Rebecca Spokony

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Genomics at Baruch College

Course Overview

Implementation

Disease Genetics Development 4015

Use the following guidelines to discover genes associated with human diseases that can be studied using Drosophila melanogaster. Report the answers to the questions in a separate report.

The following is a list of genetic diseases. Choose one of these diseases or another disease that you are interested in.

Angelman syndrome
Down syndrome
Dystonia
Kidney disease
Fanconi's anemia
Medullary thyroid carcinoma
Musculoskeletal system cancer
Stomach cancer
Tuberous sclerosis
Wagenmann-Froboese syndrome
Wolf-Hirschhorn syndrome


Go to the OMIM (Online Mendelian Inheritance in Man) website.

www.omim.org

Restrict your search by “OMIM Gene Map” to make sure there is a genetic region mapped to the disease.


Type the disease of your choice into the white search box.

http://www.omim.org/search/advanced/geneMap



If there is a known genetic cause associated with this disease, it will show up in the search results. Choose the top result.



1. Read about the disease, the gene and the gene’s relationship to the disease. Summarize these findings.
a. Make sure you understand the disease phenotype. (What tissues are effected? When during development can you tell someone has this disease? Etc.)
b. Make sure you understand what the gene does. (Is it a transcription factor? Is it a kinase? Etc.)
c. Make sure you understand how the gene relates to the disease phenotype. (Is the gene expressed in the part of the body that is effected? Is the gene required for normal development for that body part?)




Try to find this gene in Drosophila melanogaster. Go to FlyBase.

www.flybase.org

Type the gene name into the search field.




If that doesn’t work, try one of the other names from the OMIM record:

2. Can you find an ortholog in Drosophila melanogaster? Do you think there are any genes that seem like likely candidates in Drosophila melanogaster? Explain why or why not. If there is not a direct ortholog, is there another protein that performs a similar biochemical function?

Go back to the main page of FlyBase.

www.flybase.org

Click the tab that says “Human Disease”.


Fill in the disease you are researching in the white box next to the phrase “Disease term:”



Click on the first CV term.


Do any genes come up?


3. Examine the genes. Report what the gene names are.


4. Look at the flybase page for at least one of the genes on the list. Go to the part of the page that says “Human Disease Model Data”. Why is this gene listed as a model for this disease? What do you think this gene does?



5. How does the list of genes in OMIM compare with the list of genes in FlyBase? Are they similar genes? Are they involved in similar pathways or processes?

6. Explain which Drosophila genes could be used to study the disease.

Lessons Learned and Future Plans

Syllabus for

Course Syllabus: Bio 4015 - Developmental Biology Spring 2014
Lecture+Laboratory: Tuesday and Thursday 2:30-5:25 (including a 25 min break)

Instructor: Dr. Rebecca Spokony E-mail: Rebecca.Spokony AT baruch.cuny.edu
Office: 17 Lexington Ave Bldg. Rm 610A Office Hours: Wed 3:45-5:25

Course Description: An experimental and descriptive approach to the study of embryonic through adult development in various organism. Special attention is paid to the analysis of the changes in gene expression and regulation, cellular communication and dynamic movements of cells and tissues during development. The laboratory emphasizes environmental impacts on development and experimental design.

In the course we examine material that includes both descriptive and experimental components. We will examine the dynamic morphological and anatomical changes that occur as an organism goes from a single egg to a complex multicellular adult and the molecular basis of those changes.

Updates, supplements and assignments are available through the Bio 4015 Blackboard page.

Required Text: S.F. Gilbert, Developmental Biology, 10th Edition. Make sure you have access to the online materials that come with the book.

Required readings corresponding to lecture topics are listed in the syllabus; additional required readings from Wolpert and Tickle’s Principles of Development and journal articles are available through the Newman Library Reserve.

Additional suggested readings from Gilbert (particular pages and figures referred to in lecture) may be given in lecture.

Assignments:
Pre-Class Assignments (PCAs) are short, assignments based on the required readings. They may ask you, for example, to interpret a particular figure or experiment, or to explain an important developmental phenomenon. They are designed to help you prepare for lecture, and to assess your understanding of the material to better prepare for in-class discussion and exams. There will be 8 PCAs during the semester. PCAs will contribute 5% to the course grade.

Laboratory Reports are longer reports summarizing the results of your experimental manipulations. Guidelines will be provided in lab. Laboratory assignments will be shorter reports summarizing laboratory activities. There will be 2 full-length laboratory reports (25% of the course grade) and 3 shorter laboratory assignments (25% of the course grade).

Quizzes: In Lecture Quizzes are short quizzes based on the lectures and readings. They will be similar to the questions in the PCAs and exams. They are designed to help you review the lectures and prepare for the exams. There will be 6 Quizzes during the semester (see syllabus). Quizzes will contribute 10% of the course grade.

