1
DEVELOPMENTAL SYSTEMS I
FALL 2015 SCHEDULE
Course numbers:
NYUMC:
NYU:
BMSC-GA 2610
BIOL-GA 2130
Time:
Tuesdays:
2-5 PM lecture,
Fridays:
2:00-4:30PM discussion
In addition students meet in small groups (self-organized) to discuss the
papers between the lecture and discussion section
Locations:
NYUMC:
NYU:
Skirball Institute, 4th floor conference room
Room 1009G Silver Center, Conference room in the
Biology Dept. office
Depending on the week, 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. Route F also stops a few blocks from NYUMC.
DS I COURSE DESCRIPTION
This course is an introduction into Developmental Genetics. Fundamental questions, concepts
and methodologies of modern inquiry into the genetic and cellular mechanisms of development
will be explored through lectures and discussion of primary literature. Topics include embryonic
axis determination and the establishment of cellular asymmetry, cell specification through cellcell interaction and region-specific gene expression, morphogenesis and organogenesis in
different species.
The first week will cover key molecular and genetic techniques used to study Developmental
Biology in a variety of model organisms. From the second week on, two instructors will discuss
current topics in developmental biology. Each session includes a lecture and discussion part.
In the discussion part students will discuss research articles related to the topic. Lecture outlines
and discussion assignments will be posted on the course website (on ALEX) at least one week
before class. Students will read ~2 research articles as well as review article(s) or book
chapter(s) for each session. 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. You will be called upon to explain
experimental methods, results and interpretation of results in the papers.
To facilitate discussion, students will meet in small groups Wednesday or Thursday to discuss
the papers. These meetings are self-organized by the students.
The recommended text/reference book 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. The 6th edition
(2000) of the Gilbert text is available on the web via the NCBI website “books” link:
http://www.ncbi.nlm.nih.gov/books/NBK9983/
While some material is not covered in the Gilbert text, where possible, we have listed relevant
chapters from the web-accessible 6th edition of Gilbert. More recent editions (8th ed., 2006; 9th
2
2010; 10th ed., 2013) are available with additional content and are listed below as
recommended. The 8th edition is available at low cost online.
In addition each student will write a five page (not including references) research proposal.
Proposals should be sent by email as “.doc” or “.pdf” files to
jeremy.nance@med.nyu.edu by **5pm on December 11th**
The proposal should relate to a topic discussed in the sessions 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 describes an experiment with an interpretable
outcome (no fishing expeditions, please!). The experiment should be experimentally
feasible, material for the experiment should either be easy to produce or already available. The
experimental procedures used should be described clearly and potential problems should be
addressed. In the Discussion section, the possible outcomes of the experiment and their
interpretations should be discussed.
The topic of the proposal should not be directly related to the student’s project or past work in
any capacity either previous research, during rotation, as a technician, or in his/her lab. That is,
the topic should use a model organism the student hasn’t worked with, if possible, and definitely
not the one they are using for their thesis research. If someone has a particular problem (for
example, they have worked with every model organism), please contact me. The paper must be
written independently in your own words.
Both active participation throughout the course and the research proposal contribute to
the final grade.
Date
9/4/15
Lecturer(s)
Jeremy Nance/
Nick Stavropoulos
Topic
Introduction to concepts, organisms and
techniques in Developmental Genetics –
compared and contrasted in model organisms
(more details on mouse in week 4)
Model organisms Part 1: Flies
 Genetic nomenclature
 Genetic screens
 Transgenesis
 Mosaic animals and cell autonomy
Location
NYUMC
9/8/15
Matt Rockman/
Holger Knaut
Model organisms Part 2: Worms and Fish
 Genetic nomenclature
 Genetic screens
 Transgenesis
 Mosaic animals and cell autonomy
NYUMC
9/11/15
NO CLASS
(NYU Biol. Retreat)
9/15/15
Jeremy Nance/
Patrick
Eichenberger
Polarity: (B. subtilis and C. elegans)
 Binary fission, asymmetric cell division
 Coordination of cell cycle and cytokinesis
 Generating A-P polarity; PAR proteins,
NYU
3
No Gilbert for
bacteria
Gilbert Ch. 8 (pp.
