Dale Beach

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Genomics at Longwood University

Longwood Genomics Iinitiative Overview 

The Longwood Genomics Initiative seeks to bring cutting edge, "modern" genetics to students as part of a student research centered series of courses. Some of the modern genetics applications include the application of genetics to human diseases, genomic analysis of model organisms, modern sequencing methodology, the molecular mechanisms of diseases, recombinant and synthetic biology strategies,  and comparative analysis of DNA and Protein sequences. Where possible, students are encouraged to develop their own projects modeling an active research structure, including literature based hypothesis proposal, experimental testing, and public presentaion of results in oral and written formats. The GEP facilitated projects primarily support the genomic sequencing and comparative analysis. Students in our "Modern Genetics" course are expected to complete both a finishing and annotation project from the partnership. In the future, we hope to include annotation projects and comparative genomic analysis into additional courses in cellular and moleuclar biology as well as an introductory module for the general biology courses taken by first year biology majors.

Implementation 

Genome Structure, Next-Gen and traditional sequencing, and comparative analysis are the primary topics covered by the "Modern Genetics" course.The laboratory portion of hte course is primarily focused on the GEP program projects. Student begin with a Finishing project to understand DNA sequence data, contig assembly, and the modeling of a biological concept (genomic DNA sequence) in a computational environment, and then move to the Annotation to continue to develop the ideals of model building and hypothesis testing given software based gene predictions. Generally the course includes 2 hours of lecture and 4 hours of lab per week. Lecture is primarily devoted to topical discussions to develop GEP projects and discussion of pertinant literature. Students must have ocmpleted a general genetics course before enrolling in the Biol425 course. Therefore the course serves upper division students as an elective for their B.S. curriculum requirements.

Lessons Learned and Future Plans :

Spring 2013 is my first offering of the course. We have just finishined the "Finishing" portion of the course, and will begin the "Annotation" portion next. Thisngs to change for next time include better preparation for the students to use the Consed program - complete a Demonstration first, then allow them to try it out with the workshop, and then walk through a second demo to reinforce and discuss WHY they are doing each activity. The first two get them familiar with the software, use the last demo to develop the inquiry and application of the program to the Finishing project. Following this introduction, lead them through the first few lab sessions with organized activities to help them aclimate to using the program to develop their own work.


Another possible approach would be to develop a video based demo for an "inverted classroom" appraoch - then have them repeat the demo in the class to clarify the steps and the outputs from the computer.


Time well spent: In one of the first lab sessions developed a "Team Building" exercise where students assembled a Jigsaw Puzzle. The activity was compared to the Assembly of several seemingly unrelated pieces of DNA into the Contig. We have continued to reference this activity throughout the course. I will certainly use this again at the beginning of the course.

Use of GEP Curriculum Materials

Syllabus for Modern Genetics (Biol425)

MODERN GENETICS (BIOL 425) Spring 2013 Syllabus
4 Credits and Computer Laboratory Required

Lecture and Lab Days:      Tuesday and Thursday from 12:30 to 3:15 p.m., Science Center #101.

Instructor: Dr. Dale Beach        e-mail address: beachdl@longwood.edu
Office Location: Science Center# 308B Phone:   395-2198
Skype: beach.dale
Office hours: 11:00-1:00 PM (M), 1:30-2:30 PM (W), 2:00-3:00 PM (R); or by appointment.

Textbooks in reserve at the Library for your reference:
1. iGenetics: A Mendelian Appraoch.  by Peter Russel.   -  Genetics Review
2. Molecular Biology 4th Ed. by Robert Weaver - Info regarding molecular mechanisms. 

Required Textbook: Greg Gibson and Spencer Muse, A Primer of Genome Science- Third Edition.2009.  Sinauer Associates INC. ISBN-10= 0878932364
     
Course Objectives:
1. Students will actively work on nation-wide-genomic-projects through our partnership with Washington University at Saint Louis, MO. To learn more about the partnership, please visit http://gep.wustl.edu
2. Students will apply their knowledge of basic genetics to analyze and compare the putative dot chromosome of Drosophila spp to the other fly genus.  In other words, students will understand and put to practice the Central Dogma information as it relates genes (nucleotide sequence) to proteins (amino acid sequence) and their homology among different species.
3. Students will be able to learn more about Sequencing methodologies, PCR experiments and blast programs among others.
4. Students will produce high quality finished sequence for the putative dot chromosome of Drosophila spp in addition to annotate Drosophila spp of already “finished” sequences projects.
5. Students will have the opportunity to have their complete work as part of a peer-reviewed manuscript.

    Catalog Description: A study of the structure and function of hereditary material at the molecular level.  Topics include DNA-RNA structure and replication, protein synthesis, and homeostasis.  Prerequisite: BIOL 324.   3 lecture and one 3-hour lab periods. 4 credits.

Class:
    Students should check and read the lecture notes and review subjects put in blackboard PRIOR to the time that these materials are to be presented in class.  Also students need to read the articles assigned for each class. All of these will prepare the students for discussions we will have every week period.  Quizzes will cover material presented during lecture time, knowledge of the programs used in both projects as well as questions related to the assigned reading articles.  You should use the website http://gep.wustl.edu to prepare for your presentations and papers since examples are provided in it.  Guidelines will be discussed in class.
     Students are required to abide by all Longwood University policies with regard to registration and withdrawal requirements and academic honesty.  Failure to follow these policies may result in not receiving credit for the course or receiving a failing grade.  Students should turn off phones before entering any classroom.  Disrupting a class because of a ringing phone or texting will result in a 5% deduction to the student’s final grade for the first offense.  A second offense will result in 15% deduction to the final grade and so on.
   
