Biotechnological Applications of Recombinant DNA Techniques

Transcription

1 Division of Life Science The Hong Kong University of Science and Technology LIFS 3110 Biotechnological Applications of Recombinant DNA Techniques Fall semester, Credits: 2 Time: Tuesday, 14:00 17:50, Room 4160, Lift 33 Instructor: Bobby TK Yim ( bobby@ust.hk) Areas of Study The course LIFS 3110 Biotechnological Applications of Recombinant DNA Techniques comprises altogether eight laboratory exercises. The goals of these exercises are three-fold: (1) to enhance students comprehension of what they have learnt in lectures; (2) to provide hands-on experience in the fields of Biotechnology and Molecular Biology; and (3) to prepare students for advanced laboratory studies. Students will be given exposure to the following areas of molecular biology and recombinant DNA technology: Microbial culture and aseptic techniques Analysis of plasmid DNA by agarose gel electrophoresis Restriction endonuclease digestion Amplification of DNA by polymerase chain reaction DNA recovery from agarose gel Plasmid construction by Gibson Assembly Transformation of E. coli Plasmid DNA isolation Site-directed mutagenesis Quantitative analysis of recombinant proteins i

2 Learning outcomes On successful completion of this course, students are expected to be able to: 1. Acquire a sound knowledge of recombinant DNA methodology, gene structure and expression. 2. Perform practical skills relating to molecular biology and bacterial culturing to yield recombinant DNA / protein. 3. Demonstrate analytical awareness via interpretation of experimental results. 4. Plan and execute recombinant DNA techniques in order to determine and interpret genetic modifications. 5. Work and coordinate effectively in a group to accomplish laboratory based tasks. 6. Exhibit accuracy and independence in recording and reporting results. Learning activity 1. Learning environment: A group of two students will collaborate to perform the experiments during the semester. Workbench, routinely used labwares and instruments would be assigned to and managed by each group of students. 2. Pre-lab talk: Contents would focus on basic theoretical and practical issues pertaining to the experiment. 3. Pre-lab demonstration: Specific techniques will be demonstrated by the instructor prior to each laboratory exercise; real time close-up video shot will be shown live. Right after demonstration, students will perform the same techniques by themselves. Students are expected to learn a core set of techniques that will be repeatedly used throughout the semester. 4. Bench supervision: The bench supervisor, who is a technician or postgraduate student, will be in charge of several groups of students. The bench supervisor will provide assistance and instructions to students during the experiment. 5. Exit discussion: In some exercises, on completion of the experimental work, all students would be expected to present their results to the instructor. Additional discussions on data analysis and interpretation may be conducted on a large group-basis. ii

3 Method of assessment 1. Every student is required to submit 8 worksheets. Questions in the worksheets cover underlying principles of experiments, data reporting, data interpretation and statistical analysis. 2. In each laboratory exercise, practical performance, discipline and safety awareness of students will be assessed by the bench supervisor. 3. Every student will be assessed individually in the final examination, which includes written questions and practical tasks. Knowledge on concepts and principles of recombinant DNA technology, and the ability to analyze laboratory data will be evaluated in the written part. Competence on experimental techniques acquired in this course will be evaluated in the practical part. Assessment scheme Method of assessment Percentage Learning outcomes* to be assessed Worksheet 24% (1), (3) and (6) (3% per week) Laboratory performance 12% (1), (2), (4) and (5) (1.5% per week) Final examination (Written and practical) 64% (1), (2), (3), (4) and (6) *Listed on Page ii iii

4 LIFS 3110 Biotechnological Applications of Recombinant DNA Techniques Schedule of Laboratory Activities Fall Semester (Tuesday, 14:00 17:50, Room 4160, Lift 33) Activities Date Check-in 8 September Exercise 1 Aseptic and microbial techniques 15 September Exercise 2 Exercise 3 Analysis of plasmid DNA by restriction digestion and agarose gel electrophoresis Amplification of DNA by polymerase chain reaction 22 September 29 September Exercise 4 Plasmid construction by Gibson Assembly 6 October Exercise 5 Transformation of Escherichia coli by plasmid DNA 13 October Exercise 6 Plasmid mini-prep and restriction analysis 20 October Exercise 7 QuikChange site-directed mutagenesis 27 October Exercise 8 Quantitative analysis of recombinant green fluorescent proteins 3 November Final Examination 24 November iv

