I, ____________, this day of ______, hereby acknowledge that I have read, understand, and accept the requirements and expectations of Molecular Biology BIOL 433L as described in the attached syllabus.
By signing this contract, you acknowledge that you have received, read, and understand the syllabus and accept the criteria required to receive a passing grade in this course.
BIOL 433L: Molecular Biology Laboratory
Professor: Dr. Michelle M. Barthet/Parker
E-mail:
Office hours: TBD
Office/Lab: Swain 110
Phone: 349-6905
Class time: Friday 11-1:50 p.m. Swain 226
Required Texts:
None. Lab sheets will be provided or posted on Moodle.
Course objectives:
This course focuses on learning molecular techniques using in the plant sciences. Techniques covered include (but are not limited to) T-DNA insertional analysis, phenotypic and genotypic analysis, restriction digests, gel electrophoresis, PCR, cloning, sub-cloning, plant transformation techniques, and RT-qPCR.
Student learning outcomes for Biol 433L:
Upon completion of this course, students are expected to be proficient in:
- Using Model plant organisms
- Analyzing and generating genetically modified plants
- Various molecular techniques including primer design, cloning, and protein induction
- Experimental design
- Analysis of results
- Reporting of results
- Writing a paper in a format appropriate for a submission to a scientific journal
Course design:
This is a required lab to accompany BIOL 433 lecture. Concepts discussed in lecture will be applied in the laboratory. Further, students will design and implement an experiment involving cloning of a gene of interest from a cDNA library leading to expression of that gene as a protein with a reporter fusion tag. As such the aim of this course is to both provide hands-on experience for students in molecular biology as well as encourage development of investigative thinking and writing skills.
Moodle:
Moodle will be used for this class. The syllabus, power-point figures, lecture notes, grades, and other pertinent information will be posted. Please check Moodle regularly for these postings and come to class prepared.
Expectations of the student:
I expect students to attend all labs unless they have a university approved excused reason for missing. I expect all students to have read materials ahead of the lab and be on time for the lab to begin. There may be extra time requirements for this lab due to needing to repeat protocols. I expect students to then come in at times that fit their schedule for these extra requirements.
Further, in order for each student to get the most out of this class, each person is to respect their fellow classmates. So please,
-COME TO CLASS ON-TIME!
-Mute cell phones on during class, NO TEXTING!
-no loud talking during class
-read prepared lab materials ahead of time and be prepared to start lab at the beginning of the lab period
-NO FOOD OR DRINK PERMITTED IN THE LAB
-Clothing must come to the knees and shoulders much be covered!
The lecture portion of this course will be integrated with lab in a 60/40 ratio. The following is a breakdown of points awarded for each part of the laboratory portion of the course.
Grade:
Grading Scale:
Lab notebook 130 pts.90-100 A
Proposal 50 pts.80-89 B
Presentation 50 pts.70-79 C
Final paper 170 pts.60-69D
<60 F
Total 400 pts.______
B+ and C+ grades will be given for a range of 88-89.6 = B+; 78-79.6 = C+.
The design of this lab is concentrated on a singular project that you will complete by the end of the semester and present. You will work in pairs for this final project. The angle of the project and gene of choice is up to you and your partner. You will have to write a proposal for your project. ALL papers (proposal and final paper) are required to have proper citation and ONLY use peer-reviewed scientific literature (ABSOLUTELY NO WEBSITES!). NO quotations – always rephrase and cite correctly!
Grades and absences:
Grades will be posted on Moodle as soon as possible after papers/ assignments are completed. Make-up labs will not be given. If missing lab due to UNIVERSITY APPROVED excuse (sickness or death), make-up assignments may be given.
Disabilities:
Any student with special needs is encouraged to see me as soon as possible concerning those needs.
Academic Dishonesty:
A large portion of your grade in the lab is based on writing assignments. Plagiarism is the main form of academic integrity violation in the College of Science. Many of these offenses are due to mistakes, some are purposeful. DO NOT PLAGARIZE OR YOU WILL FAIL THE PAPER AND POSSIBLY THE COURSE! If any form of academic dishonesty is observed in this course, the persons responsible will be reported to the proper authorities and will receive a zero for the assignment. Please read through your
Student Handbook for the Code of Student Conduct: Section II-A pg. 37-38.
What is plagiarism?
Copying directly from a source without quotations and citation is plagiarism. Rephrasing and neglecting to include in-text citations is plagiarism. Copying incorrect citations is plagiarism.
How do you cite correctly?
Rephrase (more than just one or two words but the whole concept/ paragraph) and give a proper in-text citation. For examples of in-text citations LOOK at a peer-reviewed paper and see how they cite – follow that model!
Attendance: Attendance will not be taken for this course. HOWEVER, labs cannot be made up due to time and preparation issues. DO NOT MISS LAB UNLESS WITH A UNIVERSITY APPROVED EXCUSE!
Proper dress
You may be asked to leave the lab if you come in without proper dress according to laboratory safety rules. This includes clothed-toed shoes (and heals!), clothing that reaches to the knee, covering the shoulders.
How to keep a good notebook
You are required to obtain a composition notebook and write in it EACH LAB DAY the date, purpose/ hypothesis (sentence), methods (yes you can cut and paste the methods I give you but make sure to include any modifications!), any tables, photos, etc., results/ conclusion sentence, what is next? This lab notebook will be checked at the beginning of each lab dayto see if you have kept up with it as required. It is essential in this field to have a well-maintained lab notebook. Each lab day is worth 10 pts.!
Tentative Lab Schedule:
Week / Activity / Date1 / Model plants
2 / Plant DNA extraction/ digests / Aug. 31
3 / Gels/ligation/ transformation / Sept. 7
4 / Sequencing for insert / Sept. 14
5 / PCR for choice construct / Sept. 21 / Proposal due
6 / Gel/ PEG clean / Sept. 28
7 / BP cloning/ transformation / Oct. 12
8 / Plasmid prep / Oct. 19
9 / Gels / Oct. 26
10 / LR reaction to binary vector/ transformation / Nov. 2
11 / Plasmid prep/ gels / Nov. 9
12 / Protoplast/plant transformation / Nov. 16
13 / Phenotypic analysis of protoplasts / Nov. 30
14 / Final paper due the last day of class
I reserve the right to modify this schedule if necessary.