BI347 Comparative Developmental Cell Biology

Syllabus - Colby College - January 2023

Instructor

Dr. Dave Angelini
[e-mail]

Colby Guest Lecturer/Scientist

Dr. Christina D. Cota
[e-mail]

Meetings Times

Week 1 and Week 4 (Colby): Olin 335
MTWThF 10:30-12pm
TWTh 1-3pm

Week 2 and Week 3 (MBL):
TBD (Please refer to the course Moodle for the most up to date schedule)

Prerequisites

BI227 Cell Biology or BI279 Genetics, or instructor authorization

Course description

Our current understanding of biology is built on studies of numerous model species, using a shared set of investigative approaches and experimental methods. In this intensive course, students will practice many of these methods in investigations of several invertebrate animal models. We will examine the synthesis and regulation of melanic pigmentation, applying techniques from microscopy, cell biology, embryology and developmental biology, genomics and genetics. Students will be required to design, execute and present the results of their own experiments. The course will be conducted at the Marine Biological Laboratory in Woods Hole, Massachusetts, which presents unparalleled technical resources and expertise. Students will also have the opportunity to interact with MBL staff, and learn about the institution's history in the growth of biological knowledge.

The setting

Course activities center on hands-on examination of live animals and cells. Planned activities will build skills in molecular biology, microscopy, and experimental manipulation of the model systems. We will discuss experimental design, and students will have several opportunities to plan and conduct their own experiments with faculty and staff support. Lab activities will be interspersed with short lectures covering fundamental concepts of comparative biology, cell and developmental biology, and the use of current methods in those fields. We will also read and discuss current literature in these areas.

The Marine Biological Laboratory (MBL) is a private international center for biological research and education, located in Woods Hole, Massachusetts, and affiliated with the University of Chicago. In its 133-year history MBL has been the setting for several of the most important discoveries in modern biology. It runs annual summer courses at the graduate level, which are renowned for their rigor and intensity. To date, 58 Nobel prizes winners have been associated with the MBL. The facilities and staff of the MBL offer a unique intellectual environment and educational opportunity for Colby students.

The research topic

Diverse animals produce melanin for purposes ranging from light perception, immune defense, thermal regulation, evading predators, signaling conspecifics, warning rivals, and attracting mates. The biochemical synthesis of melanin is well-understood. However, the cellular production of melanin and its trafficking within cells and tissues is complex and varies among species. The regulation of melanin production is understood in only a few instances, but patterns of expression have enormous diversity within and among species. This course will use melanin production as a unifying research topic as we examine diverse animal models and explore various methods of investigation and experimentation.

Online resources

Moodle ( http://moodle.colby.edu/ ) will be the primary electronic method of contact for this course. Announcements and material related to the course will be posted there frequently, so please check the site on a regular basis. On the site you will also find the course syllabus and the schedule of topics, assignments, and PDF files from lecture slides.

Assessments

Final grades for the course will be calculated based on a 1000 point total as listed below.

	points
Quizzes	200
Course/Discussion participation	150
Lab notebook	250
Progress presentations	150
Final presentation	250

Accomodations for the COVID-19 pandemic

The COVID-19 pandemic presents a serious danger to the health of us all. Therefore, complete cooperation with both the college’s plan for pandemic response and the COVID-19 policies at MBL is expected.

• Information regarding the Colby Covid-19 policies can be found at:
  https://covid19.colby.edu/covid-19-health-and-safety/
• Information regarding the Covid-19 safety policies at MBL can be found at:
  https://goforward.mbl.edu/
• Information regarding the current indoor masking policy at MBL can be found at:
  https://goforward.mbl.edu/health-requirements/guidance-for-using-masks-in-mbl-work-areas/

Noncompliance with Covid-19 Health and Safety Protocols may also result in sanctions including warnings, probation, restorative justice measures, campus or community service, loss of or restrictions upon social or travel privileges, or loss of the opportunity to attend College activities or events in person, removal from College housing, loss of student employment or off-campus study opportunities, suspension and expulsion (https://my.colby.edu/ICS/COVID-19_Student_Policy.jnz).

Academic Support

If you experience difficulty in this course for any reason, a wide range of services are available from the College to support you. Please review these resources and reach out as necessary.

