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DEVELOPMENTAL AND STEM CELL SYSTEMS I (DSCS I)
FALL 2016 SCHEDULE
Course numbers:
NYUMC:
NYU:
BMSC-GA 2610
BIOL-GA 2130
Course director:
E. Jane Hubbard: [email protected]
Time:
Tuesdays and Fridays: 2-5 PM
In addition, students meet in small groups (self-organized) to discuss the papers between the
lecture and discussion section
Locations:
NYUMC:
NYU:
Meet in Skirball Institute, 4th floor conference room
Meet in room 1008 Silver Center, Conference room
adjacent to the Biology Dept. office
Depending on the class, the course will either be held in the Skirball building at NYUMC
or in the NYU Biology Department at Washington Square. The NYU Shuttle bus, Route E,
travels between NYUMC and NYU. On Tuesdays (not Fridays), Route F also stops a few
blocks from NYUMC on 3rd Avenue and 29th Street.
COURSE DESCRIPTION
This course is an introduction to Developmental Genetics and Stem Cell Biology. Fundamental
questions, concepts and methodologies of modern inquiry into the genetic and cellular
mechanisms of development and stem cell biology will be explored through coordinated
lectures, labs, and discussion of primary literature.
Course Goals
Development and stem cell biology are closely related. A deep understanding of these subjects
and of the experimental approaches that drive new discoveries in these areas is important for
students interested in both basic and applied aspects of biology and medicine, including
development, regeneration and cancer. One challenge facing researchers is the broad scientific
background required to stay abreast of progress being made, both conceptually and with
respect to different experimental systems. The latter include different organisms and organ
systems, as well as diverse molecular genetic, biochemical, and cell-based techniques. This
course – in its breadth and emphasis on molecular underpinnings and rigorous data
interpretation – aims to meet this challenge. Through this course, students will be introduced to
major concepts in development and stem cell biology, hone critical thinking skills through
analysis of recent results in the field, and achieve hands-on experience with different
experimental systems. The goal is for students to obtain knowledge, as well as both intellectual
and practical skills that will enable them to stay current with the field long into the future.
DSCS I focuses on how cell fates are acquired and changed. The companion course offered in
the spring semester, DSCS II, focuses on cell movement and organization into higher order
structures such as neural networks and organs, as well as evolution of body plans.
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Course Format
The DSCS I course is divided into 6 thematic two-week modules, each of which contains four
classes. Within each module, there are a coordinated combination of lectures, discussions, and
labs. Each module is organized by one or several faculty members and is team-taught by
members of the Developmental Genetics Program and Stem Cell Biology Program faculty from
NYUSoM and from the NYU Biology Department. Students registering for the entire class (6
credits) will take all six modules. Students may also take the class for 2 credits by participating
in two of the six modules, if space is available. The course size is limited, and registration for
the course is restricted to PhD students in the NYU Biology department or NYUMC Sackler
programs. Students in the Developmental Genetics Graduate Program (Sackler or NYU Biology
students) or Stem Cell Biology Graduate Program (Sackler) are required to take the full course
(6 credits), as well as the full companion DSCS II course in the spring semester, and will have
priority at registration if the course is overbooked.
The semester will begin with an introductory class, which is required for ALL students,
regardless of the number of credits/modules they are participating in. The first week will
provide an overview of the topics to be covered during the semester, as well as some of the key
genetic techniques used in the model organisms that will be covered throughout the semester.
During the first class, students taking the course for 2 hours credit will elect the two modules
that they will take. The final student roster for each module will be established by the course
director, taking into account student preferences as well as limits in the number of students
imposed by the need for effective laboratory classes.
