GENERAL BIOLOGY LABORATORY (HONORS) – SEA-­‐PHAGES BIOL 102 CRN 10138 (sec 08) and 10139 (sec 09) SPRING 2013 Days and Times: Laboratory Section 08 – Tuesday and Thursday, 12:40 pm – 3:30 pm Laboratory Section 09 – Tuesday and Thursday, 5:10 pm – 8:00 pm Location: EE Just Hall, Room 107 Credit Hours: 4 (includes credit hours for lecture and laboratory portion of course) Prerequisites: General Biology 101 Lecture and General Biology 101 Laboratory (Honors) Course Coordinator: Courtney J. Robinson, Ph.D., Assistant Professor, Dept. of Biology Instructor SECTION 08: Leon A. Dickson, Jr., Ph.D., Associate Professor, Dept. of Biology Email: ldickson@howard.edu Office Phone: 202-­‐806-­‐4346 Office: EE Just Hall Rm G28 Office Hours: Monday and Wednesday 2:10 – 4:00pm, and by appointment Instructor SECTION 09: Courtney J. Robinson, Ph.D., Assistant Professor, Dept. of Biology Email: courtney.robinson@howard.edu Office Phone: 202-­‐806-­‐6953 Office: EE Just Hall Rm 222 Office Hours: Monday 1-­‐2:30pm, Tuesday 10-­‐11am, Wednesday 3-­‐4:30pm, and by appointment Assistant Instructor: Ayele Gugssa, Ph.D., Sr. Research Associate, Dept. of Biology Email: agugssa@gmail.com Office: EE Just Hall Rm G41 Office Hours: Tuesday and Thursday 10:00 – 11:00 Alternate Instructor: Broderick Eribo, Ph.D., Professor, Dept. of Biology Email: beribo@howard.edu Teaching Assistant (TA): ________________________________________________________ Email: _________________________________________________ Phone: _________________________________________________ Location: EE Just Hall Rm 107 Office Hours: ______________________________________________________ Required Materials -­‐ supplied by instructor: SEA-­‐PHAGES Laboratory Manual, laboratory notebook Required Materials -­‐ supplied by student: 1 4GB flash drive, calculator, 2 Sharpie brand fine-­‐tip markers (black or blue), 2 pens, scissors, 1 ruler, 1 lab coat, 1 roll scotch (clear) tape Course description: The SEA-­‐PHAGES course will introduce students to key biological concepts using a research-­‐based laboratory course. Students will develop skills in microbiology, molecular biology and electron microscopy. During the course students will learn standard laboratory procedures such as aseptic technique, cultivation of bacteria and bacteriophages, restriction digests of DNA, and DNA amplification. Students are encouraged to work in groups of two or three and in some cases independently under the supervision of the instructor or teaching assistant. NOTE THAT THE INSTRUCTORS OF THIS COURSE RESERVE THE RIGHT TO DEVIATE FROM THIS SYLLABUS AT THEIR DISCRETION 1 General rules, regulations and procedures 1. Safety: It is important that all students familiarize themselves with the safety rules as outlined here and as described during the course. There is absolutely no eating, chewing gum, or drinking in the laboratory. We will be using an open flame, so please tie long hair back, do not wear scarves, baseball hats, long flowing sleeves, etc. in the laboratory. Do not wear open-­‐toed shoes, or shorts. Report accidents of ANY kind to your TA or instructor. 2. Grading: The laboratory and lecture grades will be combined for your final grade (total possible = 1000 points) in the course. The laboratory portion is worth 300 points and is broken down as follows: EXAMS (two worth 45 pts each) 90 LAB REPORTS (two worth 45 pts each) 90 LAB NOTEBOOK 20 QUIZZES/ASSIGNMENTS/DISCUSSION 200 TOTAL POINTS 400 3. Exams: There are no makeup exams except in extraordinary cases (as determined by the instructor) and such cases must be presented with the necessary documents (to be determined by the instructor based on the nature of the situation). The laboratory exams will be short answer, multiple-­‐choice, true or false and will include a practicum component emphasizing correct execution of techniques used throughout the semester. The exam will consist of material from mini-­‐lectures at the beginning of laboratory, material covered in the resource guide, and material from text assignments or assigned reference materials. 4. Lab Reports: Students will generate two lab reports during the semester. The reports will inform the readers of each project’s progress and the student-­‐scientist’s findings up to that point. Although students will work in pairs on the project, each student must generate his or her own original lab reports. Lab Report#2 must contain a copy(ies) of your PHAGESdb.org information page(s) (see http://phagesdb.org/phages/ICleared for an example) and your . A separate document will outline details as to how lab reports are generated. 