BIO305 Developmental Biology

Here’s an excerpt from a term paper written by a previous student in this course: Analysis of a Study Observing Development of the Oral-Aboral Axis in Nematostella vectensis

Developmental Biology teaches us not only how different groups of animals or plants develop, it also sheds light on how life has evolved and the relationships that exist between species. Continuously advancing technology allows scientists to learn more and more about the genes and proteins that are the building blocks for life. In many instances, processes or molecules that are fundamental to the most basic aspects of development are conserved throughout many different species.

Model organisms are ideal for studying mechanisms or processes that have been evolutionarily conserved and are similar across species, such as the canonical Wnt/β-catenin signaling pathway observed in this study, which was first observed in fruit flies. A common way for processes to be conserved over thousands of generations is through the creation of orthologs. Orthologs are genes that have slight variation from species to species, but that have evolved from a common ancestor and maintain the same basic function, without which, the animal would not be viable. Gene sequencing technology has made it possible to identify orthologs through internet databases, making the use of model organisms even more beneficial. It is no surprise that genes governing axial body patterning have been conserved, as they are paramount in achieving developmental success. Cnidarians do not have an anterior-posterior axis or a dorsal-ventral axis. Instead their primary body axis is oral-aboral, an end near the mouth and an end away from the mouth region. This axis is developmentally similar to the anterior-posterior axis found in vertebrates. Both types of axial patterning are regulated by the canonical Wnt/β-catenin signaling pathway. In vertebrates, the pathway begins when a Wnt signaling molecule binds to a transmembrane receptor called Frizzled. This causes a co-receptor within the cell membrane to be phosphorylated by protein kinases within the cell. Normally, these protein kinases would form a destruction complex that would degrade β-catenin, preventing it from accumulating. By preventing the formation of the destruction complexes, the extra-cellular Wnt signal allows the β-catenin molecules within the cell to enter the nucleus and activate TCF transcription factors.

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Copyright 2019 Dr. David Champlin

Class meets: Tuesdays and Thursdays, 8:45AM -10:00AM, room 202 Payson Smith attendance: Class participation is required. You probably haven’t had this requirement for a course before. Either attend class or within one week of the class meeting take notes on the lecture posted on YouTube and email your notes to me. Take notes by hand rather than on a computer. The easiest thing to do is to take pics of your notes using an app like Scanbot or GeniusScan and then email the pdf to me. Make sure you do that within one week of the class meeting because after one week the lecture will be deleted. You are required to participate in every class meeting either by attending or by emailing notes to me within one week of the class meeting. It doesn’t increase your grade to participate -- It is just a requirement. If you miss more than three class participations, the highest your final grade can be is a C. If you miss more than five class participations, you will receive an F for the course. You can also get a lower final grade if you consistently do a poor job on the notes. Your score on the notes will be: check, check plus, or check minus. If you consistently get a check minus on your notes you may receive a lower final grade. This approach doesn’t mean you can plan to miss lots of class meetings. We will have a graded assignment every class meeting that’s called a Concept Chat (described below). There will also be some quizzes and in-class assignments. I will announce those ahead of time by email. There are no make ups for missed classes. If you will have a problem with this requirement, please contact me now so we will work out a plan. This plan is dependent on equipment that might break. If so, I will notify you by email how plans need to change.

I will communicate with the class using your USM email addresses. These messages will include essential information about assignments, exams, etc.

Concept Chats During each class meeting, take notes and try to mark the most important ideas. About one hour into class, we will stop and you will discuss with the person next to you the three most important ideas/examples/concepts. On one page, write them down with your names and hand them in. Sometimes, I will then call on a series of students randomly to each describe one of the concepts.

Required Text: Principles of Development, 6th Edition, 2019. Lewis Wolpert, et al. There is a paperback version that is not expensive. ISBN-13: 978-0198800569The 5th edition is similar to the 6th edition. I’ll be using the 6th and I think you should buy the 6th because the paperback version is not expensive. It’s a good book and a very interesting topic. Most questions on the exams will come from both the book and lecture, but some questions from the exams will come from the book and not be mentioned in class.

