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:

 

overview

 
currently under construction - may change significantly before course starts
 

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

 
 

WEEK 1
Tues, 14 Jan. 2020

Introduction


 

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

+ intro to beSocratic & nota bene

how to read a paper (communally)

class 1 slides  

 
nothing required before the first day!

background reading for the class:
On teaching developmental biology
in
the 21st centrury - Klymkowsky

potentially useful reference works:
Nature: Milestones in Developmental biology

totally optional (supporting):
Ten craziest things cells do
- Marshall


 
 

Thurs. 16 Jan.

Genes and such

 

beSocratic BEORE class:
1.What is a gene?

class 2 slides  

 

read/review BEFORE class:
Genes – way weirder than you thought
- Klymkowsky
The evolving definition of the term “gene”
- Portin & Wilkins 2017.


 
 

WEEK 2:
Tues  21 Jan.

Decision making in bacteria: non-linear responses




 

beSocratic BEORE class:
2. Molecluar numbers and half-lives

3.Genotypes, phenotypes & noise

→ class 3 slides

 

read/review BEFORE class:
Molecular machines & the place of physics in the biology curriculum  - Klymkowsky
Stochastic gene expression in a single cell
- Elowitz 2002 

totally optional (supporting):
Cellular Decision Mating & Biological Noise
– Balazsi et al 2011


 
 

Thurs 23 Jan.

Aggregative
multicellularity


 

beSocratic BEORE class:
4. Community behavior & quorum sensing,

→ class 4 slides

 

read/review BEFORE class:
Aggregative & clonal metazoans – Klymkowsky
Bacterial quorum-sensing network architectures.
- Ng and Bassler. 2009.

totally optional (supporting):
The social lives of microbes. – West et al., 2007
Collective behaviour & swarm intelligence in slime moulds – Read & Latty 2016.


 
 

WEEK 3:
Tues,  28 Jan.

Clonal multicellularity

 

beSocratic BEORE class:
5. Gradients, thresholds, and decisions

→ class 5 slides

 

 read BEFORE class:
The origin animal multicellularity. - Bonner 1998

totally optional (supporting):
The evolution of metazoan axial properties
- Martindale. 2005.
The origin of animal multicellularity and cell differentiation - Brunet & King 2017.


 
 

Thurs,  30 Jan.

Cellular asymmetry


 

beSocratic BEORE class:
6. Cellular anatomy and generating asymmetries

→ class 6 slides

 

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

totally optional (supporting):
Remodeling epithelial cell organization: transitions between front-read and apical-basal polarity. Nelson 2009
The in(side) & outs(ide) of asymmetric stem cell division. - Chen et al 2016


 
 

WEEK 4:
Tues, 4 Feb.

Left-right axis

 

beSocratic BEORE class:
7. Generating chirality

→ class 7 slides

 

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

totally optional (supporting):
Daughter 3T3 cells: Are they mirror images of each other? - Albrecht-Buehler 1977
Intrinsic cellular chirality regulates left-right symmetry breaking during cardiac looping. - Ray et al., 2018.

 
 

Thurs, 6 Feb.

Morphogenis and Embryonic Axes
(A-P & D-V)

 

beSocratic BEORE class:
8. Mechanisms behind morphogens

→ class 8 slides

 

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

totally optional (supporting):
Morphogen transport  - Muller et al 2013


 
 

Weeek 5:
Tuesday, 11 Feb.

Establishing Axes

 

beSocratic BEORE class:
9. Hox clusters and their regulation

Primary Topic: Establishing embryonic axes
→ class 9 slides

 

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

totally optional (supporting):
The rise and fall of Hox gene clusters -Duboule 2007
Hox genes and evolution  - Hrycaj & Wellik 2016

         
Thursday, 13 Feb   REVIEW - CATCH UP
 

review questions on nota bene


 
 

Week 6:
Tuesday, 18 Feb.
MIDTERM #1

  MIDTERM #1  First midterm exam  
 Answer key from 2019

 
 


Thursday, 20 Feb.

Model systems

 

 

beSocratic BEORE class:
10. The logic of model organisms

→class 10 slides

 

 

Read before class: 
Model Organisms - P. Murphy
Mouse models of human disease: an evolutionary perspective - Perlman 2016.

totally optional (supporting):
Mice Fall Short as Test Subjects for Some of Humans’ Deadly Ills - McGlinn 2013.
Gene Losses during Human Origins - Wang et al 2006
Recent de novo origin of human protein-coding genes - Knowles &McLysaght 2009.
Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors - Ryu et al 2019
False analogies & logical fallacies in animal models - Sjoberg 2016


 
 

WEEK 7
Tues,  25 Feb.