Exams: There will be 2 exams during lecture time and one final exam during finals week. Exams will be cumulative. Exams will contribute 40% of the course grade.

Tentative Point Breakdown of Grading:
Assessment Points Details
Exams 400 2 in class @ 100 pts, final 200 pts.
Quizzes 100 6 @ 20 pts. Drop lowest quiz.
PCAs 50 7 @ 7 pts. Drop lowest PCA.
Lab Reports 200 2 @ 100 pts
Lab Assignments 250 3 @ 83 pts
Total 1000

Course Goals:
1. To facilitate students’ mastery of the basic concepts and skills of developmental biology recommended by the Howard Hughes Medical Institute, the Association of American Medical Colleges, and the National Science Education standards.
2. To train students to read, interpret, integrate, and communicate popular science and the scientific literature.
3. To train students in the process of science by creating a research community and developing the skills necessary to carry out scientific inquiry.

Grading Policies:
Attendance and class contribution: Regular and prompt attendance is required for this class. Students are expected to read assigned chapters before class and to participate in class discussions and activities during each class meeting. Rude behavior (including chronic tardiness, inappropriate talking during lectures or discussion or showing aggressive or disrespectful behavior towards classmates) will result in inability to participate in laboratory activities and receive credit for them. College policy, which we enforce equally for freshmen through seniors, is that you are overcut if you miss more than twice the number of class meetings held each week. It is difficult, if not impossible, to make up missed laboratory work.

Make-up Exams: Make-up exams may only be arranged if the student has a verifiable (e.g. medical) excuse and the instructor is notified prior to the original exam.

STUDENT’S RESPONSIBILITY: When you miss class or are delayed for any reason, it’s your responsibility to find out what you missed in a manner that does not disrupt or delay the course. You are responsible for information covered in class even if you are not present. Please utilize office hours.
INSTRUCTOR’S RESPONSIBILITY: I will grade all assignments in a timely manner. I will attempt to respond to all emails within 48 hours of receiving them. I will be available during my office hours and by appointment to discuss this course. I will be available for reviewing material before each exam. Where possible, I will post assignments, journal articles, handouts and some notes on Blackboard.

ACADEMIC INTEGRITY: Academic dishonesty is not acceptable. Presenting the work of others (fellow classmates, faculty, published authors, anonymous websites, etc.) as your own is considered plagiarism, and is forbidden by CUNY policy. All assignments are expected to be the work of the student, unless specifically designated as a group assignment. Enrollment in the class constitutes an agreement between you and the college to abide by the guidelines of the Student Guide to Academic Integrity (http://www.baruch.cuny.edu/facultyhandbook/documents/StudentGuideOct06.pdf) and the CUNY Policy on Academic Integrity (http://www.baruch.cuny.edu/facultyhandbook/documents/AcademicIntegrityCUNYFall2011_000.pdf)
Cheating, plagiarism, and facilitation of either one will be reported.


Contract for Ethical Conduct in a Cooperative Classroom

Adapted from Scientific Teaching Handelsman, Miller, and Pfun 2007. W.H. Freeman and Company and from course materials developed by Dr. Christine Broussard

Due 2/4/2014

I am attempting to create a cooperative learning environment that will be stimulating, demanding, and fair for this course. Because this approach to learning is different from the competitive classroom structure upon which other courses may be based, it is important to be clear about mutual expectations. Below are my expectations for students in this course. This set of expectations is intended to maximize debate and exchange of ideas in an atmosphere of mutual respect while preserving individual ownership of ideas and written words. If you do not understand or feel you cannot agree to these expectations, you must make an appointment discuss your perspective with me before 2/4/2014.
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Ethical Expectations for BIO 4015

1. Students are expected to work cooperatively with other members of the class and show respect for the ideas and contributions of other people.
2. When working as part of a group, students must strive to be good contributors to the group, to listen to others, to not dominate discussions or activities, and to recognize the contributions of others. Students must try to ensure that everyone in the group makes a contribution and recognize that everyone contributes in different ways to a group process.
3. Students will conduct experiments, engage in group activities, and develop projects as part of a group, but write/create lab assignments, exams and papers alone (i.e. do not copy from anyone else). If you use material from published sources (good idea), you must provide appropriate attribution.


I have read and understood the ethical expectations of students for BIO 4015. If I am uncertain about appropriate behavior in the class, I will ask the instructor for clarification.

I have read the syllabus carefully. I agree that it is my responsibility to ask questions about course content and requirements, if anything is unclear. I will do my best to prepare for this class and be active in the learning process by completing all required assignments and participating in classroom and laboratory activities and discussions as best I can.

