biol 4014 vertebrate embryology department of biology t/r ... · biol 4014 – vertebrate...

BIOL 4014 – Vertebrate Embryology – Department of Biology – Spring 2018 T/R Lecture 6 pm-6:50 pm New Science Building Rm 406; T/R Lab 7 pm-8:50 pm New Science

Building Rm 406

Information contained in this syllabus, other than grading, makeup work, and attendance policies, may be subject to change with advance notice, as deemed appropriate by the instructor.

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Instructor: Shaye K. Lewis, Ph.D.

Office: CARC 122

Phone: 936-261-3650

Email: [email protected]

Hours: T/R 2:00 PM – 4:00 PM

Course (Catalog) Description: Embryology examines living organisms in a very different

manner to other areas of biology; rather than examine adult structures; developmental biology

seeks to explain how these structures come about. The organization of an entire organism from a

single, undifferentiated cell is a remarkable and complex feat. This course provides an overview

of important developmental issues, questions, and experimental approaches used to study

developmental biology. As an upper level course, this course also seeks to test and reinforce

critical thinking, experimental design, and scientific writing skills through planned

experiments and accompanying lab reports.

Course Goals:

1. To provide you with the core principles of developmental biology. The lecture and the book

will introduce you to the fields of developmental biology. After this class, you will have a basic

understanding of developmental biology and will be equipped to build upon this content with

upper level courses in biology.

2. To provide you with the necessary tools for higher level thinking skills that are necessary for

scientists. You should be well equipped at remembering facts and content with good study habits.

We are looking for you to apply and analyze. Move beyond memorization. How can we

achieve this? We will have in-class questions based on out of class reading assignments to

practice this immediately (see section on TopHat). We will also explore classic experiments as a

way of thinking through the logic of experiments and to see where the foundations of this content

come from. While these may be new ways of thinking for you, practice is the most important way

to gain these skills.

3. To teach you how to think. This course should excite you about basic science and its

applications.

Learning Objectives: At the end of this course, the student will have a basic understanding of

vertebrate developmental biology, and the molecular pathways important for development of

specific body systems and body patterns important across multiple species. We will focus on both

fetal and postnatal development. Students will learn how to perform basic molecular biology

techniques applied in the study of developmental biology and how normal development is

essential for normal differentiated functions as an adult. Students will learn essential

terminologies used in developmental biology. Learning objectives are in alignment with both the

Academic Program and with the Core Curriculum.

1. to develop an understanding of experimental approaches used by developmental

biologists and embryologists

2. to develop a sufficient background for those students who wish to study more advanced

scientific topics

3. to develop an understanding of important issues and questions in developmental biology

4. to provide familiarity with the requirements for scientific writing

5. to improve student’s ability and confidence in designing, executing, and interpreting

research projects

mailto:[email protected]


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We want each of you to do well, but for this to happen we need you to do your part. Please

take advantage of all of the opportunities to learn and review the material. To facilitate this,

attendance at all classes and activities is essential. Anyone who does poorly on any exam is

strongly encouraged to meet with the professor at the earliest possible time to plan how to

improve performance on the next exam. Do not wait until the end of the semester; you will get

the grade you earn.

Please come to class prepared to ask questions. If you do not understand a point in our class

discussions or in your readings, please feel free to interrupt by asking a question or ask your

questions at the start of each lecture. Do not feel intimidated or embarrassed to ask questions!

Anyone who wishes to audio record lectures is free to do so.

Required Resources:

1. Textbook: Developmental Biology, 11th Edition, Scott Gilbert and Michael Barresi,

ISBN 978-1-60535-470-5.

2. Top Hat: We will be using the Top Hat (www.tophat.com) classroom response system in

class. You will be able to submit answers to in-class questions using Apple or Android

smartphones and tablets, laptops, or through text message.

You can visit the Top Hat Overview (https://success.tophat.com/s/article/Student-Top-Hat-

Overview-and-Getting-Started-Guide) within the Top Hat Success Center which outlines how

you will register for a Top Hat account, as well as providing a brief overview to get you up and

running on the system. An email invitation will be sent to you by email, but if don’t receive this

email, you can register by simply visiting our course website: https://app.tophat.com/e/950199

Note: our Course Join Code is 950199

Top Hat will require a paid subscription, and a full breakdown of all subscription options

available can be found here: www.tophat.com/pricing.