• First, please speak with your instructor early if you are having trouble in the course.
• The Farnham Writing Center offers support for students on basic writing and reading skills.
• The Office of the Dean of Studies offers services for students with learning differences. If you suspect you have a learning difference that might require accommodations in this course, please inquire with the Dean of Students Office.
• Counseling Services (x4460) provided from the Health Center offer professional, confidential consultations regarding family problems, stress, depression, cultural adjustments, concerns with sexuality, alcohol and drug use, trauma and other personal issues.

Academic honesty

Honesty, integrity, and personal responsibility are cornerstones of a Colby education and provide the foundation for scholarly inquiry, intellectual discourse, and an open and welcoming campus community. These values are articulated in the Colby Affirmation and are central to this course. Students are expected to demonstrate academic honesty in all aspects of this course. Academic dishonesty includes, but is not limited to: plagiarism (including quoting sources without quotation marks around the borrowed words and a citation); claiming another’s work or a modification of another’s work as one’s own; buying or attempting to buy papers or projects for a course; fabricating information or citations; knowingly assisting others in acts of academic dishonesty; violating clearly stated rules for taking an exam; misrepresentations to faculty within the context of a course; and submitting the same work, including an essay that you wrote, in more than one course. Sanctions for academic dishonesty are assigned by an academic review board and may include failure on the assignment, failure in the course, suspension or expulsion from the College. For more information on recognizing and avoiding plagiarism, see these guides:

• http://libguides.colby.edu/avoidingplagiarism
• http://web.colby.edu/farnham-writerscenter/academic-honesty/

Sustainability

Environmental degradation is a serious biological and societal issue. Colby is committed to practices that promote sustainable living. To help minimize the environmental impact of this course, please minimize paper use by reading slides on a device when possible, rather than printing copies. It is acceptable to take notes on a laptop or tablet during class. If you choose to print, please print double-sided on recycled paper. Multiple slides may be printed to a single sheet. And please recycle unwanted paper after the end of the semester.

Tentative Course Schedule*

*This schedule is subject to change. Please refer to the course Moodle site ( http://moodle.colby.edu/ ) daily for the most up to date information regarding.

Week 1, at Colby

Concepts / lecture content

• Why a comparative approach?
• Model systems
• How do you come up with questions in biology
• Cell biology of melanin
• Genetics of melanin
• How CRISPR/Cas9 gene editing works
• Reading literature for the Big Picture

Lab

• Accessing genomic information
• Design and preparation of CRISPR guide RNAs for gene editing in Vanessa
• Short presentations on plans for research projects

Week 2, at MBL

Concepts / lecture content

• Welcome to MBL/Introductions with the Director of MBL, Nipam Patel, Ph.D. (http://www.patellab.net/) and the Burroughs Wellcome Director of Education, Linda Hyman (https://www.mbl.edu/leadership/linda-hyman/)
• Stem cells and cellular differentiation
• Induction and competence
• Necessity vs. sufficiency
• Failure, negative results, and risk-taking
• Pleiotropy
• Pigmentation in different organisms
• Biological collections
• Evolutionary biology of pigmentation

Lab

• Tour the MBL Marine Resource Center
• Light microscopy
• Microinjection of insect embryos for gene editing
• Hybridization chain reaction (HRC)
• Short presentations on progress in the lab

Week 3, at MBL

Concepts / lecture content

• History of MBL/Tour of the Rare Books Collection
• Special Topics in pigmentation research: Camoflage Pigmentation in cephalopods
• The evolution and genetic basis of human pigmentation
• Graphic design principles for effective communication
• Visual representation of experimental methods
• Preparing effective scientific figures

Lab

• Fluorescent microscopy
• Students use a majority of time on self-designed experiments
• Short presentation on progress in the lab

Week 4 at Colby

Concepts / lecture content

• Scientific communication to a general audience
• Effective poster design and presentation

Lab

• Students use a majority of time on self-designed experiments
• Final presentation of independent projects in a poster session

Potential Extracurricular Activities

• Invited lectures by MBL Scientists
• Nature walks around Woods Hole
• Tour of the Woods Hole Oceanographic Institute
• Biology movie series
• Game night at MBL
• Visiting the Woods Hole Aquarium
• Visiting the Harvard Museum of Comparative Zoology