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Biology

Project Lab Syllabus


BIOL 2309, Spring 2018 (Section 02, CRN 34301)

Instructor
Desislava (Dessy) Raytcheva, Ph.D.
Email: d.raytcheva@northeastern.edu
Office: 414J Mugar Life Sciences Building
Student (Office) hours: Fridays, 12-3:00 pm in room 605 Behrakis, or by appointment.
Individual assistance is always available. Looking forward to seeing you during office
hours.

Course Information
Academic Term: Spring, 2018
Credit Hours: 4SH
Laboratory Schedule: Mondays and Wednesdays, 3:30-6:20 pm
Laboratory Location: Room 610 Behrakis Health Sciences Center

Course Description
In this guided inquiry laboratory, students will have the opportunity to design experiments and
test student-derived hypotheses. Students will generate, analyze, and present scientific data to
their peers in a multitude of authentic formats used in science. This course prepares students for
upcoming independent research positions by immersing them into a research lab setting under
supervision by lab personnel. Students are responsible for making and maintaining their own
solutions and reagents, collecting data, adjusting experimental protocols, and collaborating with
their peers to troubleshoot standard experimental issues.

Course Prerequisites
BIOL 2301 Genetic and Molecular Biology. Restricted to students in the College of Science.

Course Objectives
By the end of this course, students will be able to:
1. Apply the process of Science: formulate hypotheses; design experiments with attention to
controls to test hypotheses; properly follow and adjust protocols to collect data; maintain
detailed and accurate records of experimental procedures; interpret and evaluate data,
and determine the next steps in the research process.
2. Communicate the research findings in effective written and oral communication formats.
3. Critically evaluate scientific literature as well as the work of peers.
4. Develop as young professional researchers by practicing foundational research lab skills,
demonstrate exemplary lab safety as well as exemplary work ethic.

Required Readings
Primary literature articles and published reviews will be assigned by the instructor throughout
the semester, and will be posted to Blackboard. Students are expected to critically read these
papers prior to the assigned reading date indicated on the course calendar and come to lab
prepared to discuss each section of the paper (question/hypothesis, methods, results/data, and
conclusions).

BIOL 2309 Syllabus (Spring 2018) Page 1 of 8



Recommended Texts and Online Resources
1. At the Bench: a Laboratory Navigator, Updated Edition, Barker, K., Cold Spring Harbor
Laboratory Press, 2005.
2. Gene Cloning and DNA Analysis: An Introduction, 6th Edition, Brown, T. A., ebrary, Inc.,
Hoboken, Wiley-Blackwell 2010. Available for online reading and download via the library.
3. http://www.wormbook.org – A comprehensive, open-access collection of original, peer-
reviewed chapters covering topics related to the biology of Caenorhabditis elegans and
other nematodes.
4. http://www.wormbase.org – Facilitates insights into nematode biology.

Blackboard
In addition to published articles, the syllabus, course calendar, announcements, activities, and
assignments will also be available via Blackboard. Please note that the course schedule may be
subject to change depending on course progression and extenuating circumstances. Be sure to
check the Blackboard site often for announcements and updates. Modifications to the syllabus,
course calendar, assignments, etc. will be posted there.

Benchling Laboratory Notebooks and Group Recorders
Students will work in groups throughout the semester, and each group will be required to record
all laboratory work in a digital notebook using the Benchling website (https://benchling.com/).
This lab notebook will be maintained by all group members throughout the semester. However,
during each lab period, one individual in each group will be assigned as the official group
recorder for the day. All group Benchling projects will be accessible to the instructor.

In addition to keeping all necessary experimental records in the lab notebook on Benchling, the
recorder will also take notes summarizing team discussions and decisions. It is recommend that
this note-taking also be done on Benchling in a separate document (not in the laboratory
notebook), or via some other digital means (e.g. Google Drive). This will help to facilitate efficient
organization and communication among group members.

