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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
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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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
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.
3
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.
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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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
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.
5
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
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
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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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
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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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
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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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
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SUNDAY MONDAY TUESDAY WEDNESDAY THURSDAY FRIDAY SATURDAY
31 1 2 3 4 5 6
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14 15 16 17 18 19 20
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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February2018
SUNDAY MONDAY TUESDAY WEDNESDAY THURSDAY FRIDAY SATURDAY
28 29 30 31 1 2 3
Week 3 continued L6: Ch3 Lab 1: Histology
Recitation Time: TBD
4 5 6 7 8 9 10
Week 4 L7: Ch3 Lab 1: Histology
Exam 1 Paper topic due
Recitation Time: TBD
11 12 13 14 15 16 17
Week 5 L9: Ch4 Lab 2: RT-PCR
L10: Ch4 Lab 2: RT-PCR
Recitation Time: TBD
18 19 20 21 22 23 24
Week 6 L11: Ch5 Lab 2: RT-PCR
L12: Ch5 Lab 2: RT-PCR
Recitation Time: TBD
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
SUNDAY MONDAY TUESDAY WEDNESDAY THURSDAY FRIDAY SATURDAY
25 26 27 28 1 2 3
Week 7 continued L14: Ch6 Lab 3: Informatics
Recitation Time: TBD
4 5 6 7 8 9 10
Week 8 L15: Ch7 Lab 3: Informatics
Exam 2 First draft due
Recitation Time: TBD
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
Recitation Time: TBD
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
1 2 3 4 5 6 7
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April2018
SUNDAY MONDAY TUESDAY WEDNESDAY THURSDAY FRIDAY SATURDAY
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
Week 13 L22: Ch22 Lab: Real-time PCR
L23: Ch23 Lab: Real-time PCR
Recitation Time: TBD
15 16 17 18 19 20 21
Week 14 L24: Ch24 Lab: Real-time PCR
L25: Ch24; Ch25 Lab:
Recitation Time: TBD
22 23 24 25 26 27 28
Week 15 L26: Ch25; Ch26 Lab:
Final draft of paper and Presentations
Recitation Time: TBD
29 30 1 2 3 4 5
Week 16 Course Review Day
6 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
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May2018
SUNDAY MONDAY TUESDAY WEDNESDAY THURSDAY FRIDAY SATURDAY
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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