Genome Science Education for Engineering Majors

Transcription

1 Genome Science Education for Engineering Majors Leslie Guadron 1, Alen M. Sajan 2, Olivia Plante 3, Stanley George 4, Yuying Gosser 5 1. Biomedical Engineering Junior, Peer-Leader, President of the Genomics and Bioinformatics Club, Biomedical Engineering Sophomore, Peer-Leader 3. Biomedical Engineering Sophomore, President of the Genomics and Bioinformatics Club, Chemical Engineering Junior, Secretary of the ASEE Student Chapter at CCNY 5. Faculty adviser of the ASEE Student Chapter at CCNY, Director of Undergraduate Research & Scholarships The Human Genome project has profoundly impacted modern research, and genome science has infused into many science and engineering disciplines. The computer-lab based bioinformatics course, which has an emphasis on genomics and protein structure, was developed under the HHMI science education grant and was approved by the college s School of Engineering as a technical elective course for Biomedical and Chemical Engineering majors in the Fall of In summer 2008, we joined the nation-wide Genomics Education Partnership (GEP) that provides a research project-gene annotation- and academic support for our bioinformatics course. The experimental classes have been conducted in different teaching settings: The Special Interest Group Genomics & Bioinformatics club- during the academic year, summer bioinformatics workshop for advanced high school students (6 weeks, Sci316), and the formal 3-credit course- Sci280 with pre-requisites Chem-103 and 104 or Bio-101 and 102. The lessons learned from our practice are: a) Engineering students are interested in the research topics in genome science. In all pilot classes, 45%-55% of attendees were engineering majors, including biomedical, chemical, electrical and environmental engineering, as well as computer science. b) To offer the genomics education course to engineering students, starting from freshmen and sophomores, it is necessary to start from the Central Dogma, and then introduce protein structure visualization and homology modeling. Through the project on protein structure analysis and modeling, the students learned to illustrate a protein function with its structure by using the Protein Databank and the Pubmed literature database, and the visualization tool Pymol. c) The gene annotation project provided a focus for our bioinformatics course. The students were engaging in responsive research, from identifying the exon coordinates to constructing a gene model, to the similarity searching, and from organizing the data table to writing a complete research report. The students became familiar with genomics vocabulary, the major databases, NCBI, Flybase, and EBI, and the basic tools of comparative genomics BLAST and CLUSTALW, and learned to think like a scientist, and recognize the uncertainty in research, i.e. the unique definitive answer may not exist. d) Genome science education outreach to advanced high school students is feasible. The HS students did an annotation project from one exon for each student (the 2008 summer class), to one gene for each student (the 2009 summer class), to one contig or one fosmid with multi genes and multi-isoform for a pair of students. We conclude that expanding genomics education to engineering and non-bio major students is to meet a demand and a challenge of current science and engineering education.

2 Introduction The Human Genome project has profoundly impacted modern research, and genome science has infused into many science and engineering disciplines. The bioinformatics course at The City College of New York (CCNY) is a unique experience on campus. What makes this course different is that it gives students an opportunity to complete a research project. The computer-lab based bioinformatics course, which has an emphasis on genomics and protein structure, was developed under the HHMI science education grant and was approved by the college s School of Engineering as a technical elective course for Biomedical and Chemical Engineering majors in the Fall of In summer 2008, we joined the nation-wide Genomics Education Partnership (GEP) that provides a research project-gene annotation- and academic support for our bioinformatics course. The most important thing about the course is that it challenges the traditional idea that genomics courses can only be successfully taught to students with what are considered the necessary prerequisites. One of the goals of the course is to provide its students with a basic understanding of the fundamentals of genomics. The course also provides students with an opportunity to complete an original research project. It has become clear that undergraduate research is important for students majoring in the sciences and engineering. Participating in research provides engineering students with many benefits. It helps students develop new skills and can clarify their career path. Most importantly, taking part in research teaches students to think in new and different ways. It is known that research benefits undergraduates, but many students never get the chance to complete or take part in a research project. Normally, a student will work in a lab over the summer. However, there are students that do not have their summers free and so they miss these summer opportunities. It may also be possible for a student to work in a professor s lab during the semester. The problem here is that these spots are limited. Professors can only have so many students in their labs. The students who are not lucky enough to get into a lab, either over the summer or during the semester, may graduate without any research experience at all! This is where the importance of classes like CCNY's Sci280 Genomics and Bioinformatics course is illustrated. It gives students a chance to reap the benefits of undergraduate research in an unconventional way. It also allows engineering students to gain basic knowledge of genomics. These components of the course allow the students to get a comprehensive understanding of genome science. How to Teach Genomics to Engineering Students In summer 2008, CCNY joined the nation-wide Genomics Education Partnership. The Sci280 course was established under this partnership and it was approved as an elective for chemical and biomedical engineering students starting in the Fall 2009 semester. The prerequisites for the course are either one year of general chemistry (Chem103 and 104) or one year of general biology (Bio101 and 102). The class meets once a week for 3 hours and 40 minutes on Fridays. Half of this time is allotted for lecture and the other half is for the students to work on their