5 Pre-Lab / Follow-up Lab Session In addition to the regular lab section as listed in page iv, Exercise 1, 5, 6 and 7 will have pre-lab and/or follow-up lab session. Details of these sessions are listed as below. Pre-lab session Follow-up lab session Exercise 1 N/A 16/9/2015 Wednesday, 11:30 am 11:45 pm Exercise 5 N/A 14/10/2015 Wednesday, 11:30 am 11:45 pm Exercise 6 19/10/2015 N/A Monday, 11:30 am 11:45 am Exercise 7 N/A 28/10/2015 Wednesday, 11:30 am 11:45 pm N/A = non-applicable Only ONE student from each group is required for the above sessions. Information provided in this table is subjected to changes. You will be notified for the finalized schedule of these Pre-lab / Follow-up session. v

6 Laboratory Rules Working in a laboratory may expose one to potentially dangerous tools and equipment, and hazardous chemicals. Therefore, you need to exercise discipline and caution. The following rules are strictly enforced in the LIFS 3110 laboratory in order to ensure that experiments are conducted under the best and safest conditions. Violation to these rules will result in deduction of points in the laboratory performance evaluation. Punctuality: you should arrive at the laboratory on time. Full attendance is required for the entire duration of the experiment, except under circumstances where permission is granted. Laboratory coats must be worn at all times in the laboratory. Gloves must be worn when handling the following: bacterial cultures, hazardous chemicals or reagents, nucleic acids and proteins. Labels, notes, pens/pencils and other materials should never be placed in your mouth. The benchtop should be cleaned with 70% ethanol before and after the laboratory period. Any accidents, such as cuts, burns, and spillage of culture or toxic reagents, must be reported to the instructor immediately. Flasks, tubes and other plastic- or glasswares containing cultures or other laboratory samples must be labeled with your name, date and specimen name before they are placed in incubators. All used plastic- and glasswares, and other laboratory wastes must be disposed of in designated receptacles or garbage cans. Seek advice if you are unsure about the operation or handling of equipment and tools. The gas burners must be handled carefully. Make sure they are turned off when not in use. None of the equipment, consumables and experimental samples is to be taken from the laboratory without permission. vi

7 Laboratory Performance Evaluation Criteria In each exercise, laboratory performance of students, including practical performance, discipline and laboratory safety will be assessed by the bench supervisor / teaching assistant. This accounts for 12% of the total score of the course, (i.e. 1.5% for each exercise). The assessment will focus on the following. Motivation to accomplish the experimental tasks Proper execution of the experimental procedure Communication with group members and Teaching Assistant Completion of experiments in a timely manner Cleanliness of the bench after experiments Full marks will be awarded if all criteria are satisfied. In addition, 1-3% will be deducted from the total score of the course at the discretion of the instructor, every time the following rules are broken. Attendance a. Attendance for the entire duration of a laboratory exercise, except under circumstances where permission is granted. b. Attendance of pre-lab or follow up lab sessions. 3% 2% Dress Code a. Lab coats must be worn at all times as protection against lab hazards. b. Cover lower body with clothing i.e. no shorts, short skirts, sandals, slippers, to minimize injuries against spills. c. Long loose hair must be tied up securely to minimize contact with open flame, chemicals etc. Punctuality You should be on time (no more than 5 minutes late) for any lab session/follow-up session. 1% 1% 1% 2% Performance Follow instructions from TAs and the lab manual carefully and 2% 7

8 accurately. Laboratory Worksheet Students are required to submit a laboratory worksheet after each laboratory exercise. Therefore, a total of eight worksheets should be submitted by each student. In each worksheet, you are required to put down your Name, Student Number, Group Number, Date, and the number and title of the exercise. Answer all questions in the worksheet. Completed worksheets should be submitted on the 7th day after the related laboratory exercise. Therefore, the worksheet for an exercise on a <Tuesday> will be due the next <Tuesday>. Teaching assistants will be responsible for collecting and grading all worksheets. 8