Instructor: Dr. David Champlin Office: room 476 A Wing, Science Building, Portland Email: champlin@maine.edu Office Phone: 228-8349

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Copyright 2019 Dr. David Champlin

Office Hours: My office hours will be Tuesdays and Wednesdays, 12:00 - 2:00 PM, but you can make an appointment to meet with me at just about any time. Here is a link that can help you with that: http://media.usm.maine.edu/~champlin/advising.htm Prerequisite: BIO107 Grading: If school is cancelled for any reason, any exam/quiz/assignment will take place the next lecture period. The total number of points for the course is 540 as follows: Each is described in more detail on our course web site: http://media.usm.maine.edu/~champlin/courseW.htm

REQUIRED: attendance and/or lectures notes from missed class See info above about attendance and your final grade review paper worth 100 points (or STEM Ambassador Program) two exams each worth 100 points cumulative final worth 100 points two short writing assignments each worth 20 points quizzes and in-class assignments each worth 20 points No make-ups for missed quizzes or in-class assignments, but your lowest two scores of the total quizzes / assignments will be dropped. Each quiz will be announced at least a week ahead of time, but the in-class assignments might not be announced ahead of time.

When anything is handed back, we will go over the distribution of scores and assigned grades. Your final grade will be a weighted average of these grades (see * below) and I will also take into consideration your attendance and class participation in deciding your final grade. If you have questions or concerns about where you stand in the class at any time, please ask me. * Take the letter grade GPA and multiply it by the fraction of the total points the letter grade was worth and then add up all results. A=4.00, A-=3.67, B+=3.33, B=3.00, B-=2.67, C+=2.33, C=2.00, C-=1.67, D+=1.33, D=1.00, D-=0.67, F=0.00 Review Paper: Option to participate in the 4-H STEM Ambassador Program: Students who complete the program to the satisfaction of the 4-H director will write a Review Paper that is just a one-page summary. Here is a link to the web site: https://usm.maine.edu/service-learning-volunteering/4-h-stem-ambassadors To participate, Kristina Catomeris, usm.stemambassadors@maine.edu and let him know which of the training sessions you will attend. Antoine can work with even the busiest, craziest schedules.

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Copyright 2019 Dr. David Champlin

Here are the training dates. Students attend one session from A and one session from B. If you have done STEM Ambassadors before you probably don’t need to do the training. But you should check with Session A: Intro to STEM Ambassadors and Experiential Learning

• Wednesday, September 18, 2:00 – 4:00 pm (USM, Portland Campus) • Wednesday, September 18, 5:30 – 7:30 pm (USM, Portland Campus) • Friday, September 20, 10:00 am – 12:00 pm (USM, Gorham Campus)

Session B: STEM Ambassador Practice and Preparation

• Wednesday, September 25, 2:00 – 4:00 pm (USM, Portland Campus) • Wednesday, September 25, 5:30 – 7:30 pm (USM, Portland Campus) • Friday, September 27, 10:00 am – 12:00 pm (USM, Gorham Campus)

Development is one of the top journals in the field of developmental biology. Abstracts for the articles that appear in Development are at http://www.biologists.com/development/

You should choose an article that is in the “Research Articles” section (this is a primary research article rather than a review article). You should be able to download articles for free if they are more than six months old. Scan through abstracts in the journal and select one that covers a topic you find interesting - but you don’t need to understand any of the details of the article at this point. Once you are set on your research article, the next step will be to identify one or two review articles (These are often cited in the Introduction of the paper) and read them. Bring the article to class on October 6th and we will discuss what your article is about and learn about how to use science databases. Be prepared to describe the article - but you don’t need to understand the details at this point.

The paper is due in class on November 17th. Please turn in photocopies of the articles you read plus a paper with your own description of the following: Why were the experiments in the Development article done? What techniques were employed? What was learned? Before answering these questions, begin your paper with introductory background information you gleaned from the review articles that your classmates would need in order to understand your answers to these questions. There is no length requirement for this paper but it will likely be six pages or a bit more.

Web Resources: I don’t use Blackboard much and won’t use it at all for this course. I will email essential info about the course. Lecture recordings will each be posted for one week and then deleted.

There are tremendous resources on the web to help introduce students to developmental biology from the personal web sites of researchers to videos produced by companies selling products that facilitate discovery. The Society for Developmental Biology maintains a good web site (http://www.sdbonline.org/ ). In general, these sites are big so they are slow to load on some computers. The computers in my research lab

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Copyright 2019 Dr. David Champlin

are very fast and you are welcome to make an appointment with me to use the computers in my lab for our course. That would be great! Student Support: At any point in the semester, if you encounter difficulty with the course or feel that you could be performing at a higher level, consult with me. Students experience difficulty in courses for a variety of reasons. The following are resources on campus for students.

