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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 / Date   Topics -- jump to current week
to be completed before class


Tues, 14 Jan. 2020


class 1 slides  


– how the course orks, rules, expectations & such
– introduction to beSocratic and nota bene (or perusal or hypothesis, to be determined)
how to read a paper communally

What is the course about? 

nothing required befor the first day!

read AFTER class: On teaching developmental biology in the 21st centrury
Aggregative & clonal metazoans

optional but interesting: Ten Craziest Things Cells Do - Wallace Marshall


Thurs. 16 Jan.

Decision making in bacteria: non-linear responses

class 2 slides


next class

Primary topic
: Understanding what we already know.

Primary topic: Developmental & decision processes in bacteria. 


ineractive reading before class:
The cell as a collection of protein machines  Alberts 1998.

The Evolving Definition of the Term “Gene”
Portin & Wilkins 2017.


Tues  21 Jan.


class 3 slides


Complete: developmental decision in bacteria and unicellular organisms

Primary Topic: Origins of aggregative (temporary) multicellularity


read before classCollective behaviour & swarm intelligence in slime moulds – Read & Latty 2016.

optional but interesting: Regulated aggregative multicellularity in a close unicellular relative of metazo - Sebé-Pedrós et al., 2013.

Cellular Decision Mating & Biological Noise
– Balazsi et al 2011.

optional but interesting: Bacterial Quorum-Sensing Network Architectures - Ng & Bassler/ 2009


Thurs 23 Jan.


→ class 4 slides


Primary Topic: Evolutionary origins of (clonal) multicellularity


 read before class: Boraas et al., 1998. Phagotrophy by a flagellate selects for colonial prey: a possible origin for multicellularity

read before class: Brunet & King 2017. The origin of animal multicellularity and cell differentiation.

optional : Knoll. 2011. The multiple origins of complex multicellularity


Tues,  28 Jan.

Establishing Asymmetries

class 5 slides


Primary Topic: Establishing Asymmetries


read before class:  Neumuller & Knoblich. 2009. Dividing cellular asymmetry

optional but interesting: Chen et al 2016. The in(side) and outs(ide) of asymmetric stem cell division.


Thurs,  30 Jan.

Embryonic Axes

class 6 slides


Primary Topic: Embryonic axes introduced - Left/Right



read before class: Lebreton et al., 2018 Molecular to organismal chirality is induced by the conserved myosin 1D.

optional but interesting:.Albrecht-Buehler 1977. Daughter 3T3 cells: Are they mirror images of each other?

optional but interesting: Ray et al., 2018. Intrinsic cellular chirality regulates left-right symmetry breaking during cardiac looping.


Tues, 4 Feb.

Mophogens &

class 7 slides


Primary Topic: Morphogens and gradients: signaling systems.


read before class: Briscoe & Small. 2015. Morphogen rules: design principles of gradient-mediated patterning.

optional but interesting: Muller et al 2013. Morphogen transport


Thurs, 6 Feb.

Embryonic Axes
(A-P & D-V)

class 8 slides


Primary Topic
: Establishing embryonic axes


read before class: Genikhovish & Technau. 2017 On the evolution of bilaterality.


Tuesday, 11 Feb.

  REVIEW - CATCH UP Questions
review for exam: → class 9 slides


Thursday, 13 Feb.

  MIDTERM #1  First midterm exam  
 Answer key


Tues, 18 Feb.

Model systems

class 10 slides



Primary Topic: Considerations when selecting a model system - strengths & limitations




Read before class: P. Murphy - Model Organisms

read before class:  Perlman 2016. Mouse models of human disease: an evolutionary perspective.

interesting but optional : McGlinn 2013. Mice Fall Short as Test Subjects for Some of Humans’ Deadly Ills 

interesting but optional : Gene Losses during Human Origins

interesting but optional : Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors

interesting but optionalFalse analogies & logical fallacies in animal models


Thurs,  20 Feb.

Learning from the frog

class 11 slides


Reflecting on the first midterm 
(thinking about "I know it now")

Primary Topic: What can we learn from the clawed frog Xenopus laevis



read before class:  Houston, 2010. Cortical rotation and messenger RNA localization in Xenopus axis formation.

we will consider results from this paper: Briggs et al. 2018. The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

optional but interesting: Harland on Xenopus: part 1


Tues, 25 Feb.