Lecture classes
The module director or course administrator will post any recommended and/or required reading
material prior to the beginning of the module. Students are responsible for checking the course
site in Brightspace to see if material has been posted. For more general preparatory reading,
particularly for students who have not previously taken a Developmental Biology course, the
recommended textbook is Developmental Biology by Scott Gilbert. You are strongly encouraged
to take advantage of the textbook as well as assigned review articles before the lecture class to
acquaint yourself with each topic prior to the lecture. Copies of the Developmental Biology
textbook can be checked out for one day for photocopying. See course administrator Theresa
Walton in the Skirball 4th floor administration area if you would like to check out Developmental
Biology. Alternatively, the 6th edition (from 2000) is available online at
http://www.ncbi.nlm.nih.gov/books/NBK9983/?term=developmental%20biology
Recommended Stem Cell Biology background textbook style materials can be found online at
http://www.stembook.org and at http://www.sciencedirect.com/science/book/9780123747297
Discussion classes
In discussion classes, students will discuss one or more research articles related to the topic of
the module. The module director will post papers for discussion prior to the beginning of the
module. Students should check Brightspace to see if material has been posted. Each student
is required to read the articles before each session and to be able to present a summary, a
detailed description of the data, underlying techniques and figures, and a critique of the
research papers. Students will be called upon during the class to explain experimental methods,
results and interpretation of results in the papers. To facilitate discussion, it is strongly
recommended that students meet in small groups Wednesday or Thursday to discuss the
papers. These meetings are self-organized by the students.
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Laboratory classes
The module director will instruct students where to meet for laboratory classes. If no alternate
location is given, meet first in the normal classrooms at NYUMC or NYU, as indicated on the
syllabus. Instructors may ask students to analyze or present data that they collect during the
labs.
Grading
Half of the final grade for the class will be based on class participation, in particular during paper
discussion. The other half of the final grade will come from a written research proposal that
students turn end at the end of the semester. The proposal is required for all students, even
those taking the class for two or four credits. The proposal should be five pages (not
including references), and sent by email as a pdf file to [email protected] by
**5pm on December 16th**
The proposal should relate to a topic discussed in one of the modules and should be organized
into: An Introduction which provides background information, introduces the current knowledge
in the field and states the questions and goals addressed by the proposed experiments. An
Experimental procedure/result section, which describes an experiment with an interpretable
outcome (no fishing expeditions, please!). The experiment should be experimentally
feasible, and material for the experiment should either be easy to produce or already available.
The experimental procedures used should be described clearly, and potential problems and
workarounds should be addressed. In the Discussion section, the possible outcomes of the
experiment and their interpretations should be discussed. The topic of the proposal must not be
directly related to the student’s project or past work in any capacity either in previous research,
during rotations, as a technician, or in his/her lab. That is, the topic should use a model
organism or organ system the student hasn’t ever worked with, if possible, and definitely not the
one they are using for their thesis research. Part of the point of the assignment is to delve into a
topic that is new to the student! If someone has a particular problem (for example, they have
worked with every model organism), please contact the course director. The paper must be
written independently in your own words.
Relevant programs: Stem Cell Biology, Cellular and Molecular Biology, Developmental
Genetics, Molecular Oncology and Immunology, Molecular Pharmacology, Pathobiology,
Neuroscience and Physiology; other GSAS programs: Department of Biology, Center for
Neuroscience
Course evaluations: Will be solicited after the completion of each module, and at the end of
the course. The course administrator will prepare the evaluations anonymously.
Introductory week
Director: Jane Hubbard
Date
Tuesday
9/6
2-5pm
Instructors
Topic
Location
Jane Hubbard
Historical perspective and overview of semester
topics. Introduction to resources for genetic
methods/nomenclature relevant to model
organisms. Modules assigned for students taking
class for partial credit.
NYUMC
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Module 1: Setting the axes: Developmental determinants and morphogen gradients
Directors: Ruth Lehmann and Chris Rushlow
Date
Instructors
9/13
Lehmann,
Rushlow
9/16
Skirball
Symposium
9/20
Rushlow
9/23
Lehmann,
Rushlow
Topic
Lab and lecture. Examination of gastrulation in
wild-type and mutant flies by light microscopy.
Examination of target genes of maternal
determinants by in situ hybridization.
Students should attend the Skirball Symposium:
“Germ cells and beyond: probing immortality and
development.”
http://skirball.med.nyu.edu/news-andevents/skirball-symposium
Lab and lecture. Maternal-to-zygotic transition.
