryingUAS-polyQ in the presence and absence of polymer [48].The length of the polyQ repeat in the three strains was 22,48, and 108, respectively, and the polymer was added tothe fly food directly. Students scored and analyzed theirprogeny in a life span or morphological change assay. Ifpolymers inhibited protein aggregation, we expected to seean increase in lifespan while if polymers promoted

aggregation, we expected to see a decrease in lifespan ofthe polyQ flies.

The students were asked to determine the parametersof polymer application including concentration and inclu-sion of controls from known stock solutions of Congo redand polymer. In the interest of time, all strains wereexpanded in advance of laboratory and virgin female flieswere selected for the students. Additionally, the particularpolymer to be analyzed was preselected for each section.

Experimental Implementation and ResultsSince there were no requirements to co-enroll in bothorganic chemistry and biology laboratory courses, biologystudents normally analyzed polymers synthesized in theprevious year’s organic course. Removing the pressure todeliver compounds also provided time for organic chemis-try students to learn about the reactions and project back-ground before beginning their syntheses.

Introductory biology laboratory students have contrib-uted to the in vitro assay portions of the research projectfor four semesters, starting in Fall 2009. Each laboratory

Procedures completed, equipment used, and concepts taught are specified in the time the biology lab courses devoted

to working on the project.FIG 6



section set-up a series of samples and then monitored rightangle light scattering. Each pair of students was responsibleto collect data individually for each sample and interprettheir own results. At least two sections each semester moni-tored the same polymer to determine reproducibility of thecollected data. Results demonstrated the 100 length poly-mers displaying either glutamine or tryptophan amino acidsincrease peptide aggregation rates. Students were given theoption to design their own series of compounds for evalua-tion. Representative series are shown in Fig. 7 where stu-dents decided to systematically evaluate the effects of aminoacids tryptophan, arginine, and valine incorporation into thesynthetic polymer scaffold. The students were asked toselect their own control compounds in the biological assayto provide an opportunity for discussion of data validity.Such examples have included using the Q35 peptide alone, aknown aggregation inhibitor Congo red, or a polymer dis-playing only the diol functionality, expected to be biologicallyinert. Examples of light scattering data collected by studentsare shown in Fig. 7, where Q35 peptide control alone shows

strong light scattering indicating aggregation, and synthe-sized compounds exhibited varying degrees of decreasedlight scattering (decreased peptide aggregation).

Full implementation of the multiweek in vivo assaybegan in the Spring of 2012. Students worked in groups of4 and were assigned one polymer per section meaningeach polymer was tested in 4–6 distinct experiments. Poly-mers were rarely found to have any effect on the lifespanof flies as compared to the control. Smaller groups of stu-dents were also asked to develop tests other than astraight-forward life span assay as part of their inquiry-based laboratory design. For example, one cohort of stu-dents tested the series of polymers synthesized in Fig. 7,and the in vivo data show changes in wing structures inflies as a function of polymer application (Fig. 8). Due tothe heterogeneity of morphological changes within the flies,it was not possible to conclude whether this is indicative ofincreased or decreased aggregation in this one experimen-tal iteration. This iteration, however, did provide studentswith a realistic view of experimental design and strategy.

Time course of right angle light scattering of PolyQ peptides. Students synthesized compounds with densities of trypto-

phan, arginine, and valine shown above. Light scattering data were collected for these series in addition to a Q35 pep-

tide control, a polymer with only biologically inert diol, and a known inhibitor of aggregation, Congo red. [Color figure

can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

FIG 7

Boltax et al. 239


Assessment and Responses toStudent FeedbackA primary goal of the collaborative project described herewas to demonstrate the intersection between the distinctfields of chemistry and biology to students in our introduc-tory laboratory courses. We designed the project so that amajor motivation of the chemical synthesis was the biologi-cal application. Generation of novel compounds provided away for biology students to test a hypothesis and to runassays. In addition to the basic skills developed throughrunning reactions (in organic lab) or performing assays (inbio lab), students in each course also learned about theapplication of their work in the other field. For example,organic chemistry students learned about the biologicalassays and data interpretation as part of the project back-ground, and biology students saw novel polymeric struc-tures that they tested in their laboratory experiments.

