Course Syllabus:  Fall 2009             4 Credit hours
Meets : Tuesday and Wednesday  noon -4pm in Sci Ctr 3W02
Additional Lab Rooms: SciCtr 3W01, 3W16 and 3C30
Web-based course materials via  RPI- LMS
Prerequisites: BIOL 2120 Introduction to Cell Biology, BIOL 2500 Genetics. 
This is a communication intensive course. 

INSTRUCTOR: Dr. Donna E. Crone , Clinical Assistant Professor
Office location:  Science Center 2C38,
Office telephone number:  276-3299
Office hours:  Mon 10- 11:30am and by appointment
e-mail address: croned@rpi.edu

GraduateTeaching Assistant: Laura Stevens
TA office location: CBIS 2145
TA office hours: By appointment only
TA e-mail: stevel2@rpi.edu
Undergraduate Teaching Assistant Georgia Yalanis yalang@rpi.edu

Course Description
Students will learn a variety of modern cell and developmental biology techniques such as cell culture, genetic analysis, immunocytochemistry, fluorescence microscopy, and live cell imaging.  Using these techniques, students will investigate the function of genetically manipulated proteins in cells and developing embryos.  In the last third of the semester, students will develop independent experimental research plans to address questions of interest to the student. This is a communication-intensive course.

Course objectives:
To gain experience in modern cell and developmental biology laboratory skills including cell culture, immunocytochemistry, fluorescence microscopy and live cell imaging.
To analyze scientific data and communicate the results in a clear and concise manner.

Student Learning Outcomes
Students demonstrate competence in a set of cell and developmental biology laboratory skills
Students record steps and observations from experiments in a format that enables procedure to be reproduced.
Students apply skills to solve research question.
Students report results in writing using appropriate field-specific language and in a journal format typically used in life science.
Students design posters to supplement oral presentation of research findings  

Course text: Current Protocols Essential Laboratory Techniques, SA Gallagher and EA Wiley, John Wiley and Sons, Publisher 2008, ISBN: 9780470089934
Supplementary material will be provided in the course site in RPI-LMS
Drosophila Protocols –Ashburner etal. can be accessed electronically through RPI library

Course materials : Students should have a 1 ½ in 3 ring binder for recording notes and a USB Flash Drive (at least 512MB) for collection of images

Grading criteria
Lab quizzes     7 quizzes (10pts each /Tues weeks 2-8)                                15%    
Notebook                                                                                                        15%
should include detailed description of protocols and results; brief summary of theory including known details on mutants
Active participation     (5 points/class – week1-8)                                          15%
follows protocols, asks for help, see improvement in skills
Lab reports                                                                                                      30%
1. GFP embryo project (15% of lab report grade), 2.mutant embryo project (50% of lab report grade) , 3. S2 cell project (35% of lab report grade
Independent project                                                                                        25%
Proposal (10%), notebook (30%), poster (30%) and presentation (30%)

Labwork involves group work
Students will work in groups of 2 to 3, sharing duties and responsibilities for the group’s laboratory work equally. Violations should be reported to the instructor.
Lab reports are written independently.
Lab participation grades for individual are based on attendance, effort, and evidence of increasing skill with the basic laboratory techniques used in this course. 
For the independent project: proposal is submitted as a group effort.  Each group member should keep a separate notebook.  Poster and presentation are a group effort.  The contribution of each group member to the independent project must be explicitly stated in the acknowledgement section of the poster.

Notebooks
Lab notebooks should be kept to the highest standards of completeness; work should be recorded as it is done so that all the details needed to repeat a procedure and to prepare a report are contained in the lab notebook.  Simply copying the protocols handed out in lab is not sufficient.  Detailed notes must be included.  Notebooks must be kept up to date and may be collected and checked at any time.  Notebooks are to be turned in for grading as noted on the schedule.  All handout material must be attached securely in your notebook and should be neat and organized.  A three ring binder should be sufficient and be sure to include your name on the spine and cover of your notebook.  Be sure to include a table of contents. 

Lab Reports
This course is designated as a communication intensive course. The lab reports are designed to provide students with 1) experience at independently learning and writing about an unfamiliar subject at a high level of competence, and 2) communicate results in a clear and concise manner.  All papers should be written in the style of the modern scientific literature and include: Title, Abstract, Introduction, Methods, Results, Discussion and References.   Time will be spent going over the details of how to write a paper for this course and one revision will be allowed for the first two papers.  All papers will be written independently.

Each student will be required to write 3 descriptive lab reports.   Each lab report will be in 11 or 12pt font and double spaced.  Due dates for final reports are listed in the scheudule above.

Students will be expected to use the experience gained from initial sections of the course to demonstrate greater independence in searching out their own background information and performing the lab work. 