Learning from the frog


 

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

beSocratic BEORE class:
11. Xenopus, A/P & D/V asymmetry

→class 11 slides

 

read before class
Evidence that fold-change, and not absolute level, of b-catenin dictates Wnt signaling
- Goentoro & Kirscher 2009.

totally optional (supporting):
Harland on Xenopus: part 1
Cortical rotation and messenger RNA localization in Xenopus axis formation. - Houston, 2010.
Fold-change detection in biological systems.
- Adler & Alon -2018


 
 


Thurs., 27 Feb.

completing the frog


 

beSocratic BEORE class:
12. Emerging differentiation

→class 12 slides

 

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

totally optional (supporting):

 
 

WEEK 8:
Tue, 3 March

Learning from the fly


 

beSocratic BEORE class:
13. Drosophila and patterning

→ class 13 slides

 

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

totally optional (supporting):
Animals in Research: Drosophila (the fruit fly)


 
 

Thurs, 5 March

finishing the fly

 

 

beSocratic BEORE class:
14. The logic of genetic screens and patterning

→ class 14 slides

 

 

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

totally optional (supporting):



 
 

WEEK 9:
Tues, 10 March

Learning from worms

 

beSocratic BEORE class:
15. C. elegans, linkeage and death

→class 15 slides

 

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

Animals in Research: C. elegans (roundworm)

totally optional (supporting):
The natural history of Caenorhabditis elegans

Cell Death C. elegans development



 
 


Thurs, 12 March

Vertebrate asymmetries

 

 

beSocratic BEORE class:
15. Asymmetry in the mouse

→ class 16 slides + epitheila/mesenchyme

 

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

totally optional (supporting):
mouse embryo imaging


 
 

WEEK 10:
Tues, 17 March

Exam review

 

CATCH UP  (if needed)
+ Exam Review 
slides

 
review questions are also on nota bene

 
 

Thurs, 19 March

MIDTERM #2

  MIDTERM #2 Second midterm exam    
Answer key

 
 
Spring Break      

 
 

WEEK 11:
Tues,  31 March

Gastrulation & Neurulation

 

 

 

beSocratic BEORE class:
16. Gastrulation+Neurulation

class 16 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


 
 

Thurs, 2 April

Somite clock and wavefront.

 

 

beSocratic BEORE class:
17. Cellular and embryonic clocks

class 17 slides

 

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 and neural tube patterning

 

beSocratic BEORE class:
18. Gradients in the developming nervous system

class 18 slides

 

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

totally optional (supporting):
Specialized filopodia direct long-range transport of SHH during vertebrate tissue patterning

Wnt/beta-Catenin Signaling during Early Vertebrate Neural Development


 
 

Thurs, 9 April

Neural crest

 

beSocratic BEORE class:
19. Cellular migrations

class 10 slide

 

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

totally optional (supporting):
The neural crest migrating into the twenty-first century. Bronner & Simoes-Costa. 2016


 
 

WEEK 13:
Tues,  14 April

Limb formation

 

beSocratic BEORE class:
20. Patterning tissues (again)

class 20 slides

 

read before class (in class) Pattern formation: old models out on a limb

totally optional (supporting):
Specialized filopodia direct long-range transport of SHH during vertebrate tissue patterning


 
 

Thurs, 16 April

Environmental effects on development

 

 

 

beSocratic BEORE class:
21. Environmental and virus influences

class 21 slides

 

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

totally optional (supporting):
Impact of fetal alcohol syndrowm on body systems: a systemtic review
Fetal and neonatal abnormalities due to congenital rubella syndrome: a review of literature


 
 

WEEK 14:
Tues, 21 April

Stem & iPSC cells

class 24 slides

 

beSocratic BEORE class:
22.Cellular reprogramming

class 22 slides

 

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

optionalComparing ESC & iPSC - Based models for human genetic disorders



 
 

Thurs, 23 April

human / primate organoids

class 25 slides

 

beSocratic BEORE class:
23.Building tissues de novo

class 23 slides

 

read on NB before class: Using brain organoids to understand Zika virus-induced microcephaly

totally optional (supporting):
Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution


 
 

WEEK 15:
Tues,  28 April

Gene editing embryos

class 26 slides

 

 

beSocratic BEORE class:
24.In vivo dene editing i

 

 

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

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

totally optional (supporting):


 
 

Thurs, 30 April

REVIEW

  REVIEW for third midterm
& comprehensive exam
 

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


 
 

FINAL EXAM

  TBA next class  
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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.  2019-2020