Electronic Publishing as a Course Context for a Capstone Project on Protein Design
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The Protein Design Project is the highlight of the senior undergraduate Protein and Nucleic Acid Structure course at the University of Guelph in Guelph, Ontario, Canada. In this project, students apply problem-solving skills while working in pairs to design a zinc finger protein intended to bind to a specific sequence of DNA and act as a possible therapeutic. Problem-solving skills are critical throughout the exercise as the students define what they want their protein to do and which design elements they will include to achieve their goals. The students then report the design of their proteins and the justification of their design elements. Manuscripts are prepared and submitted using a Web-based tool that handles the administration of submission, peer review, revision, grade assignment, and correspondence with authors. Through this process students gain direct experience with the process of scientific publishing using electronic submission, review, and revision, and learn valuable lessons regarding the emotional aspects of publishing in science.
Keywords: electronic publishing, problem-solving, manuscript preparation, peer review, electronic correspondence, scientific writing.
Undergraduate science curricula typically emphasize the scientific method, but fall short when it comes to teaching the final step: dissemination of new knowledge through scientific publishing. Given the important link between publication and success in science, it is important that undergraduate students become familiar with the tasks involved in the process of publishing a scientific article today, including the experience of employing electronic submission and revision tools.
Providing undergraduate students with hands-on experiences that reflect real situations in science equips them to be future researchers and leaders. This report deals with efforts to integrate problem-solving skills and experience with scientific publishing in a senior undergraduate biochemistry course at the University of Guelph, where we use a 12-week semester system. The Molecular and Cellular Biology Department at Guelph houses researchers focusing on biochemistry, microbiology, molecular biology, genetics, and plant biotechnology and hence its undergraduate programs are quite diverse. Students enrolled in the biochemistry or molecular biology and genetics programs learn a solid base in protein structure and function through their introductory biochemistry and junior biochemistry courses. Upon entry into the senior Protein and Nucleic Acid Structure course, students have the foundation to grasp the concepts of protein folding and to tackle the Protein Design Project described here.
The Protein Design Project is arguably the most difficult project my students will complete in their undergraduate education, representing a capstone experience in biochemistry that integrates many concepts and skills. As part of this project, students must collaborate in pairs to design a zinc-finger protein that will specifically bind to DNA involved in the development of disease and act as a possible therapeutic. They must research the target genes and how zinc fingers can be designed. Then the student authors design a protein, justify its design elements, analyze the protein sequence, and generate a manuscript describing all this in detail. This manuscript is submitted to a virtual journal created for the class, Fold, named to reflect the central problem in protein science and the fact that the highest impact journals in the molecular sciences today have single-word titles. Manuscripts are reviewed by fellow students and revised before final submission and evaluation. All submission and reviews are handled by a Web object called the Fold Submission Tool that gives the students the experience of electronic submission of manuscripts, a process that is now the norm in the molecular life sciences.
Another underlying theme in the Protein and Nucleic Acid Structure course is relating what it is like to be a molecular life scientist. In completing the Protein Design Project, my students experience first hand the trials and tribulations of scientific publishing, including the pleasures and difficulties of working in teams, and writing cover letters. Through this multifaceted experience, my students gain a better perspective on the realities of science today and can make better decisions regarding their own futures.
Materials and Methods
There are two main themes associated with this project: science as a process (the flow of information), and the application of knowledge to design a novel protein with a specific function. The goals of the project are to:
- use problem-solving skills to design a novel protein;
- acquire knowledge of Web-based bioinformatics tools for the design and analysis of de novo protein sequences;
- gain experience in scientific writing;
- work collaboratively during the researching, designing, and writing processes;
- be involved in the process of scientific manuscript preparation, submission, review, revision and publication; and
- gain experience with electronic submission and peer review and revision.
Personnel and Web-based Tools
The instructor, who becomes the editor-in-chief of the virtual journal to which the students submit their manuscripts, alone administers the entire Protein Design Project. With growing class sizes, the development of a Web-based submission tool, described below, has greatly increased the efficiency with which the project can be administered. One support person who deals with the submission tool and the database associated with it is also vital. With larger class sizes, support for the assessment of the final manuscripts may be required.
