title graphic

DEVO@CU is an attempt to build a coherent introduction to the key ideas, observations & model systems used to study embryonic development.

Thoughts on course organization are outlined on the PLoS Science Education Blog: posts one, two, three & four.

DEVO is part of a larger curricular redesign effort that includes biofundamentals, Chemistry, life, the universe & everything (CLUE) & Organic CLUE (O!CLUE)(testimonial).   

 

overview

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

 
 

WEEK 1: Tuesday
15 January

Introduction

 

Introduction to the course:
– course rules, expectations & such
how to read a paper (for this class)
– introduction to beSocratic (hopefully)

What is the course about?
read post-1 class 1 slides  

 
nothing required befor the first day!

optional but interestingTen Craziest Things Cells Do - Wallace Marshall


 
 

Thursday,
17 January

Decision making in bacteria


 

Primary topic: Developmental & decision processes in bacteria. 

class 2 slides

 

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

read before class: Ng & Bassler et al 2009+ Bacterial Quorum-Sensing Network Architectures

optional but interesting: Balazsi et al 2011.+ Cellular Decision Mating and Biological Noise: from Microbes to Mammals


 
 

WEEK 2: Tuesday,
22 January

Aggregative
multi
cellularity



 

Complete: developmental decision in bacteria

Primary Topic: Origins of aggregative (temporary) multicellularity

class 3 slides

 

read before class:  Read & Latty 2016. Collective behaviour and swarm intelligence in slime moulds

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


 
 

Thursday,
24 January

Clonal
multi
cellularity

 

Primary Topic: Evolutionary origins of (clonal) multicellularity

→ class 4 slides.


 

 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


 
 

WEEK 3: Tuesday,
29 January

Establishing Asymmetries

 

 

Primary Topic: Establishing Asymmetries

 

class 5 slides

 

read before class:  Neumuller & Knoblich. 2009. Dividing cellular asymmetry: asymmetric cell division and its implications for stem cells and cancer

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


 
 

Thursday,
31 January

Embryonic
Axes
(left-right)


 

Primary Topic: Embryonic axes introduced - Left/Right

 

class 6 slides

 

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.


 
 

WEEK 4: Tuesday,
5 February

Mophogens &
non-linear
responses

 

Primary Topic: Morphogens and gradients: signaling systems.

class 7 slides

 

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

optional but interesting: Muller et al 2013. Morphogen transport


 
 

Thursday, 7 February

Embryonic Axes
(A-P & D-V)

 


Primary Topic
: Establishing embryonic axes

class 8 slides

 

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


 
 

WEEK 5: Tuesday,
12 February

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

 
 

Thursday,
14 February

MIDTERM #1

  MIDTERM #1  First midterm exam  
 Answer key

 
 

WEEK 6: Tuesday
19 February

Model systems

 

 

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

 

class 10 slides

 

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


 
 

Thursday,
21 February

Learning from the frog


 

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

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

class 11 slides

 

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


 
 

WEEK 7: Tuesday,
26 February

Mutational studies
of development


 

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,
28 February

Learning from the fly

 

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

class 13 slides

 

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.


 
 

WEEK 8: Tuesday,
5 March

Learning from the worm

 

 

Primary Topic: Finish Drosophila

class 14 slides

 

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

optional but interestingThe natural history of Caenorhabditis elegans


 
 

Thursday,
7 March

Learning from worms & flies

 

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

class 15 slides

 

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

optional but interestingCell Death C. elegans development



 
 

WEEK 9: Tuesday,
12 March

Neural Crest part 1

 

 

Primary Topic: Vertebrate development and the neural crest

Lee Niswander
class 16 slides + epitheila/mesenchyme

 

 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


 
 

Thursday,
14 March

Mouse and
Neural crest part 2

 

Primary Topic: Vertebrate development and the neural crest

Lee Niswander
class 17 slides + NC part 2

 

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: Tuesday,
19 March

 

CATCH UP + Exam Review  slides

 
review questions are also on nota bene

 
 

Thursday,
21 March

MIDTERM #2

  MIDTERM #2 Second midterm exam    
Answer key

 
 
Spring Break        

 
 

WEEK 11: Tuesday,
2 April

Limb formation- part 1

 

Primary Topic:  Link Formation Part 1

Lee Niswander class 18 slides

 
read before classPattern formation: old models out on a limb

 
 

Thursday,
4 April

Limb formation- part 2

 

Primary Topic: Limb formation Part 2

Lee Niswander

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

 
 

WEEK 12: Tuesday,
9 April

Gastrulation & Neurulation

 

Primary Topic: Gastrulation, neurulation, and neural tube patterning

class 20 slides

 

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


 
 

Thursday,
11 April

Patterning the Neural Tube

 

Primary Topic: Patterning the neural tube

class 21 slide

 

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


 
 

WEEK 13: Tuesday,
16 April

environmental effects on development

 


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

class 22 slides

 

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


 
 

Thursday,
18 April

Stem & iPSC cells

 

 

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

class 23 slides

 

 
 

WEEK 14: Tuesday,
23 April

human / primate organoids

 

 

Primary Topic: Organoids

class 24 slides

 

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



 
 

Thursday,
25 April

cancer development

 

Primary Topic: Developmental of cancer

class 25 slides

 
read on NB before classCells of origin in cancer

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


 
 

WEEK 15: Tuesday,
30 April

manipulating embryos

 


next
class

Primary Topic: Manipulating developmental: ethical and technical issues

class 26 slides

 

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

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


 
 

Thursday,
2 May

REVIEW

  REVIEW for third midterm and comprehensive exam  

Course review questions - part 1

Course review questions - part 2


 
 

Tuesday,
7 May

FINAL EXAM

  FINAL + IKIN EXAMS
1:30 PM - 04:00 PM   TUESDAY
 
Troll evolution animation

molecular buff
education

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