Should you require assistance with Top Hat at any time, due to the fact that they require specific

user information to troubleshoot these issues, please contact their Support Team directly by way

of email ([email protected]), the in app support button, or by calling 1-888-663-5491.

Grading: There will be three tests and a final exam given during the semester. The format will

include both multiple choice and open-ended questions. These are not cumulative tests and will

only cover the material specified on the course schedule. However, each part of the course builds

on the knowledge from earlier sections, so do not “mentally erase” fundamental concepts from

earlier in the semester. For all exams, and other work you turn in for grading, you will need

your class ID number as identification, do not place your name any work submitted for

grading. The instructor will give your class ID to you. Test material to study: guided readings,

discussion outlines, lecture notes, lab notebooks, and power point slides. Therefore, to succeed in

this class, it behooves you to take each reading/assignment seriously and actively engage in all

class discussions. There is no option to drop a test grade and there are no extra credit

options.

Exams must be taken on the dates indicated during the regular class period; no makeup

exams except in special circumstances, i.e., pre-planned activities where you are a

representative of the University, documented in writing prior to missing the exam. For

medical or family emergency documentation must be given to the instructor within 72

hours. The instructors reserve the right to give oral make-up exams. If you still do not

http://www.tophat.com/

https://success.tophat.com/s/article/Student-Top-Hat-Overview-and-Getting-Started-Guide

https://success.tophat.com/s/article/Student-Top-Hat-Overview-and-Getting-Started-Guide

http://www.tophat.com/pricing

mailto:[email protected]


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understand content after your exam has been graded and would like to discuss concepts or the

rationale for your answers, you will have an opportunity to defend your exam answers. If you

have a question related to points you feel you deserved, you must put it in writing no more than 5

days after an exam has been returned to you and turn it in to your instructor.

Class Participation (TopHat) (10% of your final grade): As an incentive to come to class

prepared and be engaged, 10% of your grade will come from in-class participation in question

from the assigned readings or on the textbook readings. These readings should be done before

lectures. Participation will require a subscription to a website called TopHat that you may use

through your laptop or mobile phone to answer in-class questions. Note - missing just a couple of

classes can quickly affect your participation grade! There will be no make-up opportunities for in-

class assignments if you do not class a recitation in a given week. See TopHat for the required

registration and troubleshooting and grading policy information.

Digital Etiquette: This course will require you to use your laptop and/or cell phone during class

time. While we recognize that you are an excellent multi-tasker, research suggests that your peers

are not. Please be respectful of your classmates and restrict your use of digital devices to course

content. If we see that you or your peers are distracted, we will ask you to put your devices away

and you may forfeit your ability to earn participation points that day. There will be times when

you have completed your work or answered a poll question, but your peers have not. We ask that

you assist your peers when appropriate or use the time to review your notes while you wait. I

understand that your devices connect you to your friends and family (a wonderful thing!) but the

classroom should be a place apart, however briefly (even if it seems like an eternity to you), from

the outside world and distractions. You will learn more if you concentrate on the course while

you are here and your classmates will thank you for not impeding their ability to learn.

Recitation: Attendance and participation in the recitations sections is optional but may increase

your understanding of course material. These recitations are an extension of the class and allow

time to go beyond material in class or clarify information discussed in class. They will extend

your knowledge of the field of developmental biology. Material covered in recitation may be

covered on exams too.


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Points Breakdown:

Tophat: Class Participation 140 points

Assignments 100 points

• Based on assigned at-home readings or videos to be discussed in-class

• 10 reading assignments; 10 points each

Lab Notebook: see rubric for content and assessment (100 points each) 560 points

• Each lab will have pre and post lab questions

o RNA extraction and quality control: 30

o Reverse transcription (RT): first strand cDNA synthesis: 100

o In silico: informatics: 100

o Polymerase chain reactions (PCR) – RT-PCR: 100

o Real-time quantitative PCR: 100

o Histology: tissue processing and embedding: 100

o In Situ hybridization: 30

Exams 400 points

• 4 exams, 100 points each

• No make-up exams

Paper summary and critique (instructions below) 100 points

• Paper is not optional; final exam will not replace paper

Total 1400 points


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Course Evaluation Methods: This course will utilize the following instruments to determine

student grades and proficiency of the learning outcomes for the course.

• Exams – written tests designed to measure knowledge of presented course material

• Assignments – are also brief assessments used to measure knowledge of presented

course material.

• Laboratory Notebook – see rubric at the end of the syllabus.

