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Introduction to Molecular Biology & Biochemistry Research 694:315 & |
Overview Biochemistry, molecular biology and genetics have become integrated, interdependent disciplines in part due to the exciting advances that have occurred in molecular biology over the last 25 years. Biochemists often use molecular biological approaches, and molecular biologists use biochemical approaches. Molecular biology and biochemistry are best taught through “hands on” research. It is therefore the aim of the Department of Molecular Biology and Biochemistry (MBB) to make undergraduate research an integral part of the education of our students. MBB undergraduates spend several years pursuing an independent research project under the guidance of a faculty mentor that will result in an undergraduate thesis. A central component of the MBB curricula is the Introduction to Research in Molecular Biology & Biochemistry (694:315) course, which is used to train students in the basic molecular biology and biochemistry techniques and expose them to many of the joys and problems of real research. Over the past 15 years, we have trained over 800 students in the 315 course and these students have gone on to perform independent research projects in laboratories at Rutgers and UMDNJ. The majority of these students have continued with graduate or medical training in the biological sciences or have found research positions in academia or industry. We have designed this course to give students the theoretical background and practical experience with many of the techniques that will likely be used during an undergraduate research project. We will also provide assistance to help students identify research labs that they may be interested in. In designing the Introduction to Research in Molecular Biology & Biochemistry courses, we wanted to avoid the problems of other lab courses in which the experimental outcome is already known and the aim of the laboratory exercises is to simply reproduce the expected results as closely as possible. Students will therefore carry out a research project for which the results are unknown and the outcome could potentially lead to new and exciting avenues of research. Since the outcomes of the research in the course is often unknown the course instructor, lab coordinator and a teaching assistant will be present during all the labs, which will provide extensive opportunities for interactions with the professors teaching the course. The Project: After some initial training in several techniques used in molecular biology, students will start to work on their main research project. The project involves sequencing random clones from a cDNA library. The sequences derived from these experiments will be used to query a database for sequence similarity using the appropriate computer software. When matches are found, students will then search the scientific literature for information on the genes that they have identified. Students in the course will identify genes that have never been sequenced before and students will have the opportunity to publish their sequence on GenBank the international sequence database of the National Center of Biotechnology Information (NCBI). Reading Material: All lecture and laboratory notes will be posted on the course web site. The laboratory notes contain the protocols you will performing the lab. It is essential that you come to the lab with a hard copy of the lab notes. Students that forget their notes will not be able to take the lab. It is essential that in order for your lab work to run smoothly and for completion of the required tasks, it is essential that you understand your laboratory experiments before you enter the lab. Therefore, you should read your Lab Manual before coming to each class. Figures used in the lectures will also be posted before each class. Pod casts of each class will be posted after the lecture. Office Hours: This course is designed to provide students with a unique, specialized laboratory experience. Thus, course participants are likely to require individualized attention at irregular and unpredictable intervals. In order to accommodate this unusual situation, the instructors have arranged to be as accessible as possible. Therefore, we are not restricting you to pre-scheduled office hours; instead, students are encouraged to email or call us to make an appointment if you have problems or questions. We are always here during the week and most of us are available on line at some points on nights and weekends. Course Coordinator: Dr. Andrew Vershon, Waksman Rm. 234, 445-2905 vershon@waksman.rutgers.edu Lab Coordinator: Dr. Janet Mead, Waksman Rm. 19, 445-4661 mead@waksman.rutgers.edu Grading in 215: Exams will be in class and will account for 25% of the grade. The exams will focus on the material covered in the lectures and assigned reading. Quizzes: Brief, unannounced quizzes will be given at the beginning of lectures to test your understanding of the lecture material covered in the previous week and the lab exercises planned for the upcoming week. these will account for 25% of your grade. Clickers: Several times during each lecture there will be questions that the students will respond to using the I-clicker response systems. Many of these responses will be graded. The accumulated scores will account for 10% of the total grade. Correct answers will account for 3 points while wrong answers will account for 1 point. Grades for lectures with the two lowest scores will be dropped. It is your responsibility to bring your clicker to each class and keep it in working order. Presentation of Results: At the end of the course each student will give a 10-15 minute presentation of their results and interpretation of the data. The presentation of your results will account for 25% of the grade. To help you prepare for your talk, on Week 10 a table listing all of the clones you have purified, sequenced, and the results of the Blast search on each must be submitted. At this point you must choose a clone for further investigation and a summary on the gene of interest you are going to do your presentation on is due (Week 11). In Week 12, an outline of your presentation as well as a list of the publications you have used in researching your topic, must be handed in. A copy of the first page of a primary research article on the protein you are basing your presentation on must be included in this. During Week 13, an abstract of your presentation must be handed in. Finally, a copy of your Powerpoint presentation is due to by 10:00 AM on Week 13. This presentation is due even if you are talking the next week. Please note that you will not be able to make any change to your presentation even after you hand it in. Failure to turn in these materials will result in a lower presentation grade. Remember, these are new experiments! There is no right or wrong to your results or analysis of the data and so you will not be graded on whether or not the experiment fails or that there were no “correct” results. Lab Participation: Students will be expected to be active members of the lab. This means being prepared for the labs, taking part in all of the experiments, being helpful and courteous to other members of the lab, and cleaning up after your self. Ten percent of your grade is based on lab participation. Timely data entry: During the lab part of this course you will generate DNA sequence data that you will analyze in several different ways. At the end of this analysis you will give an oral presentation concerning one (or more) of the genes you sequenced. As a result, you will generate a lot of data. To simplify and better organize the analysis of your DNA sequences we have developed several data entry forms (some are hard copy and some on-line). Towards the end of the project you are expected to follow the instructions and complete the different data entry forms in a timely manner. This will help you to better analyze your data and also organize it a way that can be readily assessed. These comprehensive analyzes will help you select an “interesting” gene to form the basis of your oral presentation and will provide “hands-on” experience in how to analyze DNA sequences, knowledge that will be beneficial to you on the class exams. Furthermore, there is a high probability that the data you generate will be novel and a goal of the project is to deposit your findings in the public genomic databases. For every entry you provide, your name will be associated with the “discovery” as a co-author in the public databases. However, submitting DNA sequence is a serious undertaking and requires a thorough analysis of the data. If you follow the required data analysis and do so in a timely manner, your findings should be of the quality appropriate for submission to the DNA sequence databases. If you do not perform the data analysis, your findings will not be able to be submitted. Therefore, there are many good reasons to do the data analysis, including that it is part of your grade! Notebooks: Each student is required to keep a notebook of their experiments. The notebooks will be examined periodically at random and, along with your timely data entry, will account for 15% of the final grade. Groups: Collaborations in science are usually very beneficial, if not unavoidable. If you examine any recent scientific journal you will find that most research articles are by a group of people from the same lab or by several different groups that work in collaboration to conduct the research. Each member of a group adds experience, reagents, or effort to a project that would otherwise be very difficult for one person to perform on their own. Contact Dr. Andrew Vershon for more information about the course |
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last updated 1/8/08 |
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