Biology 4202L - Biotechnology Laboratory Course Syllabus - Fall 2012 Individuals with disabilities who need to request accommodations should contact the Disability Services Coordinator, Student Center 214, 678-466-5445, disabilityservices@mail.clayton.edu. Course Description: Number and Title: BIOL 4202L (CRN 87102 and CRN 89471), Biotechnology Laboratory Credit Hours: 3.0 semester credit hours Catalog Description: An experiment-based course in which students use DNA technology to explore topics such as DNA fingerprinting, gene cloning, DNA amplification, genetically modified foods and organisms, gene therapies, inheritance and paternity, and human genetic diseases. Course Requirement: Pre-requisite: BIOL3250 and BIOL3250L; BIOL3201 Computer Requirement: Each CSU student is required to have ready access throughout the semester to a notebook computer that meets faculty-approved hardware and software requirements for the student's academic program. Students will sign a statement attesting to such access. For further information on CSU's Official Notebook Computer Policy, please go to http://www.clayton.edu/hub/itpchoice/notebookcomputerpolicy. Computer Skill Prerequisites: Able to use the Windows TM operating system. Able to use the Microsoft Word TM word processing program.
Able to send and receive e-mail using the Outlook TM or Outlook Express TM program. Able to use a Web browser (preferably Microsoft Explorer TM ). Able to print documents either on your home computer's printer or Smart Print (networked printers on campus). In-class Use of Student Notebook Computers: Student notebook computers will be required periodically in this class. Students will also use the computers to access supplemental lectures, laboratory assignments, protocols, review sheets, internet information, and to communicate with the instructor. Course Objectives: To understand the fundamentals of molecular biotechnology To understand the processes involved in DNA replication, RNA synthesis, and protein translation To describe the basic application of recombinant DNA technology To understand commercial application of DNA technology and use in medicine and research To learn to use basic biological laboratory equipment To understand and use laboratory math and chemistry To learn to perform basic molecular biology techniques To learn to prepare laboratory notebooks and write laboratory reports based on experimental data, results and conclusions To apply critical thinking and problem-solving skills to laboratory situations To learn how to prepare research proposals To understand the regulation and patenting of biotechnology inventions Student Learning Outcomes: BIOL 4202L supports the following outcomes: 1. Effectively demonstrate knowledge of the basic principles of major fields of biology. 2. Demonstrate a mastery of a broad range of basic lab and technology skills applicable to biology. 3. Apply knowledge of physical sciences, mathematics, and statistics to biological concepts. 4. Communicate scientific information in a clear and concise manner both orally and in writing.
5. Demonstrate the ability to collect, evaluate and interpret scientific data, and employ critical thinking to solve problems in biological science and supporting fields. 6. Collaborate effectively on team-oriented projects. 7. Demonstrate the ability to identify and describe the impact of biological and physical sciences on the environment and society. Instructor Information: Dr. Fran Norflus Office: Natural and Behavioral Sciences Building (NBS), Room 153 Phone: 678-466-4852 e-mail: FNorflus@clayton.edu Internet: http://a-s.clayton.edu/fnorflus/ Office Hours: Monday, Tuesday, Wednesday and Thursday 1:00 2:15 PM Class Meetings: CRN 87102, Tuesday and Thursdays, LAB 210, 9:45 AM 12:35 PM CRN 89471, Monday and Wednesdays, LAB 210, 10:00 AM 12:50 PM *You must attend only the section of the class that you are signed up for.