At the end of each semester, students were given univer-sity standard course evaluations without any compensationor academic bonus for completing the evaluations. Thecourse evaluations included two free response questions, andalthough the generic evaluation did not include specific ques-tions about the Huntington’s project, many students com-mented upon its incorporation in the class. This indicatedanecdotally that the Huntington’s project impacted them in amemorable fashion. Course evaluations were reviewed oversix semesters during which the project was offered.

A total of 60 responses to the question “Please identifythose aspects of the course you found most useful or valua-ble for learning.” broadly fit into two categories, with rep-resentative examples shown in Fig. 9.

1. Enhanced engagement through the project’s practicalapplications was indicated by students that felt they weredoing “real science” as opposed to predicted cannedexperiments. A few students noted the value of the inter-play between the organic chemistry procedures and theassociated biological processes, and some students

commented on the value of the inquiry-based approach incomparison to traditional cookbook laboratory procedures.

2. The research project experiment structure and activitiesinvolved comments from many of the students thatdescribed the enjoyable or interesting aspects of researchitself including the collaborative nature of projects, theintegrative aspects of the material, and the reading of pri-mary literature to supplement their learning.

Overall, most evaluation comments concerning theinquiry-based Huntington’s project were positive, althoughsome students did point out shortcomings in the process. Atotal of 24 responses to the question “What suggestionswould you make to the instructor for improving thecourse?” broadly fit into two categories, with representa-tive examples shown in Fig. 10.

1. Project structure and confusion was largely focused inthe first semester the organic chemistry part of the pro-ject was offered (Spring 2009), and fortunately wasaccompanied by constructive suggestions that were inte-grated into future course design. Several students com-mented on the slightly disorganized nature of the projector suggested a need for stronger background or integra-tion into other course work. These issues wereaddressed by modification of some of the assigned litera-ture readings, integration of a project overview in thecourse handout, and by taking several laboratory lec-tures to discuss the project background and design. Posi-tive feedback increased in subsequent semesters withthese modifications and as the biology labs integratedcomplementary experiments starting with Fall 2011.

2. Too difficult or too time intensive for an introductorycourse comments were accompanied by a large numberof suggestions to increase the current organic chemistrylaboratory course status from a “half course” to a “fullcourse”, a reasonable suggestion currently under consid-eration. When inquiry- or project-based experiments areimplemented in introductory courses, we create a

Representative images of wing morphologies observed on day 12 of Drosophila expressing Q48. Polymer used in these

experiments was an average 10 units long with vTrptophan 5 0.5, vArginine 5 0.1, and vdiol 5 0.4 ligands. Treatments from

left to right are as follows (1) no treatment, (2) 0.5% polymer, (3) 0.5% polymer, 10 mM Congo red, and (4) 0.5% poly-

mer, 2.5 mM Congo red. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

FIG 8




Representative examples of comments responding to the question “Please identify those aspects of the course you

found most useful or valuable for learning.” broadly fit into two categories.FIG 9

Boltax et al. 241

multiple week experiment that covers fewer topics, butin greater depth than a standard course. Although sev-eral students suggested we move away from a multiweekproject format and cover more topics, there were alsosuggestions to increase the amount of crossover betweenlaboratory courses. Finally, allowing students to refineparameters or have an active hand in the experimentaldesign may lead to unpredictable or uninterpretableresults or potentially failed experiments, akin to aresearch laboratory experience. Several of the sugges-tions for course improvement in the biology laboratoryindicated that a small number of students were frus-trated with the lack of results produced in the course.While the level of difficulty of the project is a very realpotential instructor concern, our assessment did not sug-gest the project workload to be generally problematicconsidering only 6 negative comments were receivedover several years of offering the project with enroll-ments of about 200 organic students and about 250 biol-ogy students each semester. However, if an instructordesired, difficulty and time of project can be adjusted byleaving out certain parts, for example, NMR analysis fororganic students could be done by the instructor or

Teaching Assistants, and biology students could performone rather than two assays as part of the courses.

