BIOL 155 PHAGE ISOLATION AND PURIFICATION FALL 2014 MON/WED 10:00 11: HAWORTH OPEN LAB: BY APPT.

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1 Attachment #3 CAC Agenda 9 Dec 2014 Proposal to consider BIOL 155 as a lab/field experience course for the BA Degree Specific Requirements INSTRUCTORS: Robert Ward robward@ku.edu Haworth Hall Brad Williamson bwilliam@ku.edu Dole Hall BIOL 155 PHAGE ISOLATION AND PURIFICATION FALL 2014 MON/WED 10:00 11: HAWORTH OPEN LAB: BY APPT. TA: Erin Suderman dillerin@gmail.com 4004 Haworth Hall COREQUISITES: ENROLLMENT INTO BIOL 150. COURSE DESCRIPTION: This course is a two semester open-ended research laboratory course where students will purify bacteriophage from soil, visualize phage using electron microscopy, isolate genomic material for nucleic acid sequencing, and annotate the genome of at least one phage isolated by the class. As such, students will learn techniques used in microbiology, molecular biology and bioinformatics. Students will also develop oral and written communication skills through informal lab meetings, formal presentations (including poster presentations) and written reports. COURSE OBJECTIVES: 1. Students will isolate their own bacteriophages, and in the process gain a mastery of wet lab microbiological and molecular techniques. 2. Students will be able to describe bacterial viruses, their ecological importance, life cycle, and the purification process. 3. Students will record, analyze and communicate their scientific findings. **DATES AND COURSE CONTENT ON THIS SYLLABUS ARE SUBJECT TO CHANGE** Due to the nature of this lab, we will need to be flexible with our dates and requirements. Anything is subject to change at anytime GRADING Requirement Participation 20 Laboratory Benchmark Achievement 20 % Grade

2 Notebook 15 In Class Exercises 10 Written Report 15 Oral presentation/poster 20 Total 100 PARTICIPATION An important component of your grade in this course is participation. Obviously your work cannot go on when you are not present. Excused absences (either emergency or known in advance) must be officially documented. Your course instructors must be notified before the next class period following an absence. Unexcused absences (5% off, each) will result in lower participation grades. Participation also includes demonstrating good research habits of mind (intrinsic curiosity, independence, asking good questions, critical evaluation of results, lab courtesy, not giving up, etc). LABORATORY BENCHMARK ACHIEVEMENT This class focuses on mastering skills appropriate to microbiology and molecular biology labs. You will be graded on completing the following tasks: pipetting, aseptic technique, direct plating, enrichment plating, identification of plaque, purification of plaque, production of web plate, isolation of high-titer lysate, DNA purification, restriction digest, and EM Visualization. NOTEBOOK You will be required to keep a detailed record of all that you do in the phage lab. This is REAL research that will one day be published, and you have a responsibility to properly document your experiments. You will be provided a lab notebook in the first full week of class. Lab notebooks must remain in lab at all times. IN CLASS EXERCISES There will be a variety of in class exercises that may or may not be announced in advance. These may include, but are not limited to, math quizzes, reading quizzes, journal discussions, and on-the-fly media preparation calculations. If it is in your lab guide, you should know how to do it. ADDITIONAL LAB HOURS You will occasionally need to come to the lab between classes. We will post times when instructors will be available to help you and which will not interfere with other classes. You should record all work in your notebook, including the dates and times you are in the lab. RELIGIOUS HOLIDAYS, STUDENT ATHLETES, AND STUDENTS WITH DISABILITIES If you need special consideration (i.e. quiet room, extra time for exams, etc.), you must provide me with a letter stating exactly what you need and proof of this necessity (e.g. a letter from Disability Services). Students with special requirements are responsible for self-identification prior to requesting services. LAB MANUAL AND ASSIGNED READINGS The laboratory manual for this course is entitled SEA-PHAGES Student Lab Manual In Situ. It is available as a pdf file in the Course Documents section of Blackboard. You may print it out and bring it to class, or you can have a copy on your laptop computer or tablet. We will have files available

3 on the computers in the lab as well. You will be assigned readings from the lab manual throughout the semester. Additional readings will be assigned and made available on Blackboard as needed. Useful websites will be posted on Blackboard as they come up in the course. ONLINE SURVEYS FOR HHMI You will be asked periodically to complete online surveys about your experience in this course for HHMI and NIH. The surveys are voluntary and have no impact on your grade in the course. We would appreciate your participation in these surveys and it will help shape the future of undergraduate biology in this country. The first survey should be completed before the second class. The survey can be found at: ACADEMIC INTEGRITY (from the Statement on Academic Integrity from the School of Business Honor System): Academic integrity is a central value in higher education. It rests on two principles: first, that academic work is represented truthfully as to its source and its accuracy, and second, that academic results are obtained by fair and authorized means. Academic misconduct occurs when either of these principles is knowingly violated. The responsibility of academic integrity does not rest solely in the hands of the faculty and administration. It depends also on the attitude and spirit of the student body to create an atmosphere that promotes strong integrity. In other words, the students determine a school's level of character. The job of educators, therefore, is to foster and encourage a feeling of honesty and quality. In this class, the concept of individual honor is designed to promote mutual trust and respect between students and faculty. (continued on next page)

4 SEPTEMBER 1 OCTOBER 1 TENTATIVE SCHEDULE OF LAB ACTIVITIES Date Typical timeline Activities No class, Labor Day 3 Course overview, Safety, Distribute phage collection Capture tools Learn basic lab 8 Direct plating, start enrichment techniques samples Collect soil 10 Pick plaques, plaque assays samples 15 Direct and 17 enrichment 22 plating Tame 24 Isolate pure population Plaque 29 isolation Titer phage Plaque 6 purification 8 Empirical test and titer 13 No class, Fall Break plate lysate (HTL) 27 Extract phage DNA 29 DNA quantification/restriction analysis Run agarose gel 5 EM sample prep 10 EM1/DNA QC gel 12 EM2/DNA QC gel 17 NOVEMBER 3 19 Phage Olympics!! Defend Your Phage 24 Archive reports and samples due 26 No class, Thanksgiving Oral presentations 3 Poster session 8 10 Papers Due DECEMBER 1 Dissect DNA purification DNA restriction digest and QC gel Electron microscopy Communicate Papers Presentations Celebrations

5 Laboratory Benchmark Achievement Skill Pipetting Data Aseptic technique Direct plating Enrichment plating Soil Sample Collection GPS 1: Identification of plaque Purification of plaque Phage Name: Number of serial dilutions performed: Clear/turbid/halo/comet/size/multiple Describe final plaque morphology Production of web plate Isolation of high-titer lysate DNA purification DNA quantification Restriction digest EM Visualization Empirical/Intuitive Titer: Volume: Concentration: Head Diameter: Tail length: