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BIOL 451

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BIOL451 - Biology of RNA

Spring 2015


MW 11:15AM-12:05PM 009 Huck Life Sciences Bldg.

M 2:30PM-4:00PM 143 Stuckeman Family Bldg.

Instructor: Michael Axtell, Ph.D.

Office: 260 North Frear Lab


Office Hours: Tu 1:00PM-4:00PM and by appt.

Course Goals

Students will become conversant with the many biological roles of RNA

Students will gain familiarity with analyzing and discussing data from journal articles

Students will develop computational and statistical methods relevant to modern biological research

Course Objectives

Describe key concepts and molecular pathways involving RNA across prokaryotes, eukaryotes, and viruses during exams.

Analysis and critical summarization of current journal articles by essay assignments and worksheets.

Development of scientific writing skills, and writing skills in general via essay assignments and laboratory reports.

Introduction to programming with a focus on biological data analysis in the perl language.

Use and application of the R statistical language for analysis and visualization of data.

Use of aligners, genome browsers, and other common tools for genome-wide analyses of RNA data.

Complete analysis of RNA-seq datasets to test specific hypotheses.

Preparation of detailed written laboratory reports.

Presentation of experimental results in an oral format.


BIOL230 or BMB251 or MICRB251 (can be waived after discussion with instructor).

Required Textbook



Attendance is required and is noted by the instructor at every lecture and lab. The instructor will contact students with a pattern of missing classes and labs.


All grades will be maintained in the ANGEL gradebook.  This course uses a "points" system; there are a total of 1,000 points to earn during the course of the semester.  The breakdown of points is below

Assignment type                     weight              points               frequency

Mid-Term Exams                    25%                 250                  1 @ 84pts., 2 @ 83pts.

Weekly Lab Homework          25%                 250                  10 @ 25pts. each

Weekly Lecture Homework    25%                 250                  10 @ 25pts. each


Independent Project                25%                 250                  1 @ 250 pts.

The final course grade will be computed using the following weightings:

Point Range                Rounded Percentage Range              Letter Grade

950-1000                     95%-100%                                          A

900-949                       90%-95%                                            A-

867-899                       87%-90%                                            B+

833-866                       83%-87%                                            B

800-832                       80%-83%                                            B-

767-799                       77%-80%                                            C+

700-766                       70%-77%                                            C

600-699                       60%-70%                                            D

< 600                           < 60%                                                  F         

 Note:  Under extreme circumstances, grades may be adjusted to achieve a C+ mean grade for the course

Lecture and Lab Homework

Nearly every week there will be homework assignments for both lecture and lab. Overall, homework accounts for 50% of the course grade. Homework will include review components (of topics just covered in lecture / lab), AND preview components (of topics that will be covered in the next lecture / lab).

Mid-Term Exams

There are three mid-term exams in the course. Each one covers BOTH lecture AND lab material from the preceding unit. Exams are given during a lecture period, on Wednesdays, as noted in the schedule. Practice exams will be distributed before-hand.

Independent Projects 

Each student will perform an independent research project centered on the analysis of various RNA-seq datasets. Projects will involve computational analyses of data, production of a 15 minute presentation, and a written research report. Students can work together if they wish to devise experimental approaches, but the writing and analysis of data must be independent. Detailed guidelines for this project will be provided during the course of the semester.

No Final Exam

There is no final exam in this course. The independent project (see above) is used in lieu of a comprehensive final.

No Extra Credit

There is no extra credit available in this course.

Absence and Make-Up Policy: 

Make-ups of missed assignments will only be considered for the following types of absences:

Conflicts with University sanctioned events (such as athletic events for athletes, etc.)

Holy day(s)

Illness or injury serious enough to prevent attendance at class

Death in the family

Other unforeseen circumstances, subject to the instructor's judgment

If an absence occurs because of a legitimate reason (list above), student must contact the instructor as soon as possible (email to to arrange to make up any missed work (quizzes, worksheets, exams). The instructor reserves the right to judge whether or not make-up work is accepted depending on his judgment of the student's situation. Final Projects will not be accepted late except under truly extraordinary circumstances.