Course Format and Procedure
a. BIOL 2309 is a laboratory-based course. There is no lecture component for this course.
Each laboratory section will meet twice a week. Each lab session runs for 2 hours and 50
minutes.

b. For the group project work, student will work in groups of 3-4 members. Group work
requires a commitment to efficiency and mutual respect. Every group member is
responsible for ensuring that the group experience is pleasant and successful during each
lab period. Group members will each be peer-reviewing their fellow group members
throughout the semester. These reviews will assess each member’s attendance,
preparedness, contribution, and flexibility.

c. During each lab period, every group member will be assigned a role. These roles will rotate
every few days among the members of each group. Responsibilities for group members are
as follows:

BIOL 2309 Syllabus (Spring 2018) Page 2 of 8


All Group Members
a. Ensure that all group members are dressed appropriately for lab, and are utilizing proper
safety protocols during laboratory.
b. Strive to create a harmonious and positive team atmosphere, and ensure that the group
reaches a consensus during discussion after allowing full expression of ideas.
c. Raise counter-arguments and constructive objections.
d. Contribute alternative perspectives, hypotheses, and analyses of data.

Facilitator
a. Moderates team discussion and keeps the entire group, as well as each member, on task.
b. Distributes work among group members as needed and ensures that each member has the
opportunity to contribute and learn.
c. Ensures that all group members understand the scientific concepts and the group’s
conclusions.
d. Keeps the group aware of time constraints and deadlines.

Recorder
a. Keeps all necessary experimental records in lab notebook on Benchling.com
b. Takes notes summarizing team discussions and decisions on some digital format
(Benchling, Google Drive, etc.).

Reporter
a. Serves as group spokesperson to the class or instructor, summarizing the group’s
activities and/or conclusions.
b. Keeps the recorder updated on the details of the performed experimental procedures.

Prepper (combined with Facilitator duties in groups of 3)
a. Plans the group’s work for next class period and includes the plan in the Benchling group
folder as well as remind the group about the planned work for that day.
b. Perform literature search tasks such as finding new papers or lab protocols for next class
period.
c. Ensures that the workspace is free of clutter during work and properly cleaned and
organized at the end of class.

General Note for All Assignments:
Specific instructions for assignments will be provided during lab by the instructor and will be
posted to Blackboard. These instructions will contain detailed expectations for each assignment
and will indicate the due date and the submission location (Benchling, Turnitin, hard copy, etc.)
for the completed assignment. It is also noted on the course calendar whether each assignment
should be done as an individual or as a group. Please keep in mind that late submissions will be
penalized.

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Evaluation and Grading
Final course grades will be determined as follows:

Category Percentage
Laboratory Research
● Attendance, Professionalism & Safety 10%
● Homework & Assignment Sheets 10%
● Practical Exam 10%
● Benchling Lab Notebook 10%
● Quizzes 5%
Written and Oral Communication
● Annotated Bibliography 5%
● Chalk Talks 10%
● Journal and Exit Cards 5%
● Peer-Reviews 5%
● Results and Discussion - Draft 5%
● Results and Discussion - Final Paper 10%
● Final Group Presentation 15%

Attendance
● You are expected to attend all lab sections on time, properly dressed, and prepared to conduct
scientific experiments.
● Absences will only be excused if you have: (a) notified your primary instructor via email in
advance; and (b) you have a documented excuse (e.g. University-sponsored event, proof of
family emergency, religious or legal conflicts, illness with a doctor’s note*). All
documentation must be received within one week of your absence. Unexcused absences
will negatively affect your grade.
*Please be aware that Health Services doesn’t provide documentation for short-term
illnesses, but you may be able to get an appointment card signed and dated by a nurse or
physician.
● Students who are absent from lab are responsible for coordinating with the instructor as
well as with their group members to catch up on missed material and to ensure that they
will compensate for lost time. Groups may also discuss these circumstances with the
instructor as needed.
● Once you start working on your group projects, you will not have regular homework
assignments but you will probably have to come outside of class to work on your projects.
You will make arrangements within your groups based on the schedule of your project.