251-257)
9/18/15
09/22/15
Eichenberger/
Nance
Steve Small/
Jeremy Dasen
Gilbert ch. 9
09/25/15
09/29/15
Small/Dasen
Adrian Erlebacher
Including paper
discussion
Gilbert ch. 11 and
Parts of ch 4, 5 and
19
Gilbert ch 7
10/02/15
Ruth Lehmann
Including paper
discussion
Rho signaling, actin, myosin and
cytoskeletal control
 Techniques/experimental concepts:
maternal effect phenotypes, RNAi,
reporter fusions and antibody staining
Discussion
NYU
Segmentation in Drosophila and Vertebrates
 Pre-planning the Drosophila body
in the embryo. Area-specific
transcription in the early embryo.
Refinement of pattern via a
transcriptional cascade.
 Target gene responses to
gradients.
 Complex promoters. Independent
activity of multiple enhancers that
use a common basal promoter.
SYSTEMS ASPECTS
Classical experiments:
 Segmentation screens and the
proposal of a patterning cascade.
 bcd activation of hb (DNA-binding,
cotransfection, reporter genes).
 eve promoter dissection, and
stripe 2 regulation.
NYU
Discussion
From egg to embryo in mice; ES cells and
reprogramming
 fertilization
 blastocyst, implantation, decidualization,
reproductive endocrinology
 Axis specification
Tools
 static, video – markers, Lineage tracing
(physical versus genetic marking), Cell
ablation
 Chimeras, Knockout mice, Forward and
reverse genetics
ES cells and Stem cell lines from early embryos,
cloning
From egg to embryo in flies
 Polarity and Morphogen gradients
 Maternal effects
 Preformation/prepattern
 Localized determinants
 RNA localization by microtubules and
Translational control
NYU
NYUMC
NYUMC
4
10/06/15
Jessica Treisman/
Cindy Loomis
Gilbert ch. 15-16
Gilbert ch. 18
10/9/15
10/13/15
10/16/15
10/20/15
Treisman /Loomis
Claude Desplan/
Anna Di Gregorio
Gilbert 8th edition:
ch. 10 (pp.359-367)
ch 20 (pp. 890-715)
Desplan/
Di Gregorio
Jeremy Nance/
Lionel Christiaen
Gilbert ch. 8-10
Appendage development; compartments and
developmental fields
Imaginal disc development
 compartments
 boundaries
 organizers
Limb development:
 Early specification of limb field
 Subsequent autonomous outgrowth and
patterning
proximal-distal outgrowth and AER
anterior-posterior patterning and ZPA
dorsal-ventral patterning and non-AER
ectoderm
 Differentiation of musculoskeletal and skin
structures
Discussion
Evolution and Development
 Conservation of eye
development
 Regressive (eye) evolution
 Evolution of vision
NYUMC
Discussion
NYU
Gastrulation, morphogenesis and organogenesis
(worm, fly, Xenopus, zebrafish, Ciona, mouse)
 Gastrulation in C. elegans, Drosophila,
fish, amphibians and mouse
 Convergent extension, apical constriction
 Morphogenesis and organogensis
 Signaling pathways and adhesion that
regulate gastrulation, morphogenesis,
and organogenesis
Morphogenesis (migration, proliferation,
looping)
 Cardiac specification, heart fields
 Multipotent cardiovascular progenitors,
differentiation, heart stem cells
 Conserved cardiac gene network
(“kernel”)
 Heart evolution in chordates
NYUMC
Concepts/techniques:

Explants

Maternal-effect vs. embryonic
phenotypes

Organizer
NYUMC
NYU
5
10/23/15
10/27/15
Nance/ Christiaen
Jessica Treisman/
Erika Bach
Gilbert ch. 6 (6th ed;
pp 397-398 in 8th ed);
ch.15
Additional Gilbert for
germ line ch 19 (6th
ed) and stem cells –
from new edition
10/30/15
11/03/15
Treisman/ Bach
Esteban Mazzoni
Including paper
discussion