Students are introduced to a version of the Osborn / Parnes creative problem solving process, (1) providing them with the structure into which the course content related to protein structure and bioinformatics falls, and provides a real context for that content. As a result, there is less emphasis on memorizing content and more emphasis on seeing how that content fits into the bigger picture of the predominant problem in protein science today: How do proteins fold? Not only do students see how problem solving applies to the field of protein folding, they apply the steps of problem solving to the Protein Design Project, where the students use each step to complete the project.
Protein Design Project
In this project, students work in pairs to design a DNA-binding protein. I allowed students to select their own partners first, and I paired the remaining. Scientists need to choose collaborators, and this enables my students to learn the value of being a good collaborator or of choosing a collaborator wisely. Interestingly, the self-selected and assigned groups do equally well on their papers.” The outline for the project, guidance aimed at providing some structure to the manuscript that students prepare, and advice on how to peer review, are posted on the server at the University of Guelph.
Problem Finding: The students must first define the problem to be solved, based on some general directions. Problems I have chosen focus on diseases in which changes in DNA affect the amount of normal protein being made; these changes are called non-coding mutations. In the past, I have employed the maspin or phospholamban genes in breast cancer or heart disease development, respectively.
As part of this problem, students must consider additional details, such as how to target a specific sequence in the human genome without affecting other genes. Moreover, no two consecutive zinc-finger domains may be 65% identical or 80% homologous with known proteins found in the protein database, so students cannot simply take a natural protein, make the necessary substitutions, and arrive at their sequence. This requirement forces students to make design decisions based on their knowledge of amino acids and protein structure.
Assumption Finding: The fundamental assumption for this project is that binding to the promoter region of a target gene by the designed DNA binding protein will affect its ability to be transcribed. This is an assumption that can be discussed by the students as part of their assignment, but for the most part this assumption has to be accepted for the students to proceed.
Fact Finding: The concepts of DNA binding proteins and specific disease development require further investigation to provide the students with the facts to be able to solve the problem.
Students are told that there are published rules for the design of proteins to bind to specific DNA sequences (2) (Figure 1). Included in these rules is the need for protein linkers between designed binding domains (3) (4) (5, 6).
Solution Finding: Students must first decide which DNA sequence their protein will recognize. This decision involves balancing the limitations of DNA binding by zinc-finger domains with potential sites on the gene being targeted and the probability that the target DNA sequence is unique in the human genome.
Once the target DNA sequence is chosen, designing the protein sequence to bind to that sequence is relatively simple, providing the rules of zinc finger domain design are followed correctly.
Verification Finding: Once the students have designed a protein, they analyze their designed protein sequence using bioinformatics tools to explain any discrepancies or structural features. Students are asked to perform a number of bioinformatics analyses on their protein design and produce a theoretical structure of their designed proteins. Finally, the students are asked to critically think about the overall problem and are asked to answer the question, “Do you think your design will solve the problem?”
Using Reference Tools
As part of the first assignment, students are introduced to RefWorks, a subscription-based online reference manager tool available to all University of Guelph students, and they use it to organize their information.
To guide the reading required for the project, I provide an on-line help corner containing eight papers that deal with topics directly related to the project (Table 1). An informative annotated bibliography that includes three references that will be used in the protein design project is required halfway through the course to motivate groups to meet and begin reading for the project. Of these three referenced articles, only one can be from the “Help Corner” and at least one article must deal with the maspin protein or with zinc fingers.
The format for the annotated bibliography is relatively simple: students use the reference style of the Proceedings of the National Academy of Science USA (PNAS) and then write a paragraph or two explaining the purpose or hypothesis of the paper and the findings that are of most interest or applicable to the protein design project.
The Fold Submission Tool: A Web-based submission tool.
All of the documents related to the protein design project are handled through the Fold Submission Tool (FST). This tool was developed with the cooperation of Teaching Support Services at the University of Guelph.
FST provides students with an experience that is relevant to scientists today: electronic preparation and submission of documents to a journal’s server. In this case, the journal is Fold, a virtual journal created just for this course. FST is designed to reflect electronic scientific journals today and, as such, could be employed by a real scientific journal to manage submissions and peer review before final evaluation and production of published articles.