A general grading rubric for each paper is as follows:
Grammar and clarity of writing                    40%
Even if you fully understand the material, poor grammar and lack of clarity can make the most intelligent person sound incompetent. All papers should observe the conventions of Standard English e.g., correct usage, sentence structure, spelling, and punctuation. 

Style (conciseness)                                      35%
There is a general style to writing scientific papers.  Methods are always written in past tense.  The results should be written in past tense, and should describe your results, graphs and pictures.  The best sentences are short, brief and to the point.  There are so many papers to read today, that the papers must be written concisely or else readers will get frustrated.  Included in this is using the appropriate vocabulary necessary for describing the background of molecular biology and the purpose of your experiments.

Organization                                                 25%
The paper needs to be in the format of a scientific journal article, which consists of an abstract, introduction, methods, results, and conclusions/discussions.  It is important that each section contains information only for that section.  For example, methods should only be described in the methods section.  Enough information should be contained to allow a researcher to replicate your experiments.  The Results section should describe the data, i.e. a picture showing bands from a western blot or fluorescently labeled proteins in cells and/or embryos.   Then, state the conclusions and whether or not they support the original hypothesis or the goal of the experiment.  The discussion section should describe relevance to other published work or ways to improve the accuracy or discrepancies (or agreement) between papers and what was expected originally. 

Knowing your audience                              
The information provided in the paper should cover enough background information and presented in a logical manner that a sophomore or a junior can understand and follow the purpose and reasoning in the paper. 

Independent Project
Students will work in groups to gather data for independent project and will present results of their independent projects in the form of a poster.  The poster and its presentation will be a group effort.  Posters will be prepared following the instructions for poster preparation for annual meeting of the American Society for Cell Biology.  Poster will include title and authors, abstract, introduction, methods and results, conclusions and references.  Ideally, posters should be prepared and printed before Thanksgiving to avoid the end of semester crunch (and possibility that poster is still in the print queue when it is time to present.) Students should prepare a 5-10 minute presentation to explain their poster. Each student will present a portion of their presentation: either the introduction, methods, results or discussion.  The will be a short question and answer period after each presentation for the entire group.  The instructor and the TAs will grade the presentation. 

Student presentations will be evaluated based on the scientific data presented as well as the ability to present the information in a clear and logical manner.  Presentation of the poster is not a reading of the text of the poster but rather a summarization of the key points of the poster.  Presentation should be at a level that can be understood by a classmate who is not familiar with the specific details of the individual project.

Attendance
 Timely attendance at both laboratory and recitation sessions is mandatory.   If you must miss a class due to an extenuating circumstance, you must contact the professor as soon as possible.  However, in most cases, a missed laboratory session cannot be made up.  Excessive lateness and unexcused absences will result in the reduction of grade.

Penalty for Late Assignments
Assignments turned in late will be penalized one letter grade for each day or fraction thereof that they are tardy.

Grading Appeals
Appeals of grades must be made to the instructor within one week of the return of graded material to the student. Since grades are assigned both in consideration of the instructor's absolute standards and relative to the performance of the rest of the class, it is unlikely that grades will be changed unless a clear error on the part of the instructors can be demonstrated.

Academic integrity
Student-teacher relationships are built on trust. For example, students must trust that teachers have made appropriate decisions about the structure and content of the courses they teach, and teachers must trust that the assignments that students turn in are their own. Acts, which violate this trust, undermine the educational process. The Rensselaer Handbook of Student Rights and Responsibilities defines various forms of Academic Dishonesty and you should make yourself familiar with these.
This course requires that students work together, in groups of two or three.  Lab work and data analysis must therefore be shared within each group.  Consultation between groups on lab procedures and data handling is also allowed; however, each student is required to keep an independent and detailed notebook.  Copying of data from one notebook to another is only permitted during lab time unless explicit permission to do otherwise is obtained.  The notebooks are considered the property of the course until the semester is over.  Unless otherwise indicated, you should cooperate with one another in and outside of class on the solution of problems.  You may collaborate with your partner on reports.  Each student’s research report and final lab report must be independently written with your name listed as first author and other group member names following.  You may not collaborate on examinations or misrepresent another person's work as your own on examinations.  You may not bring crib sheets to examinations, and you may not write on or alter examination materials that you submit for regrading.  The minimum penalty for cheating is an F on the assignment in question; clear cut or persistent cheating will result in a grade of F overall.
Students who violate the spirit or letter of these rules are subject to penalties according to the principles outlined in the Rensselaer Handbook.

Course calendar overview – detailed calendar in LMS (will be updated regularly with links to protocols and supplemental information
This is a tentative schedule and subject to change depending upon the progress of the class.