3 projects. The two major assignments completed are the gene annotation project and the protein structure-function research project. It is essential to start the course with an overview of the Central Dogma of biology. This gives the engineering students a good foundation for the rest of the semester. It truly is necessary to start from this point because engineering students normally have not taken any biology courses in college. From there protein structure visualization and homology modeling are introduced. One of the projects to be completed is the gene annotation project. For this project, the students are assigned a contig, which is a segment of DNA on a chromosome that is tens of thousands of kilo base pairs in length. The students must discover which parts of their DNA segment are coding for proteins. This means that all of the different genes in the contig must be identified. Then the coordinates of every exon for every gene must be located and the data is organized in a table in order to construct a gene model. To accomplish this, the students must learn how to use a number of online databases. They are taught how to navigate flybase.org, which is a database that contains fruit fly sequences, and NCBI BLAST. BLAST is a tool that can find alignments between two different sequences. They also become familiar with Gene Record Finder, Expasy, EBI, Swiss Model Maker, ClustalW, which is used for homology modeling, and Gene Model Checker. The final step for completing the project is to fill out an annotation report. This is the formal report that will be submitted to the GEP. Once the annotation is finished, the students complete a project on one of the proteins that is encoded in their contig. The student must research the function of their protein. They need to make the connection between the function and structure of their protein. As part of this project, the students must learn how to use Pymol, which is a protein visualization tool. This program allows the students to download a model of their protein and highlight different areas to show the active sites or any other features of interest. Students also learn how to find journal articles in datbases, like Pubmed. Besides learning more about protein structure and function, the goal of this project is to teach students to read and extract information from journal articles and to present their newfound knowledge in the form of a Power Point Presentation. Outreach to High School Students It is plausible to implement this type of class for advanced high school students. Since 2005, bioinformatics courses have been offered to high school students in a six week long summer workshop (Sci316) to prepare them for majoring in science and engineering. The students have done well in the course, particularly in the gene annotation project. In summer of 2009, 11 high school students annotated eight different contigs/fosmids. Each student was able to annotate one isoform from every gene. In the summer of 2010, 16 students were able to annotate all isoforms

4 in 14 fosmids/contigs with an approximate passing rate of 80%. This proves that it is feasible to bring research-oriented genomics education to advanced high school students. How Does Genomic Knowledge Impact Engineering Students? Engineering students are willing to learn about genomics and bioinformatics. In the Sci820 course at CCNY and in all pilot classes, nearly half of all the enrolled students were engineering majors. 45% to 55% of the students were biomedical, chemical, electrical, and environmental engineering majors. The genomics and bio informatics class at City College is an asset to any engineering education. The class allows a student to participate in research and learn about a new subject. Many engineering students seldom take a biology course while in college simply because it is not a requirement. Nevertheless, having knowledge of biology is important and can open new doors for a person s career. Mechanical, electrical, and chemical engineers can all benefit from taking a course that teaches them about protein structure and gene annotation. They may even discover a new interest or career path. The gene annotation project requires that the student identify the coordinates of all the exons in their assigned genes. By doing so, the students learn a great deal about genetics and become familiar with genomics vocabulary. They also learn how to use some major online databases, like Flybase.org and NCBI BLAST. There are many online programs and databases that the students learn how to use throughout the semester. Another benefit that a student may gain from this course is the chance to participate in research. It is made clear to the students that their annotation project is considered original research. The location of the exons of the genes is something that the students themselves have discovered by using comparative genomics concept and evidence. They even have the chance to have an article published once they submit their annotation reports to the Genomics Education Partnership (GEP) at Washington University in St. Louis. This is really a great opportunity because having research experience is something that will make engineering students more competitive when applying to jobs or graduate school. Sometimes engineering students have difficulties making time for research during the semester. This course gives students a chance to complete a research project while keeping up with the rest of their classes during the semester. Engineering students will learn a lot of valuable and indispensible information by taking a genomics and bioinformatics course. Having an understanding of DNA, genetics, and proteins is as important as having some knowledge of basic chemistry principles. The analogy can be made between a genomics course and a general chemistry course. Many students are required to take a general chemistry course because of the importance of understanding the world around you. It may be that the student will not take any higher level