Rather than administering all of the documents manually, including cutting and pasting an enormous number of form-letter style e-mails, I can use FST to save all submissions and cover letters in a central database on the local ColdFusion server. All confirmation e-mail and other letter-based communications are handled through FST. Moreover, the entire review process, complete with comments and numerical score tabulation, for both the student reviewers and the final evaluation by the editor-in-chief, are handled through FST. It has become an integral part of the Protein Design Project, as it permits the administration of this intensive course to large classes. A flow chart of the activities involved in the Protein Design Project is presented in Figure 2.
First Submission: Each group uploads its manuscript and a cover letter that outlines the main points in the paper and requests that the manuscript be reviewed. Importantly, each cover letter must contain a paragraph outlining the contributions of the authors to the manuscript that is agreed upon by both authors. Cover pages for the manuscripts are not included with the initial submission, so that the student authors’ names do not appear anywhere on the manuscript. To overcome computer platform differences, each manuscript must be converted to a PDF file before being uploaded to FST. Thus, students become familiar with PDF file conversion tools available on the Web. Upon receiving both of these submissions, FST automatically sends a confirmation e-mail to the authors stating that their submissions have been received.
Peer Review: FST automatically assigns two peer reviewers—students in the class, chosen randomly except that they are not collaborators in this project—to each submitted manuscript and sends a form e-mail and a copy of the manuscript to each reviewer requesting that they review it. The message provides instructions on how to review the paper using FST. Since the authors’ names are not included on the manuscript, the student reviewers do not know who wrote the manuscript that they are reviewing.
Each reviewer then reads the manuscript and provides feedback. When students access FST, the comments they provide are automatically linked to the papers that they review, along with their overall numerical assessments of the manuscripts. FST permits students to input comments and save them as they go, so that they can complete the review over several sessions.
Editoral Assessment of Reviews: As editor, I read each review to ensure that there are no inflammatory comments and to assess the quality of the review. I have the ability to edit the review in FST before it is returned to the authors, and I can provide comments to the reviewer in a separate text box. When the editorial assessment is complete, the review is officially submitted to FST. Part of the review received by the student authors is a standard cover letter from the editor-in-chief (me) that I modify to suit the specific papers. In these letters, the major comments of the reviewers are highlighted and the authors are reminded of the deadlines for submission of the final manuscript.
Manuscript Revision: Each review is immediately available for the student authors to see through their FST Web pages. With reviews in hand, the students make revisions to their manuscripts and address the concerns of the reviewers in a cover letter. Depending on the quality of the initial submission, these revisions can be minor or complete overhauls. Some groups have had to re-evaluate their entire designs based on the astute observations of some of their peer reviewers.
Final Submission and Assessment: When the final version of the manuscript is ready, the student authors again use FST to submit their manuscript and final cover letters in PDF format. At this point, the editorial office (me) performs its assessment using the same review tool used by the peer reviewers. The comments and editor’s assessment are automatically updated on the student’s FST page when the editor’s review is officially submitted.
Time Use Data Collection: At the time of submission, each group is requested to complete a form that tracks the number of hours employed to complete different tasks associated with the Protein Design Project. I have used this data in the past to understand how my students organize their time to complete this project.
Acceptance or Rejection: Letters of acceptance and rejection are sent through FST. Standard letters are modified to suit the specific paper, highlighting strengths and weaknesses and providing encouragement for future work. The papers that are accepted are based solely on the assessment of the reviewers and the editor. Depending on the class size, I accept three or four papers for publication.
Publication: Accepted manuscripts are formatted for publication in our online journal, Fold. A cover page is generated and the published papers are uploaded to a Web page that is accessible through the course Web page (Figure 3). In this way, others can view the students’ work and they can point their friends and family to their “published” work. Although Fold is published online, access to the journal and the articles is restricted to those in the course to avoid plagiarism, as the research topics are employed with multiple cohorts of students. This mirrors the situation with many scientific electronic journals that require registration and a password to access the published articles, even though the justification (remuneration vs. restricted access) is much different.
Assessment of the Project: The students’ overall grade for the protein design project is a combination of several tasks that are assessed over the course of the semester: annotated bibliography: (10%), doing peer review (10%), time data sheet (5%), cover letter (5%), peer review assessments (just over 10% each), and final editorial assessment (just under 50%).
