BIOS 221 Genetics Laboratory
Fall 2014
This is the syllabus for BIOS 221, Genetics Laboratory. The class
meets in room 3085 SELE for 8.00 am, 11.00 am and 2.00 pm sessions
and in room 3099 SELE for 9.00 am, 12.00 pm and 3.00 pm sessions.
Course Coordinator : Dr Shalu Shiv, sshiv1@uic.edu
Office Hours : Starting from September 9 th on Tuesdays at 5.30 pm in
room 3085 (unless otherwise announced/cancelled on Blackboard or
email)
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.
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 0536897999
2. REQUIRED: Schaum’s Outlines Genetics Fourth or Fifth Edition by Susan Elrod
and William Stansfield. Used copy is allowed.
ISBN 0071362061
3. (Optional) Flagg, R.O.; Carolina Drosophila Manual, Burlington, NC: Carolina
Biological Supply;
ISBN 0892780274
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.
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 email.
- 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
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 email 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.
- 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,
email 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 email.
GRADING:
The points for this course are derived from labs, quizzes, lab reports,
presentations and exams.
Possible Number of Points = 500
Activity
Lab participation and
Completion
Quizzes (top 10)
10 points per lab
Lab Report
10 points per
quiz
80 points
Lab Presentations
Exam 1
20 points
100 points
% of final grade
Scaled to12% of final
grade
Scaled to12% of final
grade
Scaled to12% of final
grade
4%
20%
Exam 2
Final Practical
100 points
100 points
20%
20%
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
http://www.uic.edu/ucat/catalog/GR.shtml
BIOS 221 Genetics laboratory
Lab Schedule
SOG (4) = SCHAUM’S OUTLINES GENETICS 4th edition
SOG (5) = SCHAUM’S OUTLINES GENETICS 5th 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
Aug 25/26
Aug 27/28
Introduction
Human Chromosomes
Quiz 1
Human Karyotype
Sep 1/2
Sep 3/4
Page
Syllabus
- Handout
- LM 41 -51
- SOG(4) p. 217-254
- SOG (5) p.182-211
Labor day 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
Sep 8/9
Probability and Pedigree Analysis
Quiz 3
a. Probability and Probability practice questions
b. Pedigree Analysis Handout
Sep 10/11
- Handout
- SOG(4) p. 6-27
- SOG(5) p. 2-22
Principles of Genetics and Chi-square analysis
Quiz 4
a. Corn Genetics
Ignore ‘duplicate genes with cumulative effect’
- Handout
- SOG(4) p.43-49
SOG(5) p.31-34, solved
problems 2.8-2.12 on
p.46-47
- LM p. 19-26
- Handout
- SOG(4) p. 64-65, and
73
SOG(5) p.42, solved
problem 2.22 p.52, 2.822.83 p.59
- LM p. 119-121
- Handout
- SOG(4)p.28-38, p.4955 and p.117-124
-SOG(5)p.23-29, p.35-38
and p.97-99, solved
problems 2.1-2.4 p.4344, 2.13-2.15 p.47-49
and 4.1-4.2 and 4.4-4.6
p.101-105
- LM 8-10, 11, 14-15
b. Chi - Square Analysis
- Handout
- LM 27-39
- SOG(4)p.58-64
- SOG(5)p.40-42, solved
problem 2.18-2.21 p.5052
Sep 15/16
Genetics of Co dominant genes
Quiz 5
- Handout
a. Blood Groups
b. Polygenic Inheritance: Finger print ridge count
Sep 17/18
- Handout
- LM p. 97-105
- LM p. 112-114
Drosophila Genetics
Quiz 8
a. Stages of life cycle, identify male & female,
identification of mutants
b.Sex determining Mechanism
- Carolina Drosophila
Manual p. 4-18 ( upto
Experimental Crosses)
- SOG p. 140-144
- SOG p. 146-149
- LM p. 1-8, 11-14
- Handout
c. Sex-linked inheritance
d.Set up Monohybrid and Dihybrid Drosophila
Crosses
Review for Exam I
Sep 22/23
EXAM I
Sep 24/25
Micro-Measuring and Bacterial Conjugation
Covers material from
Human Chromosomes to
Drosophila Genetics
- Handout
Quiz 6
a. Micro-Measuring
b. Bacterial Conjugation Part I
Sep 29/30
a. Bacterial Conjugation Part II
Oct 1/2
Viral Transduction
Quiz 7
a. Viral Transduction
b. Bacterial Conjugation Part III
c. Drosophila Genetics : Check for larva and remove
parents (F1)
Oct 6/7
- Handout- SOG(4)p.367-376
- SOG(5)p.302-308,
solved problem 11.1
p.320
- Handout
-
a. Viral Transduction II
b. Drosophila Genetics : Check for larva and remove
parents (F1)
Handout
Oct 8/9
Bacterial Transformation
Quiz 9
a. Bacterial Transformation, Part I
a. Bacterial Transformation, Part II
b. Drosophila Genetics : Collect data
Oct 13/14
- Handout
-SOG(4)p.336-338
-SOG(5)p.275-276
- Handout
- Handout
TBD
b. Drosophila Genetics : Collect data
Oct 15/16
Yeast Complementation
- Handout
Quiz 10
a. Complementation in Yeast-Part I
b. Drosophila Genetics : Collect data
Oct 20/21
- Handout
- LM p. 69-74
a. Complementation in Yeast-Part II
Exam 1 returned
Oct 22/23
Oct 27/28
a. Complementation in Yeast-Part III
b. Sordaria Genetics
Restriction Endonuclease Digestion of DNA
Quiz 11
a. Restriction Endonuclease Digestion of DNA, Part I
b. Complementation in Yeast-Part IV
c Drosophila Crosses (continued)
Oct 29/30
a. Restriction Endonuclease Digestion of DNA, Part II
- Handout
- Handout
- LM p75-78
- SOG(4) p. 410-419
-SOG(5) p.334-339,
solved problem 12.2
p.359
- Handout
- LM p85-87
Drosophila Lab Report is due on Blackboard safe assign by 11.30 PM on
Nov 1st for everyone regardless on their section.
Room 3085
Nov 3/4
Quiz 12 covers PCR Amplification of DNA
a. PCR-I
Room 3099
Presentations
Lab Report hard copy due in class for room 3085
and room 3099
- Handout
- SOG(4) p. 419- 421
- SOG(5)p.339-341
Nov 5/6
Room 3085
a. PCR- II- Analysis of PCR product
- Handout
Room 3099
Presentations
Nov 10/11
Room 3085
Presentations
Room 3099
Quiz 12 covers PCR Amplification of DNA
- PCR-I
Nov 12/13
Room 3085
Presentations
- Handout
- SOG(4) p. 419- 421
- SOG(5)p.339-341
- Handout
Room 3099
a. PCR- II Analysis of PCR product
Nov 17/18
Linking Genes to Diseases
- Handout
a. DNA Microarray
Nov 19/20
Population Genetics
a. The Hardy-Weinberg Principle -PTC tasting
Review for Exam II
Nov 24/25
EXAM 2
Drosophila report returned
Nov 26/27
Dec 1/2
- Handout
-SOG(4) p. 299-306
- SOG(5) p.248-251,
solved problems 9.1-9.6
p.255-257
- LM p. 107-112 (upto
“Part III”)
Covers topics from Viral
Transduction to end of
syllabus
Thanksgiving Holiday. No Classes
EXAM 2 returned
Topics covered after
exam to end of class
Final Review Session
Dec 3/4
FINAL PRACTICAL EXAM
Covers all topics