Textbook and Supply Information: Textbook Information: 1. Biotechnology: A laboratory skills course by J. Kirk Brown This is a relatively new book and you will probably only be able to purchase this textbook through the bookstore. The book is published by Biorad. You will probably NOT be able to purchase it online. ISBN #: 978-0-9832396-0-4 http://www.biorad.com/prd/en/us/adirect/biorad?cmd=catproductdetail&isfromsearch=true&prod uctid=166-1025edu&vertical=lse&parentcategoryguid=lkn6r715 Text Coverage: required readings will be listed in the course schedule. It is essential that you read the background in the textbook and have the laboratory protocols. But, if you want, you may share your textbook with ONE other student in the class. Dr. Norflus will assign lab groups by the second class meeting. You may wait until then to purchase books or purchase them beforehand and then swap so you can share with a partner. This book is NOT optional. If you do not have the book, you will not be able to perform the laboratory experiments and will not be able to pass the class. Note: Additional reading and laboratory materials will be provided by the instructor. It is also recommended that you have handy your microbiology or genetics textbook. You may want to refer back to these books for additional background information on the laboratory techniques that we will be performing. 2. Writing Papers in the Biological Sciences, Fourth Edition, Victoria McMillan, Bedford/St. Martin s, ISBN: 0-312-44083-1. Students must bring to class a laboratory coat. It is also recommended that students have pencils and pens to draw the results. These will be stored in your lab drawer. Or, you may use digital cameras in the lab to take pictures or bring
your own camera. If you want to use your cell phone to take pictures, you may only use it to take pictures and not for any other uses. Each lab group will also be REQUIRED to purchase a combination lock for your drawer or take the risk and leave your drawer open. Dr. Norflus will not be responsible for any lost items. In the beginning of this class, we will learn how to use certain equipment and how to perform calculations. Once we start performing experiments, each student will be required to wear his/her laboratory coat. NO EXCEPTIONS!!! If you do not have a lab coat, you will be asked to leave the lab and will get a 0 on any assignments for the day. There will be only 2 exams in this class but MANY other different assignments. They are explained below:
Evaluation: item Introduction to class on GA View points 5 points 3 other posts to GA view discussion board which are not part of the introduction Drawings of protocol (INDIVIDUAL) Presentation of protocol (GROUP) Other lab write-ups 15 points 50 points 10 points 50 points Assignments/Quizzes (different from lab write-ups) Skills test 100 points 50 points Midterm exam 100 points Lab report 1 (based on pglo experiments and modifications) GROUP PROJECT Lab report 2 (based on PCR experiments) GROUP PROJECT Poster analysis based on poster you will be given by Dr. Norflus GROUP PROJECT Project poster based on original research project GROUP PROJECT Resume Final exam 100 points 100 points 30 points 70 points 10 points 100 points
Total 790 points Description of assignments: At the beginning of the class, you will need to participate in an introductory discussion in GA View. You should answer the questions below. If your answer is yes, please describe what you have done. 1. Have you done research before at CSU or elsewhere? 2. Have you performed DNA or protein electrophoresis before? 3. Have you performed PCR before? 4. What do you want to do before you graduate? There will then be a separate discussion for you to participate in at various times throughout the semester. This will be more like a chat board for students. This will be an area for you to post questions and/or comments about the class. Maybe you have a question about something we learned in class or you want to know if different groups had different results on their lab. You will be required to post three responses to this discussion. Your 3 posts can be a combination of 3 original posts starting a discussion or responses to other student s posts. Dr. Norflus will not grade this discussion until the end of the semester. However, if you just write, I agree, you will not get any credit. You must write a substantial statement or question. Drawings of protocol Prior to many laboratories, you will be required to make a drawing of the protocol for the day. This assignment will be due at the beginning of class. There will be a 5 minute grace period but after then, if you show up late, you will get a grade of 0, even if the lab is not going to be performed for another 30 minutes. If you come to me and tell me you left it at home or need to go photocopy it, then you will get a 0. You cannot hand in this assignment if you are not in class. I will grade these assignments out of 100 points and then take an average at the end of the semester. I will drop your two lowest grades. What you will need to do for these drawings is diagram out what you will do in the laboratory. You can and should use your textbook to complete these assignments. However, you will not just write out in words what is written in the book. You should make a sort of flow chart and use diagrams when possible. For example, in some experiments, we will add 1 or more things to a tube and then centrifuge the tube. So, you might draw a tube, show what is added and then show what happens after centrifuging. Maybe, we need to keep the supernatant so you would indicate that in your flow chart. You are encouraged to use colored markers for this assignment. DO NOT find a similar protocol on the Internet. Use the written protocol that is in your