Students may be penalized for lazy or bad science. There is a 20% penalty from the editorial assessment for a design that includes any stretch of two consecutive zinc finger domains that is more than 60% identical and 85% homologous with any protein in the protein database as assessed by a BLAST search. This 20% penalty is meant to force students to include de novo design of proteins using knowledge of the properties of amino acids acquired during the course. Simply taking a natural zinc finger protein and modifying the DNA binding amino acids is not enough; students must make other changes. The other penalty is an approximately 5% penalty from the editorial assessment for including a major flaw by designing a zinc finger protein in the incorrect orientation. In these cases, the students have applied the DNA recognition rules correctly, but have failed to recognize that zinc finger proteins bind to DNA with a specific orientation. As a result, the design concept is correct, but the final design will never work as intended, thereby defeating the design goals of the project.
Assessment of Impact: To measure changes in experience, anonymous entrance and exit surveys were administered to students (Table 2). Not all questions were answered by all students, resulting in different totals for the various questions in each cohort. Owing to student attendance on the day of the survey or students withdrawing from the course, the number of respondents of the entrance and exit surveys was different. The intention of the entrance survey is to gauge the previous experience of the students with scientific literature and the scientific publishing process. The exit survey is intended to revisit some of the concepts covered on the entrance survey and allow the students to provide direct feedback regarding the best and worst parts of the Protein Design Project. The entrance and exit surveys are not exactly the same and are meant to measure general knowledge and experience before and after the Protein Design Project. Part of the exit survey includes a survey of student attitudes about the Protein Design Project and is discussed in the following section (Table 3).
Results and Discussion
By completing the Protein Design Project, students experience a problem-based learning process designed to teach the fundamentals of zinc-finger domain structure and how zinc-finger proteins can be engineered to target specific DNA sequences. While this information is part of the course content, it is not taught in class. It is hoped that by learning it on their own and applying it to a real situation, students will better retain the knowledge.
In addition, through their research into the maspin protein and how zinc-finger proteins may be used as a therapeutic, students become more aware of the connections between disease and protein structure and function. While my students design proteins that are hypothetical, there are biotech companies such as Achillon Pharmaceuticals and Sangamo BioSciences that focus on the design and production of zinc-finger proteins as therapeutics. Through in-class presentations about these companies, my students also make the connection between their knowledge and the biotechnology sector.
Scientific Publishing: Measures of Attitudes and Direct Feedback
While many undergraduate science curricula successfully emphasize the scientific method, they often overlook teaching the final step of the dissemination of new knowledge. The entrance survey showed that my students had a limited knowledge of the details of scientific publishing; while some knew what the roles of a primary and senior author are, far fewer knew what a corresponding author is or to whom manuscripts are sent for consideration for publication (Table 2). A very limited number of students recognized references as an essential section of a paper, and no one had an idea of the costs involved in publishing papers or that there may be costs involved at all. In short, while my students have read primary literature by the time they reach my course, they have very limited understanding of how these papers were published.
The exit survey revisits some of the concepts covered on the entrance survey and allows the students to provide direct feedback regarding the best and worst parts of the protein design project (Table 2). In contrast to the beginning of the course, nearly all of my students knew that they should submit a manuscript to the editor of a journal, and almost as many realized that a cover letter should accompany that manuscript upon submission. Almost every student knew the chronological order of events for getting a paper published. Based on these findings, my objective of providing the experience of the process of scientific article publication has been met through the Protein Design Project.
I also ask my students to provide feedback regarding their attitudes to the protein design project (Table 3). These are 25 attitude statements that the students agree or disagree with on a scale of 1-5 with 1 strongly disagreeing, 3 neutral, and 5 strongly agreeing. There are eight categories of questions that are shuffled in the survey. Analysis of the results reveals excellent attitude indicators in each category.
The highest overall attitude score (4.28) indicated that the project helped students link protein structure and function with disease, indicating depth and breadth of understanding. Other strong indicators speak to the students’ acquisition of research and analytical skills related to the project, and their appreciation of the pros and cons of using electronic submission. My students also responded favorably to statements relating to their ability to write a manuscript in the future and to act as peer reviewers, indicating positive attitudes towards literacy, forms of inquiry, and moral maturity.
In addition, my students responded negatively to the idea that they would perform better working alone, showing an appreciation for collaboration that will be essential for future work. Similarly, students disagreed that working with electronic documents takes more time than working with paper copies, another reality of science that will serve them well in the future. My students also responded negatively to the idea that the Protein Design Project was too hard for the level of this course.