Engaging Students in ScientificResearchA telling sign of student interest in the scientific process as aresult of these courses was the direct involvement of any-where from 5 to 10 students each year who sought under-graduate research positions with us to continue workrelated to the Huntington’s project. Since 2009, 33 under-graduate students have worked in the Pontrello researchlaboratory, many in collaboration with Kosinski–Collins tocomplete biological assay development and compound eval-uation. These students were drawn from diverse majors andminors including chemistry, biology, neuroscience, biochem-istry, business, mathematics, studio art, and economics.Depending on the students’ interests, their research focusedon chemical synthesis and/or biological evaluation.

Perspectives and Future InitiativesWe have described an inquiry-based project in the area ofchemical biology focused on Huntington’s disease research

Representative examples of comments responding to the question “What suggestions would you make to the instruc-

tor for improving the course?” broadly fit into two categories.FIG 10



for introductory organic chemistry and biology laboratorycourses serving over 200 students per semester. In theorganic laboratory, students synthesized multivalent ligandsdesigned to inhibit or promote polyQ aggregation. In the biol-ogy lab, students tested the polymers using in vivo and in vitromodels of polyQ aggregation. As a result of these courses, stu-dents became more aware of the relevance and application ofsynthesis in biomedical problems and were more engaged inand knowledgeable of scientific research. By offering theselaboratories simultaneously, we emphasized the interdiscipli-nary nature of modern science to our students.

This type of project required us to be prepared to fail withrespect to our research while still allowing students to com-plete the laboratory course. Such an experience is an impor-tant feature of authentic research; however, a lack of datacan create logistical problems. We addressed this importantissue by always being sure a group of students ran “control”experiments utilizing commercially available materials andknown results. For example, while most students in organiclaboratory synthesized novel compounds using new ligands, asmall group always utilized a commercially available controldiol to be sure there would be data to use in collaboration tofulfill laboratory report requirements. Similarly, some biologystudents always worked with the commercially availableknown inhibitor of aggregation, Congo Red.

In response to the requests of some students to furtherengage in the scientific research project, we are using the pro-ject model reported here to create additional, intensiveresearch experiences for self-selecting groups of students co-enrolled in both laboratory courses. These students will haveadditional freedom in individual project design, synthesizing,and testing their own compounds under the supervision of aTA experienced in both courses. Additional work and activitieswill further explore project background and implications.

The Huntington’s experiments represent the principle ofdrawing from the research capabilities of science depart-ments and the interests of faculty to design an open-endedproject. Replicating and/or building on this project in anothersetting would require initial polymer synthesis using all com-mercially available materials (see Supporting InformationLaboratory Preparation file). However, rather than present-ing a project to be simply replicated, we wish to inspire otherscientists in other research areas to think about how someaspect of authentic work can be brought into the undergrad-uate laboratory, and hope we have demonstrated that thebenefits to student learning are well worth the effort. On theother hand, we also understand that this cannot be done inevery setting, and so we welcome partnerships with otherlaboratory courses, including at other universities, toincrease the scope of the synthetic component as well as thediversity of experiments for more extensive biological evalua-tion. For example, work is currently underway to integrateatomic force microscopy analysis of aggregates into the pro-ject as part of the biology laboratory course. We hope that byfurther expanding the scope of the project, students will

continue to learn that their work is built on the contributionsof others, and collaborations are often necessary to advanceinterdisciplinary research.

Supplemental InformationChemistry laboratory Project Handout and Advanced Stoi-chiometry assignment are included as well as the FinalProject Report. The biology laboratory procedures for invitro and in vivo experiments are included. A LaboratoryPreparation file is included that indicates specific hazardsas well as lists and costs of chemicals/equipment.

AcknowledgementsWe would like to thank Brandeis University for allowing thefreedom and support to develop and explore new methods ofscience education. We would also like to thank DeborahBordne for expansion and maintenance of the polyQ flystrains, and Gary Koltov for continued work in chemistry labo-ratory preparation. We thank the Division of Science SummerUndergraduate Research Fellowship and the Jerome A. SchiffUndergraduate Fellows Program at Brandeis University forfinancial support of our undergraduate research students. Wealso thank Brian P. Coppola for thoughtful review and sugges-tions on this manuscript and Laura L. Kiessling whose innova-tive graduate research projects made envisioning the polymerapplication of this work possible. Finally we thank our out-standing Teaching Assistants and students who have allowedrealization of this research.

