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

 
Syllabus - may change significantly before course starts
 

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 & 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 (blog)


potentially useful reference works:
Nature: Milestones in developmental biology


 
 

Thurs. 16 Jan.

Genes, experimental methods, and outcomes

 

beSocratic BEORE class:
#1 What is a gene


class 2 slides  

 

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

- Klymkowsky (blog)
The evolving definition of the term “gene”
- Portin & Wilkins 2017.


totally optional (supporting):
Your Cancer Targets may not be real - Lowe. 2019
Off-target toxicity is a common mechanism of action of cancer durgs undergoing clinical trials. Lin et al. 2019
watch/review: Cre-Lox recombinase
CRISPR: Gene editing and beyond
& RNA interference (RNAi)


 
 

WEEK 2:
Tues  21 Jan.

Decision making in bacteria: stochastic behaviors, sampling phenotypic space, and non-linear responses




 

beSocratic BEORE class:
#2. Molecular 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 (blog)
Stochastic gene expression in a single cell
- Elowitz 2002 


totally optional (supporting):
Biology education in the light of single cell/molecule studies - Klymkowsky (blog)
Distinct mods of cell competition shape mammalian tissue morphogenesis - Ellis et al., 2019
Cellular decision making & biological noise
– Balazsi et al 2011


 
 

Thurs 23 Jan.

Aggregative
multicellularity


 

beSocratic BEORE class:
#4. Community behaviosr & quorum sensing,

→ class 4 slides

 

read/review BEFORE class:
Aggregative & clonal metazoans – Klymkowsky (blog)
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 Clonal behaviors

→ class 5 slides

 

 read BEFORE class:
The origins of 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 polarity and asymmetry


 

beSocratic BEORE class:
#6 Emerging cellular polarities

→ 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
Front–Rear Polarization by Mechanical Cues: From Single Cells to Tissues - Ladoux et al 2016.
Orienting muscle stem cells for regeneration in homeostasis, aging and disease. Feige et al. 2018.
The in(side) & outs(ide) of asymmetric stem cell division. - Chen et al 2016


 
 

WEEK 4:
Tues, 4 Feb.

Molecular asymmetrie and left-right axis

 

beSocratic BEORE class: TBA
#7 Molecular and cellular left-right asymmetry

→ 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.

Morphogensis & axes: signaling gradients, and decision making

 

beSocratic BEORE class:
#8 Gradients and threshold effects

→ 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 continues (Hox)

 

beSocratic BEORE class:

#9 Establishing axis & tissue polarity


→ class 9 slides

 

read before class:
Hox genes, homeosis and the evolution of segment identify: no need for hopeless monsters - Akam 1998


totally optional (supporting):
On the evolution of bilaterality
- Genikhovish & Technau. 2017
The rise and fall of Hox gene clusters -Duboule 2007
The enigmatic HOX genes: can we crack their code? Luo et al 2019
Control of Hox transcription factor concentration and cell-to-cell variability by an auto-regulatory switch - Papadopoulos et al. 2019.

         
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 Characteristics of model systems

→class 10 slides

 

 

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


totally optional (supporting):
Model organisms - P. Murphy
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. Axis formation in Xenopus: change detection systems

→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 (emerging cell types)


 

beSocratic BEORE class:

#12 Developmental trajectories

→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):   watch this space!

 
 

WEEK 8:
Tue, 3 March

Learning from the fly & genetic screens


 

beSocratic BEORE class:
#13 Genetic screens in the fly

→ 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 Homeotic mutations

→ class 14

 

 

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


totally optional (supporting): watch this space!



 
 

WEEK 9:
Tues, 10 March

Learning from worm: lineages and cell death

 

beSocratic BEORE class:

#15 Cell lineage (C. elegans)

→class 15 slides

 

read on before class
A transparent sindow into biology: a primer on Caenorhabditis elegans


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

Cell Death C. elegans development
Animals in Research: C. elegans (roundworm)



 
 


Thurs, 12 March

Vertebrate asymmetries

 

 

beSocratic BEORE class:

#16 Emerging asymmetric (mouse)

→ →class 16 slides

 

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:

#17 Morphogenic movements (gastrulation / neurulation)

class 17 slides

 

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

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


totally optional (supporting): watch this space


 
 

Thurs, 2 April

Rregulatory network, clocks & wavefronts

 

 

beSocratic BEORE class:
#18 Somites clocks and wavefronts


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

class 19 slide

 

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:
#20 Neural Crest induction and epithelial-mesenchymal transition

class 20 slides

 

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

 

beSocratic BEORE class:
#21. Pattering the vertebrate limb

class 21 slides

 

read / review before 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:
#22 Environmental and viral influences

class 22 slides

 

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


totally optional (supporting):
Impact of fetal alcohol syndrome 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

 

beSocratic BEORE class:
#23. Cellular reprogramming

→class 23 slides

 

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


totally optional (supporting):
 Comparing ESC & iPSC - Based models for human genetic disorders



 
 

Thurs, 23 April

human / primate organoids

 

 

beSocratic BEORE class:
24.Building tissues de novo

class 24 slides

 

read / review 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

 

 

beSocratic BEORE class:
25.In vivo gene editing

class 25 slides

 

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

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


totally optional (supporting):


 
 

Thurs, 30 April

REVIEW

 

REVIEW for third midterm
& comprehensive exam

class 26 slides

 

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