Signed:___________________________ ____________________________
Sign your name Print your name


M Lecture Reading(s)
January 28, 2014 Introduction, Commitment of cell fate W&T Ch1: p 1-13
January 30, 2014 (PCA1) Major events of morphogenesis & axis formation W&T Ch1: p 14-19;
G Ch1: p 6-12
February 4, 2014 Induction & Cell Fate Specification (Quiz 1) G p 17-23, p 109-119
February 6, 2014 (PCA2) Differential Gene Expression I G p 35-42
February 11, 2014 Differential Gene Expression II G p 42-52
February 13, 2014 Genomic Equivalency, Differential Gene Expression III (Quiz 2) G p 53-66, 107-116
February 18, 2014 (PCA3) Pattern formation and cell-cell communication I G p 69-84
February 20, 2014 No class, Monday Schedule.
February 25, 2014 Pattern formation and cell-cell communication II (Quiz 3) G p 84-98, p 170-177
February 27, 2014 Pattern formation and cell-cell communication III G p 98-106
March 4, 2014 Exam 1.
March 6, 2014 Introduction to Nuclear Receptors in metamorphosis and cancer
March 11, 2014 Introduction to Nuclear Receptors in metamorphosis and cancer
March 13, 2014 (PCA4) Axis specification in Drosophila (Cleavage and Gastrulation) G p 179-185, 77
W&T p 35-50
March 18, 2014 Axis specification in Drosophila (anterior-posterior, dorsal-ventral) (Quiz 4) G 185-202, 84-86
W&T p 56-79
March 20, 2014 Axis specification in Drosophila (homeotics), G 209-213
W&T p 80-88
March 25, 2014 Long and Short Germband Insects. Journal Club. Dual mode of embryonic development is highlighted by expression and function of Nasonia pair-rule genes. http://elife.elifesciences.org/content/3/e01440
March 27, 2014 Dr. Shulman: (PCA5) Stem Cells G 319-331, 656-659
April 1, 2014 Work on Metamorphosis lab report
April 3, 2014 Stem Cells (Quiz 5) W&T Ch 8 p289-306, G 252-262
April 8, 2014 Stem Cells W&T Ch 8 p309-320, G 263-272
April 10, 2014 Exam 2
April 15, 2014 Spring break
April 17, 2014 Spring break
April 22, 2014 Spring break
April 24, 2014 (PCA7) Morphogenesis W&T Ch 8 p289-306, G 252-262

April 29, 2014 (Quiz) Nervous system & Neural Crest I G 333-341
May 1, 2014 (PCA8) Nervous system & Neural Crest II: Guest Lecture: Dr. Jean-Pierre Saint-Jeannet
May 6, 2014 Nervous System & Neural Crest III G 342-358
May 8, 2014 Nervous System & Neural Crest IV G 375-385
May 13, 2014 Nervous System & Neural Crest V G 386-395

May 15, 2014 Review for Final

Date Lab Readings and Assignments
January 28, 2014 Introduction to signaling pathways and planaria. Using the microscope. Introduction to Planaria. Drawings and Observations. Handout Planaria Lab. Assignment to read and design experiment.
Clay models.
January 30, 2014 Discuss plan for experiment. Start Planaria experiment..
February 4, 2014 Observe and document results of planaria experiment. Think about model for discussion. Write up experimental design and lab report outline.
February 6, 2014 Discuss Planarian signaling paper. Observe and document results of planaria experiment. Due: experimental design and lab report outline.
http://scienceintheclassroom.org/research-papers/heads-or-tails/university

February 11, 2014 Continued observation and documentation of planaria experiment. Introduction to Genomics and GEP Annotation. Write Planaria lab report.
February 13, 2014 Continued observation and documentation of planaria experiment. Introduction to genome annotation software: BLAST, Genome Browser, GeneScan. Go over GEP annotation project report. Write Planaria lab report.
February 18, 2014 Annotation Practice Activity 1. Due: Planaria Lab Report. Computer RM VC6155.
February 20, 2014 Monday Schedule, no class
February 25, 2014 Annotation Practice Activity 2. Computer RM VC6155.
February 27, 2014 Start GEP annotation. Computer RM VC6155.
March 4, 2014 GEP annotation Computer RM VC6155. Write up GEP assignment
March 6, 2014 GEP annotation Computer RM VC6155. Write up GEP assignment
March 11, 2014 Observation and documentation of metamorphic stages. Hormone and control treatments of prepupae. Due: GEP assignment.
Write up metamorphosis experimental design, expected results and lab report outline.
March 13, 2014 Observation and documentation of hormone treatment.
March 18, 2014 Observation and documentation of hormone treatment. Due: Metamorphosis lab report outline
March 20,2014 Work on graphs of data. Fit model? Combine class data.
March 25, 2014 Repeat treatment. Write developmental effects of hormone exposure lab report.
March 27, 2014 Repeat observations and documentation. (Prof Spokony at Conference) Write developmental effects of hormone exposure lab report.
April 1, 2014 Repeat observation and documentation. (Prof Spokony at Conference) Write developmental effects of hormone exposure lab report.
April 3, 2014 TBD Due: Metamorphosis lab report.