Safety
● You will be required to complete a few online trainings through the Environmental Health
and Safety Department webpage. Check the calendar to earn the credit for on-time
completion.
● You will be expected to demonstrate exemplary safety at all times during the lab.
● Repeated safety violations will be reflected in your final grade.
BIOL 2309 Syllabus (Spring 2018) Page 4 of 8
Professionalism
In preparation for your career as a researcher, part of your grade will be based on your
professionalism.
• You are therefore expected to attend each lab section on time, properly dressed, and
prepared to conduct scientific experiments.
• You will be responsible for cleaning your lab stations before and after working in lab,
setting up your own experiments, properly storing your samples, and disposing of waste
in accordance with Environmental Health and Safety standards.
• Every student will be an active contributor to experimental design and execution, as well
as discussion of results and analysis of data within your group. This applies both to in-
class as well as outside work on the group project.
• You will also be expected to optimize experimental protocols as needed to ensure that the
research project is progressing at a suitable pace. You are expected to perform literature
search as needed, and contribute ideas and suggestions to the group discussions in a
timely manner as well as listen carefully to the input of others, e.g., groupmates,
classmates, UAs, instructors, etc.
You can find the complete list of professional skills that will be assessed on Blackboard under
Syllabus. Please review the list and keep it in mind as you work in the lab.

Homework and Assignment Sheets
● Throughout the semester, you will complete and submit homework assignments, and
assignment sheets for in-class activities.
● These assignments will allow you to monitor your understanding, prepare for the Practical
exam, as well as receive feedback from the instructor.
● These assignments will be assessed primarily on their completeness, clarity and on-time
submission.

Practical Exam
● The Practical exam will assess your knowledge of and competency with laboratory material
and techniques.
● During the exam, you will answer both theoretical and practical questions related to:
execution of lab procedures, proper use of equipment, experimental design, as well as data
analysis and interpretation.
● The practical exam will also allow you to assess your competencies in the lab prior to the
start of your research project.

Benchling Lab Notebook
● Keeping a proper lab notebook is a very important skill for a researcher. Throughout the
semester, two notebook entries written on Benchling during your time as group recorder
will be chosen at random and graded. Your lab notes will be assessed for accuracy,
completeness, and clarity. You are encouraged to use the provided feedback to improve
your note-taking skills.

Quizzes
● There will be a few quizzes in the course. They will be administered through Blackboard.
● The quizzes will provide feedback on your understanding of the material as well as prepare
you for the Practical exam.
BIOL 2309 Syllabus (Spring 2018) Page 5 of 8
Written and Oral Communication
In this course, you will have numerous opportunities to practice reporting your research findings
both in oral and written formats.

Journal and Exit Cards
The purpose of this ongoing assignment is to provide an opportunity for you to honestly reflect
on your experiences as a nascent research scientist and reflect on your own learning.
● Regularly throughout the semester you will be asked to compose and submit written
responses to Journal/Exit cards prompts provided by the instructor.
● Some of the entries will be completed at the end of class, others outside of class and will be
due before the beginning of the next class.
● These assignments will be assessed on the quality, completeness, clarity, and on-time
submission.

Peer-Reviews
Each student will provide feedback on oral and written assignments completed by other groups
and students.
● Each group member will also provide and receive feedback on their performance as a
teammate based on the quality of their group work via Teammates.
● The peer-review assignments will be assessed on the quality, completeness, clarity of the
reviewer’s feedback, and on-time submission.

Annotated Bibliography
The annotated bibliography is a collection of brief summaries of relevant papers from the
primary literature that will serve as a resource as you and your groupmates design and execute
your project as well as prepare the final presentation and papers.
● As you are thinking about potential projects, you should be familiarizing yourself with the
literature. Therefore, your first annotated bibliography submission will be due before you
start brainstorming your project as a group (check the calendar for the exact date).
● Throughout the semester, when you are assigned the Prepper role for the week, it will be
your responsibility to find, read and summarize papers that are relevant to your group’s
activities for the week.
● As you conduct this research, you will be expected to update the bibliography with your
findings and share it with everyone.
● This assignment will be assessed primarily on its completeness, clarity, and on-time
submission.