Interpretation of the prepattern by early zygotic
gene expression
Discussion
Location
NYUMC
NYUMC
NYUMC
NYUMC
Module 2: Asymmetric division: segregation of information
Directors: Erika Bach
Date
Instructors
Topic
Location
9/27
Bach
Lecture and Discussion. Asymmetric divisions in
stem cell-niche contexts.
NYUMC
Bach
Lab (half of class). Asymmetric division in fly
testes. Immunostaining and confocal microscopy.
NYUMC
9/30
(again on
10/4)
10/4 (also
on 9/30)
10/7
Desplan
Nance
Lab (half of class). Stem cell divisions in fly larval
brains. Immunostaining and confocal microscopy.
Lecture and Discussion. Asymmetric cell division
and polarity in the C. elegans embryo.
NYU
NYUMC
Module 3. Spatiotemporal patterns of gene expression in embryos and stem cells
Director: Lionel Christiaen
Date
Instructors
10/11
Small, Christiaen
10/14
Small, Christiaen
10/18
Small,
Di Gregorio
10/21
Small, Christiaen
Topic
Lecture. Gene expression and positional
information.
Lab and Discussion. Lab 1: examining and
modulating gene expression in Ciona embryos.
Lab 2: Creating position weight matrices for DNAbinding proteins (data analysis).
Lecture. Enhancers and spatio-temporal patterns
of gene transcription in embryos and stem cells
Lab and Discussion. Lab 1: Whole mount in situ
on fly embryos (wild-type and mutant). Lab 2:
Using ATAC-seq data to design guide RNAs for
CRISPR
Module 4. Cell-cell signaling and patterning
Location
NYU
NYU
NYU
NYU
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Director: Jessica Treisman
Date
Instructors
Topic
Location
10/25
Treisman, Dasen
Lecture. Imaginal disc developmental and somite
patterning
NYUMC
10/28
(also on
11/1)
Treisman
Lab (half of students). Imaginal disc development
NYUMC
11/1 (also
on 10/28)
Loomis
Lecture and lab (half of students). Limb
development and craniofacial development. Lab:
Mouse embryo dissection.
NYUMC
11/4
Treisman, Dasen
Discussion
NYUMC
Module 5. The basis of inheritance
Directors: Agnel Sfeir and Andreas Hochwagen
Date
Instructors
Topic
Location
11/8
S. Smith,
Hochwagen
Lecture. Chromosome segregation
NYUMC
11/11
Sfeir
Discussion and Lab. Immortal strand hypothesis.
Lab: Telomere co-FISH
NYUMC
11/15
Reinberg,
Armache
Lecture. Epigenetic inheritance
NYUMC
11/18
Tahiliani, Erçan
Discussion and Lab. Regulation of cell identity.
Lab: ChIP Seq
NYU
Module 6: Developmental Plasticity
Director: Esteban Mazzoni
Date
Instructors
Topic
Location
11/22
Mazzoni,
Stadtfeld,
Birnbaum
Lecture and Discussion. Development, cell
differentiation, and plasticity.
NYU
11/25
No class
Thanksgiving break
Mazzoni,
Stadtfeld,
Birnbaum
NYU
Developmental
Genetics
Symposium
Mazzoni,
Stadtfeld,
Birnbaum
Mazzoni,
Stadtfeld,
Birnbaum
Lecture and Discussion. Plant development,
plasticity, regeneration. Reprogramming
mechanism in mammals.
NYU
Students should attend the NYU Developmental
Genetics Symposium.
NYU
11/29
12/2
12/6
12/9
Lab. Lab 1: ESC differentiation. Lab 2: Fate
mapping and laser tissue dissection in Arabidopsis.
Lab 3: iPS cells.
Lab and Discussion. Cell fate transitions in vitro
and in vivo. Lab: Examine results from labs on
12/6
NYU
NYU
**Proposals are due December 16th by 5PM. Email pdf to [email protected]