BIOS 221 Genetics Laboratory

Transcription

1 BIOS 221 Genetics Laboratory This is the syllabus for BIOS 221, Genetics Laboratory. The class meets in room 3085 SEL for 8.00 am, am and 2.00 pm sessions and in room 3099 SELfor 9.00 am, pm and 3.00 pm sessions. Course Coordinator : Dr Shalu Shiv, sshiv1@uic.edu Office Hours will be held once every week alternating between Tuesdays and Wednesdays. - Starting from January 21 st on alternate Wednesdays at 5.30 pm in room Please see the 'office hours' file for exact dates - Starting from January 27 th on alternate Tuesdays at 5.30 pm in room Please see the 'office hours' file for exact dates - Any changes to office hours will be communicated via so please make sure that your id is accurate. During office hours I will be conducting review of the labs that were covered. I will discuss questions that can be asked on the exam from those topics. I will be answering any questions that students have. -Students are also always encouraged to and ask questions. Course Teaching Assistant : specific for each section. LEARNING OBJECTIVES: Genetics Laboratory course focuses on Classical Genetics and Molecular Genetics. Genetics Lab course will - Acquaint the students with the mechanics of experimentation and the methods and techniques of experimental genetics - Familiarize the students with the genetic principles in a first hand manner as they see these principles operate in a controlled experimental setting - Introduce students to learn plant and animal chromosomes and their behavior in somatic cells and in sex cells. - Introduce students to learn about eukaryotic genetics using yeast as a model.

2 - Introduce students to classical genetics as they perform experiments with the model organism Drosophila. - Introduce students to genetics laboratory skills like bacterial transformation, viral transduction, bacterial conjugation, restriction endonuclease digestion of DNA, gel electrophoresis and amplification of DNA by Polymerase Chain Reaction, and microarray technology. - Train the students to learn and perform experiments, collect data, analyze the data learn to interpret the data and draw conclusion from it. - Provide students with opportunities to develop science writing skills. It is required that you are concurrently enrolled in Bios 220 or have taken this course before Bios 221. Consequently, it is presumed that you will have access to a general genetics text that will serve to provide the background and theory about most of the experiments in the lab course. In addition during this course you will be provided with handouts that will further enhance your understanding of the concepts and methodologies of the experiments that you will be performing in the laboratory. Carefully study the syllabus and pay special attention to deadlines, exam dates etc. Immediately notify me if you have a conflict. BOOKS: 1. REQUIRED: Symbiosis Custom Lab Manual. Used copy will NOT be allowed. BIOS 221-Genetics Laboratory ISBN REQUIRED: Schaum s Outlines Genetics Fourth or Fifth Edition by Susan Elrod and William Stansfield. Used copy is allowed. ISBN (Optional) Flagg, R.O.; Carolina Drosophila Manual, Burlington, NC: Carolina Biological Supply; ISBN COURSE MATERIAL: - Lecture notes and other reading handouts. These will be posted on the course blackboard website in the folder in Course Documents - Reading and Exercises from the Symbiosis Custom Lab Manual (LM). These will be completed in class as part of lab exercises. - Reading and Exercises from the Schaum's Outlines Genetics (SOG). These will need to be self-completed in class as part of lab exercises.

3 LAB: - Students are required to attend and complete all labs. - Students are expected to go over the schedule and inform the TA and coordinator of any date conflicts or anticipated circumstances that may lead to missed lab so that appropriate arrangements can be made in advance for making up the lab. - If students miss a lab due to unforeseen situation, inform the coordinator immediately so that appropriate arrangements can be made for making up the lab. - Without having a justifiable reason, students will be penalized after more than two missed or incomplete labs. - Students must not enter the lab without the TA, even if the door is open. - Students must be prepared to show the I card if asked by the TA. - Students are required to read the handouts posted on Blackboard. They will be tested on their knowledge of the material covered in handouts during Quizzes. This material includes lecture notes and other reading materials posted on Blackboard. - The teaching assistants will be teaching the lab. The teaching assistant is required to explain the background, objective and methodology of the lab exercise. The TA is required to facilitate discussion regarding expected and observed results and analysis of the results. The TA is required to be available and answer questions while students are conducting the lab. - If students feel that the teaching standards described above are not being met, then students must inform the coordinator immediately. A delay in reporting such concerns lead to incomplete understanding of the material and reflects later in student's grades - The students are responsible for making sure they understand the lab exercises and the concepts behind the exercise. Students are encouraged to ask questions to the TA during the lab and to the coordinator during office hours or via . - Students are encouraged to ask questions during review sessions held before the exams to further enhance their understanding of the material. - Labs will be graded. The grading will be based on participation and completion of labs. Students are required to complete all lab exercises as directed and show them to the TA BEFORE leaving the lab. For labs where there are no lab manual

