Course URL Spring 2014- Mon/Thur 11:00 to 1:00 PM (Advanced undergraduate or first year graduate level course) Location MSB

R3351

Saima Riazuddin, PhD  Office Phone: 513‐803‐2888  Email: Saima.Riazuddin@cchmc.org  Office location: CCHMC, R building  R2‐2407  Optional discussions (by appointment  via email) 

The beginning of the 21st century has revolutionized the world of genetics. Geneticists are immersed in exciting science, technology and medical breakthroughs every day. The recent technological advances have allowed the scientific community to discover the complete genomic sequences of organisms ranging from microbes to humans. These discoveries have enabled a shift from pedigree based studies to analysis of populations of unrelated individuals, and consequently from single gene to complex disease. We are learning how life evolved, and the genetic differences that separate one species from another. The study of human genetics impacts almost every aspect of our society, from medicine to law enforcement to how we view ourselves. In addition, human genetics is a topic that gets frequent attention in the press. Reports about genes for traits ranging from breast cancer to criminal behavior are constantly in the news. The capability to comprehend the fundamental of genetic analysis will assist you throughout your life journey, where it’s assured that you’ll be faced with a major decision involving your heredity; and society will be forced to make reforms in medicine and law due to our vastly increasing genetic knowledge. This course will introduce you to the very latest strategies in human genetics; will cover the full spectrum of human disease and will empower students to become critical readers of the primary literature.

About  5000  disease  are  known  or  suspected  to  have  a genetic  etiology.  During  recent  years  the  genetic  and molecular  basis  of  many  genetic  disorders  has  been unraveled.  In  this  course  the  students  will  learn  about  the different  experimental  designs  for  identifying  disease genes  and  use  of  model  organisms  for  modeling  disease and investigating gene function.

The figure on the right is a revised version of “Bloom’s Taxonomy”. Bloom’s Taxonomy was created as a method of classifying educational goals for student performance evaluation. At this stage of your career, you should already be equipped at remembering facts and contents with good study habits. In this course, I am looking for you to move beyond memorizing to applying and analyzing. In order to achieve these goals, we will have in-class questions to answer and in class problems to solve. You will also be assigned homework problems to practice on your own. You will be expected to review data sets and primary research articles and come up with hypotheses and design experiments for unanswered questions. Briefly, by the end of this course, student will be able to:     

The revised Bloom’s taxonomy.  http://www.learnnc.org/lp/pages/4719 

Explain the core principals of genetics and molecular biology. Review latest genetic and genomic technologies for analyzing data. Demonstrate the significance of research in genetic model organisms to understand fundamental and biological phenomena. Interpret and critically review primary research articles. Develop hypotheses and design experiment for unanswered questions in human genetics, in order to gain higher level thinking skills that are necessary for scientists.

Undergraduate level classes in biochemistry and molecular genetics, or the equivalent.

Human Molecular Genetics 4th Edition, T. Strachan and A.P. Read, Garland Science Press, April 2010 Advanced Genetic Analysis: Genes, Genomes and Networks in Eukaryotes. Philip Meneely, ISBN-13: 978-0199219827 Oxford University Press. 2009

Genetics: From Gene to Genomes Leland Hartwell, Leroy Hood, Michael Goldberg, Ann Reynolds and Lee Silver. 2011 Additional readings from the literature or online will be made available through blackboard PubMed: http://www.ncbi.nlm.nih.gov/pubmed?dr=cita tion&holding=cnchlib,ohiolinklib,ucmclib,cnc hlib_fft NCBI: http://www.ncbi.nlm.nih.gov OMIM:http://www.ncbi.nlm.nih.gov/sites/entr ez?db=omim BLAST: http://blast.ncbi.nlm.nih.gov/Blast.cgi RCSB Protein Data Bank: http://www.rcsb.org/pdb/home/home.do
UCSC genome bioinformatics: http://genome.ucsc.edu/

Course Policies
Electronic Communication  If you have a laptop with  wireless capability, bring it  to the class to facilitate in‐ class searches on questions  that arise.   As a courtesy to the all the  members of our classroom  and online community,  please turn off your cell  phones and keep your side  conversations to a  minimum.  No cell phones and laptops  will be allowed in class on  the exam days.  You will need to purchase a  personal response system  (PRS) transmitter (or clicker)  from the book store or  online. Its is called a  Response Card RF by a  company that makes it  (http://www.turning  technologies.com  Blackboard will be used for  posting course documents,  online quizzes, for  posting/receiving  assignments and for posting  grades. Use the links here to  Log in to Blackboard or  connect to Blackboard  support. 

