FIRE 155 - FIRE SEMESTER 2: Terrapin Genome Project, 2015
Instructor: Dr. Amy Voltz
Email:
Office: avoltz@umd.edu
Microbiology 1126 A/B
Lab: Microbiology 1202
Office Hours: Mondays 2– 4 PM (right after class) or by appointment
Class Time: Mondays, 1:00 – 1:50 PM
Class Location: Hornbake 1108
Course Description
A collaborative research engagement focusing on the reconstruction and annotation of the genome of the diamondback terrapin, the Maryland State reptile and mascot of our
University. Students will be involved both in biological activities related to high-throughput
DNA and RNA (cDNA) sequencing, and in the bioinformatics analysis of the data generated.
Specifically, the students will learn to perform molecular biology techniques such as the
Polymerase Chain Reaction (PCR) to fill in sequence gaps in the terrapin genome assembly.
A basic understanding of DNA structure and function will be gained in order to understand how the laboratory techniques work and how to trouble-shoot them when they don’t.
Using bioinformatics tools such as NCBI’s BLAST, students will analyze the genomic sequence data they have produced by comparing it to the genomes of other turtles.
This is the second course in the FIRE (First-Year Innovation & Research Experience) program sequence and is for students participating in the Terrapin Genome Project innovation and research stream.
This course will focus on the concepts related to the process of independent research, including collaboration with peers, communication of ideas, troubleshooting unexpected outcomes and discipline-specific methodologies. Scheduled class meetings will focus on the discussion of primary literature, troubleshooting research issues and continual review of

individual and group research progress. The course requires each student to commit 8 additional hours of independent research per week.
Course Objectives
Students will:
1.
demonstrate proficiency in basic lab techniques such as micro pipetting, serial dilutions, weighing and measuring
2.
keep an accurate and up-to-date laboratory notebook containing experimental notes, procedures, results and analyses
3.
understand the basic properties of DNA
4.
learn to perform molecular biology lab techniques Polymerase Chain
Reaction (PCR), agarose gel electrophoresis, and DNA purification
5.
participate in lab meetings where they will trouble shoot and discuss their own lab results and those of their peers
6.
demonstrate a basic understanding of the Unix computational environment by working at the command line to manipulate files and perform data analyses
7.
become familiar with on-line bioinformatics tools for genome analyses such as NCBI’s BLAST suite and PCR primer design tools
8.
turn in a formal lab report containing introduction, materials and methods, results and discussion sections
9.
participate in discussions of published scientific papers to learn how to analyze data and incorporate it into their own research objectives

Course Calendar (topics are subject to change as research progresses)
Be sure to check CANVAS weekly for background reading, slides, research papers, helpful videos and other class materials.
Monday Jan 26 – Introductions to course, instructor and students. Background on project goals and how they will be achieved.
In the lab -> learn how to keep a laboratory notebook and basic lab techniques including measurement, dilutions and pipetting. Introduction to the Unix computational environment.
Monday Feb 2 – Lab safety training in class, online training on your own. Mandatory attendance. You must complete this training to work in the lab.
In the lab -> continue with basic lab techniques and Unix
Monday Feb 9 – the structural and replicative properties of DNA
In the lab -> demonstrate proficiency in basic lab techniques
Monday Feb 16 – theories of Polymerase Chain Reaction (PCR) and gel electrophoresis
In the lab -> begin doing PCR and running gels
Monday Feb 23 – Bioinformatics – BLAST and PCR primer design
In the lab -> more PCR and gels. Learn to design PCR primers and run a BLAST search.
Monday March 2 – Class lab discussion – informal progress reports
In the lab -> PCR! Gels! Prep your DNA for sequencing. PCR primer design. BLAST your contigs.
Monday March 9 – Class lab discussion – informal progress reports
In the lab -> can’t get enough of that PCR! Run gels. Prep DNA. BLAST stuff!
Monday March 16 – No class, no lab – Spring Break
Monday March 23 – Bioinformatics – analyzing DNA sequence data and genome assembly
In the lab -> more PCR and gels! Use BLAST and other sequence analyses tools.
Monday March 30 – Reading the Scientific Literature I
In the lab -> BLAST and sequence analyses, PCR and gels. Genome annotation.
Monday April 6– Class Lab Discussion – informal progress reports
In the lab -> PCR and gels, genome annotation
Monday April 13 – Class Lab Discussion – informal progress reports
In the lab -> PCR and gels, genome annotation

Monday April 20 – Reading the Scientific Literature II
In the lab - > Practicums - demonstrate proficiency in PCR, gels and DNA purification.
Monday April 27 – Class Lab Discussion – informal progress reports
In the lab -> Practicums – demonstrate proficiency in PCR, gels and DNA purification.
Monday May 4 – Reading the Scientific Literature III
In the lab -> Practicums – demonstrate proficiency in PCR, gels and DNA purification.
Monday May 11 – Last day of class – lab cleanup, course evaluation, instructor feedback

Due Dates for Lab Report
Monday April 6 - Lab Report – Introduction due
Monday April 13 - Lab Report – Methods due
Monday April 20 - Lab Report – Results due
Monday April 27 - Lab Report – Discussion due
Monday May 4 – Final Complete Lab Report due
Course Organization
Students will work as both individuals and in small groups on projects related to the continually evolving research agenda of the stream. The dedicated research space will be open and available with the Research Educator and/or peer mentors present to provide guidance at specific times each week.

