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 

 

overview


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

 

WEEK 1
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
class
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


 

WEEK 2:
Tuesday  21 Jan.

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

beSocratic BEORE
class
:
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
class
:
Aggregation & multicellularity

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
A mechanism for the sharp transition of morphogen gradient interpretation -Saka & Smith 2017


 

WEEK 3:
Tuesday 28 Jan.

Clonal multicellularity

beSocratic BEORE
class: Cell specification

→ 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
class
:
  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


 

WEEK 4:
Tuesday, 4 Feb.

Molecular and cellular asymmetries and embryonic
left-right axis

beSocratic BEORE
class
:
Molecular, cellular, & embryonic left-right asymmetry

→ 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
Cellular chirality regulates left-right symmetry breaking during cardiac looping.
- Ray et al., 2018

 

Thursday, 6 Feb.

Morphogensis, axes and signaling systems

beSocratic BEORE
class
:
Patterning by gradients

→ class 8 slides

 

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


totally optional (supporting):
Morphogen transport  - Muller et al 2013
Morphogen rules: design principles of gradient-mediated patterning.
- Briscoe & Small. 2015
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):

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

→class 10 slides

 

beSocratic BEORE class: #9 Model systems considered

Read before class: 
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


 

WEEK 7

Tues,  25 Feb.

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

Learning from the frog (and the fish)

→class 11 slides

 

beSocratic BEORE class: #10 Axis formation in Xenopus: change detection systems

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


totally optional (supporting):
Richard Harland on Xenopus: part 1
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 (and the fish) - emerging cell types

→class 12 slides


 

beSocratic BEORE class: #11 Developmental trajectories

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):  
Principle Component Analysis, explained simply - BioTurning
Volcabo plot | Violin plot - Wikipedia


 

WEEK 8:

Tue, 3 March

Learning from the fly
& genetic screens

→ class 13 slides


 

beSocratic BEORE class: #12 Genetic screens in the fly

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


totally optional (supporting):
Drosophila as a model organism - Yamaguchi & Yoshida 2018


 

Thurs, 5 March

finishing the fly

→ class 14

 

beSocratic BEORE class: #13 Homeotic mutations

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!


 

WEEK 9:

Tues, 10 March

Learning from worm: lineages & cell death

→class 15 slides

 

beSocratic BEORE class: #14 Cell lineage (C. elegans)

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

class 16 slides

 

beSocratic BEORE class: #15 Emerging asymmetric (mouse)

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
→ 
slides

 
review questions are also on nota bene

 

Thurs, 19 March
MIDTERM #2

  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
Xenopus:
Time-lapse through neurulation
Richard Harland on gastrulation:

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


 


 

Thurs, 2 April

Rregulatory
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
patterning

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):
 Specialized filopodia direct long-range transport of SHH during vertebrate tissue patterning - Sanders et al 2013


 

Thurs, 16 April

Environmental
effects on
development

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
organoids

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

watch:
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

REVIEW
class 26 slides

 

REVIEW for third midterm & comprehensive exam

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


 

FINAL EXAM

 
TBA

last year's answer key

  cell and molecular and developmental
education


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