5. Lab Notebooks: Students will record each experiment and laboratory activity in their notebooks. The required format will be discussed in class. Dr. Gugssa, the TA, and/or the instructor will conduct random unannounced checks of notebooks. Notebooks will be graded primarily on completeness (i.e. Can someone repeat the student’s experiments based on what was recorded in the notebook?). Other considerations will be legibility and organization. 6. Quizzes: Both unannounced and announced quizzes will be given during the semester and can cover any information covered in the lecture or laboratory. There are ABSOLUTELY no makeup quizzes. 7. Assignments: Both out-­‐of-­‐class and in-­‐class assignments will be used to help students develop skills related to understanding and communicating scientific data. Assignments can cover a number of topics, including, but not limited to: scientific articles, information from the previous class period, popular science, and questions from the lab manual. Students will be graded on level and quality of participation. 8. Discussion: During certain class periods students will be expected to participate in discussions facilitated by Dr. Gugssa, the TA, and/or the instructor. Like assignments, discussions can cover a broad range of topics relating to the biological sciences. Points for discussion can also be earned by participation in the biweekly lab meeting. The lab meeting is an informal presentation during which students update colleagues, instructors and TAs on their progress. Certain lab meetings will focus on specific information as described in the course schedule, but most will cover information of the students’ preference. Students will be graded on level and quality of participation. 9. Blackboard: Students are responsible for accessing Blackboard. Announcements, assignments and electronic versions of most of the material used in this course will be posted to Blackboard. Some assignments will be submitted to the instructor via Blackboard. Grades for the laboratory course will be maintained on Blackboard. 10. Open laboratory time: This is a research-­‐based course. Therefore, there may be times when your attendance (or a labmate’s attendance as your proxy) is required outside of the normal class period. Students will not be NOTE THAT THE INSTRUCTORS OF THIS COURSE RESERVE THE RIGHT TO DEVIATE FROM THIS SYLLABUS AT THEIR DISCRETION 2 permitted access to the lab without supervision. The only guaranteed open laboratory time is during TAs’ office hours, however other times may be requested. During these times students can practice techniques, complete lab work, ask questions, get extra help, etc. If there is a specific technique you want to practice or lab work that requires specific reagents, then you MUST notify the TA (or instructor, etc.) ahead of time. 11. Tips on how to do well: a.
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read and be thoroughly familiar with this syllabus read laboratory material/assignments before coming to lab do not wait until the last day before reports are due to seek help from the instructor or TAs do not wait until the last day before exams to go over the study materials, or seek help from the instructor or TAs 12. CHEATING WILL NOT BE TOLERATED. ANYONE CAUGHT CHEATING WILL BE DEALT WITH ACCORDING TO THE RULES OF THE COLLEGE OF ARTS AND SCIENCES. 13. In compliance with the law (Section 504, Rehabilitation Act and the American with Disabilities Act, "ADA"), Howard University is committed to providing its disabled students with reasonable accommodations. In accordance with this policy, students in need of accommodations due to a disability should contact the Office of the Dean for Special Student Services for verification and determination of reasonable accommodations as soon as possible after admission to the University, or at the beginning of each semester. The Office of the Dean for Special Student Services can be reached at (202) 806-­‐2420. SCHEDULE This is a research-­‐based course, and because research is unpredictable there is a limited schedule of set activities. Activities are listed in order to give you context for your project’s progress. Certain milestones must be achieved by certain times. Those milestones and dates, as well as other important dates are indicated on the schedule. Specific readings and assignments will be given during the class period, except were noted. Brief review of last semester and overview of the semester Regroup and plan for the semester 1. Review lab notebooks and determine what the next steps are for your project 2. Determine what needs to be done with your partner from last semester and what you can do on your own. 3. Begin developing wet lab projects 1/8/13 Tuesday 1 Lab meeting: 1. What do you need to complete or repeat from last semester? Will you complete these tasks working with your partner from last semester? 