Students will build expertise in the following areas:
1) Collaboration and discussion of data
2) Reviewing of primary literature and discipline understanding
3) Record keeping and professional writing
4) Practical methodological experience
Collaboration and discussion of data:
Owing to the increasingly collaborative nature of research, students, working within the framework of small groups and the stream, will learn to discuss data, troubleshoot problems encountered during the course of their work, and otherwise gain confidence and capacity with the collaborative nature of research.
Review of primary literature and discipline understanding:
Students will gain experience researching the background of an experimental hypothesis.
This will include understanding the proper methods required to approach a question, what has been done already within the field, and what questions still remain. Through analysis of published articles, students will gain an understanding of the expected format and tone of discipline-specific research articles, which will prepare them for the production a manuscript presenting the findings of their own research. Aggregate guided review of contemporary literature will facilitate broad understanding of the discipline engaged.
Record keeping and professional writing:
The maintenance of proper records is critical for research credibility and experimental reproducibility, thus students will be responsible for maintaining a notebook of their experimental procedures and data. Students will also prepare a final written manuscript in the form of a Research Report to outline their specific studies. Data may be collected and prepared for publication, dependent on results.
Practical methodological experience:
Students will be responsible for conducting experimental research and will be trained in the theoretical background and practical execution of basic methodological techniques needed to further stream research goals.

Required Texts
Students will review scientific articles related to the research being conducted, which will be provided through Canvas.
Online Resources
Unix and Perl for Biologists -> http://korflab.ucdavis.edu/Unix_and_Perl/current.html
NCBI BLAST -> http://blast.ncbi.nlm.nih.gov/Blast.cgi
Attendance
Due to the independent nature of research, in addition to scheduled weekly class meetings, students will be required to work in the dedicated stream research setting for a minimum of 8 hours each week.
Students will be required to sign in and out with the Research Educator to ensure that research hours are correctly noted.
University sanctioned absences for scheduled class time will be excused, however, the
Research Educator must be notified prior to the absence. Additionally, absences due to illness require a medical excuse.
Evaluation
Evaluation of student progress will be based on participation in discussions and evidence of work rather than research results. Assignments will be divided into Formative and
Summative categories.
All assignments will be assessed based on whether they meet (M) the expectations set forth in the rubric or are incomplete (I).

Weekly Meeting Attendance ** – Students will attend a weekly meeting to allow for group discussion of student progress, troubleshooting research issues and to review results. Students will be assessed on whether they have attended meetings and participated during discussion. (M = 12/14 lectures attended, I = 11 or fewer lectures attended)

Informal Progress Reports ** – Every student will be required to deliver ~2 informal progress reports over the course of the semester. (Content = 1 pt., communication = 1 pt., ability to answer questions = 1 pt.) M = 2/3 pts. I = less than 2 pts.
 Literature Analyses ** – There will be ~3 discussed scholarly papers over the course of the semester. A report including a brief summary of the background (1 pt.), methods

used (1 pt.), and conclusions (1 pt.) of each article to be reviewed during the weekly lab meeting. (M = 2/3 pts. I = less than 2 points)
 Notebook Checks ** – To ensure proper documentation of experimental methods and data, notebooks will be checked ~3 times at random over the course of the semester.
(Title and data = 1 pt., purpose = 1 pt., results and conclusion = 1 pt.) M = 2/3 pts. I = less than 2 pts.
 Research Report Draft Sections – Drafts of each of the component sections of each student’s final cumulative report will be submitted over the course of the semester. (M
= all components of research report submitted, I = any components of research report missing)
 Methods Practical – An evaluation of the student’s ability to perform the disciplinespecific methodologies of the stream, including evaluation of the student’s knowledge of basic methodological procedures and research-setting safety. (Proper lab technique
= 1 pt., lab safety = 1 pt., understanding of why you are doing what you are doing = 1 pt.) M = 2/3 pts., I = less than 2 pts.

Final Research Report – The final research report will be an aggregation and refinement of draft sections developed throughout the semester. (All sections complete = 1 pt., comprehension = 1 pt., presentation = 1 pt.) M = 2/3 pts. I = less than
2 pts.
** A cumulative grade will be assigned for multiple evaluations.