• For writing skills or time management, you can make an appointment to see a student tutor at the Learning Commons located in both the Portland and Gorham libraries. For more information, visit http://www.usm.maine.edu/learningcommons. The Writing Center at LAC is also available to all USM students and is a great option for students living in the greater Lewiston/Auburn area. For more information, please visit http://usm.maine.edu/writingcenter.

• If you need accommodations due to a disability, please contact the Disability Services Center for confidential assistance and accommodation authorization. Timely notification of accommodations is essential. For more information, visit http://usm.maine.edu/dsc.

• University Health and Counseling Services is a student resource that promotes the health and well-being of the USM community. More information can be found at www.usm.maine.edu/uhcs.

• The University of Southern Maine shall not discriminate on the grounds of race, color, religion, sex, sexual orientation, national origin or citizenship status, age, disability or veteran's status in education, employment, and all other areas of the University. Discrimination inquiries should be directed to Betsy Stivers, Director, Equal Opportunity Center of Excellence. She can be reached at 780-4709 or elizabeth.stivers@maine.edu.

The University of Southern Maine is committed to making our campuses safer places for students. Because of this commitment, and our federal obligations, faculty and other employees are considered mandated reporters when it comes to experiences of interpersonal violence (sexual assault, sexual harassment, dating or domestic violence, and stalking). Disclosures of interpersonal violence must be passed along to the University’s Deputy Title IX Coordinator who can help provide support and academic remedies for students who have been impacted. More information can be found online at http://usm.maine.edu/campus-safety-project or by contacting Sarah E. Holmes at sarah.e.holmes1@maine.edu or 207-780-5767.

If students want to speak with someone confidentially, the following resources are available on and off campus: University Counseling Services (207-780-4050); 24 Hour Sexual Assault Hotline (1-800-871-7741); 24 Hour Domestic Violence Hotline (1-866-834-4357).

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Copyright 2019 Dr. David Champlin

Day Date Reading Topic T 9/3 watch videos that will be emailed to the class Th 9/5 pp.235-241 and 248-253 (sections on nematodes in Ch. 6)

C. elegans, model systems, molecular genetics T 9/10 QUIZ 1 (answer questions about gene expression from emailed videos 1A,

1B, 1C) Ch. 1 An introduction to developmental biology Th 9/12 QUIZ 2 (answer questions about gene expression from emailed videos 2A,

and 2B) T 9/17 more intro Th 9/19 Ch. 3 Vertebrate life cycles

T 9/24 Ch. 4 Vertebrate axial patterning Th 9/26 T 10/1 More vertebrate body plan Th 10/3 Ch. 5 Early patterning of vertebrate nervous systems T 10/8 Ch. 2 Molecular development of Drosophila Th 10/10 On Thursday, 10/10, Please bring a copy of the primary research article you have selected (or more than one if you haven’t decided) plus your notes on the article. T 10/15 NO CLASS – Fall Break Th 10/17 Ch. 13 Plant development T 10/22 EXAM 1 Chapters 1, 3, 4, parts of Ch 5 (In Ch 5, for this exam emphasize selected Figs described in an email), and part of Ch 6 (pp.235-241 and 248-253), plus course videos. Th 10/24 Ch. 7 Mechanisms of morphogenesis T 10/29 Th 10/31 Ch. 8 Cell differentiation T 11/5 Th 11/7 Stem cells T 11/12 Ch. 10 Organogenesis Th 11/14 T 11/19 Ch. 11 Development of the nervous system Th 11/21 T 11/26 EXAM 2 Chapters 2, 7, 8, 10, 11, plus parts of Ch5 Th 11/28 NO CLASS – Thanksgiving Break T 12/3 Ch. 9 The saga of the germ cell Your review paper is due at the beginning of class on Thursday, 12/3 Th 12/5 More on reproduction T 12/10 parts of Ch 12 Growth

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Copyright 2019 Dr. David Champlin

Th 12/12 parts of Ch 12 Growth The Final Exam will be in our regular classroom on: Thursday, Dec. 19, 8:00 AM – 10:00 AM. The exam will cover all the material in the course.

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Copyright 2019 Dr. David Champlin