Susan Parrish

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Biology 3312: Genomics Lecture & Laboratory (Spring 2013)

Lecture: Lewis Recitation Hall 325; M/W/F 9:10 – 10:10 am Laboratory: Eaton Hall 207; T 1:00-4:00 pm

Professor: Dr. Susan Parrish Eaton Hall, Room 212 (410) 871- 3122 sparrish@mcdaniel.ed

Laboratory Classroom Assistant (for annotation project): Ms. Carol Marques dos Santos Vieira

Texts and Required Materials:

1) A Primer of Genome Science. 3rd edition. Gibson, G. and Muse, S. (2009) Sinauer Associates, Inc. (Recommended)

2) Short Guide to Writing about Biology. 7th edition. Pechenik, J. (2009) Longman. (Recommended)

3) Exploring Genomes. 2nd edition. Young, P. G. (2008) W.H. Freeman and Company.

4) A flash-drive and a small spiral notebook are required for the laboratory annotation project.

Course Description and Objectives:

Welcome! ☺ You are about to embark into the realm of Genomics, one of the newest and most rapidly expanding fields of modern Biology. The term Genomics describes the study of scientific questions through analysis and comparison of whole genomes, a feat only recently possible with the advent of modern sequencing technology. Intertwined closely with Genomics, the field of Bioinformatics allows for the development of computational methods to archive, organize, and analyze the enormous amount of sequence information gathered from genome sequencing projects. In this course, we will explore how scientists are taking global Genomics approaches to answer fundamental questions in all aspects of Biology. In addition, Genomics is a Writing in the Disciplines (WID) course; therefore scientific writing will be significantly emphasized. You are encouraged to use the Writing Center (x4645, Hill Hall) as a resource for this course.

Our learning objectives for the course include the following:

1) To explore the concepts and implications of genomics and bioinformatics Biology Department Objectives: Students investigate the unifying principles of Biology; Students explore several different areas and sub-disciplines of Biology

2) To read and evaluate scientific literature General Education Objectives: Critical Thinking; Communication; Biology Department Objective: Students explore the scientific literature in the field of Biology

3) To deliver and convey scientific information in written and oral formats General Education: Communication; Biology Department: Students demonstrate effective oral and writing skills

4) To utilize genomic databases and algorithms to answer scientific questions General Education: Critical Thinking; Creative Expression and Problem-Solving; Biology Department: Students engage in science as a process; Students demonstrate laboratory skills; Students understand and, where possible, practice using the technology appropriate to the discipline

5) To perform an original Genomics research project in collaboration with the Genomics Education Partnership (GEP) General Education: Critical Thinking; Creative Expression and Problem-Solving; Communication; Biology Department: Students demonstrate effective oral and writing skills; Students engage in science as a process; Students demonstrate laboratory skills; Students understand and, where possible, practice using the technology appropriate to the discipline

Learning Format:

To foster the learning process, the class period will consist of lectures and interactive classroom activities, such as concept mapping, journal club discussions, student presentations, etc. The laboratory component of the course is entirely computer-based and will consist of in-class weblems and the Genomics Education Partnership (GEP) annotation research project.

Blackboard:

The class syllabus, lectures, primary literature, and grades will be available on Blackboard. Please note that the lectures will be posted prior to the class period and that the grades on Blackboard are not weighted. You are strongly encouraged to take notes during class and to use the posted lectures to supplement your notes taken in class.

Grading Breakdown:

• Lecture

1) 3 exams each worth 10% each = 30%

2) Disease Gene Case Study Paper = 15%

3) Journal Club Discussion Presentation = 10%

4) Assignments = 5%

5) Attendance/Promptness (Lecture & Lab) = 5%

• Laboratory

6) Laboratory Weblems & GEP Notebook = 10%

7) Laboratory Annotation Paper = 15%

8) Laboratory Annotation Presentation = 10%  Laboratory Weblems and GEP Notebook Checks (10%):

• Weblems During the laboratory, you will be required to solve assigned problems using genomic web resources (a “weblem”). You are strongly encouraged to complete the weblem during the laboratory class (highly recommended by all of the 2009-2012 Genomics students!) Weblems are due by the next laboratory period. Late weblems will receive 1-letter grade reduction if turned in outside of the laboratory period and an additional 1-letter grade reduction per day late.

