BIOL 4740 Syllabus:  Fall 2011                    4 Credit hours
Meets : Tuesday and Friday   12 noon -4pm in Sci Ctr 3W02
Additional Lab Rooms: SciCtr 3W01, 3W10, 3W16, 3C30and 3C31
Web-based course materials via  RPI- LMS
Prerequisites: BIOL 2120 Introduction to Cell Biology and BIOL 2500 Genetics. 
This is a communication intensive course. 

INSTRUCTOR: Dr. Donna E. Crone , Lecturer
Office location:  Science Center 3C11,       Office telephone number:  276-3299
Office hours:  Tues and Friday 4-4:30p and by appointment

GraduateTeaching Assistant:  Josh McLane      
TA office location: 2119 CBIS                                        TA office hours: by appt                    

 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 culture of model organisms, 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 as assessed by notebook.
Students apply skills to solve research question assessed by independent project poster and presentation.
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:
Required: Short Guide To Writing About Biology (P), Author:Pechenik ISBN:9780205667277
            This is the 7th edition 2010.  Earlier edition  (5th or 6th should be fine)
Additional course material is accessible on the web (links will be provided in the course site in RPI-LMS) and via electronic access at RPI Library (Drosophila Protocols –Ashburner etal)

Course materials : Students should have a 1 in or 1 ½ in 3 ring binder for recording notes, a USB Flash Drive (at least 512MB) for saving images and safety glasses.

BIOL 4740

























Below 60%




Grading criteria
Lab quizzes     5 quizzes (10pts each /Fri  weeks 2-6)                                   10%    
Lab exam        2 exams (Oct 14 and Dec 6)                                                  10%
Notebook                                                                                                        15%
should include detailed description of protocols and results; brief summary of theory
Active participation     (5 points/class – week1-8)                                          15%
follows protocols, asks for help, see improvement in skills
Lab reports                                                                                                      30%

Independent project                                                                                        20%
50% of project grade is based individual performance (notebook 30%/ participation 20%)
50% of project grade is based on group performance (poster 25%/presentation 25%)

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.

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. 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 following format in 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 2 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 accompanying schedule.

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 posterThe 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.

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 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.





Tentative schedule for cell and developmental lab course




week of 8/29

8/30  Introduction to Microscopy
embryo plate prep

9/2  Introduction to imaging
Image J

HW: virtual compound microscope tutorial (link in LMS)

 solution prep

week of 9/5

9/6  Flies: male/female, phenotype markers, media/ fly husbandry

9/9  Quiz1

Preliminary Embryo observation

Live embryo imaging

Set up embryo cages (+/- GFP flies)

Standard embryo collection/ fixation

week of 9/12

9/13  GFP embryo fixation

9/16  Quiz 2

DNA stain—standard /GFP fix


LacZ assay

Day 1  Embryo immunofluorescence

set up embryo cages


week of 9/19

9/20  Day 2 embryo immunofluorescence

9/23  Quiz 3


Microscope imaging – time slots

Notebooks collected at end of class check #1

initial work with C elegans

week of 9/26

9/27  C elegans /prep for RNAi

continue microscope imaging from immunofluorescence

9/30  Quiz 4

prep for RNAi



week of 10/3

RNAi 16C/ 22C

10/7  Quiz 5


independent project planning


10/7 Paper1 due – Drosophila embryo analysis

Week of 10/10

No class Tues 10/11 (Mon Sched)

10/14 Notebooks collected at beginning of class check #2

10/14 Exam 1
independent project prep

week of 10/17

independent projects

independent projects

week of 10/24

independent projects

independent projects

week of 10/31

independent projects

independent projects

11/4 Paper 2 due –C elegans: mutants and RNAi

week of 11/7

independent projects

independent projects

week of 11/14

independent projects

independent projects

week of 11/21

All lab work for independent projects must be completed by 4pm 11/22

No class Nov 24 – Thanksgiving break

week of 11/28

Lab cleanup!

Poster drafts displayed as powerpoint in class for comments before printing

week of 12/5

12/6 Exam 2

12/10 Poster presentations
Notebooks due

Students are required to maintain live material (cells and/or flies) throughout semester.