title graphic

DEVO@CU is an attempt to build a coherent introduction to the key ideas, observations & model systems used to study embryonic development. It is built on the biofundamentalist perspective (link)

Thoughts on course organization are outlined on the bioliteracy.blog:

Syllabus: There may well be changes before the course starts and along the way  -  and we will be using CatchBox to facilitate engagement 



Date / Topic   to be completed before class                                 jump to current week.


Tuesday, 14 Jan. 2020

What is the course about, how does it work & what do I expect from you?

class 1 slides  


nothing required before the first day,

but if you are curious read:
On teaching developmental biology in the 21st centrury

Introduction to beSocratic +
a useful reference work: Nature: Milestones in developmental biology


Thursday 16 Jan.

Genes, experimental methods & outcomes

beSocratic BEORE
What is a gene

class 2 slides 


read/review BEFORE class:
Genes – way weirder than you thought

watch/review (if necessary): Cre-Lox recombinase
CRISPR: Gene editing and beyond & RNA interference (RNAi)

totally optional (supporting):
The evolving definition of the term “gene” - Portin & Wilkins 2017
Conceptual simplicity, mechanistic complexity & unintelligent design - 2020
Your Cancer Targets may not be real - Lowe. 2019
Off-target toxicity is a common mechanism of action of cancer drugs
- Lin et al. 2019
Biological plasticity rescues target activity in CRISPR knock outs
- Smits et al 2019
Genetic paradox explained by nonsense - Wilkinson, 2019


Tuesday  21 Jan.

Stochastic gene expression: sampling phenotypic space with a single genotype.

beSocratic BEORE
Stochastic gene expresssion

class 3 slides


read/review BEFORE class: next
Stochastic gene expression in a single cell - Elowitz 2002 

totally optional (supporting):
Bacterial persistance as a phenotypic switch - Balaban et al 2004
Programmed cell death in bacteria - Allocati et al 2015
Metabolic interactions betweeen dynamic bacterial subpopulations
- Rosenthal et al 2018
Modeling network dynamics: the lac operon, a case study - Vilar et al 2003
Global quantification – mammalian gene expression control
- Schwanhäusser et al 2011
Molecular-level tuning of cellular autonomy controls the collective behaviors of cell populations - Maire & Youk 2015


Thursday 23 Jan.

Quorum sensing & aggregative multicellularity

beSocratic BEORE
Gradients ...

class 4 slides


read/review BEFORE class:
Aggregative & clonal metazoans
(and review: On teaching developmental biology in the 21st centrury)

totally optional (supporting):
Aggregative multicellular & cell-cell communication in Dictyostelia
- Du et al 2015
Cell competition and its role in the regulation - Di Gregorio et al 2016
Collective behaviour ... in slime moulds– Read & Latty 2016
Construction of a genetic toggle switch -Gardner et al 2000


Tuesday 28 Jan.

Clonal multicellularity

beSocratic BEORE
class: Multicellularity

class 5 slides


 read BEFORE class:
Evolution of individuality during the transition
from unicellular to multicellular life
- Michod 2007

totally optional (supporting):
Phagotrophy by a flagellate selects of colonial prey: a possible
origin of multicellularity
- Boraas et al 1998
The multiple origins of complex multicellularity - Knoll 2011
The origin of animal multicellularity - Brunet & King 2017


Thursday,  30 Jan.

Cellular polarity & asymmetries

beSocratic BEORE
  Emerging cellular polarities

class 6 slides


read BEFORE class
Dividing cellular asymmetry - Neumuller & Knoblich. 2009

totally optional (supporting):
Remodeling epithelial cell organization: front-read and apical-basal polarity - Nelson 2009
Front–Rear Polarization by mechanical cues - Ladoux et al 2016
Orienting muscle stem cells - Feige et al. 2018
The in(side) & outs(ide) of asymmetric stem cell division. - Chen et al 2016


Tuesday, 4 Feb.