• GEP Notebook During the GEP laboratory annotation project, your notebook will be periodically checked by Dr. Parrish to ensure adequate progress and proper project documentation.

What information should be documented in the GEP notebook? a) Date, b) project description (species, contig # and size), c) gene id #, d) procedure used to acquire data (i.e. BLAST algorithm), e) D. melanogaster ortholog BLAST hits (include BLAST alignment numbers, E-value, % identity, gaps #, frame number, etc.), f) D. melanogaster ortholog synteny, g) # of splice isoforms and differences between them, h) D. melanogaster ortholog function and conserved domains, i) start and stop codon coordinates, and j) splice junction coordinates and any other relevant information.

You are also required to “capture” web images along the way and save them on your flash drive. This documentation will help you immensely with your final paper and presentation and also will be useful if your data is included in a GEP publication.

• Please note: The GEP research project cannot be used as your capstone research project since it is performed in-class.

Laboratory Annotation Project Paper (15%):

• Introduction & Methods Draft Due Date (double-spaced): Wednesday, April 24th (worth 5% of final paper score)

• Results/Discussion/Abstract Draft Due Date (double-spaced): Monday, May 6th (worth 5% of final paper score)

• Paper and Electronic Version Due Date: Final Exam Period: Monday, May 13th 8:30 am-11:30 am

• Length: However long you need (will have lots of images from web capture) + references

• Topic: A description of your laboratory annotation project written in your own words (must be distinct from laboratory partner or will be considered plagiarism and a violation of the McDaniel College Honor Code)

• Paper Format: This paper will be written as a scientific research article (since after all, it is an actual research project!). The paper will be divided into the six following sections: I) Abstract II) Introduction III) Methods IV) Results V) Discussion VI) References

• What should be discussed in the Annotation Project Paper? Please see Syllabus Appendix E: GEP Annotation Paper for a detailed description of the areas to discuss for each section of the paper and the reference format. Also, you can visit the Genomics Education Partnership webpage http://gep.wustl.edu/ and select “Curriculum” (on green bar), followed by “Student Work” to view samples of student papers on annotation projects.

• How will the Annotation Paper be graded? Please see Syllabus Appendix E: GEP Annotation Paper for the rubric that will be used to grade the annotation paper. Late papers will receive 1-letter grade reduction if turned in outside of the final exam period and an additional 1-letter grade reduction per day late. If it is clear that one partner is doing most of the work (and this is verified by this partner), grade reductions in both the final annotation paper and presentation will be taken for the non-contributing partner.

Laboratory Annotation Project Presentation (10%):

• Presentation Date: Final Exam Period: Monday, May 13th 8:30 am -11:30 am

• Length: ~ 20 minute Power Point presentation + 5 minute Q&A session

• Topic: A description of your laboratory annotation project delivered by you and your GEP partner

• Additional Information: Please see Syllabus Appendix D: Scientific Presentations for advice on delivering scientific presentations. Also, you can visit the Genomics Education Partnership webpage http://gep.wustl.edu/ and select “Curriculum” (on green bar), followed by “Student Work” to view samples of student presentations on annotation projects.

• How will the presentation be evaluated? Please see Syllabus Appendix D: Scientific Presentations for the rubric that will be used to grade your presentation. If it is clear that one partner is doing most of the work (and this is verified by this partner), grade reductions in both the final annotation paper and presentation will be taken for the non-contributing partner. This is the final exam for the course and participation is mandatory.

Bio 3312 Genomics Laboratory: Tentative Laboratory Schedule (subject to change)

T Jan 29 Welcome: Science Paper & Genomics Education Partnership Pre-Quiz

T Feb 5 Intro to Genomic Databases Young 1-5 & Introduction to Entrez Young 6-10 & Introduction to Pubmed/OMIM Young 22-29

T Feb 12 2/5 Weblem due; Introduction to Blast Young 11-21& BLAST papers

T Feb 19 2/12 Weblem due; Finding Conserved Domains Young 30-33 Clusters of Orthologous Groups Young 34-36

T Feb 26 2/19 Weblem due; Functional Analysis Young 42-44 & Cancer Genome Project Young 45-49 & ClustalW 

T March 5 2/26 Weblem due; Introduction to Annotation Project

T March 12 3/5 Weblem due; GEP Annotation Project 

T March 19 Spring Break 

T March 26 NB check; GEP Annotation Project 

T April 2 NB check; GEP Annotation Project

T April 9 NB check; GEP Annotation Project 

T April 16 NB check; GEP Annotation Project

T April 23 NB check; GEP Annotation Project

T April 30 NB check; GEP Annotation Project 

T May 7 Project Submission! ☺ & GEP Post-Quiz Syllabus Appendix D: Scientific Presentations: GEP Presentation

1) Slide Layout: Use a slide background that confers some visual interest but is not distracting or blocking text or visual images. Keep the slide layout consistent throughout the presentation.

