Justin DiAngelo Hofstra University

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Genomics at Penn State Berks

Course Overview

BMB 448 is an inquiry-based laboratory course that combines lectures, traditional wet lab protocols and computer lab research experiences to introduce bioinformatics skills in the context of genome annotation and gene expression analysis. Designed as part of the Genomics Education Partnership (GEP), funded in part by the National Science Foundation, the course is intended for upper division Biochemistry and Molecular Biology and Biology undergraduates. Students are expected to prepare their annotated sequence information for publication in a professional journal. Students will also choose one of their in silico gene models to test in vivo using standard cell and molecular biology laboratory techniques. In order to prepare students for a task of this magnitude, I will lecture, assign readings and exercises and collect homework at regular intervals. An expected outcome, among others listed below, will be the students’ names on a collaborative publication involving members of the GEP nationwide.

Implementation

The first implementation of Genomics using GEP materials at Penn State Berks included a large portion of an upper level Biochemistry and Molecular Biology lab course, BMB 448 - Model Systems and Approaches in Cell Biology Inquiry in Fall 2015.  I started with an introduction to the GEP Research Question, the basics of genome sequencing, an introduction to BLAST and then an introduction to the basic annotation workflow.  Then my students spent ~4 weeks annotating their fosmid in pairs culminating in an oral presentation.  I finished up the course by having the students test one of their gene models using standard wet lab techniques.

Lessons Learned and Future Plans

We'll see how it goes...more info on this to come!


Syllabus for


BMB 448 Model Systems and Approaches in Cell Biology Inquiry
Fall 2015
T 1:40 – 2:30pm, R 3:05-5:55pm
Luerssen 102

Instructor: Justin DiAngelo, Ph.D.
Phone: 610-396-xxxx
Email: jrd5671@psu.edu (email is the preferable way to contact me)
Office: Luerssen 101J
Office hours: M 3:30-4:30pm, T 2:30 – 3:30pm and W 11:30-12:30pm or by appt

Course Description: BMB 448 is an inquiry-based laboratory course that combines lectures, traditional wet lab protocols and computer lab research experiences to introduce bioinformatics skills in the context of genome annotation and gene expression analysis. Designed as part of the Genomics Education Partnership (GEP), funded in part by the National Science Foundation, the course is intended for upper division Biochemistry and Molecular Biology and Biology undergraduates. Students are expected to prepare their annotated sequence information for publication in a professional journal. Students will also choose one of their in silico gene models to test in vivo using standard cell and molecular biology laboratory techniques. In order to prepare students for a task of this magnitude, I will lecture, assign readings and exercises and collect homework at regular intervals. An expected outcome, among others listed below, will be the students’ names on a collaborative publication involving members of the GEP nationwide.

Course Objectives: At the conclusion of this course, the student will be able to:
1. Use genome analysis software to develop sequence data into an annotated genome segment.
2. Search sequence databases and identify the putative function of genes as well as their structure and organization within the genome.
3. Use cell and molecular biology techniques to determine the validity of an annotated gene model in vivo.
4. Communicate clearly and professionally, both in oral and written format, the details of a scientific investigation.

Required Materials: There is no required textbook for this course – all protocols and background reading will be posted on ANGEL. However, a bound laboratory notebook and a minimum of 1 GB flash drive are required to enable you to collect data throughout the semester. I also expect that you will have goggles with UV protection. Please also get a small 3-ring binder to organize your protocols and handouts and an ultra-fine sharpie to label tubes (blue or black only). You should bring all of these items with you to each lab session.

Prerequisites: BMB 251 or BIOL 230W; MICRO 202 or BMB 442. I expect that you have some basic molecular biology laboratory skills!

Course Communications: Email is the main method of communication outside of class time, so make sure that you check your Penn State email account daily or have your Penn State email forwarded to the account you check most often.