11/06/15
Sevinc Ercan
Including paper
discussion
Discussion
Signaling in the context of development: Eye and
germ line
 Hedgehog signaling and progressive
differentiation
 Receptor tyrosine kinase signaling and
photoreceptor identity
Germ cells and gonadogenesis
 Stem cell - niche interaction
SIGNALING, TRAFFICKING:
HH, JAK/STAT, RTKs
Discussion
Genomes and development
 RNAi (si-, sh-, miRNA) and High
Throughput Screens
 Functional genomics and proteomics
 Network analysis and integration of “omic”
datasets
 Chemical genomics
NYUMC
NYUMC
Genomes and development
 RNAi (si-, sh-, miRNA) and High
Throughput Screens
 Functional genomics and proteomics
 Network analysis and integration of “omic”
datasets
 Chemical genomics
NYU
NYUMC
NYU
11/10/15
Jesús TorresVazquez/
Holger Knaut
Gilbert ch. 13, 15
The cell biology of motility
 Types of migration:
Amoeboid
Fibroblast
Cell sheets
 Types of migratory signals:
Gradients/long-range
Contact mediated/short-range
Attractive, Repulsive
 ECM REMODELING, INTEGRINS
 GPCR SIGNALING IN MIGRATION
 Specific examples:
Germ cells
Border cells in Drosophila
Neural crest
Endothelial migration
Axon guidance
 Migration and disease
NYUMC
11/13/15
Torres-Vazquez/
Knaut
Discussion
NYUMC
6
11/17/15
Don Ryoo/
Ken Birnbaum
Gilbert ch. 1, part of
ch. 18, Gilbert ch.20
(PDF)
Control of growth in development
Animals
 Growth control at the cell, organ and
organism level
 Cell survival, competition, death and
proliferation
 TOR SIGNALING
Plants
 Self-organization and patterning with
indeterminate growth
 Stem cells and stem cell niches in plants
and animals
 Plasticity of plant cells and totipotency
NYU
11/20/15
11/24/15
Ryoo/Birnbaum
Jane Hubbard
Discussion
Aging (one class, lecture and discussion
together)
 INSULIN, NHR SIGNALING
 Metabolic influences on aging
NYU
NYUMC
Neural patterning
Anterio-posterior and Dorso-ventral patterning of
neuroepithelium, Proliferation and migration
 Anterio-posterior and Dorso-ventral
patterning of neuroepithelium
 Neuromeric development
 Stem cell and transit amplifying cell
proliferation
 NOTCH SIGNALING
 Tangential versus Radial Migration in the
PNS and CNS
NYUMC
Discussion
NYUMC
Including paper
discussion
Gilbert ch.18
11/27/15
12/1/15
NO CLASS Thanksgiving
Gord Fishell/
Jean-Pierre SaintJeannet
Gilbert ch. 12-13
12/4/15
Fishell/
Saint-Jeannet
12/11/15
FINAL PAPERS
DUE 5PM
7
FACULTY DIRECTORY – DS I FALL 2015
Erika Bach
Ken Birnbaum
Lionel Christiaen
Jeremy Dasen
Claude Desplan
Anna Di Gregorio
Patrick Eichenberger
Sevinc Ercan
Adrian Erlebacher
Gord Fishell
Jane Hubbard
Holger Knaut
Ruth Lehmann
Cindy Loomis
Esteban Mazzoni
Jeremy Nance
Niels Ringstad
Matt Rockman
Don Ryoo
Jean-Pierre Saint-Jeannet
Stephen Small
Nick Stavropoulos
Jesús Torres-Vázquez
Jessica Treisman
erika.bach@nyu.edu
ken.birnbaum@nyu.edu
lc121@nyu.edu
Jeremy.dasen@med.nyu.edu
cd38@nyu.edu
and2015@med.cornell.edu
pe19@nyu.edu
se71@nyu.edu
adrian.erlebacher@med.nyu.edu
Gordon.fishell@med.nyu.edu
jane.hubbard@med.nyu.edu
Holger.Knaut@med.nyu.edu
Ruth.lehmann@med.nyu.edu
Cynthia.loomis@nyumc.org
eom204@nyu.edu
Jeremy.nance@med.nyu.edu
Niels.ringstad@med.nyu.edu
Mrockman@nyu.edu
HyungDon.Ryoo@nyumc.org
jsj4@nyu.edu
sjs1@nyu.edu
Nicholas.Stavropoulos@nyumc.org
Jesus.Torres-Vazquez@med.nyu.edu
Jessica.treisman@med.nyu.edu
Theresa Walton –
COURSE
ADMINISTRATOR
Theresa.walton@med.nyu.edu