textbook or that Dr. Norflus handed out for the steps of the experiment. Your grade will be based on the details provided and quality of the work, not necessarily the art work. But, your diagram should be interesting. You will need to make 2 copies of your drawing one to hand in and one to use during the class to perform the experiment. This is an individual assignment. Dr. Norflus or a student volunteer will then randomly pick out one group who will draw the protocol on the board and explain to the class what needs to be done. The details of the drawings with different members of the group should be similar. Dr. Norflus will fill in any missing material. Some groups might present more than others during the semester but each presentation will be worth 10 points and an average will be taken at the end of the semester. Other lab write-ups At the end of many of the labs, you will need to submit your data and/or answer various questions. Sometimes, you might have to answer the pre or post lab questions in the textbook. These assignments will be due at the end of class unless otherwise indicated. These assignments will be graded separately from the protocol drawings. I will drop your lowest 2 grades. You may not hand this in if you are not in class or if you leave early before the lab exercise is completed. Assignments/Quizzes Many of these assignments will be based on math calculations and most will be done in class but are separate from the protocols and lab write-ups. These assignments will be more based on the background material than on the actual experiments. I will drop only the lowest assignment grade. Skills test This in class test will require you to demonstrate various skills for instance, you will be required to pour a gel, load a gel, hook up the electrophoresis equipment and demonstrate how to read and use various pipets. You will also need to perform various calculations. Lab Report 1 This will be a group project and you will submit one lab report. There will be one series of experiments that are related to each other. You will perform a transformation with a special plasmid called pglo that glows green under UV light. You will then grow up the colonies, and isolate and quantitate the DNA. The last part of the experiment will be to perform chromatography and isolate the GFP protein.
In addition to performing the experiments described in the textbook, each group of students will test 2 ways on two different days to improve/modify the experiments. Prior to performing the experiment, students will submit a 1 page proposal of what they will modify in the experiments. Dr. Norflus will either comment on the proposal and/or discuss the plans with the different groups. The proposal will count towards the final grade of the lab report. Everyone in your group will receive the same grade on this assignment. However, if any group member misses class, points will be deducted from their grade. If you have an excused absence documented by a note handed to Dr. Norflus the day you return to class, you will not be penalized. If it is not a valid excuse or you do not bring in a note, then you I will deduct points. You will only be allowed one documented absence for the lab periods that count towards the lab report. Lab Report 2 This will be a group project and you will submit one lab report. In these experiments, you will need to go to the supermarket and purchase normal food and genetically modified or organic food. You will then extract the DNA from these food products and then perform PCR with the primers provided. In this experiment, you will also write a 1-2 page proposal explaining what you will do. You can also make some modifications to the procedure to get better results or just see how changing some conditions in the PCR can alter the results. In this lab report, you will analyze the results and explain the use of the different controls. The proposal will count towards the final grade of the lab report. Everyone in your group will receive the same grade on this assignment. However, if any group member misses class, points will be deducted from their grade. This lab will only last 2 class periods so if you miss a lab period, you will be missing the bulk of the experiment. If you miss the laboratory, you will need to have a very good excuse and an alternate assignment that you will need to do by yourself will be assigned. Poster analysis 1 Dr. Norflus will give your group a poster to analyze. You will have to get together with your group members and answer various questions based on this poster.