L-R asymmetries / overview of signaling systems

beSocratic BEORE
polarity and & left-right asymmetries

class 7 slides


read BEFORE class:
Molecular to organismal chirality ... conserved myosin 1D
- Lebreton et al., 2018

totally optional (supporting):
Daughter 3T3 cells: Are they mirror images of each other?
- Albrecht-Buehler 1977
From cytoskeletal dynamics to organ asymmetry: a non-linear, regulative pathway underlies left-right patterning - McDowell et al 2016
Cellular chirality arising from the self-organization of the
actin cytoskeleton
- Tee et al., 2015
A conserved role of the unconventional myosin 1d in laterality determination
- Tingler et al et al., 2018


Thursday, 6 Feb.

finish overview of signaling systems

beSocratic BEORE
Patterning by gradients

class 8 slides


read BEFORE class
Communication codes in developmental signaling pathways
- Li & Elowitz 2019.

totally optional (supporting):
A mechanism for the sharp transition of morphogen gradient interpretation
-Saka & Smith 2017
A role for actomyosin contractility in notch signaling - Hunter et al., 2019
Cell competition shape mammalian morphogenesis - Ellis et al., 2019
Cellular competition corrects noisy Wnt morphogen gradients to achieve
robust ratterning in the zebrafish embryo
– Akieda et al., 2019


Weeek 5:
Tuesday, 11 Feb.

Establishing (AP) axes and Hox genes

beSocratic BEORE
class: Establishing axis & tissue polarity

class 9 slides


read before class:
Constrained architecture of mammalian Hox gene clusters
- Darbelley et al 2019.

introduction to nota bene

totally optional (supporting):

On the evolution of bilaterality - Genikhovish & Technau. 2017
Hox genes – no need for hopeless monsters - Akam 1998
The rise and fall of Hox gene clusters -Duboule 2007


Thursday, 13 Feb


2020 review questions on nota bene  / 2019 review questions
  emo 1beSocratic explainations ← emo 2


Week 6:
Tuesday, 18 Feb.

  MIDTERM #1  First midterm exam 2020  Answer key from 2019


Thursday, 20 Feb.

Model systems and their uses

class 10 slides


Read for beSocratic: 
Mouse models of human disease: an evolutionary perspective
- Perlman 2016.

totally optional (supporting):
Mice fall short as test subjects - McGlinn 2013
False analogies & logical fallacies in animal models - Sjoberg 2016
Gene losses during human origins - Wang et al 2006
Recent de novo origin of human protein-coding genes
- Knowles & McLysaght 2009
Human accelerated regions in neural progenitors - Ryu et al 2019


Tues,  25 Feb.

Learning from the frog & the fish (Exams returned)

beSocratic BEORE
Model systems & Xenopus Axis formation

→class 11 slides


read before class
Watch – Richard Harland Xenopus: part 1
optional: Cellular basis of gastrulation: part 2
Spemann organizaton (twins): part 3

totally optional (supporting):
A matched set of frog sequences - Burgess 2016
Evidence that fold-change not absolute level of β-catenin dictates
Wnt signaling
- Goentoro & Kirscher 2009
Cortical rotation and mRNA localization in axis formation. - Houston, 2010
Fold-change detection in biological systems. - Adler & Alon 2018


Thurs., 27 Feb.

Completing the frog & the fish - emerging cell types

beSocratic BEORE
Developmental gene expression trajectories

→class 12 slides


read before class
The dynamics of gene expression in vertebrate embryogenesis at single-cell
- Briggs et al. 2018 (focus onsummary page)

totally optional (supporting):  
Single-cell mapping of gene expression landscapes and lineage
in the zebrafish embryo
- Wagner et al 2018
Principle Component Analysis, explained simply - BioTurning
Volcabo plot | Violin plot - Wikipedia


Tue, 3 March

Learning from the fly
& genetic screens

beSocratic BEORE
Mutants and phenotypes ( in the fly)

→ class 13 slides


read on before class
How the dorsal gradient works: insights from postgenome
- Hong et al., 2008

totally optional (supporting):
Drosophila as a model organism - Yamaguchi & Yoshida 201


Thurs, 5 March

finishing the fly

beSocratic BEORE class: #13 Homeotic mutations

→ class 14



read on before class
The Heidelberg screen for pattern mutants of Drosophila: a personal account
- Wieschaus & Nusslein-Volhard 2016

totally optional (supporting):  watch this space!


Tues, 10 March

Learning from worm: lineages & cell death

beSocratic BEORE clas: Cell lineage (C. elegans)

→class 15 slides


read on before class
A transparent sindow into biology: a primer on Caenorhabditis elegans
- Corsi et al 2015

totally optional (supporting):
The natural history of Caenorhabditis elegans
- Felix & Braendle 2010
Cell Death C. elegans development
- Malin & Shaham 2015


Thurs, 12 March

Vertebrate asymmetries

beSocratic BEORE class: #15 Emerging asymmetric (mouse)

class 16 slides


read on before class: :
Cell fate decisions and axis determination in the early mouse embryo