• Research Article Critique and Presentation – See above grading criterion

• Class Participation – daily attendance and participation in class discussions

Attendance Policy: Students are responsible for all material discussed in class, including

arranging with classmates to obtain material from missed class sessions. Students must notify the

instructor before an absence on an exam day to have the option of completing the exam at another

time outside of class, which must be completed no later than the following class session. Makeup

exams may be oral.

Cell Phones: Please respect the learning environment of others by turning-off or silencing cell

phones, tablets, computers or other electronic devices. Failure to control your electronic device

will result in a pop quiz for all students. The quiz will count for a grade.

Test and Quizzes: Please leave bags and electronic devices at the perimeter of the room during

all exams and quizzes.

Scientific Writing Project

Following the Scientific Method, critique current peer-review original research article. This assignment gives you the

opportunity to choose a topic related to development or developmental genetics that is of interest to you and develop

further knowledge and understanding that will be demonstrated through a written critique and an oral presentation to

the class.

Paper Selection – Due February 8, 2018

Submit the paper selection for your project. Include a copy of the first page of article (not title page or abstract only)

with your topic. These items must be submitted electronically through e-Course. Your paper can be anything related to

developmental biology or developmental genetics. You are encouraged to discuss your topic idea with the professor to

confirm it will be appropriate for the assignment. I will prepare a list of papers to choose from.

Written paper (1-3 pages) –First draft Due March 8, 2018; Final draft due April 28, 2018; see course calendar

provided on eCourse

Paper guidelines:

• Typewritten in an easily readable font

• Line spacing is 1.5 and font is 12 point

• Body of paper approximately 2-3 pages (see below)

• Do not select a review article; must be an original research article (consult w/the instructor, see calendar)

• Topic and article should be current information (2009-2018)

• Direct quotations only when appropriate (not necessary in most cases)

• Include your own personal evaluation and interpretation of information!!

• No plagiarism

• Submit paper via eCourse. Do not submit by direct email. I will not grade them.

• Late papers receive a 20 point grade reduction

Body of Paper:

• Question under investigation?

• Relevance of the question under investigation?

• Objectives of the current research written in the paper?

• Hypothesis under investigation (or problem statement)?

• What is the null hypothesis (opposite)?

• How did the authors test their hypothesis (methods used to answer the question)?

• Did the authors data support their hypothesis (in part or whole)?

• What were their finding?

• Include your own personal evaluation and interpretation of the approach and results written by the

authors of the paper (were their methods/approach valid to answer the question (look-up methods to

understand what they are measuring), were the authors conclusions valid based on the result presented or do

they overreach in their assessment the results in the conclusion/discussion)

Grading considerations: see rubric below.

Student Resources

Learning Resources:

Below are a few resources for locating information. You are encouraged to utilize the interlibrary loan system

available through the PVAMU library to obtain free articles from journals not in the PVAMU library or e-Databases.

The PVAMU campus Library e-Databases are an excellent resource. Either the Librarian or myself can show you how

to access these tools. Industry magazines, extension fact sheets, textbooks, and other reliable publications are also

good resources.

PVAMU Library:

• Phone: 936-261-500

• Learning or research resources at PVAMU:

• Website: http://www.tamu.edu/pvamu/library/

Search websites

• Cell biology laboratory manual online: http://homepages.gac.edu/%7Ecellab/index-1.html

• National Library of Medicine (www.pubmed.gov)

• Scitable

• GudMap

• GenePaint

• Gene Cards

• Edinburgh mouse Atlas EMAP (eMouseAtlas)

• Human Protein Atlas

• Allen Brain Atlas

• Human Developmental Biology Resources: http://www.hdbr.org

• Human developmental studies network: http://hudsen.eu

• Heirloom Collection

• https://www.shadygrovefertility.com/blog/treatments-and-success/the-beginners-guide-to-the-

embryology-lab/

• http://www.austinivf.com

• http://atlanticfertility.com/embryology-lab-blastocyst/

Journals related to vertebrate embryology

• Development

• Developmental Dynamics

• Developmental Biology

• Development, Growth, and Differentiation

http://www.tamu.edu/pvamu/library/

http://homepages.gac.edu/~cellab/index-1.html

http://www.hdbr.org/

http://hudsen.eu/

https://www.shadygrovefertility.com/blog/treatments-and-success/the-beginners-guide-to-the-embryology-lab/

https://www.shadygrovefertility.com/blog/treatments-and-success/the-beginners-guide-to-the-embryology-lab/

http://www.austinivf.com/

http://atlanticfertility.com/embryology-lab-blastocyst/

University Rules and Procedures

Disability statement (See Student Handbook): Students with disabilities, including learning disabilities, who wish to

request accommodations in class should register with the Services for Students with Disabilities (SSD) early in the

semester so that appropriate arrangements may be made. In accordance with federal laws, a student requesting special

accommodations must provide documentation of their disability to the SSD coordinator.