References

[1] Lunetta, V. N. (1998) The School Science Laboratory: Historical Perspec-

tives and Contexts for Contemporary Teaching, Kluwer Academic Pub-

lishers, Dordrecht.

[2] Gabel, D. (1998) The Complexity of Chemistry and Implications for

Teaching, Kluwer Academic Publishers, Dordrecht.

[3] Hofstein, A. (2004) The laboratory in chemistry education: Thirty years

of experience with developments, implementations, and research.

Chem. Ed. Res. Pract. 5, 247–264.

[4] National Research Council. (2003) Bio 2010, Transforming Undergradu-

ate Education for Future Research Biologists, National Academies

Press, Washington, DC.

[5] Cianciolo, J., Flory, L. and Atwell, J. (2006) Evaluating the use of

inquiry-based activities: Do student and teacher behaviors really

change? J. Coll. Sci. Teach. 36, 50–56.

[6] Lord, T. and Orkwiszewski, T. (2006) Moving from didactic to inquiry-

base instruction in a science laboratory. Am. Biol. Teach. 68, 342–345.

[7] Fairweather, J. (2010) Linking evidence and promising practices in sci-

ence, technology, engineering, and mathematics (STEM) undergraduate

education: A status report for the National Academies National

Research Council Board of Science Education. BOSE, Washington, DC.

[8] Aronson, B. D. and Silviera, L. A. (2009) From genes to protein to

behavior: A laboratory that enhances student understanding in cell and

molecular biology. CBE Life Sci. Educ. 8, 291–308.

[9] Rissing, S. W. and Cogan, J. G. (2009) Can an inquiry approach improve

college student learning in an introductory laboratory? CBE Life Sci.

Educ. 8, 55–61.

[10] Treacy, D. J., Sankaran, S. M., Gordon-Messer, S., Saly, D., Miller, R.,

Isaac, S. R. and Kosinski-Collins, M. S. (2011) Implementation of a

Boltax et al. 243

project-based molecular biology laboratory emphasizing protein struc-

ture–function relationships in a large introductory biology laboratory

course. CBE Life Sci. Educ. 10, 18–24.

[11] Kroll, L. (1985) Teaching the research process via organic chemistry lab

projects. J. Chem. Educ. 62, 516–518.

[12] Ruttledge, T. R. (1998) Organic chemistry lab as a research experience.

J. Chem. Educ. 75, 1575–1577.

[13] Gottfried, A., Reynolds, B. P. and Coppola, B. P. (2004) In Honors Cup:

Incorporating a Synthetic Project Competition in an Undergraduate

Organic Chemistry Lab, 18th Biennial Conference on Chemical Educa-

tion, University of Iowa, Ames, Iowa.

[14] Horowitz, G. (2007) The state of organic teaching laboratories. J. Chem.

Educ. 84, 346–353.

[15] Mohrig, J. R., Noring Hammond, C. and Colby, D. A. (2007) On the suc-

cessful use of inquiry-driven experiments in the organic chemistry labo-

ratory. J. Chem. Educ. 84, 992–998.

[16] Slade, M. C., Raker, J. R., Kobilka, B. and Pohl, N. L. B. (2014) A

research module for the organic chemistry laboratory: Multistep synthe-

sis of a fluorous dye molecule. J. Chem. Educ. 91, 126–130.

[17] Auchincloss, L. C., Laursen, S. L., Branchaw, J. L., Eagan, K., Graham,

M., Hanauer, D. I., Lawrie, G., McLinn, C. M., Pelaez, N., Rowland, S.,

Towns, M., Trautmann, N. M., Varma-Nelson, P., Weston, T. J. and

Dolan, E. L. (2014) Assessment of course-based undergraduate research

experiences: a meeting report. CBE Life Sci. Educ. 13, 29–40.

[18] Speth, E. B., Momsen, J. L., Moyerbrailean, G. A., Ebert-May, D., Long,

T. M., Wyse, S. and Linton, D. (2010) 1,2,3,4: Infusing quantitative liter-

acy into introductory biology. CBE Life Sci. Educ. 9, 323–332.