Mutational studies
of development

class 12 slides


Primary Topic: Complete Xenopus, start Experimental manipulation of embryonic development

class 12 slides

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


Thursday, 27 Feb.

Learning from the fly

class 13 slides


Primary Topic: Finish Experimental manipulation of embryonic development  and start "What can we learn from the fruit (vinegar) fly Drosophila"



read on before class Animals in Research: Drosophila (the fruit fly) & Wieschaus & Nusslein-Volhard 2016 The Heidelberg screen for pattern mutants of Drosophila: a personal account.


Tue, 3 March

Learning from the worm

class 14 slides



Primary Topic: Finish Drosophila



read on before classAnimals in Research: C. elegans (roundworm)

optional but interestingThe natural history of Caenorhabditis elegans


Thurs, 5 March

Learning from worms & flies

class 15 slides


Primary Topic: Hox and "What can we learn from the nematode C. elegans - cell death!"



read on before class A Transparent Window into Biology: A Primer on Caenorhabditis elegans

optional but interestingCell Death C. elegans development


Tues, 10 March

Neural Crest I

class 16 slides + epitheila/mesenchyme



Primary Topic: Vertebrate development and the neural crest


 read on before class: The Neural Crest Migrating into the Twenty-First Century

→Read & comment on NB: Cell fate decisions and axis determination in the early mouse embryo

interesting: mouse embryo imaging


Thurs, 12 March

Mouse &
Neural crest II

class 17 slides + NC part 2


Primary Topic: Vertebrate development and the neural crest


continue reading for class: The Neural Crest Migrating into the Twenty-First Century

→Read & comment on NB: Cell fate decisions and axis determination in the early mouse embryo


WEEK 10:
Tues, 17 March


CATCH UP + Exam Review  slides

review questions are also on nota bene


Thurs, 19 March


  MIDTERM #2 Second midterm exam    
Answer key

Spring Break        


WEEK 11:
Tues,  31 March

Limb formation I

class 18 slides


Primary Topic:  Link Formation Part 1


read before classPattern formation: old models out on a limb


Thurs, 2 April

Limb formation II

class 19 slides


Primary Topic: Limb formation Part 2


read before class (in class activity)Specialized filopodia direct long-range transport of SHH during vertebrate tissue patterning


WEEK 12:
Tues,  7 April

Gastrulation & Neurulation

class 20 slides


Primary Topic: Gastrulation, neurulation, and neural tube patterning



Xenopus: Time-lapse through neurulation
Richard Harland on gastrulation:
watch through [link] to ~12:20

Mouse : Animation: Second Week Of  Development
Animation: Gastrulation | Neurulation

start on NB before classWnt/beta-Catenin Signaling during Early Vertebrate Neural Development


Thurs, 9 April

Patterning the Neural Tube

class 21 slide


Primary Topic: Patterning the neural tube



finish on NB before class: Wnt/beta-Catenin Signaling during Early Vertebrate Neural Development


WEEK 13:
Tues,  14 April

environmental effects on development

class 22 slides


Primary Topic
: Environomental effects on development (fetal alcohol syndrome / viral infection



read on NB (in class activity):  in vitro neural tube patterning with a microfluidic device

read on NB (next topic):  Impact of fetal alcohol syndrowm on body systems: a systemtic review

optional: Fetal and neonatal abnormalities due to congenital rubella syndrome: a review of literature


Thurs, 16 April

Stem & iPSC cells

class 23 slides



Catching up and on to Primary Topic: Understanding stem cells reprogramming somatic cells




WEEK 14:
Tues, 21 April

human / primate organoids

class 24 slides



Primary Topic: Organoids



complete: Using brain organoids to understand Zika virus-induced microcephaly

read on NB (in class activity)Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution


Thurs, 23 April

cancer development

class 25 slides


Primary Topic: Developmental of cancer


read on NB before classCells of origin in cancer

optionalEchos of the embryo: using the developmental biology toolkit to
study cancer


WEEK 15:
Tues,  28 April

manipulating embryos

class 26 slides



Primary Topic: Manipulating developmental: ethical and technical issues



watch: Gene editing is here. It’s an enormous threat.

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


Thurs, 30 April


  REVIEW for third midterm and comprehensive exam  

Course review questions - part 1

Course review questions - part 2



Troll evolution animation

molecular buff

The original version of DEVO@CU by M.W. Klymkowsky/virtuallaboratory/beSocratic, llc.| part of the the biofundamentals cooperative
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