Academic misconduct (See Student Handbook): You are expected to practice academic honesty in every aspect of

this course and all other courses. Make sure you are familiar with your Student Handbook, especially the section on

academic misconduct. Students who engage in academic misconduct are subject to university disciplinary procedures.

Forms of academic dishonesty:

1. Cheating: deception in which a student misrepresents that he/she has mastered information on an academic

exercise that he/she has not mastered; giving or receiving aid unauthorized by the instructor on assignments or

examinations.

2. Academic misconduct: tampering with grades or taking part in obtaining or distributing any part of a

scheduled test.

3. Fabrication: use of invented information or falsified research.

4. Plagiarism: unacknowledged quotation and/or paraphrase of someone else’s words, ideas, or data as one’s own

in work submitted for credit. Failure to identify information or essays from the Internet and submitting them as

one’s own work also constitutes plagiarism.

Nonacademic misconduct (See Student Handbook): The University respects the rights of instructors to teach and

students to learn. Maintenance of these rights requires campus conditions that do not impede their exercise. Campus

behavior that interferes with either (1) the instructor’s ability to conduct the class, (2) the inability of other students to

profit from the instructional program, or (3) campus behavior that interferes with the rights of others will not be

tolerated. An individual engaging in such disruptive behavior may be subject to disciplinary action. The Dean of

Students under nonacademic procedures will adjudicate such incidents.

Sexual misconduct (See Student Handbook): Sexual harassment of students and employers at Prairie View A&M

University is unacceptable and will not be tolerated. Any member of the university community violating this policy

will be subject to disciplinary action.

Attendance Policy: Prairie View A&M University requires regular class attendance. Excessive absences will result in

lowered grades. Excessive absenteeism, whether excused or unexcused, may result in a student’s course grade being

reduced or in assignment of a grade of “F”. Absences are accumulated beginning with the first day of class.

Student Academic Appeals Process: Authority and responsibility for assigning grades to students rests with the

faculty. However, in those instances where students believe that miscommunication, errors, or unfairness of any kind

may have adversely affected the instructor's assessment of their academic performance, the student has a right to

appeal by the procedure listed in the Undergraduate Catalog and by doing so within thirty days of receiving the grade or experiencing any other problematic academic event that prompted the complaint.

Course Calendar: See below calendar (subject to change)

Laboratory Notebook


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Student Laboratory Notebooks: All students must maintain a laboratory notebook detailing the

labs completed in the course.

Laboratory Manual Rubric Science Writing Paper

Introduction

15

Pre-Lab Questions 20

Discussions/Results (Pictures with Labels)

30

Post Lab Questions 20

Conclusion (overview of the lab/what you learned/importance of the lab)

15

Total: 100

Laboratory Notebook


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Lab Scoring Rubric Grading considerations

Introduction

0-5 The introduction was sparse (1-2 Sentences) Did not provide background information for the lab.

5-10 A short (3-4 sentences) intro that gave the reader vague information pertaining to the lab/organism.

10-15 Provided detailed information (4-6 sentences) that gave the reader background information on the lab and the organism.

Pre-Lab Questions 0-5 Did not answer all questions. Gave answers that were vague.

5-10 Answered some questions thoroughly.

10-20 Answered all questions thoroughly.

Discussions/Results (Pictures with Labels)

0-5 Did not provide pictures or commentary about the lab

5-15 Short commentary, pictures with no labels or description.

15-30 Provided labeled pictures with additional description of topics covered in the lab

Post Lab Questions 0-5 Did not answer all questions. Gave answers that were vague.

5-10 Answered some questions thoroughly.

10-20 Answered all questions thoroughly.

Conclusion (overview of the lab/what you learned/importance of the lab)

0-5 The conclusion was sparse. (1-2 Sentences). Did not elaborate on the lab or summarize.

5-10 A short (3-4 sentences) conclusion that gave an overview of the lab.