4 exercises, students are required to submit a short write up BEFORE leaving the lab for that day. The write up is expected to be short (1-2 page) and handwritten during the lab. The write up will be returned in future sessions after being graded. More details and instructions on the write up will be provided. QUIZZES - Quizzes will be based on ALL the material posted on Blackboard. Quizzes will not include lab manual pages as they need to be completed in lab. - Quizzes will be distributed at the beginning of the lab and will be collected after ten minutes. - Students who come late to the lab may still take the quiz, however whether the quiz is included in the grade or not will be decided by the coordinator. Students are required to inform the TA and the coordinator of the reason for delay. The coordinator will then decide whether the reason is compelling to allow the quiz grade or not. - There will be 12 quizzes of which the lowest two quiz scores will be dropped in the calculation of the final grade. - Students are expected to always be prepared with the readings as there may be pop quizzes on any of the days. Students who miss pop quiz will not be allowed to make it up. LAB REPORT: - Students are required to write a detailed lab report on Drosophila Genetics Lab. Instructions regarding writing the lab report will be provided close to the date. - Students are encouraged to ask any questions regarding writing the lab report either to their TAs or the coordinator during office hours. - Students can always the coordinator to ask questions regarding writing the lab report. - Students may not ask the TA to 'preview' the report to see if it looks ok. - ALL students are required submit the lab report on safe assign on the date and time mentioned in the syllabus. Late submissions will be heavily penalized.

5 - Students are required to bring a hard copy of the lab report and turn it in to the TA in their lab section. If an emergency prevents you from coming to lab that day, the coordinator immediately to arrange for alternatives. LAB PRESENTATIONS: - Students will be required to give a brief presentation on a topic assigned to them. The presentation will be during the regular lab section. More details on the presentation will be provided closer to the date. EXAMS: - There will be three exams in the course. First exam will cover syllabus from the first half of the course (see the schedule below for exact topics) and second exam will cover syllabus from after exam 1 to the end. The third exam would be a comprehensive practical. Further details regarding the exam will be provided closer to the date. - All students are required to take the exams. The exam dates are provided in the syllabus. If students have a valid conflict with the date, they MUST inform the coordinator immediately so that alternative arrangements can be made. If students miss the exam they will be heavily penalized which may include getting a zero for the exam. - On the day of the exam, students are strongly recommended to allow enough time to reach the lab to account for traffic or transit delays and any other circumstances. - In case of an emergency that prevents you from coming to the University, you MUST inform the Coordinator as soon as possible. Whether you will or will not be penalized will depend on a case by case situation. It is strongly advised to avoid this situation if possible. COMMUNICATION: - Students are strongly encouraged to communicate with the Coordinator and the Teaching Assistants regarding their understanding of the topics, concerns, lab issues or any questions. Students can bring their questions and concerns to the coordinator during office hours or discuss via .

6 GRADING: The points for this course are derived from labs, quizzes, lab reports, presentations and exams. Possible Number of Points = 500 Activity Lab participation (10 points per lab) Quizzes (top 10 and 10 points per quiz) Lab Report Lab Presentations Exam 1 Exam 2 Final Practical Points Scaled to 60 points Scaled to 60 points 60 points 20 points 100 points 100 points 100 points SAFETY RULES NO TARDINESS. Your TA reserves the right to lock the door once the lab begins. You must get to the lab on-time. Absolutely NO FOOD OR DRINKs IN THE LAB. NO dirty hands wash your hands before and after each lab session. NO unattended open flames. NO careless handling of ethanol or other flammable solvents. NO long and loose hair. NO loose or baggy sleeves. NO fancy fashion. Wear clothes that you don t mind getting dirty and/or smelly. NO sandals or open-toe shoes. NO cell phone use during Lab. If you fail to follow any of these safety rules, your TA reserves the right to deduct points from your grade and/or make you leave the laboratory. ACADEMIC INTEGRITY Cheating will not be tolerated. During the tests we will assume that you are cheating if your eyes wander from your test paper to another s. You will not be allowed to carry cell phones, calculators etc to the exam. Any act of academic dishonesty will be punished severely. Cheating includes, but is not limited to falsification of data, plagiarism of published material, copying another student s work and accepting or giving help during quizzes or exams. The UIC Guidelines regarding academic Integrity may be found at

7 BIOS 221 Genetics laboratory Lab Schedule SOG (4) = SCHAUM S OUTLINES GENETICS 4 th edition SOG (5) = SCHAUM S OUTLINES GENETICS 5 th edition LM = SYMBIOSIS LAB MANUAL ***The syllabus is subject to changes due to availability of reagents*** ***The yellow and blue shaded sections indicate that classes in room 3085 and 3099 will be doing different activities*** Date Lab Activities Page Jan 12/13 Introduction Syllabus Jan 14/15 Human Chromosomes Quiz 1 Human Karyotype - LM SOG(4) p SOG (5) p Jan19/20 Jan 21/22 Martin Luther King Jr Holiday. No classes. Mitosis and Meiosis Quiz 2 a. Making slides for different stages of mitosis from onion root tip b. Observing slide sets 1. Plant Mitosis 2. Animal Mitosis 3. Meiosis - SOG(4) p SOG(5) p. 2-22