Oral Presentations
There will be two types of oral presentations:
● The Chalk talks will be short overviews of your project and will allow you to obtain
feedback from your peers and the instructor on your project direction, progress and
experimental troubleshooting as well as on your presenting skills.
● In the Proposal Chalk talk, you will present the proposal for your group project. It will
include the concept map of your project as well as proposed figure(s) with your expected
results.
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● In the Mid-project Chalk talk, you will present your preliminary findings of your research
project.
● The Final presentation will provide a detailed and final summary of your project findings.

Results and Discussion – Draft and Final Paper


You will practice summarizing your project and its findings in a written format specialized for a
scientific audience.
● You will first submit a draft of the Results and Discussion. You will receive feedback from
the instructor as well as your peers.
● You are encouraged to use the provided feedback to improve your writing skills and to
perfect your final report.
● The Final Results and Discussion Paper will summarize your final and edited findings.

Group Assignments
● Assignments which will be completed as group work will be graded with strong or exclusive
emphasis (depending on the assignment and as described in its instructions) on the
performance of the entire group.
● Should any conflicts or concerns arise among group members during preparation please
address them immediately and, if needed, contact the instructor for assistance before the
assignment due date.
● Complaints (about individual teammates displaying poor participation or performance) that
are presented to the instructor after the assignment has been submitted will not be
sufficient cause for a regrade of the submitted assignment.
● Students are strongly encouraged to fairly and constructively assess their groupmates
contributions during the provided opportunities throughout the semester for peer-review
assessments within the group. These reviews will be anonymous.

Grading Scale
● There will be no curve unless the overall, final average for the entire class falls below 70%.
However, this rule may be amended as deemed necessary by the instructor.
● Individual quizzes, homework, assignments, and exam grades will not be curved during the
semester.
● Final letter grades will not be assigned until the end of the course.
● Final letter grades will be assigned according to the following convention: 93-100% = A,
90-92% = A-, 86-89% = B+, 83-85% = B, 80-82% = B-, 76-79% = C+, 73-75% = C,
70-72% = C-, 66-69% = D+, 63-65% = D, 60-62% = D-, 0-59% = F.
● COS students who receive an F will automatically fail a course. Any higher grade (A through
D) is considered a passing grade, however students need to maintain a C (2.000) average in
math/science and a 2.000 overall to graduate.

Academic Honesty
The process of scientific research often involves reading and expanding on previous published
research. For this reason, you will be expected to design authentic research projects and to cite
previous research appropriately. Additionally, many assignments in BIOL 2309 will require you
to work independently. In these cases, you are expected to submit assignments that are
exclusively your own. Academic dishonesty includes (but is not limited to) cheating, fabrication,
plagiarism, unauthorized collaboration, participation in dishonest activities, and facilitating

BIOL 2309 Syllabus (Spring 2018) Page 7 of 8


academic dishonesty. Students caught cheating will get an automatic 0 on the assignment and
will be reported to OSCCR. The university policy on academic integrity is detailed at:
http://www.northeastern.edu/cos/wp-content/uploads/2014/11/Northeastern-COS-Policies-
Template.pdf

Northeastern Resources and Policies
Title IX
The University strictly prohibits sex or gender discrimination in all university programs and
activities. Information on how to report and incident of such discrimination (which includes
sexual harassment and sexual assault) is located at http://www.northeastern.edu/titleix/

Disability Resource Center (DRC)
Students who have disabilities who wish to receive academic services and/or accommodations
should follow the standard Disabilities Resource Center (DRC) procedures:
http://www.northeastern.edu/drc/getting-started-with-the-drc/

Academic Support
The instructor will have regularly scheduled student (office) hours. Looking forward to seeing
you during these sections. Individual appointments outside of office hours are always available.
Please don’t hesitate to email the instructor to schedule one.
In addition, the university policy on tutoring and other resources can be found at:
http://www.northeastern.edu/cos/wp-content/uploads/2014/11/Northeastern-COS-Policies-
Template.pdf

Class Discussions
Classrooms are a place for respectfully challenging open discussions. All expressions will be
peaceful and orderly, conducted in a manner consistent with the Student Code of Conduct
(http://www.northeastern.edu/osccr/wp-content/uploads/2017/06/code-of-student-conduct-
2017-2018.pdf) and University policies, and in such a way that University business and respectful
academic discourse are not unduly disrupted.