Project poster During the course of the semester, you will learn different techniques. The final assignment for the semester will be to design your own experiment and make a poster showing the results that you expect. You will not actually be doing the experiment. This will be a GROUP project and ideally, each group will have to have a different idea. Some potential ideas are listed on page 319-336 of your textbook. You can use these ideas or come up with your own idea. Towards the end of the semester, each group will need to meet with Dr. Norflus to discuss what they want to do. Each GROUP will then make a PowerPoint of their project as if you were going to a scientific conference to present your findings. Later in the semester, Dr. Norflus will go over how to make a poster. Briefly, on your poster, you should have the following sections Extra credit Title and your name Abstract/introduction Material and methods Expected results Discussion/conclusion/future direction References You will need to use at least 2 references that are NOT from the Internet but are from primary scientific literature. You can use your textbook as an additional reference. You can use pictures from the Internet but cannot use the Internet as a source of information. There will be two extra credit assignments in this class. There will be NO others so please do not ask. 1. You are not allowed to use your cell phone in this class unless approved by Dr. Norflus. Everyone will start the class with 10 extra credit points. For each time
that a student uses their cell phone, 1 point of extra credit will be deducted from everyone in the class for each unapproved use of a cell phone. 2. Dr. Norflus will present to the seminar class on Friday, October 19 from 2:15 4:05 PM. If you attend the seminar come on time and stay until the end, you will get 10 points. This is a one time event so plan ahead. There will not be any other opportunities. Grading: Your final grade will be determined as follows: grade percentage range A 90-100% B 80-89% C 70-79% D 60-69% F below 60% Mid-Term Progress Report The mid-term grade in this course will be based solely on your grade for the first exam. Based on this grade, students may choose to officially withdraw from the course by October 5, 2012 and receive a grade of "W". The following link gives instructions for withdrawal: http://www.clayton.edu/registrar/withdrawal The course schedule will be posted in a separate document. Final Examination Schedule: CRN Instructor Date of final exam Time of final exam 87102 Norflus November 29 9:45 AM 11:45 AM
89471 Norflus November 28 10:00 AM 12:00 PM Course Policies: Laboratory Safety: Students must follow safety rules and guidelines at all times. These rules will be discussed during the first meeting. Students are encouraged to report any violations of the safety rules to the instructor immediately. Failure to follow specified safety rules will result in dismissal from the laboratory and receive a grade of zero for that lab. Under no circumstances, may you come to class in sandals, flip flops, high heels, shorts or short skirts/dresses. If you do, you will need to leave the laboratory and receive a grade of 0 on all lab assignments for that day. You must wear covered shoes!!!! You must comply with this dress code even if we are not performing a laboratory exercise on a specific day. You will need to wear to class what is commonly regarded as acceptable attire. For instance, no ripped clothes will be allowed. If you are wearing something that Dr. Norflus deems unacceptable, you will be asked to leave. This is not a fashion show. No eating or drinking will be allowed in the lab. You may not bring any food or beverages to the laboratory. If you do have anything, it must be in your book bag covered and out of site. You may not have any beverages on the bench tops, even if they are closed. If you are caught with any food or beverages, I will deduct 5 points from your next exam. I will also take away your food and/or drink and throw it in the garbage or down the sink. Laboratory Attendance: Students are expected to attend all class meeting. However, I will not take attendance. But, you will need to explain to your lab partners why you could not do the laboratories but they needed to do them. You will not get credit for any lab assignments that are due that day. You will also be required to submit 2 lab reports. If you miss a laboratory, you will have points deducted from your lab report.