[19] Matthews, K. E., Adams, P. and Goos, M. (2010) Using the principles of

BIO2010 to develop and introductory, interdisciplinary course for biol-

ogy students. CBE Life Sci. Educ. 9, 290–297.

[20] Dillner, D. K., Ferrante, R. F., Fitzgerald, J. P., Heuer, W. B. and

Schroeder, M. J. (2007) Integrated laboratories: Crossing traditional

boundaries. J. Chem. Educ. 84, 1706–1711.

[21] Lipkowitz, K. B., Jalaie, M., Robertson, D. and Barth, A. (1999) Interdisci-

plinary learning with computational chemistry: A collaboration between

chemistry and geology. J. Chem. Educ. 76, 684–691.

[22] Megehee, E. G., Hyslop, A. and Rosso, R. J. (2005) Interlaboratory col-

laborations in the undergraduate setting. J. Chem. Educ. 82, 1345–1348.

[23] Scott, W. L. and O’Donnell, M. J. (2009) Distributed drug discovery, part

1: Linking academic and combinatorial chemistry to find drug leads for

developing world diseases. J. Comb. Chem. 11, 3–13.

[24] Scott, W. L., Alsina, J., Audu, C. O., Babaev, E., Cook, L., Dage, J. L.,

Goodwin, L. A., Martynow, J. G., Matosiuk, D., Royo, M., Smith, J. G.,

Strong, A. T., Wickizer, K., Woerly, E. M., Zhou, Z. and O’Donnell, M. J.

(2009) Distributed drug discovery, part 2: Global rehearsal of alkylating

agents for the synthesis of resin-bound unnatural amino acids and vir-

tual D3 catalog construction. J. Comb. Chem. 11, 14–33.

[25] Dillner, D. K., Ferrante, R. F., Fitzgerald, J. P. and Schroeder, M. J.

(2011) Integrated laboratories: Laying the foundation for undergraduate

research experiences. J. Chem. Educ. 88, 1623–1629.

[26] Latch, D. E., Whitlow, W. L. and Alaimo, P. J. (2012) Science education

and civic engagement: The next level ACS symposium series. American

Chemical Society, Washington, DC, pp 17–30.

[27] Rabago Smith, M., McAllister, R., Newkirk, K., Basing, A. and Wang, L.

(2012) Development of an interdisciplinary experimental series for the

laboratory courses of cell and molecular biology and advance inorganic

chemistry. J. Chem. Educ. 89, 150–155.

[28] Wells, G. and Haaf, M. (2013) Investigating art objects through collabo-

rative student research projects in an undergraduate chemistry and art

course. J. Chem. Educ. 90, 1616–1621.

[29] Ross, C. A. and Poirier, M. A. (2004) Protein aggregation and neurode-

generative disease. Nat. Med. 10, S10–S17.

[30] Labbadia, J. and Morimoto, R. I. (2013) Huntington’s disease: Underly-

ing molecular mechanisms and emerging concepts. Trends Biochem.

Sci. 38, 378–385.

[31] McGowan, D. P., Van Roon-Mom, W., Holloway, H., Bates, G. P.,

Mangiarini, L., Cooper, G. J., Faull, R. L. and Snell, R. G. (200) Amyloid-

like inclusions in Huntington’s disease. Neuroscience 100, 677–680.

[32] Bodner, R. A., Outeiro, T. F., Altmann, S., Maxwell, M. M., Cho, S. H.,

Hyman, B. T., McLean, P. J., Young, A. B., Housman, D. E. and

Kazantsev, A. G. (2006) Pharmacological promotion of inclusion forma-

tion: A therapeutic approach for Huntington’s and Parkinson’s diseases.

Proc. Natl. Acad. Sci. 103, 4246–4251.

[33] Pittman, D. (2010) Amyloid’s functions expand. Chem. Eng. News 88,

29–30.

[34] Soscia, S. J., Kirby, J. E., Washicosky, K. J., Tucker, S. M., Ingelsson,

M., Hyman, B., Burton, M. A., Goldstein, L. E., Duong, S., Tanzi, R. E.

and Moir, R. D. (2010) The Alzheimer’s disease-associated amyloid b-

protein is an antimicrobial peptide. PLoS One 5, e9505.

