Consuelo Alvarez - Longwood University

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Genomics at Longwood University in Farmville, Virginia

At LU, Dr. Consuelo Alvarez, a biochemist in the BES department taught this spring 2008 a 4 credit course, Biology 425: Modern Genetics. I decided to spend the entire course working on GEP projects. The first part of the semester, we worked with "mojavensis" finishing projects and then, we moved to "erecta" annotation projects. There were 4 students in the class, who worked individually with the assistance of TA, Matthew Wadsworth, who also did his own projects.

Comments

General Comments

Time: I was able to secure a schedule that allowed me to work with the students twice a week for 3 hours each time we met. That probed to work very well. We spent more time than the allocated half of the semester working with the finishing projects since we want to "call for reads" at least 3 times and be able to incorporate them in the respective project. Overall, all students make progress on the projects; a couple of them completed their projects. Regarding annotation, all students completed their projects (naming genes with exon/intron boundaries) but we did not do Clustal, Repeats and Synteny analysis.

Projects versus Exercises: For the Finishing part, we spent only 3 classes going through projects files 16B18, XBAA7G24 and M_BB0112A10. At the third week of class, the first reads for claimed projects were called. Similarly, for the annotation part, we only spend 3 classes going through blast exercises 1 and 2. Then, we jumped straight into the finishing and annotation projects according to the schedule provided in the syllabus. We all shared information, learned and discussed along the way. We were in such a small room that any problem or success was immediately known by everyone in the class. And especially, anyone's problem became everyone's problem and at the end of the project time, other students besides the TA or I were helping or guiding in the class. TA, Matthew Wadsworth went through an "annotation walkthrough" presentation with his own completed project after students had gone through the practice exercises, and this turned out to be useful.

Outcomes: The students learned a lot from the experience of doing something that had not been done here before. They made progress on projects that they did not finished completely. All the students prepared oral presentations for the class and wrote papers about each finishing and annotation project. Only done at the end of the semester and taking Dr. Anya Goodman suggestions of possible annotation assessment questions, I wrote an internal assessment for this LU class related to both finishing and annotation projects. The summary of the students' results can be seen below.


FINISHING PROJECTS (4 students' answers)

  • For all questions written below, answer Yes/No, and why by providing any example that support your answer.
Question Responses
Is a finisher able to provide the absolute sequence an organism has? No(3) due to polymorphisms, mutations, variation.
Yes(1) if enough reads are correct.
Do you feel confidant to explain the terminology and concepts related to DNA sequencing? Yes(4) fairly confident and more so after taking this class; repetition helps.
Are you able to design a. PCR sequencing reactions or just b. PCR experiments? a. No(4) know concepts but more experience is needed; I don’t quite have the background.
b. Yes(3) and No(1)
Are you capable to maneuver the computer program consed? Yes(4) absolutely, we spent most of our time working with it.
Can you explain accurately the definition of high quality readings? Yes(4) no discrepancies found, multiple levels of coverage, trace peaks are high and well separated designating the base clearly.


  • From the following subjects, which ones do you think you will recommend other finishers to review before starting up their very first finishing project? Write Yes/No on each one’s side.
Subject Responses
The meaning of consensus sequence Yes (3)
No (1) b/c it is fairly obvious
The meaning of N in dNTP Yes (2)
No (2) b/c it is very obvious
The limitations of sequencing reactions Yes (4)
The definition of clones Yes (4)
The direction of DNA replication Yes (2)
No (1)
Maybe (1)
The mechanism of PCR reactions Yes (4)
The definition of polymorphism Yes (3)
No (1) b/c it is pretty easy


  • According to you own personal experience, what subjects to review are not mentioned above and you will recommend?
    • Know more detail about reactions 4:1 type and know all the capabilities/limitations of the consed program
    • Write below any additional comments (limitations, advantages, etc).
    • We work more in class than any other class we have taken and have less limitation on ordering reads


ANNOTATION PROJECTS (4 students' answers)

  • For all questions written below, answer Yes/No, and why by providing any example that support your answer.
Question Responses
Do you think that the nature of scientific knowledge is absolute? No(4) constant discoveries, exception in the rule to apply, new technology shed light on old ideas and although we strive for, we can’t know everything.
Do you feel confidant to explain and use the terminology and concepts related to genomics? Yes(4) especially in papers and presentations, at least much better than before.
Have you used and apply the central dogma of molecular biology and understand how molecular evolution uses it? Yes(3) it is an easy analogy between finishing and transcription and annotation and translation; the importance of exons in evolution;
No(1)
Are you capable to choose the appropriate web-based tools to find information about specific genes, proteins and genomes? Yes(4) definitions of different sites and tools; blast options (n, p, x, t to x, etc.)
Are you able to compare two or more nucleotide or protein sequences using BLAST and make inferences regarding molecular evolution and function? Yes(4) this seems simple now.
Analyze and synthesize information from various databases and BLAST experiments to predict novel gene structure and function (genome annotation). Yes(4)