Finally, I asked my students to tell me anonymously what was the best and worst part of the protein design project (Box 1). I considered these comments very seriously and adapted some recommendations from the 2004 cohort for following cohorts. Most significantly, I introduced the requirement for a mid-semester annotated bibliography for the project to guide the students to do the research for the project and in this way avoid groups attempting to complete the entire project in the last week before the deadline. I also ensured that the referencing style I expected in the manuscript was one that is available through RefWorks.
In general, these comments indicated that the project took a lot of time and effort and the students wanted the weighting for the project within the context of the course to reflect that. To begin to address this concern, the value of the project was increased in 2005 to 35% from 30%. I am considering increasing this percentage in the future.
On the positive side of things, many students found that the project was a fantastic opportunity to do something “real,” with direct applications both in the science they were doing and in the process of scientific writing and publishing. They thought it was relevant and would prepare them for the future. My students accepted the standard publishing paradigm of peer review and revision without protest. They accepted the concept that within the realm of scientific endeavor, the number of other scientists who can provide insightful and effective reviews of the details of another’s work is very limited, and hence review by a peer is a reasonable method.
Disciplinarian and Emotional Lessons
Electronic Publishing: Apart from acquiring the knowledge to complete the Protein Design Project, there are many emotional lessons my students faced related to learning to be a molecular life scientist. All documents are electronic to reflect the powerful influence of the Internet on scientific publishing today. This affords the students the luxury of producing big, high-quality figures (commonly on black backgrounds) without the fear of having to print the document on their ink-jet printer and using their resources.
The students learn how to convert their documents to PDF files for viewing across platforms. Without access to the full version of Acrobat, some students struggled with finding on-line services that converted their documents to PDF files for free, but through collaboration between groups several solutions were found.
For the most part, students are familiar and comfortable with working with electronic documents. As a result, my undergraduate students had no bias against electronic publication. For the most part, undergraduate students are now accessing and reading scientific journal articles almost exclusively online, so they do not perceive a difference between electronic publishing and traditional publishing. The extension of this attitude is a natural acceptance of electronic processes involved with publishing, including the peer review and revision processes. Our future scientists will very rarely access printed forms of scientific literature, so learning about electronic publishing as part of their undergraduate experience is formative.
Collaborative Work: For many, this is the first time that they have worked closely with another student to produce a term project. The experience of collaboration on a major project is important for my students as almost all scientific endeavor today is performed within teams. For example, the total number of research articles published in the top-ranked journal Cell between 1996-2005 was 2,733; of these, the number of papers written by single authors is 14 (0.5%).
My students experience the spectrum of problems and advantages with collaboration during this project that reflect real situations. For some, the workload is not equally shared, for others each collaborator has different goals or expectations for the project. Still others learn hard lessons regarding taking joint responsibility for parts of the project that they did not complete first-hand. To overcome problems with sharing the work, each group must write a paragraph as part of their first cover letter describing the work that each collaborator performed. Both parties sign this letter, and so they must agree on the wording of that statement.
Other groups experience the joys of bouncing ideas off another expert and building on another’s creative ideas. Some enjoy overcoming challenges with another person, receiving feedback and encouragement to continue with a difficult and multifaceted task. For the most part, my students appreciate working in pairs to divide the labor for the project. In addition, a surprising number of my students do not know each other by name, although they have been in most of their classes together throughout their university education, and this project gives some of them the opportunity to become acquainted with each other and make friends.
Experiencing Peer Review: Receiving feedback from peer reviewers also brings forth a complex range of feelings for the student authors. Knowing that their peers have been through the same experience and have made similar efforts to complete the project make the reviewers somewhat sympathetic to the authors of most manuscripts, but for the most part the reviewers have high standards for their fellow classmates. Some comments from reviewers are welcomed and appreciated, while others are not. It is a valuable experience for my students to understand these feelings and discuss them. All scientists who go through the peer review process for papers and grants have to come to terms with criticism from others, good or bad.
My students are accustomed to receiving feedback from professors, but not from others at the same level as themselves. I tell my students that in science there are typically very few people in the world who have the expertise to effectively review a detailed manuscript, and so we all have to learn to be diplomatic in our responses to reviewers who may seem inadequate. This is why it is so important to learn to write very clearly and concisely so that others can read and understand your work. Too often students write with the attitude that the professor will know what they mean, but when they are faced with reviewers at the same level, they realize that they must write more effectively.