10-15 Provided detailed information (4-6 sentences) that gave the reader an overview of the lab as well as highlighted the importance of the lab, and included what they got out of it

Science Writing Project


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Science writing grading rubric Total Points For breakdown of assessment; follow the lab scoring rubric

Brief Summary 20

Question under investigation

5

Relevance of the question under

investigation 10

Objectives of the current research

written in the paper 5

Hypothesis under investigation (or

problem statement) 5

What is the null hypothesis

(opposite) 10

How did the authors test their

hypothesis (methods used to answer

the question)

10

Did the authors data support their

hypothesis (in part or whole) 10

What were their finding 5 Include your own personal

evaluation and interpretation of

information

20

Total Points 100

DecemberS M T W T F S26 27 28 29 30 1 23 4 5 6 7 8 9

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January2018

SUNDAY MONDAY TUESDAY WEDNESDAY THURSDAY FRIDAY SATURDAY

31 1 2 3 4 5 6

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Week 1 L1: Syllabus, Lewis lab research, lab experiments, expectations, TopHat

L2: Ch1

21 22 23 24 25 26 27

Week 2 L3: Ch1 cont. Ch2 Lab 1: Histology

L4: Ch2 Lab 1: Histology

Recitation Time: TBD

28 29 30 31 1 2 3

Week 3 L5: Ch2 Lab 1: Histology

4 5 6 7 8 9 10

FebruaryS M T W T F S28 29 30 31 1 2 34 5 6 7 8 9 10

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JanuaryS M T W T F S31 1 2 3 4 5 67 8 9 10 11 12 13

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February2018


28 29 30 31 1 2 3

Week 3 continued L6: Ch3 Lab 1: Histology


4 5 6 7 8 9 10

Week 4 L7: Ch3 Lab 1: Histology

Exam 1 Paper topic due


11 12 13 14 15 16 17

Week 5 L9: Ch4 Lab 2: RT-PCR

L10: Ch4 Lab 2: RT-PCR


18 19 20 21 22 23 24

Week 6 L11: Ch5 Lab 2: RT-PCR

L12: Ch5 Lab 2: RT-PCR


25 26 27 28 1 2 3

Week 7 L13: Ch6 Lab 3: Informatics

4 5 6 7 8 9 10

MarchS M T W T F S25 26 27 28 1 2 34 5 6 7 8 9 10

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FebruaryS M T W T F S28 29 30 31 1 2 34 5 6 7 8 9 10

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March2018


25 26 27 28 1 2 3

Week 7 continued L14: Ch6 Lab 3: Informatics


4 5 6 7 8 9 10

Week 8 L15: Ch7 Lab 3: Informatics

Exam 2 First draft due


11 12 13 14 15 16 17

Week 9 Spring Break Spring Break Spring Break Spring Break Spring Break

18 19 20 21 22 23 24

Week 10 L16: Ch7 Lab: RNA Extraction Midterm Grades

L17: Ch9 Lab: ISH


25 26 27 28 29 30 31

Week 11 L18: Ch9 Lab:

Founders day/honors convocation

L19: Ch12 Lab:

Good Friday Easter Good Friday Easter

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AprilS M T W T F S1 2 3 4 5 6 78 9 10 11 12 13 14

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MarchS M T W T F S25 26 27 28 1 2 34 5 6 7 8 9 10

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April2018


1 2 3 4 5 6 7

Week 12 L20: Ch12 Lab: Real-time PCR

Exam 3 Recitation Time: TBD

8 9 10 11 12 13 14


L23: Ch23 Lab: Real-time PCR


15 16 17 18 19 20 21


L25: Ch24; Ch25 Lab:


22 23 24 25 26 27 28

Week 15 L26: Ch25; Ch26 Lab:

Final draft of paper and Presentations


29 30 1 2 3 4 5

Week 16 Course Review Day

6 7 8 9 10 11 12

MayS M T W T F S29 30 1 2 3 4 56 7 8 9 10 11 12

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AprilS M T W T F S1 2 3 4 5 6 78 9 10 11 12 13 14

15 16 17 18 19 20 2122 23 24 25 26 27 2829 30 1 2 3 4 56 7 8 9 10 11 12

May2018


29 30 1 2 3 4 5

Week 17 Course Review Day Embryology Final Exam TBD??

6 7 8 9 10 11 12

Week 18 Embryology Final Exam TBD??

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3 4 5 6 7 8 9

JuneS M T W T F S27 28 29 30 31 1 23 4 5 6 7 8 9

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biol 4014 vertebrate embryology department of biology t/r ... · biol 4014 – vertebrate...

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