College of Science Academic Course Policies
These policies hold across all courses taught in the College. The complete policies are available
for review at:
http://www.northeastern.edu/cos/wp-content/uploads/2014/11/NortheasternCOS-Policies-
Template.pdf.

Course Evaluation
At the end of the semester you will be expected to participate in Teacher Rating and Course
Evaluation (TRACE). Details will be provided closer to the end of the semester. Your feedback is
appreciated and is important for course improvement.

BIOL 2309 Syllabus (Spring 2018) Page 8 of 8


BIOL 2309 Biology Project Lab: Course Calendar
Monday-Wednesday Sections, Spring, 2018

Date Laboratory Topics and Assignments Due Quizzes, Homework, and
Activities Assignments*
Jan 8, v Welcome! v Read Iatsenko et al., 2014
Mon v Student Information Survey v Journal Club Activity
v Syllabus & Calendar v Chemical Hygiene 1 and
v Class Community Agreement Chemical Hygiene 2
v Laboratory Rules & Online EH&S Trainings -
Regulations Upload Certificates to
v Biosafety Guidelines Contract Turnitin
v Pre-Test v Read Rubio-Infante and
Moreno-Fierros, 2015
v Laboratory Safety Quiz
Jan 10, v Journal Club Discussion v Journal Club Activity
Wed (Iatsenko et al., 2014)
v Exit card #1
Jan 15, Martin Luther King Jr.’s Birthday - No Classes
Mon
Jan 17, v Journal Club Discussion - v Laboratory Safety Quiz v Mini-Project
Wed wrap-up v Chemical Hygiene 1 and Experimental Plan
v Mini-Project, Part 1 Chemical Hygiene 2 v Bacteria & Nematode
v Obtaining Pure Cultures via Online EH&S Trainings - Quiz
Quadrant Streaking Upload Certificates to v Read review articles on
v Exit card #2 Turnitin Bacillus and C. elegans
(needed for “Bacteria and
Nematode Homework”)
Jan 22, v Mini-Project, Part 2 v Mini-Project v Calculations Homework
Mon v Observing Bacterial Growth Experimental Plan v DNA Purification
(Quadrant Streaks) v Bacteria & Nematode Homework
v Start Liquid Cultures Quiz
v Gram Staining and Light
Microscopy
v Pipetting Activity
v Exit card #3
Jan 24, v Measuring Optical Densities v Calculations Homework v PCR Homework
Wed v DNA Purification v DNA Purification v DNA Purification Quiz
v Exit card #4 Homework
Jan 29, v Calculations Activity v PCR Homework v PCR Quiz
Mon v PCR Activity v DNA Purification Quiz v Gel Electrophoresis
v Mini-Project, Part 3 Homework
v Exit card #5
Jan 31, v Gel Electrophoresis Activity v PCR Quiz v Gel Electrophoresis Quiz
Wed v Pouring and Seeding NGM v Gel Electrophoresis v Data Analysis Homework
Plates Homework v Bacteria and Nematode
v Assigning Groups for Group Homework
Projects
v Exit card #6