Assignments: At the beginning of the course, you will be assigned various homework assignments to help you learn how genomes are sequenced and to prepare you to annotate your piece of a Drosophila genome. Throughout the annotation process, students will also give progress reports as short, informal oral presentations. At the completion of the GEP annotation project, students will give a 10-minute oral presentation. Additionally, a standard report file must be completed for submission to the GEP. The major written portion of this course involves a final paper written in the style of a professional publication focusing on the wet lab portion of the course. A rubric outlining the expectations of the final manuscript style paper will be distributed in class.

NOTE: All assignments are DUE at the start of class on the day the assignment is to be handed in. Assignments handed in late will be assessed a 10% penalty per day.

Laboratory notebooks: Each student is required to keep a laboratory notebook (bound written laboratory notebook and/or electronic notebook as a Word document). The notebook will be checked periodically and will count for 10% of your final grade in this course. Collecting data on a computer is just as valid as collecting data during a wet lab protocol and should be documented as such. It is imperative that the notebook be updated consistently and thoroughly, as this data will be used for a professional scientific publication. In a paper notebook, the first few pages initially will be left blank for completion of a table of contents at the end of the semester. All pages will be numbered and entries will be recorded in permanent ink not pencil. At the beginning of each class period, you will start an entry in the notebook with the date (day/month/year) and write down each procedure that you perform (i.e., which Blast algorithm you use, what website you found it at, etc.) and the results that you obtain (i.e., coordinates of splicing junctions, potential gene names, etc.). Any printouts of data that you collect throughout each class period will be stapled into the notebook. Primary data not entered into the notebook like digital files or images should be indexed in the lab notebook and their location and labeling clearly noted. Screen shots of data can be included in the electronic notebook but should be clearly labeled. Your notebook will serve as a permanent record of the work that you have completed as well as a reference for any questions that may come about during the data analysis and preparation for final publication by the GEP. It is essential that you document your findings and failure to do so will prevent authorship on any publication that arises from this course.

Grading: The course will be graded on the +/- system and weighted as follows:
Sequencing Quiz 10 points
PCR Quiz 10 points
Laboratory Notebook 30 points
Workshops/Assignments
Intro to BLAST Exercise 10 points
Sequencing Workshop 20 points
Annotation Workshop 40 points
Oral Annotation Progress Report 10 points
Oral Presentation on Annotation 50 points
GEP File for Annotation 50 points
Methods and Results Draft 20 points
Final Lab Report 50 points
Total Points 300 points

Grading Scale: A (92-100%) C+ (78-79%)
A- (90-91%) C (70-77%)
B+ (88-89%) D (60-69%)
B (82-87%) F (less than 60%)
B- (80-81%)

Attendance: You're adults and I expect you to be responsible, present, and on time. In return, I’ll do my best to always be prepared and on time, and to help you learn and understand the material. Since we will be working with biological reagents that are time and temperature sensitive there can be no make-up assignments or laboratories for this course. However, if you anticipate that you might miss class because of sports / music/ other course-related activity / religious activity, you MUST tell me at least two weeks in advance, in writing, so that I can make alternative arrangements for you before the scheduled time.

The bulk of the computer-based exercises should be worked on during the lab period although you may need additional time outside of this period to complete projects. You are expected to come to class having thought about your progress in lab and prepared to discuss your experiences.

Assessment: The annotation project is part of nationwide collaborations designed to improve undergraduate education and involve students in real research experiences. To evaluate the effectiveness of these exercises, students are asked to complete pre- and post-surveys throughout the semester. This is purely voluntary and will not affect a student’s grade in any way. Individual results of the surveys will not be available to the instructor at any time.

Academic Integrity: Everyone assumes responsibility for the content and integrity of their work. Academic dishonesty will not be tolerated. Please refer to the University Regulations (Student Handbook) or Policies and Rules for Students available in the Office of Student Affairs (14PSC). Definition and expectations: Academic integrity is the pursuit of scholarly activity in an open, honest and responsible manner. Academic integrity is a basic guiding principle for all academic activity at Penn State, and all members of the University community are expected to act in accordance with this principle. Consistent with this expectation, the University's Code of Conduct states that all students should act with personal integrity, respect other students' dignity, rights and property, and help create and maintain an environment in which all can succeed through the fruits of their efforts. Academic integrity includes a commitment not to engage in or tolerate acts of falsification, misrepresentation or deception. Such acts of dishonesty violate the fundamental ethical principles of the University community and compromise the worth of work completed by others.