  • What papers that you read during this class have helped you understanding more the field of genetics and genomics? Choose your top three selections by ordering them as 1, 2, and 3.
3 1 - - The 12 Drosophila’s genomes, evolution of genes and genomes
- - - 3 Drosophila transforming developmental biology and cell biology
- - - - Metabolic homeostasis
1 - 3 2 The next generation of sequencing, sequence census methods
- 2 - - Imaging Drosophila gene activation
2 3 2 1 Orchestrating size and shape during morphogenesis
- - 1 - Neurogenetics


  • From the following subjects, which ones do you think you will recommend others annotators to review before starting up their very first annotation project? Write Yes/No on each one’s side.
Question Responses
The difference between genomic DNA and cDNA Yes(4)
The meaning of locus Yes(3)
No(1) b/c we are not finding a locus
Differences between exons and introns Yes(3)
Maybe(1)
The sequence of standard splice sites Yes(4)
The sequences of potential cryptic splice sites Yes(4)
The sequence of a start codon Yes(3)
No(1)
The sequence of the stop codons Yes(3)
No(1)
When using blast, the significance of the E-value Yes(4)


  • According to you own personal experience, what subjects to review are not mentioned above and you will recommend?
    • More on the programs and less on Genetics; that covers about everything.
  • Write below any additional comments (limitations, advantages, etc).
    • More time for annotation; not as frustrating as finishing.


Future: I am planning to teach this class again in spring 2009 and to check with former students for outside the University presentations about their work (probably NCUR 09 in WI) as well as an in house presentation before recruiting students for the spring 2009.


Syllabus for Biology 425 - Modern Genetics

Last Taught Spring 2011, Longwood University, College of Liberal Arts and Sciences, BES department

MODERN GENETICS (BIOL 425, Section 01)
4 Credits and Computer Laboratory Required
Spring 2011 Syllabus
Lecture and Lab Days: Tuesday and Thursday from 9:30 to 12:15 p.m., Science Center #101
Instructor: Dr. Consuelo Alvarez e-mail address: alvarezcj@longwood.edu
Office Location: Science Center# 306 Phone: 395-2847
Office hours: 11:00-1:00 PM (M), 1:30-2:30 PM (W), 2:00-3:00 PM (R); or by appointment.


Textbook in reserve at the Library:

  1. Discovering Genomic, Proteomics and Bioinformatics by A. Malcolm Campbell and Laurie J. Heyer.
  2. Genetics. Analysis and Principles by Robert Brooker. Published by Mc Graw Hill, 3rd edition.
  3. Color Atlas of Genetics by Eberhard Passarge, 3rd edition.


Course Objectives:

  1. 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 mojavensis or grimshawi 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 mojavensis or grimshawi in addition to annotate either Drosophila mojavensis or grimshawi of already “finished” sequences projects.
    5. Students will have the opportunity to have their complete work as part of a peer-reviewed manuscript.
    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 put in blackboard PRIOR to the time that these materials is 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 class period. Quizzes will cover material presented during lecture time 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 the classroom (this is probably true for all classes-not just this one). Disrupting a class because of a ringing phone 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, 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 papers 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. The instructor will not accept any work put into her mailbox. 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) 25% (250 pts) >90% A
Reading assignments 25% (250 pts) 80-89% B
*Presentations, 2 20% (200 pts) 70-79% C
+First draft papers,1 10% (100 pts) 60-69% D
*Final version papers, 2 20% (200 pts) <59% F


*One for each project, that is one for Finishing and one for Annotation

+ Only for Finishing

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 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
1-8  01/18-03/11
  • Overview of Modern Genetics.
  • Finishing project
    • Introduce to Consed software.
    • Practice with the Mouse 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, 01/25 at 5:00 PM

Grades estimates due 02/28, noon

Withdraw dateline, 03/08 at 5:00 PM

8   03/11 

First draft paper and presentation, Tuesday 

In class time
9 03/14-03/18                        Spring break vacation
 **11   03/29

Final Finishingpaper, Tuesday 

In class time 
10-15  03/21-04/29 
  • Annotation project
    • 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 begins 03/24

16  05/16

Final version paper and presentation for Annotation, Thursday 

11:30 AM


Earth day Events: during first 20 minutes of each class on April 19th and 21st we will have guests visiting our class! 

Handouts for programs and other materials will be given to you one time but you can also access them at the web site: http://gep.wustl.edu

We will read assignments from Nature, Vol 450, issue 7167, Nov. 8, 2007 Pgs 1-36; Nature Methods, Vol 5, number 1, Jan. 2008 Pgs: 11-21; American Laboratory, Nov-Dec 08, 48-53 as well as from other sources if needed. The tentative schedule will be posted on blackboard.