 

Course materials will be handled through the course’s web page (http://blackboard.uc.edu). Check this page regularly for announcements, assignments, reading material, other class-related material, including changes to the syllabus schedule. Basic lecture notes will be posted.

Before class students are expected to read assigned text, watch assigned videos and carefully read assigned journal articles, take notes and complete online quiz. Students are expected to bring questions and notes to class.

We will break the class time into three portions. First portion: Discuss and review assigned readings or lecture, answer questions (15-20 mins). Second portion: Group activities that require higher level thinking skills and individual quiz with higher level thinking skills (15+ 5 mins).

Third portion: Formal students (20 mins).

group

presentation

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Course Policies
Attendance
If you want to do well in this course  you should attend every lecture.  Because the field of human  genetics is progressing at such a  rapid rate, any text book published  to dates is already outdated. There  will be considerable amount of  material in the lecture that is not  included in the text. The material  will not be made available to those  who do not attend the class, unless  the student has a legitimate excuse. 

Learning requires student to actively contribute both inside the class room and after class. Class participation is an integral part of the learning process. Answering questions posed during lecture and energetically being a member of group during activities will reinforce your learning and help make the class enjoyable for all participants.

You will give one 20 minutes formal group presentation during the semester on a genetic disorder of your choice; it must be the one that we do no otherwise cover. No two groups can choose the same topic, so clear your topic with me early on. Background information on the disease should take up about half of your presentation. Analysis of an original research paper should take up the other half. I must approve your research paper choice and you must have it in hand at least seven days before your presentation. Don’t try to explain the entire paper- instead pick the most crucial two or three figures and explain those in detail. You must prepare a handout with an outline and any important image to distribute to the class. The grading rubric is as follows: background section, 25 points; explanation of research paper, 25 points, fielding questions from audience, 20 points; handouts, 10 points, effectiveness of method (powerpoint etc.), 10 points; public speaking presence (voice, posture, enunciation), 10 points. 

Bad Weather
This course will follow the  University policy on bad weather. 

Disability
This course will involve a large  amount of reading and writing. If  you have a special need related to  your participation in this course,  please contact the instructor at  Saima.riazuddin@cchmc.org 

Late work
Generally, late work will not be  accepted. This said, I understand  that there are often occasions  which occur that will make finishing  assignments on time difficult. If  such a circumstance comes up,  please contact me as soon as you  can, and I will work with you. 

There will be five individual problem sets (40 points) that will be passed out one week before they are due. Your grade will be based on the top four. Late homework assignments will not be accepted. If you must miss a problem set then your score will be based on the remaining four. In addition there will be group problems (25 points) which will be solved in groups. All group members will receive the same credit. Before coming to class, students will complete online quiz that will be based on assigned material. During the class, students will individually take daily quizzes using their PRS transmitter. Written PRS answers will not be accepted if your

clicker is lost or broken. You must correctly answer 80% of these questions to earn the full credit for your final grade. The quizzes will address key points from the module, including lectures and presentations. There will be two midterm exams and a final. Exam material will be drawn from required readings, lecture material, and in class activities. No make-up exams will be given. In case of emergency please contact Dr. Riazuddin (Saima.Riazuddin@cchmc.org).
Quizzes Mid-term exam Final Exam Formal group presentation Final Project (written summary evaluation of a research paper) 60 points Class participation and general participation 15 points

Problem sets

40+25=65 60 points points

50*2=100 100 points points

100 points

Your final grade for the course will be calculated as follows: A+ A AB+ B B490-500 465-489 450-464 440-449 415-339 400-414 C+ C CD+ D DF 390-399 365-389 350-364 340-349 315-339 300-314 <300

We want this class to be beneficial and fair to all students. If you don’t hold yourself to a high standard of honesty and personal integrity, please don’t sign up for this course. We will apply the rules if we are forced to. The University Rules, including the Student Code of Conduct, and other documented policies of the department, college and university related to academic integrity will be enforced. Any violation of these regulations will be dealt with on an individual basis according to the severity of the misconduct. See the following websites for complete information: http://www.uc.edu/conduct/Code_of_Conduct.html http://www.uc.edu/conduct/Academic_Integrity.html

Policies for adding, dropping, or withdrawing from a class can be found through the office of the Registrar at the University of Cincinnati (http://www.uc.edu/registrar/policies_and_procedures/add_drop_withdrawal.html). Generally a student is allowed to drop from a course by the 15th day of the semester with no academic penalty. A course withdrawn because of excessive absence is not

eligible for academic credit or refund of fees. If you are receiving financial aid, there could be repercussions for withdrawing http://financialaid.uc.edu/eligibility/recalculation.html.
 

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