5 chemistry course or that they won t use this knowledge directly in their major. But it is important for them to understand chemistry because we encounter it every day. Students understand why ice floats in their drinks, or why soap can clean hair better than water alone, or that you shouldn t mix bleach and ammonia, and why we throw salt on the roads after a snowstorm. 1 These are things that we come to have an understanding of due to our knowledge of chemistry. The same importance can be attributed to a genomics course. The Sci280 course at City College hopes to instill this same sort of basic knowledge in its students. In the case of the engineering students who take the course, they are really learning this to enhance their general knowledge. They may never use this information in their future careers, but they will have an understanding of everyday occurrences. Many new technologies that involve genes raise concerns and cause debates because they impact our everyday lives. Some of the major issues related to genetics are the use of DNA evidence in criminal trials, genetically engineered food products, cloning, and genetic screening. 2 Engineers should be able to form informed opinions about these subjects because they will most likely encounter them in their lives. At some point, they may have to decide whether or not they will choose to eat genetically modified food. This course should provide them with enough knowledge so that they can look up information about how the food products are made and if they are possibly dangerous and, most importantly, understand the information. This would enable them to come to their own conclusions about the other controversial topics and any other new technologies that may arise in the future. This knowledge can also be applied to specific career paths for biomedical engineers (BME) and chemical engineers (ChemE). BME students may decide that they want to learn more about genomics so that they can eventually get into the field of genetic engineering. This type of elective course will help give them an advantage in that field because they will have a better understanding of the basics of the subject. The ChemE students may want to get involved in the field of biomaterials after taking the course. They would be better prepared than other engineers because they would have an understanding of genomics that is necessary. If having this knowledge is so important, than why not take a genomics course? The answer is that genomics courses require too many prerequisites. Engineering students do not have free space in their curriculum to take these prerequisite courses just to take a genomics class. The only prerequisites for Sci280 are Bio 101 and 102 or Chem103 and 104. The two chemistry courses are part of the engineering curriculum at CCNY to begin with, so there would be no need to take any extra courses. And because the class has been approved as a technical elective for chemical and biomedical engineers, they even get credits towards graduation. Engineers have done exceptionally well in the Sci280 course. It turns out that they can do just as well as biology students. This is most likely due to the fact that engineers have well developed

6 reasoning and problem solving skills. That may make it easier for them to learn the material and apply it to the gene annotation project. Conclusion The course fairly new, but so far we see that engineering students are successfully grasping the material. Not only that, but they were able to engage in responsive research. From constructing a gene model to writing a complete research report and making a PowerPoint presentation on protein structure-function, they became familiar with genomics vocabulary, major databases, and basic bioinformatics tools. We conclude that expanding genomics education to engineering and non-bio major students is to meet a demand and a challenge of current science and engineering education. Bibliography 1. Helmenstine, Anne Marie. "Chemistry Questions You Should Be Able to Answer." About.com:Chemistry. Web. 29 Sept < 2. Sartori, Marc B., and Carrie L. Pogany. "An Internet WebQuest on Genes." Genes: The Building Blocks of Life. University of Richmond, Web. 29 Sept <