[35] Zhang, X., Smith, D. L., Meriin, A. B., Engemann, S., Russel, D. E.,

Roark, M., Washington, S. L., Maxwell, M. M., Marsh, J. L., Thompson,

L. M., Wanker, E. E., Young, A. B., Housman, D. E., Bates, G. P.,

Sherman, M. Y. and Kazantsev, A. G. (2005) A potent small molecule

inhibits polyglutamine aggregation in Huntington’s disease neurons

and suppresses neurodegeneration in vivo. Proc. Natl. Acad. Sci. 102,

892–897.

[36] Herbst, M. and Wanker, E. E. (2006) Therapeutic approaches to polyglut-

amine diseases: Combating protein misfolding and aggregation. Curr.

Pharm. Des. 12, 2543–2555.

[37] Lanning, J. D., Hawk, A. J., Derryberry, J. and Meredith, S. C. (2010)

Chaperone-like N-methyl peptide inhibitors of polyglutamine aggrega-

tion. Biochemistry 49, 7108–7118.

[38] Perutz, M. (1995) Polar zippers: Their role in human disease. Pharm.

Acta Helv. 69, 213–224.

[39] Hoffner, G. and Dijan, P. (2002) Protein aggregation in Huntington’s dis-

ease. Biochimie 84, 273–278.

[40] Krishnamurthy, V. M. E., Estroff, L. A. and Whitesides, G. M., in Jahnke,

W. E., Erlanson, D. A., Eds. (2006) Fragment-based Approaches in Drug

Discovery, 1st ed., Wiley-VCH, Weinheim, pp. 11–53.

[41] Strong, L. E. and Kiessling, L. L. (1999) A general synthetic route to

defined, biologically active multivalent arrays. J. Am. Chem. Soc. 121,

6193–6196.

[42] Puffer, E. B., Pontrello, J. K., Hollenbeck, J. J., Kink, J. A. and Kiessling,

L. L. (2007) Activating B cell signaling with defined multivalent ligands.

ACS Chem. Biol. 2, 252–262.

[43] Nagai, Y., Tucker, T., Ren, H., Kenan, D. J., Henderson, B. S., Keene, J.

D., Strittmatter, W. J. and Burke, J. R. (2000) Inhibition of polyglutamine

protein aggregation and cell death by novel peptides identified by

phage display screening. J. Biol. Chem. 275, 10437–10442.

[44] Ren, H., Nagai, Y., Tucker, T., Strittmatter, W. J. and Burke, J. R. (2001)

Amino acid sequence requirements of peptides that inhibit polyglut-

amine–protein aggregation and cell death. Biochem. Biophys. Res.

Commun. 288, 703–710.

[45] Nagai, Y., Fujikake, N., Ohno, K., Higashiyama, H., Popiel, H. A.,

Rahadian, J., Yamaguchi, M., Strittmatter, W. J., Burke, J. R. and Toda,

T. (2003) Prevention of polyglutamine oligomerization and neurodegen-

eration by the peptide inhibitor QBP1 in Drosophila. Hum. Mol. Genet.

12, 1253–1260.

[46] The Nobel Prize in Chemistry. (2005). http://www.nobelprize.org/nobel_

prizes/chemistry/laureates/2005/accessed August 2014.

[47] O’Nuallain, B., Thakur, A. K., Williams, A. D., Bhattacharyya, A. M.,

Chen, S., Thiagarajan, G. and Wetzel, R. (2006) Kinetics and thermody-

namics of amyloid assembly using a high-performance liquid

chromatography-based sedimentation assay. Methods Enzymol. 413,

34–74.

[48] Kazantsev, A., Walker, H. A., Slepko, N., Bear, J. E., Preisinger, E.,

Steffan, J. S., Zhu, Y. Z., Gertler, F. B., Housman, D. E., Marsh, J. L. and

Thompson, L. M. (2002) A bivalent Huntingtin binding peptide sup-

presses polyglutamine aggregation and pathogenesis in Drosophila.

Nat. Genet. 30, 367–376.



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