Blackboard:
     Students should access in BIOL 425 on Blackboard within the first week of class.  (http://blackboard.longwood.edu) Syllabus, Lecture notes, Assigned reading articles, Quizzes schedule, Internet links, and other useful information will be distributed through Blackboard.  Messages concerning the class will also be posted on Blackboard.

Attendance:
     Attendance is mandatory and it will be recorded daily.  Students are required to attend a minimum of 75% of the course sessions in order to receive a final grade in the course.  The student is responsible for being aware of announcements/schedule changes that may be made during any class and for any material covered during an absence.  No additional class time will be devoted to covering material for the benefit of someone who has missed a class.  Students should check Blackboard regularly for messages concerning class. 
     Missed work that is the direct result of an excused absence must be made-up before the 2nd class period after returning to class.  Missed work that is the direct result of an unexcused absence cannot be made up and will be graded as a zero. Missed quizzes CAN'T be retaken.  Missed papers datelines and presentation datelines are not to be rescheduled.  If you miss a session, your participation grade for that session is "ZERO".  Dismissal from the session for any reason will result in the student obtaining a "zero" for that activity, and that session will be counted as an absence.  Missed sessions will need to be done on your own time so you can complete the work.
     Dismissal from the computer laboratories and a zero for the session in question will be granted to students who do not follow the computer laboratory guidelines.  That is, 1) food, drink, and smoking are never allowed in the computer labs, 2) the computer lab is a serious environment and there is no room for horseplay or joking around, and 3) violations for using cellular phones.  Any such inappropriate behavior will result in the student(s) being dismissed from the session.
     The definitions of excused absences are given in the Longwood University handbook.  All unexpected excused absences must be documented by the student and discussed with the professor on the first day that the student returns to class.  Failure to provide documentation immediately upon returning to class from an excused absence will cause the absence to be counted as unexcused.  If a student knows that he/she will be absent on the day of a graded exercise due to a sanctioned school event, it is the responsibility of the student to provide the professor with written verification of the student’s participation in the event prior to the day of the class to be missed.  Failure to provide advance notice will result in the absence being counted as an unexcused absence. 
     Participation is mandatory in class throughout the semester.  In every class, questions about troubleshooting problems of any project or class material as well as reading material will be asked and all students are required to answer them and be prepared to discuss.

Grading:
     All students begin the class with ZERO points, and the grade received depends upon the number of points accumulated throughout the semester compared to the total number of points possible.  Students can earn points towards their final grade in the following areas: Quizzes, Reading assignments, Presentations, First draft paper and Final version papers.  There will be no extra credit work.  There will be no makeup work of any type.  No late work will be accepted.  Every effort should be made to hand graded work directly to the instructor.  Every effort will be made to return graded materials within one week of the due date.  The point distributions and grading scale are shown below.  Grades are not curved, but for borderline cases, special consideration may be given to those students who clearly and consistently demonstrate a serious work ethic in the class.  Students should maintain records of all grades received and are encouraged to calculate the cumulative point total as the semester progresses. 

Point Distribution              Grading Scale:        
    Quizzes (5)    50 pts each  25%  (250 pts)   >90% A
    Reading assignments (10) 25 pts each  25%  (250 pts)        80-89% B
  *Oral Presentations (2) 100 pts each 20%  (200 pts)    70-79% C
  #First draft paper (1) 100 pts         10%  (100 pts) 60-69% D
  *Final version papers (2) 100 pts each 20%  (200 pts)    <59% F

  • One for each project, that is one for Finishing and one for Annotation.
    # Only for the Finishing project.

Course-work Assistance:
     Individual help may be obtained from the instructor during assigned office hours [11:00-1:00 PM (M), 1:30-2:30 PM (W), 2:00-3:00 PM (R); or by appointment in the science building room # 306], but the professor reserves the right to limit the time spent with a student.  Students may use e-mail and Skype to ask questions, but it may not be possible to answer all questions immediately.  Study groups are strongly encouraged.  Small groups of students may come together to office hours.
    
Class Schedule (Note: schedule may be changed at instructor’s discretion).
Weeks Dates Major lecture topics Notes



1-7


01/15 - 02/28 Overview of Modern Genetics.

Finishing project
Introduction to Consed software.
Practice with demo finishing project.
Claim projects.
Find High Discrepancy regions.
Call for readings (PCR oligos order)
Fill in gaps.
Assemble final sequence.
Check and send back to WUSTL

Last day Add/Drop  01/24 at 5:00 PM

Grades estimates due 02/25, noon

Withdraw dateline 03/13 at 5:00 PM

7 02/28 Presentations / First draft Paper
Thursday In class time

8

03/04-03/08



Spring break vacation

DUE
Date 03/15 Final version Finishing Paper
Friday by 5PM Finishing Paper DUE
(10% penalty per late day)



9-15


03/12– 04/27

Annotation project
Introduction to Blast programs.
Web sites to use.
Chimpanzee annotation project.
Claim projects.
Find Genes. Comparisons.
Validation.  Intron-Exon boundaries.
Isoforms detection.
Check and send back to WUSTL


Registration Advising begins 03/21


16
05/02 Final Version Paper/Presentation 
Annotation
Friday
11:30 AM


    

     Readings and  Handouts and other materials will be available on the Blackboard Site, and you can also access them at the web site: http://gep.wustl.edu
   
Reading Assignments and Quiz Dates will be posted in separate files on the Blackboard Site.