Formative Assignments:
# Assignments
1 Weekly Meeting
Attendance
Course Objective
The student attends and participates during the meetings, contributing to research discussion.
2
3
4
5
Informal Progress
Reports
Literature Analyses
Notebook Checks
Draft Report Part 1 –
Introduction
The student is able to relate the progress of his/her research verbally to the rest of the class in an informal setting in order to receive feedback and suggestions.
The student is able to discover and analyze the available scientific literature to determine relevant information for their final research report.
The student is capable of keeping an organized notebook that contains up-to-date data and experimental protocols.
The student can author a methods section relating the proper information to duplicate experiments utilized during their research.
6
7
8
Draft Report Part 2 –
Methods
Draft Report Part 3 –
Results
Draft Report Part 4 –
Discussion
The student can author an introduction to their research report containing background to introduce the research topic and explain the purpose of the current research.
The student can author a results section, including figures to illustrate and descriptions of the research results obtained.
The student can author a discussion section, including an analysis of the current work, alternative theories, and future directions.
9 Methods Practical The student is capable of working independently in the lab with a basic understanding of the methods, both practical and theoretical, being utilized for the research project.
10 Research Setting
Attendance
The student can work independently within the research setting for a require minimum of 8 hours a week in order to work toward the goals of his/her research project.
M I

Summative Assignments:
# Assignments Course Objective M I
B-
C+
C
C-
A
A-
B+
B
D+
D
F
10 Research Report
11
The student can combine the draft sections of the research report into a cohesive document outlining his/her research and experience over the course of the semester.
The score for each assignment will be made by a majority score on the individual rubric with the higher graded awarded in the event of a majority-score tie.
The cumulative score for assignments that have multiple evaluations (#1, #2, #3 and #4) will be the majority score of individual evaluations with the higher score awarded in the event of a majority-score tie.
The following grade scale will be used to assign final grades based on number of assignments earning an M or I designation for the 11 total assignments.
Meets (M) Incomplete (I)
5
4
7
6
11
10
9
8
3
2
1
0
1
2
3
4
5
6
7
8
9
10

Research Setting Policies
The following policies are strictly enforced within the research setting.
 No eating or drinking in the research setting, including gum or candy. All food and drink must be kept in the hallway.
 All safety procedures and clothing requirements must be strictly adhered to.
 Be respectful. This includes but is not limited to:
 Listening to instructions from me and/or fellow researchers

Behaving civilly to those in research setting
 Keeping conversation to a volume so as not to disturb others that are working

All efforts to troubleshoot should be made amongst fellow group members and the class as a whole before the instructor becomes involved.
Rules for Lab Safety
1.
Know the locations of all laboratory exits, emergency eye wash stations, emergency showers and fire extinguishers.
2.
No food or drink in the lab ever! Do not put anything in your mouth while in the lab.
3.
Appropriate clothing must be worn at all times – no open toed shoes or sandals, no shorts. Lab coats must be worn.
4.
Wear laboratory gloves at all times. Wash your hands before and after lab.
5.
No personal items on the lab bench – only your lab notebook.
6.
UV eye protection must be worn while using the gel light box.
7.
Dispose of waste properly.
8.
Keep your lab bench working area neat and clean.
9.
Understand the hazards involved with the materials you are working with such as reagents and equipment. (i.e. EtBr is a carcinogen, always wear gloves!)
10.
Report any accidents or injuries to the lab instructor.
Class Cancellations and Emergencies
All assignments are due before the beginning of the weekly meeting and are submitted online, therefore assignments will still be due even in the event of a university cancellation.
In the event of an emergency, follow all UMD announcements, guidelines and policies.
Class will not be held when the university is closed due to emergency, weather or other

unforeseen event. Any other cancellations will be communicated through the course website.

Academic Integrity
The University of Maryland, College Park Code of Academic Integrity is strictly enforced in this class. Assignments and classwork must reflect your own, original work and must including proper citation and attribution for work that is not your own. Academic dishonestly includes:
- “Cheating: Intentionally using or attempting to use unauthorized materials, information or study aids in any academic exercise.
- Fabrication: Intentional and unauthorized falsification or invention of any information or citation in an academic exercise
- Facilitating academic dishonesty: Intentionally or knowingly helping or attempting to help another to violate any provision of this Code
- Plagiarism: Intentionally or knowingly representing the words or ideas of another as one’s own in any academic exercise.”
For information concerning the Code of Academic Integrity see: http://www.shc.umd.edu/SHC/Default.aspx
Academic Accommodations
If you require academic accommodation, please provide proper documentation by the second class period and contact Disability Support Services so that we can arrange an appropriate accommodation for your needs
DSS Phone: (301) 314-7682
DSS Web: http://www.counseling.umd.edu/DSS/
Copyright
Please note that all classroom lectures and materials are copyrighted by the instructor and cannot be reproduced for anything other than personal use without my permission.