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Date Laboratory Topics and Assignments Due Quizzes, Homework, and
Activities Assignments*
Feb 5, v Review of Bacteria & v Gel Electrophoresis Quiz v Prepare for Practical
Mon Nematode Biology HW v Data Analysis Homework Exam
v Chunking & Observing v Bacteria and Nematode
Nematodes Homework
v Data Analysis Discussion
v Practice for Practical
v Exit card #7
Feb 7, v Practical Exam v Group Work Articles (for
Wed Journal Entry #1)
v Literature Research
Homework
v Annotated Bibliography,
First Entry
Feb 12, v Scientific Method v Literature Research v Group Proposal Chalk
Mon v Project Proposal/Concept Homework Talk (Concept Map &
Mapping Activity v Annotated Bibliography, Expected Results Figure,
v Expected Results Figure and First Entry and Methods Figure)
Methods Schematics Draft v Journal Entry #1
v Exit card #8
Feb 14, v Group Projects: continue v Journal Entry #1 v Finalize Group Proposal
Wed working on Group Proposal Chalk Talk
Chalk Talk
Feb 19, President’s Day – No Classes
Mon
Feb 21, v Group Proposal Chalk Talk v Proposal Chalk Talk v Peer-Review of Group
Wed (Concept Map & Expected Members via Teammates,
Results Figure, and Methods part 1
Figure) v Journal Entry #2
v Chalk Talk Peer Reviews
v Maintaining a Laboratory
Notebook and Group Roles
Feb 26, v Making Media and Solutions v Journal Entry #2
Mon v Group Projects
Feb 28, v Group Projects v Peer-Review of Group v Journal Entry #3
Wed v Mock Data Presentation Members via
Activity Teammates, part 1
Mar 5-7 Spring Break – No Classes

Mar 12, v Group Projects v Journal Entry #3


Mon
Mar 14, v Group Projects v Journal Entry #4
Wed
Mar 19, v Group Projects v Journal Entry #4
Mon
Mar 21, v Group Projects v Journal Entry #5
Wed v Group Mid-Project Chalk Talk v Peer-Review of Group
(Group # TBD) and Peer Members via Teammates,
Reviews part 2

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Date Laboratory Topics and Assignments Due v Quizzes, Homework, and
Activities Assignments*
Mar 26, v Group Projects v Journal Entry #5 v Results and Discussion
Mon v Group Mid-Project Chalk Talk Draft
(Group # TBD) and Peer
Reviews
Mar 28, v Group Projects v Peer-Review of Group
Wed v Group Mid-Project Chalk Talk Members via
(Group # TBD) and Peer Teammates, part 2
Reviews
Apr 2, v Group Projects v Results and Discussion v Peer-Review of Results
Mon v Group Mid-Project Chalk Talk Draft and Discussion Draft
(Group # TBD) and Peer v Journal Entry #6
Reviews
Apr 4, v Group Projects
Wed
Apr 9, v Group Projects v Peer-Review of Results v Group Final Presentation
Mon and Discussion Draft Draft
v Journal Entry #6
Apr 11, v Group Projects v Group Final v Optional (Strongly
Wed v Post-Test Presentation Draft Encouraged): TRACE
Survey
v Group Final Presentation
Apr 16, Patriot’s Day – No Classes
Mon
Apr 18, Last day of class! v Results & Discussion Final
Wed v Group Final Presentations Paper
(Note: visiting professors may be
present)
v Annotated Bibliography – All
Entries
Apr 26, No Class v Results & Discussion Final Paper
Wed v Optional (Strongly Encouraged): Copy of TRACE Survey
Completion Email or Screen Shot

*Important Notes for Quizzes, Homework, and Assignments:
1. All quizzes, homework, and assignments must be completed as individual work, unless otherwise noted (i.e.
“Group”).
2. All quizzes, homework, and assignments are due at the start of lab, unless otherwise noted.
3. All quizzes will be available via Blackboard.
4. Each homework/assignment will be accompanied by explicit instructions for completion and submission.
Please follow these instructions carefully to obtain full credit on each assignment.

**This schedule is subject to change based on the needs of the class. All changes will be announced in
class and posted on Blackboard. Please pay attention to any changes in order to adhere to the updated
schedule.

***Important dates:
January 22, 2018 – last day to drop the class without a “W” grade
April 19, 2018 – last day to drop the class with a “W” grade

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