2) Text: The minimum font size should be 24. Font should be in stark contrast to the slide background for optimal visibility (for example: either black font on white background or yellow font on blue background). Ensure that text is not blocked by the slide layout or any images. Avoid putting too much text per slide and do not write out complete sentences. Keep the font consistent through the presentation. Spell-check the text.

3) Titles: Include a title slide with the name of the presentation and the presenters. Each subsequent slide should have a title that summarizes the main point of the slide. The size of the title font should be larger than the text on the slide.

4) Figures: Whenever possible, use an image to convey the point of the slide and keep text to a minimum (try to have an illustrative image on every slide). Visual images are generally easier to understand than text and help keep audience interest. Do not use images that are fuzzy or unclear. If you cannot find an appropriate image, consider making a diagram or figure in PowerPoint. Make sure that images are large enough for the audience to see. Include the website address below the figure for an image acquired from the Internet.

5) Slide content: Keep slides simple. Try to make only one major point per slide. When presenting a journal article, show each figure as a slide as you go through the data. If the figure is complicated, separate the figure panels onto different slides for clarity.

6) Talk Organization: I) Title Slide, II) Outline of sections of talk, III) Introduction (example: background and questions addressed), IV) Results/Main Part of the Talk (example: figures from paper, one by one), V) Conclusions (a visual model is a great way to conclude a talk), VI) References

7) Talk Preparation: Rehearse your talk numerous times and make sure that you are within the mandated time period. Ensure that you know how to transition between slides and the overall order that you will go through each section of a particular slide. Make sure you know how to correctly pronounce the words in your talk (you can type into Google “Pronounce ….” to get a spoken example).

8) Day of Talk: Bring your talk on a flash drive, saved both in the older 97-2004 version of Powerpoint (.ppt) and the newer PowerPoint version (.pptx). To be cautious, you may want to also e-mail your presentation to yourself. Although not required, professional attire always makes a good impression!

9) Delivery: Make eye contact and face your audience while presenting. Do not read directly from the slides and I encourage you not to use note cards. Go through each slide as slowly as possible. Actively point out important part of figures and diagrams. If you use a laser pointer, do not wave it around, as this is distracting. Most importantly, be enthusiastic! ☺

Dr. Parrish’s Presentation Rubric

Presenter_____________________________________ Presentation__________________________________

Each item below is worth 10 points:

Introduction:

• sufficient

• appropriate for audience

Visual Aids:

• slide layout

• images

Language:

• text

• titles

• spelling

• pronunciation

Delivery:

• eye contact

• facing audience

• proper pointing

• appropriate pace

• enthusiasm

• professionalism

Organization:

• title, outline, background, main, conclusions, references

• each section organized

• within time limit

Conclusions:

Clarity of Content:

Thoroughness:

Interpretations:

Question/Answer Session: Grade:  / 100

Syllabus Appendix E: GEP Annotation Paper

I) Abstract

Briefly:

• Define annotation

• Describe major results: Drosophila species annotated, chromosome, contig, size, predicted genes, annotated genes, Drosophila orthologs, number of isoforms in D. melanogaster, gene features annotated, etc.

• Define overall, big picture project goal (chromatin structure?)

II) Introduction

Describe:

• Genomics education partnership (can reference Science paper)

• Comparative genomics of Drosophila (phylogenetic tree)

• Dot chromosome description and differences in chromatin structure in other species, links to type of repeats

• What is annotation?

• Brief description of annotation strategy (computational, comparative), gene features annotated, etc.

• What you will discuss in this paper: species, chromosome, contig #, gene identification, start and stop of translation, exon/intron boundaries/UTRs and repeats

III) Methods

• Describe methods (including all algorithms, etc.) used to annotate your contig/fosmid (how determined D. melanogaster ortholog, Gene Record Finder, etc.) with relevant screen shots

• Provide one example of exon annotation with relevant screen shots (blastx with exon aa sequence melanogaster ortholog vs. translated contig, E-values and % identity, UCSC genome browser picture, GT marks beginning of intron, AG marks end)

• Gene Model Checker method for verification

IV Results

A) • Define species, chromosome, contig/fosmid, size

• GenScan prediction description (Please remember this is the hypothesis you are testing!)