Handling Rejection: Students submit a cover page either requesting consideration of the manuscript in the first instance or responding to the comments of the reviewers following revision. They also receive an acceptance or rejection letter from the journal following final consideration by the editor. One question I always ask my students is: what does it feel like to receive a rejection letter after you have spent so much time and effort on a difficult project? Scientists worldwide feel the emotions that are raised upon receiving a rejection letter, and I tell my students that they are not alone. I also tell my students that they must learn to deal with publications-rejection letters, as they are relatively common. It is important to stress to my students that the process of review is an extension of the scientific method, in which other scientists in the field analyze the data and make suggestions or comments. In this way, the peer review process can be used as a means to improve the work, however painful it might be to receive the comments.
Accepted papers are formatted in the style of the Fold journal, converted to PDF files, and the issue of Fold for that class is published online (I design the covers) for the class to see. Permission of student authors is obtained for the online publication of their work and for the use of their work in demonstrations of the Protein Design Project and the Fold publication process.
Wrap-up Session: During the last day of class, I have a wrap-up session with the students to cover the emotional aspects of the project and the protein designs that were created by the class members. Since all the groups had the same design target, the designed proteins generally have very similar sequences. Proteins with similar sequences can be analyzed with phylogenetic tools to determine the level of relatedness between the sequences (tools such as CLUSTALW, for example). In this way, I present to the class the sequence relationships of the proteins that they designed and point out common features and some of the more unique design elements that some groups introduced. Students usually enjoy seeing the different strategies and which proteins are most closely related and why. In general, the designs fall into two categories: those with three zinc fingers and those with six zinc fingers. Other obvious features are the position of nuclear localization signals (N- vs. C-terminal) and whether transcriptional activation domains have been fused to the protein. As iterations of the project go forward, the database of designed sequences will grow. My students enjoy seeing how their sequences compare with the legacy of designs that have been created in their year and other years combined.
Through the Protein Design Project, students go through the entire protein solving strategy to solve a specific problem. The amount of guidance given to students is intentionally limited so that students learn to solve problems themselves. Some students thrive in the atmosphere of creativity and self-directed learning, while others are frustrated by the lack of the strict guidelines that they have come to expect in their education. I receive feedback that speaks to both of these points of view. Moreover, my goals of giving my students the experience of being molecular life scientists are being met. My students are more aware of what science is really like, apart from the standard laboratory experiences they have through their undergraduate courses. I think this course empowers them to make better decisions regarding their futures in science.
Parnes, S. J., et al. (1977) Guide to creative action, Scribners, New York.
Sera, T., and Uranga, C. (2002) Biochemistry 41, 7074-7081. [doi: 10.1021/bi020095c]
Kim, J. S., and Pabo, C. O. (1998) Proc Natl Acad Sci U S A 95, 2812-2817. [doi: 10.1073/pnas.95.6.2812]
Coleman, J. E. (1992) Annu Rev Biochem 61, 897-946. [doi: 10.1146/annurev.bi.61.070192.004341]
Nagaoka, M., et al. (2001) Biochem Biophys Res Commun 282, 1001-1007. [doi: 10.1006/bbrc.2001.4672]
Nagaoka, M., et al. (2001) Biochemistry 40, 2932-2941.
Box 1: Student Comments about the Protein Design Project
The relevance of the project!! So good to be doing real(istic) and valuable assignments. Also it was really good working together to write the paper, discussing ideas, etc.And being reviewed / doing reviews with people at the same level was great. It did take a long time, but was definitely worth it. By far one of the best projects in my time here! (Next time, please use a reference style that is available in Refworks)
Overall the project was fun, and something very different from all other university projects / assignments that I have done in the 4 years here. Thank you. Great project idea, especially to prepare for future research within the field of science.
A lot of time was spent on it. I’ve spent far less time on exams worth 30% and come out with a good grade. Although, what I did learn in doing this assignment, it looks like that knowledge will stick with me unlike after exams when you forget almost immediately. Also I’m actually proud of this project (despite major design flaws) and it’s been a while since I could say that about a school project.
This was fun! The project definitely built on concepts from class and was a good opportunity to learn about and use computer programs relevant to this field. Creativity was encouraged, which is appreciated in a 4th year science course. I really feel I learned a lot through this project.