- Takaoka & Hamada 2012

totally optional (supporting):
watch : mouse embryo imaging


WEEK 10:
Tues, 17 March

CATCH UP + Exam Review

review questions are also on nota bene

  emo 1beSocratic explainations ← emo 2


Thurs, 19 March

  MIDTERM #2 Second midterm exam  

Spring Break    


WEEK 11:
Tues,  31 March

Gastrulation & Neurulation

class 17 slides


beSocratic BEORE class: #16 Morphogenic movements (gastrulation / neurulation)

watch through [link] to ~12:20
Time-lapse through neurulation
Richard Harland on gastrulation:
Mouse : Animation: Second Week Of  Development
Animation: Gastrulation | Neurulation

totally optional (supporting):


Thurs, 2 April

network, clocks
& wavefronts

class 18 slides


beSocratic BEORE class: #17 Somites clocks and wavefronts

read / review before class
The mechanism of somite formation in mice– Saga 2012.

totally optional (supporting):
Patterning embryos with oscillations: structure, function anddynamics of the vertebrate segmentation clock - Oates et al 2012


WEEK 12:
Tues,  7 April

Spinal cord &
neural tube

class 19 slide


beSocratic BEORE class: #18 A/P and D/V Neural patterning

read / review before class
Development-on-chip: in vitro neural tube patterning with a microfluidic device - Demers et al 2016

totally optional (supporting):
Wnt/β-Catenin Signaling during Early Vertebrate Neural Development
- Brafman & Willert 2017
Establishing neuronal diversity in the spinal cord
- Sagner & Briscoe 2019


Thurs, 9 April

Neural crest

class 20 slides


beSocratic BEORE class: #19 Neural Crest induction & epithelial-mesenchymal transition

read / review before class
Identification of a rudimentary neural crest in a non-vertebrate chordate - Abitua et al 2012

totally optional (supporting):
Ancient evolutionary origin of vertebrate enteric neurons from trunk-derived neural crest
- Green et al 2017
The neural crest migrating into the twenty-first century
. Bronner & Simoes-Costa. 2016


WEEK 13:
Tues,  14 April

Limb formation

class 21 slides


beSocratic BEORE class: #20 Pattering the vertebrate limb

read / review before class
On the Formation of Digits and Jointsduring Limb Development

- Hiscock et al 2017

totally optional (supporting):
Hox Genes in the Limb: A Play in Two Acts - Deschamps 2004
 Specialized filopodia direct long-range transport of SHH during vertebrate tissue patterning
- Sanders et al 2013


Thurs, 16 April

effects on

class 22 slides


beSocratic BEORE class: #21 Environmental and viral influences

read / review before class
 In vitro neural tube patterning with a microfluidic device

- Demers et al 2016

totally optional (supporting):
Impact of fetal alcohol syndrome on body systems: a systemtic review
- Caputo et al, 2016
Fetal and neonatal abnormalities due to congenital rubella syndrome: a review of literature

- Yazigil et al 2017


WEEK 14:
Tues, 21 April

Stem (ES) &
iPSC cells

→class 23 slides


beSocratic BEORE class: #22 Cellular reprogramming

read / review before class
 Impact of fetal alcohol syndrowm on body systems: a systemtic review

- Demers et al 2016

totally optional (supporting):
 Comparing ESC & iPSC - Based models for human genetic disorders
- Halevy & Urbach 2014
Embryoids, organoids and gastruloids: new approaches to understanding embryogenesis
- Simunovic & Brivanlou 2017


Thurs, 23 April

human / primate

class 24 slides


beSocratic BEORE class: #23.Building tissues de novo

read / review before class
 Using brain organoids to understand Zika virus-induced microcephaly

- Qian et al 2017

totally optional (supporting):
Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution
- Pollan et al 2019
Cell types of the human retina and its organoids at single-cell resolution: developmental convergence, transcriptomic identity, and disease map - Cowan et al 2019


WEEK 15:
Tues,  28 April

Gene editing
in embryos

class 25 slides


beSocratic BEORE class: #24 In vivo gene editing

Gene editing is here. It’s an enormous threat.
- Thiessen 2018

read on NB before class
What are the Ethical Concerns of Genome Editing?

totally optional (supporting):


Thurs, 30 April

class 26 slides


REVIEW for third midterm & comprehensive exam

Course review questions - part 1 + Course review questions - part 2




last year's answer key

  cell and molecular and developmental

The original version of DEVO@CU
by M.W. Klymkowsky/virtuallaboratory/beSocratic, llc.| part of the the biofundamentals cooperative
Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License
.  2019-2020