Week 1: Sept 1 and 2                        Introduction to working with Drosophila
            Reading: Lab Safety (Text appendix A1), handouts on working with flies
Tues Sept 1     Rec:  Introduction: syllabus review, Lab safety, Introduction to Drosophila,
Lab: male vs female flies, markers and phenotypes
Introduction to reading a scientific paper
Wed Sept 2     Rec: basic fly pushing skills
Lab: 1) working with fly mutants, 2)collect flies for  complementation crosses, 3) collect flies for mutant embryo analysis
Special Rec at 3pm Microscopy techniques 
Guest lecture: Dr. Chris Bjornsson, Director of Microscopy Core, Biotech Center

Week 2: Sept 8 and 9            working with Drosophila embryos
            Reading: handout on Drosophila embryos
Tues Sept 8     QUIZ1 :  Lab safety/ fly husbandry
Rec:  working with fly embryos
Lab: fly embryo collection and preabsorption of antisera
Wed Sept 9     Rec: introduction to fly mutants
Lab: 1) fly embryo collection and visualization, 2) fly maintenance –complementation crosses

Week 3 Sept 15 and 16         working with Drosophila mutants 1
            Reading: Nuf mutation paper / Ethical handling of images (Text : appendix 3)
Tues Sept 15   QUIZ 2: embryos preparation
Rec: Studying mutations and their effects on development
Lab: collect and visualize embryos (flies with GFP tagged gene)
            Notebook collected at the end of today’s class to be graded and returned Wed
Wed Sept 16   Rec: How to write a research paper/ Ethical handling of image data
Lab: 1) collect and sort progeny from complementation crosses (groups share data with class) and 2) set up fertility cross

Week 4 Sept 22 and 23         working with Drosophila mutants2
            Reading: Immunofluorescence (Text: Unit 9.2)
Tues Sept 22   QUIZ 3: fly mutant biology/ complementation tests
                        Rec: immunohistochemistry in theory and practice
                        Lab: 1) collect mutant embryos then fix, block and incubate in primary antibody
                        2) plate embryos from fertility cross
            Paper 1 (GFP embryo) due at beginning of class
Wed Sept 23   Rec: lysate preparation
Lab: 1) secondary antibody, DNA stain, mount, fix mutant embryos, 2)results of fertility cross, 3) whole fly lysates

Week 5 Sept 29 and 30         Immunoblot / Introduction to Cell culture
            Reading: Immunoblotting (Text: Unit 8.3) and Asceptic Technique (Text unit 4.1)
Tues Sept 29   QUIZ 4: immunohisotchemistry
                        Rec:in vivo protein expression analysis / immunoblots
Lab: 1) immunoblot day1 (end with blot in primary antibody)
            Notebooks collected at end of today’s class
Wed Sept 30   Rec: ethical processing of blot data/ asceptic technique
Lab: 1) immunoblots day2, 2) S2 cell culture – split cells for next week’s experiments

Week 6 Oct 7 and 8               Cell Culture 1
Reading: Drosophila cell supplement / Immunofluorescence (Text: Unit 9.2)
Tues Oct 6      QUIZ 5: immunoblots
                        Rec: experiments in culture vs in vivo
Lab: cell immunofluorescence day1 (plate on ConA, permeabilize, fix, block, primary antibody
            Paper 2 (Developmental mutants) due at beginning of class
Wed Oct 7       Rec: cell culture maintenance
                        Lab: immunofluorescence day2

Week 7 Oct 14                       Cell Culture 2
            Reading: Ashburner ch 20
Tues Oct 13    No class – Monday Schedule
Wed: Oct 14    QUIZ 6: S2 immunofluorescence
                        Rec: working with conditional mutants
                        Lab: Live Cell imaging.          
            Independent project proposals due at the beginning of class

Week 8 Oct 20 and 21           Live imaging in Drosophila embryos (tentative)
            Reading: Asburner ch 17
Tues Oct 20    QUIZ 7: conditional mutants
                        Rec: introduction to live embryo imaging
                        Lab: 1) live imaging of GFP embryos, 2) set up for independent projects
            Notebooks collected at the end of class for grading
WedOct 21      Lab: 1) continue live imaging. 2) independent projects

Weeks 9 -12   INDEPENDENT PROJECT
No quizzes or formal recitations during this time.
Tues Nov 3: S2 cell paper due at noon.
            DATA collection must be completed by Tues Nov 24 5pm

Week 13 Dec 1 and 2                       
Tues Dec 1     Lab cleanup
Wed Dec 2      Draft of poster reviewed --comments by instructors and classmates

Week 14 Dec 8 and 9            Poster Presentation
Tues Dec 8     Practice presentation
Wed Dec 9      Poster presentations – Bio Dept invited (posters and presentations to be graded)    Notebooks will be collected for project grading