First project that I feel like I am almost 100% sure about the subject matter. The size of the project is what made it good; there was a very good feeling of accomplishment at the end.
The actual design of a protein. Most papers at this level (term papers) consist of research, then compilation of research into a paper format. This project included research, actual design and analysis,
as well as compilation of ideas in paper format. This extra step was the best part.
It was very interesting. It was great to see the real-life applications of what we learn in the classroom. It was nice to have independence, but also some guidance if it was asked for.
Working in a group and design ZFP. That was a lot of fun!
I loved designing the protein and having to consider the myriad of variables required to produce a single coherent product.
The project was NOT just make busy work. The project was a great introduction into the world of scientific writing.
You learn exactly what the real-world is like.
Table 1: Help Corner Articles
Maspin and Breast Cancer
- Costello JF, Plass C. Methylation matters. J Med Genet. 2001 May;38(5):285-303.
- Futscher BW, Oshiro MM, Wozniak RJ, Holtan N, Hanigan CL, Duan H, Domann FE. Role for DNA methylation in the control of cell type specific maspin expression. Nat Genet. 2002 Jun;31(2):175-9.
- Domann FE, Futscher BW. Editorial: maspin as a molecular target for cancer therapy. J Urol. 2003 Mar;169(3):1162-4.
Phospholamban and Heart Disease
- Minamisawa S, Sato Y, Tatsuguchi Y, Fujino T, Imamura S, Uetsuka Y, Nakazawa M, Matsuoka M. Mutation of the phospholamban promoter associated with hypertrophic cardiomyopathy. Biochem Biophys Res Commun. 2003. 304:1–4.
- MacLennan DH, Kranias EG. Phospholamban: a crucial regulator of cardiac contractility. Nat Rev Mol Cell Biol. 2003. 4:566-77.
- Haghighi K, Gregory KN, Kranias EG. Sarcoplasmic reticulum Ca-ATPase-phospholamban interactions and dilated cardiomyopathy. Biochem Biophys Res Commun. 2004. 322:1214-22.
- Hoshijima M. Gene therapy targeted at calcium handling as an approach to the treatment of heart failure. Pharmacol Ther. 2005. 105:211-28.
Zinc Finger Protein Design
- Choo Y, Isalan M. Advances in zinc finger engineering. Curr Opin Struct Biol. 2000. 10:411–416.
- Pabo CO, Peisach E, Grant RA. Design and selection of novel Cys2His2 zinc finger proteins. Annu. Rev. Biochem. 2001. 70:313–40.
- Sera T, Uranga C. Rational design of artificial zinc-finger proteins using a nondegenerate recognition code table. Biochemistry 2002. 41:7074-7081.
- Beerli RR, Barbas CF 3rd. Engineering polydactyl zinc-finger transcription factors. Nat Biotechnol. 2002 Feb;20 (2):135-41.
Table 2: Entrance / Exit Survey Results
✔ : correct; ✕ : incorrect/no answer. Surveys were anonymous and not all questions were answered by all students, resulting in different totals for the various questions in each cohort. Owing to student attendance on the day of the survey or withdrawals from the course, the number of respondents of the entrance and exit surveys are different.