Note to students with disabilities: Penn State welcomes students with disabilities into the University’s educational programs. Every Penn State campus has an office for students with disabilities. Please contact Michelle Strawley, Disability Services Coordinator, at mns136@psu.edu or 610-396-6410. Her office is located in room 169 Franco. For further information, please visit the Office for Disability Services Web site: http://equity.psu.edu/ods.

In order to receive consideration for reasonable accommodations, you must contact Michelle Strawley, participate in an intake interview, and provide documentation: http://equity.psu.edu/ods/guidelines. If the documentation supports your request for reasonable accommodations, the Disability Services Office at Penn State Berks will provide you with an accommodation letter. Please share this letter with your instructors and discuss the accommodations with them as early in your courses as possible. You must follow this process for every semester that you request accommodations.

LAB RULES:

• You may NOT eat, drink, or smoke in the laboratory at any time.

• Eye protection MUST be worn at all times. The goggles you had from chemistry are sufficient. If you need to purchase a pair you can find them in the bookstore.

• It is also advisable not to wear your Sunday best. Lab coats can be worn if needed. If enough are interested I can have the bookstore order them for you to purchase.

• You must wear closed toe shoes at all times. You can never be barefoot or wear open toe shoes such as sandals, Birkenstocks, etc.

• Please clean up after yourself. There will be waste receptacles for trash and tubs for glassware - please remove labels/tape from tubes and beakers before leaving them to be washed.

• It is important to wash your hands thoroughly prior to leaving the laboratory

• Working with live organisms and performing experiments that require incubations may result in laboratories that take more than our allotted time slot, or require you to come back later on that evening. Sometimes you may need to come for a short time at other points during the week to prepare for experiments or to record data.

• Please be on time for lab. I will give instructions, clarifications and changes in protocol at this time. You will keep a separate laboratory notebook that you will be required to bring to lab to record your protocols and data. Write in ink! In research laboratories, one’s notebook stays in the laboratory, and is frequently used as a resource by others. Although you may bring your notebook home and keep it, your notes and data should be clear enough that someone could reproduce your experiment or analyze your results. I will tell you when they will be collected for review during the semester.

• All assignments will be due at the beginning of each laboratory period. If you have questions about your results or about the assignment please see me before the beginning of lab.




Date Lecture/Lab Topic Readings/Assignment
Aug 25, 27 Introduction to the Course
Lab Safety
Research Question/Heterochromatin Complete GEP pre-course survey and quiz
Sept 1, 3 Chemistries used to Sequence Genomes – Sanger and Next Generation Sequencing
RNA-Seq Sequencing Workshop
Sequencing Quiz (on 9/8)
Sept 8, 10 Basics of BLAST Intro to BLAST exercise

Sept 15, 17 How do you annotate a gene?
Ab initio gene finding
The annotation workflow Annotation Workshop
Sept 22, 24 Annotation (staggered start on 9/24)
Sept 29,
Oct 1 Annotation Progress Report – What genes do you have? (on 10/6)
Oct 6, 8 Annotation
Oct 13, 15 Annotation
Oct 20, 22 Oral presentations on annotation and GEP files Complete GEP File
Oct 27, 29 RNA isolation Design primers
Nov 3, 5 RNA gels and quantitate samples

Nov 10, 12 cDNA synthesis and PCR set up RNA isolation and gel Methods and Results draft (due on 11/12)
Nov 17, 19 Gel electrophoresis of PCR products PCR quiz (on 11/17)

Nov 24, 26 No Class – Thanksgiving Break
Dec 1, 3 Analyze Data; Write paper
Dec 8, 10 Analyze Data; Write paper Final paper due 12/10
Dec 14-18 Final Exam Period Complete GEP post-course survey and quiz