For each Putative Gene:

B) Putative Gene 1 (or Feature 1 or example: 17.1)

• Include all relevant screen shots

• D. melanogaster ortholog; E-value and % identity and why this is the most likely ortholog (BLAST screen shots critical!)

• Function of protein in D. melanogaster and conserved domains

• Chromosome location of D. melanogaster ortholog (synteny?)

• Ensembl or Gene Record Finder picture of isoforms

• Discussion of isoforms

• Must have gene model diagram for all genes and splice isoforms (Indicate clearly non-coding vs. coding exons, translation start and stop coordinates, splice junction coordinates)

• Repeat for unique isoforms

• If applicable: Use of small exon finder algorithm

• If applicable: UTR annotation process (blast n using nt exons from ensembl vs. contig, ESTs- flybase blastn of contig vs. EST database (include with putative gene where appropriate)

• If applicable: ClustalW analysis (include with putative gene above where appropriate)

C) Repeat analysis (define types of repeats present) and speculate as to higher order chromatin structure

V) Discussion

• Summarize all major findings

• Thoughtful analysis of data

• Contribution to overall project goal

VI) References:

References must be included to receive credit.

A) In-text citations:

Within the text of the paper, please use (Author, Year) format for single author publications, (Author and Author, Year) for two author papers, and (Author et al., Year) for papers with more than two authors. Example: (Pug, 2010) or (Pug and Chow, 2010) or (Pug et al., 2010). For websites, please put the web address in parentheses.

B) References: 1) If you use an Internet source: List the complete web address. Please do not use Wikipedia as a source of information. 2) If you use a journal article, use the following reference format: Brennan P, Kaba H, Keverne E. 1990. Olfactory recognition: A simple memory system. Science 250: 1223-1226. 3) If you use a book, use the following reference format: McKusick V. Mendelian inheritance in man. 12th ed. Baltimore: Johns Hopkins University Press; 1999.

GEP Annotation Paper Rubric:

5 pts: Abstract

• Annotation definition

• Major results: species, chromosome, contig, size, predicted genes, annotated genes, Drosophila orthologs, number of isoforms in D. melanogaster, gene features annotated

• Overall, long-term project goal

10 pts: Introduction

• Genomics education partnership (can reference Science paper)

• Comparative genomics of Drosophila (phylogenetic tree)

• Dot chromosome description and differences in chromatin structure in other species, links to type of repeats

• What is annotation?

• Brief description of annotation strategy (computational, comparative), etc.

• What you will discuss in this paper: species, chromosome, contig #,ortholg identification, start and stop of translation, exon/intron boundaries/UTRs and repeats

10 pts total: Methods

• Describe methods (including all algorithms, etc.) used to annotate your contig/fosmid (how determined D. melanogaster ortholog, Gene Record Finder, etc.)

• Provide one example of one exon annotation with relevant screen shots (blastx with exon aa sequence melanogaster ortholog vs. translated contig, E-values and % identity, UCSC genome browser picture, GT marks beginning of intron, AG marks end) • Gene Model Checker method for verification

35 pts total: Results

• 5 points: Species, chromosome, contig, size and GenScan prediction For each putative gene:

• 10 pts: D. melanogaster ortholog E-value and % identity, function of protein, conserved domains, synteny

• 5 pts: Ensembl or Gene Record Finder picture of isoforms and discussion

• 10 pts: Gene model diagram for all genes and splice isoforms (Indicate clearly non-coding vs. coding exons, translation start and stop coordinates, splice junction coordinates)

• Points adjusted if applicable: UTR annotation process (blast n using nt exons from ensembl vs. contig, ESTs- flybase blastn of contig vs. EST database for yakuba and erecta); ClustalW analysis

• 5 pts: Repeat analysis (define types of repeats present)

5 pts: Discussion • Summarize major findings

• Thoughtful analysis of the data

• Contribution to overall project goal

10 pts: Interpretations/Thoroughness

10 pts: Writing Quality (Spelling, Grammar, Organization)

5 pts: Clarity

10 pts: Completion of drafts