|Fall 2004||Fall 2005||Fall 2006||Overall|
|what is a primary author?||14||9||12||23||18||16||44||48|
|what is a senior author?||14||9||8||28||11||23||33||47|
|corresponding author role?||3||19||6||29||2||32||11||81|
|sections of an article?||0||22||0||35||2||32||2||90|
|what is a half-tone figure?||1||23||1||34||0||34||2||90|
|who do you send manuscripts to?||10||14||5||30||7||37||22||68|
|how much $ for colour figures?||no clue|
|who do you send manuscripts to?||17||1||38||0||16||2||71||3|
|chronological order of events?||18||0||37||1||15||3||70||4|
|what else is submitted? (cvr ltr)||18||0||36||2||16||2||70||4|
|Fall 2004||Fall 2005||Fall 2006||All-time|
|1. Relating to coursework||a. The project built on concepts covered in class.||3.61||1.04||3.61||0.90||3.54||0.74||3.60||1.01|
|b. The project made me aware of the bigger picture of the topics we covered in class.||4.00||0.69||3.78||1.01||3.90||0.77||3.92||0.86|
|c. The project helped me to see a link between protein structure / function and disease.||4.28||0.67||4.39||0.69||4.28||0.64||4.28||0.67|
|2. Skills in research||a. The project built my confidence in researching new areas of interest.||4.17||0.79||3.89||0.78||4.10||0.82||3.94||0.81|
|b. The project helped me focus my reading to areas that were relevant to the topic at hand.||3.94||0.73||3.72||0.72||4.00||0.71||3.92||0.71|
|c. The project helped me distill the most important information from research articles.||4.11||0.83||3.89||0.61||4.14||0.64||4.02||0.67|
|3. Skills in writing||a. The project built my confidence in scientific writing.||3.72||0.83||3.89||0.68||3.86||0.83||3.82||0.76|
|b. I understand enough of the process to write a draft scientific manuscript for submission to a journal on work that I might do in the future.||3.94||0.87||4.00||0.70||3.89||0.88||3.81||0.80|
|c. I am now more aware of issues like plagiarism in science.||3.56||1.42||2.72||0.97||3.21||1.01||3.24||1.09|
|4. Skills in Design and Analysis||a. I feel confident that I could design a protein that would bind a specific 10 bp sequence.||3.94||0.73||4.22||1.02||3.76||1.09||3.87||0.99|
|b. I could analyze the secondary and tertiary structure of a given protein sequence.||4.11||1.37||4.28||0.81||4.28||0.84||4.18||0.95|
|c. The project built my confidence in producing good figures.||3.61||0.92||3.72||0.78||4.07||0.90||3.85||0.86|
|5. Skills in Publishing||a. I would feel confident reviewing another's work for a journal on topics that I know about.||4.17||0.71||3.89||0.76||3.79||0.94||3.85||0.82|
|b. I would be able to correspond with scientific journals regarding manuscript submissions and peer reviews.||4.00||0.69||3.72||0.81||3.54||0.74||3.69||0.78|
|6. Working in a Team||a. The project helped develop my teamwork skills.||3.72||1.27||3.56||0.89||3.69||0.84||3.65||0.96|
|b. I would have produced a better project if I had worked alone.||2.28||1.02||1.94||1.24||2.28||1.30||2.19||1.21|
|c. My partner and I communicated effectively regarding the planning and production of the project.||3.89||1.23||3.78||1.13||3.83||1.14||3.72||1.15|
|7. Electronic Submission||a. The project made me aware of technical issues regarding the production and submission of electronic documents.||3.94||1.00||4.11||0.87||3.86||0.71||3.95||0.84|
|b. Working with electronic documents took more time than hard copies.||2.44||1.34||2.00||1.14||2.31||1.07||2.33||1.15|
|c. I felt anxious about handing an assignment using email.||2.89||1.49||2.00||1.30||2.28||1.39||2.38||1.38|
|8. Attitudes||a. The project was too hard for the level of this course.||2.28||0.67||2.28||1.03||2.17||1.10||2.27||0.99|
|b. The project was fun.||3.78||0.88||3.61||1.13||3.38||1.12||3.52||1.08|
|c. The expectations for the project were clear.||3.89||1.08||3.67||1.10||3.72||0.96||3.64||1.05|
|d. The value of the project toward the final grade was too low.||2.83||1.15||2.78||1.07||3.59||1.21||3.85||0.86|
Figure 1. A. Cartoon of zinc finger domains from protein database file 1A1F.pdb showing amino acids coordinating the zinc ion and the four amino acids in the DNA recognition helix, numbered 6, 3, 2, and -1, relative to the start of the helix. Amino acids 6, 3, and -1 recognize three bases on one strand of the DNA double helix, while amino acid 2 recognizes the fourth base on the other strand. This fourth base is complementary to the first base recognized by the zinc finger domain that precedes it.
Figure 1. B. The nondegenerate DNA recognition code as determined by Sera and Ungara (2), used to design zinc finger proteins to bind to specific sequences of DNA.
Figure 2. Flow chart of activities involved in the Protein Design Project. At left are the tasks required; the middle column represents the different documents to be submitted at the times in the course indicated in the right column.
Figure 3: Covers of the issues of Fold for the three cohorts described in this article. The target protein for the project is listed below the covers.
From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
Address correspondence to: John F. Dawson, Department of Molecular and Cellular Biology, University of Guelph, Ontario, Canada, N1G 2W1; E-Mail:firstname.lastname@example.org.