8 Jan 26/27 Jan 28/29 Feb 2/3 Feb 4/5 Quiz 3 Probability and Pedigree Analysis a. Probability and Probability practice questions b. Pedigree Analysis Handout Principles of Genetics and Chi-square analysis Quiz 4 a. Corn Genetics Ignore duplicate genes with cumulative effect b. Chi - Square Analysis Quiz 5 Genetics of Co dominant genes a. Blood Groups b. Polygenic Inheritance: Finger print ridge count Quiz 6 Drosophila Genetics a. Stages of life cycle, identify male & female, identification of mutants b.sex determining Mechanism c. Sex-linked inheritance d.set up Monohybrid and Dihybrid Drosophila Crosses Review for Exam I - SOG(4) p SOG(5) p.31-34, solved problems on p LM p SOG(4) p , and 73 SOG(5) p.42, solved problem 2.22 p.52, p.59 - LM p SOG(4)p.28-38, p and p SOG(5)p.23-29, p and p.97-99, solved problems p.43-44, p and and p LM 8-10, 11, LM SOG(4)p SOG(5)p.40-42, solved problem p LM p LM p Carolina Drosophila Manual p ( upto Experimental Crosses) - SOG p SOG p LM p. 1-8, 11-14

9 Feb 9/10 EXAM I Covers material from Human Chromosomes to Drosophila Genetics Feb 11/12 Feb 16/17 Feb 18/19 Feb 23/24 Feb 25/26 Mar 2/3 Mar 4/5 Mar 9/10 Mar 11/12 Micro-Measuring and Bacterial Conjugation Quiz 7 a. Micro-Measuring b. Bacterial Conjugation Part I a. Bacterial Conjugation Part II b. Drosophila Genetics : Check for larva and remove parents (F1) Exam 1 returned Viral Transduction Quiz 8 a. Viral Transduction b. Bacterial Conjugation Part III c. Drosophila Genetics : Check for larva and remove parents (F1) a. Viral Transduction II b. Drosophila Genetics : Check for larva and remove parents (F1) or c. Drosophila Genetics : Collect data if F2 emerged Bacterial Transformation Quiz 9 a. Bacterial Transformation, Part I b. Drosophila Genetics : Collect data if F2 emerged a. Bacterial Transformation, Part II b. Drosophila Genetics : Collect data if F2 emerged TBD b. Drosophila Genetics : Collect data if F2 emerged Quiz 10 Yeast Complementation a. Complementation in Yeast-Part I a. Complementation in Yeast-Part II b. Sordaria Genetics - - SOG(4)p SOG(5)p , solved problem 11.1 p.320 -SOG(4)p SOG(5)p LM p Mar 16/17 Restriction Endonuclease Digestion of DNA Quiz 11 LM p SOG(4) p

10 a. Restriction Endonuclease Digestion of DNA, Part I a. Complementation in Yeast-Part III -SOG(5) p , solved problem 12.2 p.359 Drosophila Lab Report is due on Blackboard safe assign by PM on Mar 17th for everyone regardless on their section. Mar 18/19 a. Restriction Endonuclease Digestion of DNA, Part II b. Complementation in Yeast-Part IV - LM p85-87 Lab Report hard copy due in class Spring Break March 23-March 27, No Classes Mar 30/31 Room 3085 Quiz 12 covers PCR Amplification of DNA a. PCR-I - SOG(4) p SOG(5)p Room 3099 Presentations Apr 1/2 Room 3085 a. PCR- II- Analysis of PCR product Room 3099 Presentations Apr6/7 Room 3085 Presentations Room 3099 Quiz 12 covers PCR Amplification of DNA - PCR-I Apr 8/9 Room 3085 Presentations - SOG(4) p SOG(5)p Apr 13/14 Room 3099 a. PCR- II Analysis of PCR product a. DNA Microarray Linking Genes to Diseases Drosophila report returned Apr 15/16 Population Genetics -SOG(4) p

11 a. The Hardy-Weinberg Principle -PTC tasting Review for Exam II - SOG(5) p , solved problems p LM p (upto Part III ) Apr 20/21 EXAM 2 Covers topics from Viral Transduction to end of Apr 22/23 EXAM II returned Final Review Session syllabus Topics covered after exam to end of class Apr 27/28 FINAL PRACTICAL EXAM Covers all topics