Students are expected to come to class on time and bring laboratory materials to each class meeting. If you come in late, please don t ask me to explain the lab that I already explained. Quizzes and Assignments: All assignments must be typed unless the instructor directs otherwise. All assignments that are more than one page must be stapled. If you use paper clips or fold the pages over, the assignment will be returned to you. All reports/assignments are due at the beginning of class and must neat and stapled. For each day that the assignment is late, 10 points will be deducted. Late means after I start lecturing for the day or the lab begins. No assignments will be accepted after 3 days past the due date. Some assignments will be math calculations and these will be allowed to be handwritten. I will drop your lowest quiz/ assignment grade. I will not collect any excuses that you have but if you miss 2 assignments, regardless of the excuse, you will be given a grade of 0. Laboratory Class Meeting and Exams: Absences from EXAMS must be accompanied by a signed physician's or judge's excuse (there are no exceptions). The instructor must be notified immediately before or after missing an exam. THERE WILL BE NO MAKEUP LABS OR EXAMS. Without an excuse provided within one week, a grade of zero points will be assigned for the missed work. If the student has a valid excuse, the final exam will be doubled to make up for the missed exam. If a student misses the final exam and has a valid excuse, a makeup will be administered. If you miss the skills test, your assignment grade will count twice. However, you must provide a valid excuse upon returning to class. E-mail accounts: All students must establish and maintain their CSU e-mail accounts. For many laboratory exercises, students will be expected to download laboratory pre-lab assignments and protocols from the course web page. Group Work: Students will work in groups of 3-4 to complete laboratory experiments and other assignments. Students are encouraged to work in groups to discuss laboratory experiments but all written work must be unique and completed separately be each student. All tests and quizzes are to be completed by each student individually.
Course Policies: Students must read course policies as stated below on first day of class. Students must abide by policies in the http://www.clayton.edu/portals/46/docs/studenthandbook.pdf and the http://www.clayton.edu/portals/5/basicundergraduatestudentresponsibilities.pdf. No disruptive behavior of any kind will be tolerated. Disruption of the Learning Environment Behavior which disrupts the teaching learning process during class activities will not tolerated. While a variety of behaviors can be disruptive in a classroom setting, more serious examples include belligerent, abusive, profane, and/or threatening behavior. A student who fails to respond to reasonable faculty direction regarding classroom behavior and/or behavior while participating in classroom activities may be dismissed from class. A student who is dismissed is entitled to due process and will be afforded such rights as soon as possible following dismissal. If found in violation, a student may be administratively withdrawn and may receive a grade of WF. A more detailed description of examples of disruptive behavior and appeal procedures is provided at: http://www.clayton.edu/portals/5/disruptiveclassroombehavior.pdf University Attendance Policy Students are expected to attend and participate in every class meeting. Instructors establish specific policies relating to absences in their courses and communicate these policies to the students through the course syllabi. Individual instructors, based upon the nature of the course, determine what effect excused and unexcused absences have in determining grades and upon students ability to remain enrolled in their courses. The university reserves the right to determine that excessive absences, whether justified or not, are sufficient cause for institutional withdrawals or failing grades. No electronic devices are allowed while in the biotechnology laboratory. Use of electronic devices in the laboratory is considered a violation of laboratory safety procedures and the university s disruptive behavior policy. Dr. Norflus talked to the class on Feb. 23, 2012 and stated that the use of cell phones during class is a violation of the class and university s disruptive behavior policy. If a student is caught using their phone after this date, they will be dismissed from the class with a grade of WF. If you need your cell phone to tell the time, record lectures or any similar activities, you will need to find a different way to do it. The only exception will be to take pictures of gels with your cell phone or if there is an emergency. These calls must be taken in the hallway. Routine texting is NOT considered an emergency.
Most of the lab protocols are in the textbook. If you need to print additional materials, you must print them BEFORE coming to class. Visitors (friends, children, etc) are strictly prohibited from attending class without the permission of the instructor. No smoking, eating or drinking is permitted at any time in the laboratory. If you are caught, you will have 5 points deducted from your next test. NO CHEATING. Cheating is defined as copying anything that is not your own work. This applies to laboratory report, laboratory notebooks, laboratory assignments, laboratory quizzes and exams. You are not to copy word for word what I post as background for the labs in your lab notebook or lab reports. You must write it in your own words. You are also not to copy word for word what you find on the Internet. Cheating in any form will result in a zero on the assignment and academic misconduct forms will be filed with the Office of Judicial Affairs for any violation. Judicial procedures are described at http://adminservices.clayton.edu/judicial/ Last update: 8/8/12