Plagiarism: If the instructor suspects plagiarism in a student-submitted written assignment, he will have a conference with the student to discuss it.  Penalties for plagiarism in submitted work will depend upon the severity of the case, and include a warning, a grade reduction, a zero on the assignment, or in extreme cases a grade of XF (Failure with academic dishonesty) for the course. 

Statement of Requirement For Academic Integrity

"All Penn State policies regarding ethics and honorable behavior apply to this course. Academic integrity is the pursuit of scholarly activity free from fraud and deception and is an educational objective of this institution. Academic dishonesty includes, but is not limited to, cheating, plagiarizing, fabricating of information or citations, facilitating acts of academic dishonesty by others, having unauthorized possession of examinations, submitting work of another person or work previously used without informing the instructor, or tampering with the academic work of other students. For any material or ideas obtained from other sources, such as the text or things you see on the web, in the library, etc., a source reference must be given. Direct quotes from any source must be identified as such. All exam answers must be your own, and you must not provide any assistance to other students during exams. Any instances of academic dishonesty WILL be pursued under the University and Eberly College of Science regulations concerning academic integrity. " There will be zero tolerance of academic dishonesty in this course.


“Penn State welcomes students with disabilities into the University's educational programs. Every Penn State campus has an office for students with disabilities. The Office for Disability Services (ODS) Web site provides contact information for every Penn State campus. For further information, please visit the Office for Disability Services Web site.

In order to receive consideration for reasonable accommodations, you must contact the appropriate disability services office at the campus where you are officially enrolled, participate in an intake interview, and provide documentation. If the documentation supports your request for reasonable accommodations, your campus’s disability services office 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."

Course Schedule (subject to change)

Week 1 (Jan 12, 14)

Lectures: Nucleic acid structure and basics

Lab: Introduction to the Terminal

Week 2 (Jan 21)

No Lecture or Lab Monday Jan 19 - MLK Holiday Observance

Lecture: Central dogma and overview of RNA types

Week 3 (Jan 26, 28)

Lectures: Overview of RNA-seq methods

Lab: perl 1

Week 4 (Feb 2, 4)

Lectures: Transcription 1

Lab: perl 2

Week 5 (Feb 9, 11)

Lectures: Transcription 2

MID-TERM EXAM 1: Wed. Feb 11th

Lab: perl 3

Week 6 (Feb 16, 18)

Lectures: RNA processing 1

Lab: R 1

Week 7 (Feb 23, 25)

Lectures: RNA processing 2

Lab: R 2

Week 8 (Mar 2, 4)

Lectures: Translation

Lab: R 3

-- Spring Break: Mar 9, 11. No Lectures or Lab --

Week 9 (Mar 16, 18)

Lectures: RNAi 1

Lab: Genomes, genome browsers

Week 10 (Mar 23, 25)

Lectures: RNAi 2

MID-TERM EXAM 2: Wed. March 25th

Lab: RNA-seq alignments and samtools

Week 11 (Mar 30, Apr 1)

Lectures: RNA viruses

Lab: Small RNA-seq alignments and ShortStack

Week 12 (Apr 6, 8)

Lectures: RNA transposons 1

Lab: Differential expression analysis and edgeR

Week 13 (Apr 13, 15)

Lectures: RNA transposons 2

Lab: Independent Projects .. work and discussions

Week 14 (Apr 20, 22)

Lectures: CRISPR

MID-TERM EXAM 3: Wed Apr. 22.

Lab: Independent Projects .. work and discussions

Week 15 (Apr 27, 29)

Lectures: Independent Project Presentations

Lab: Independent Project Presentations

Week 16 (May 4)

Materials for Independent Projects due by 11:59PM