2. Report on wet lab study project for the semester a. What project ideas do you have? b. How will you and your partner work together on this project? For example, will you both work on the same 1/10/13 Thursday experiment simultaneously or will you divide the work? Continue Lab Meeting presentations and planning for the semester if necessary 1/15/13 Tuesday 2 Begin wet-­‐lab experiments Written version of semester plans due beginning of class period (10pts). 1/17/13 Thursday Continue wet-­‐lab experimentation Mini-­‐Lecture: Review of Nucleic acids 1/22/13 Tuesday 3 Continue wet-­‐lab experimentation – Must start new project today NOTE THAT THE INSTRUCTORS OF THIS COURSE RESERVE THE RIGHT TO DEVIATE FROM THIS SYLLABUS AT THEIR DISCRETION 3 1/24/13 Thursday 1/29/13 Tuesday 4 1/31/13 Thursday 2/5/13 Tuesday 5 2/7/13 Thursday 2/12/13 Tuesday 6 Lab Meeting (5pts) Continue wet-­‐lab experimentation Mini-­‐Lecture: Manipulation of DNA in the laboratory All phages will be archived in the -­‐80o freezer today Continue wet-­‐lab experimentation Mini-­‐lecture: DNA sequencing Continue experimentation Submit HUBison113 and all other phages to PhagesDB (5pts) Mini-­‐lecture: Introduction to In Silico portion of course (need computer lab/laptops) -­‐ Practice Genome: Etude Continue wet-­‐lab experimentation Mini-­‐lecture/In Silico activity: DNA Master, BLAST, and auto-­‐annotation Continue wet-­‐lab experimentation Continue experimentation with Etude Continue wet-­‐lab experimentation Begin prep for Undergraduate Research Symposium Abstract 2/14/13 Thursday Exam Review -­‐ come with questions 2/19/13 Tuesday 7 2/21/13 Thursday 2/26/13 Tuesday 8 2/28/13 Thursday 3/5/13 Tuesday 9 EXAM #1 Lab Meeting (5pts) Mini-­‐lecture/In Silico activity: Phamerator Continue experimentation with Etude Continue wet-­‐lab experimentation Undergraduate Research Symposium Abstract DUE to Course Instructors (even if you do not plan to actually participate) (10pts) Lab Report #1 DUE Phage Genome Annotation Assignment Begin annotation process for our phages Continue all other experimentation Mini-­‐lecture: Gene-­‐by-­‐gene evaluation and annotation Continue in silico experimentation with Etude and our phages Continue in silico experimentation with Etude and our phages Continue wet-­‐lab experimentation Lab Meeting (5pts) Continue in silico experimentation with our phages Continue wet-­‐lab experimentation No Class – Spring Recess 3/7/13 Thursday 3/12/13 Tuesday 10 3/14/13 Thursday 3/19/13 Tuesday 11 3/21/13 Thursday 3/26/13 Tuesday 12 3/28/13 Thursday 4/2/13 Tuesday 13 4/4/13 Thursday 4/9/13 Tuesday 14 No Class – Spring Recess Continue in silico experimentation with our phages Continue wet-­‐lab experimentation Begin prep for Undergraduate Research Symposium Posters Continue in silico experimentation with our phages Continue wet-­‐lab experimentation Continue prep for Undergraduate Research Symposium Posters Continue in silico experimentation with our phages Continue wet-­‐lab experimentation Continue prep for Undergraduate Research Symposium Posters Lab Meeting (10pts) -­‐ practice for Undergraduate Research Symposium Continue in silico experimentation with our phages Continue wet-­‐lab experimentation Continue in silico experimentation with our phages Merge Annotations Continue wet-­‐lab experimentation Lab Meeting (5pts) – graded by classmates Continue wet-­‐lab experimentation Continue in silico experimentation with our phages Continue of in silico experimentation with Merged Annotation Continue wet-­‐lab experimentation NOTE THAT THE INSTRUCTORS OF THIS COURSE RESERVE THE RIGHT TO DEVIATE FROM THIS SYLLABUS AT THEIR DISCRETION 4 4/11/13 Thursday 4/16/13 Tuesday 15 4/18/13 Thursday 4/23/13 Tuesday 16 Final Merged Annotations DUE to Instructors Submit names for consideration –two representatives for the SEA-­‐PHAGES symposium (June 7-­‐9th HHMI Janelia Farm Research Campus, Ashburn, VA) Continue wet-­‐lab experimentation Presentations by candidate representatives for the SEA-­‐PHAGES symposium – Class, Instructors, and TAs will vote Submit Final Annotation to Dr. Graham Hatfull’s lab at the University of Pittsburg Final Day of wet-­‐lab experimentation Exam Review Lab Report #2 DUE Exam Review Exam #2 NOTE THAT THE INSTRUCTORS OF THIS COURSE RESERVE THE RIGHT TO DEVIATE FROM THIS SYLLABUS AT THEIR DISCRETION 5