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DEVO@CU is built on a biofundamentalist / bioliteracy perspective; introducing key ideas, observations & model systems through a molecular, celllular, and evolutionary perspective.

thoughts on the course:  the syllabus adapts to our pace (and viruses), so stay tuned in.  



Date / Topic                            


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

beSocraticWhat is a gene

class 2 slides 


watch/review (if necessary):
Cre-Lox recombinase
CRISPR: Gene editing and beyond & RNA interference (RNAi)

supporting: Genes – way weirder than you thought
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


Tuesday  21 Jan.

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

beSocratic: Stochastic gene expresssion

class 3 slides


supporting: Stochastic gene expression in a single cell - Elowitz 2002 
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: Gradients ...

class 4 slides


supporting: Aggregative & clonal metazoans
(and review: On teaching developmental biology in the 21st centrury)
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


Tuesday 28 Jan.

Clonal multicellularity

beSocratic: Multicellularity

class 5 slides


supporting: Evolution of individuality during the transition
from unicellular to multicellular life
- Michod 2007
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:  Emerging cellular polarities

class 6 slides


supporting: Dividing cellular asymmetry - Neumuller & Knoblich. 2009
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


Tuesday, 4 Feb.

L-R asymmetries / overview of signaling systems

beSocratic: polarity and & left-right asymmetries

class 7 slides


supporting: Molecular to organismal chirality ... conserved myosin 1D
- Lebreton et al., 2018
Daughter 3T3 cells: Are they mirror images of each other?
- Albrecht-Buehler 1977
From cytoskeletal dynamics to organ asymmetry: a non-linear, regulative pathway underlies left-right patterning - McDowell et al 2016
Cellular chirality arising from the self-organization of the
actin cytoskeleton
- Tee et al., 2015
A conserved role of the unconventional myosin 1d in laterality determination
- Tingler et al et al., 2018


Thursday, 6 Feb.

finish overview of signaling systems

beSocratic: Patterning by gradients

class 8 slides


supporting: Communication codes in developmental signaling pathways - Li & Elowitz 2019.
A mechanism for the sharp transition of morphogen gradient interpretation
-Saka & Smith 2017
A role for actomyosin contractility in notch signaling - Hunter et al., 2019
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: Establishing axis & tissue polarity

class 9 slides


introduction to nota bene

Constrained architecture of mammalian Hox gene clusters
- Darbelley et al 2019.
On the evolution of bilaterality - Genikhovish & Technau. 2017
Hox genes – no need for hopeless monsters - Akam 1998
The rise and fall of Hox gene clusters -Duboule 2007


Thursday, 13 Feb


2020 review questions on nota bene  / 2019 review questions
  emo 1beSocratic explanations ← emo 2


Week 6:
Tuesday, 18 Feb.

MIDTERM #1  First midterm exam 2020 answer key 


Thursday, 20 Feb.

Model systems and their uses

class 10 slides


supporting: Mouse models of human disease: an evolutionary perspective
- Perlman 2016.
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


Tues,  25 Feb.

Learning from the frog & the fish (Exams returned)

beSocratic: Model systems

class 11 slides


before class:  Watch – Richard Harland Xenopus: part 1
read for next beSocratic: Gurdon: The egg and the nucleus

supporting: Cellular basis of gastrulation: part 2
Spemann organizaton (twins): part 3
A matched set of frog sequences - Burgess 2016
Evidence that fold-change not absolute level of β-catenin dictates
Wnt signaling
- Goentoro & Kirscher 2009
Cortical rotation and mRNA localization in axis formation. - Houston, 2010
Fold-change detection in biological systems. - Adler & Alon 2018


Thurs., 27 Feb.

Frog & the fish - completed

beSocratic: Xenopus + axes

class 12 slides


supporting:   The dynamics of gene expression in vertebrate embryogenesis at single-cell
- Briggs et al. 2018
Single-cell mapping of gene expression landscapes and lineage
in the zebrafish embryo
- Wagner et al 2018
Principle Component Analysis, explained simply - BioTurning
Volcabo plot | Violin plot - Wikipedia


Tue, 3 March

complete single cell flow analysis - begin
Learning from the fly

beSocratic: Developmental trajectories

class 13 slides


Watch before class:   Pattern formation overview video

supporting: Levin: Transcriptional Precision: Enhancers
Patel: Anterior-Posterior Axis Patterning: Homeotic (Hox) Genes
Wieschaus - Patterning development in the embryo
How the dorsal gradient works: insights from postgenome
- Hong et al., 2008
Drosophila as a model organism - Yamaguchi & Yoshida 2018
Understanding the Effect of Gene Expression Noise in Biological Development - Holloway 2018


Thurs, 5 March

finishing the fly

beSocratic: Regulatory progressions

→ class 14 slides


watch before class
Patel: Anterior-Posterior Axis Patterning: Homeotic (Hox) Genes
Levin: Transcriptional Precision: Enhancers

supporting:  The Heidelberg screen for pattern mutants of Drosophila: a personal account
- Wieschaus & Nusslein-Volhard 2016
A short history and description of Drosophila melanogaster classical genetics - Kaufman 2017


Tues, 10 March

Learning from worm: lineages & cell death

beSocratic: reviewing the fly

class 15 slides


supporting: A transparent window into biology: Caenorhabditis elegans - Corsi et al 2015
Nobel lectures Sydney Brener | John Sulston | Robert Horowitz
The natural history of Caenorhabditis elegans
- Felix & Braendle 2010
Cell Death C. elegans development
- Malin & Shaham 2015


Thurs, 12 March

Considering mammals

beSocratic: reflecting on the worm

class 16 slides


supporting: Polarity and cell division orientationin the cleavage embryo: from worm
to human
- Ajduk & Zernicka-Goetz 2016
Cell fate decisions and axis determination in the early mouse embryo
- Takaoka & Hamada 2012
watch : mouse embryo imaging


WEEK 10:
Tues, 17 March

review questions + on nota bene 2019 exam answer key (different from this year's)
  emo 1beSocratic explanations ← emo 2


Thurs, 19 March
MIDTERM postponed


MIDTERM #2 postponed until after Spring Break

Spring Break    

WEEK 11:    

Tuesday, 31 March
beSocratic 2 to 4PM

MIDTERM #2 Second midterm exam  Answer Key
Dr. K. will be online (via zoom) during the exam for questions


Thurs, 2 April
Gastrulation & Neurulation
class 17ZOOM


watch through [link] to ~12:30
Time-lapse through neurulation
Mouse : Animation: Second Week Of  Development
Animation: Gastrulataion | Neurulation


WEEK 12:
Tues,  7 April
Somite formation
beSocratic: gastrulation neurulation
class 18  →ZOOM


supporting: The mechanism of somite formation in mice– Saga 2012.
Patterning embryos with oscillations: structure, function anddynamics of the vertebrate segmentation clock - Oates et al 2012


Thurs, 9 April

Neural tube patterning beSocratic: somites
class 19  →ZOOM


supporting: Establishing neuronal diversity in the spinal cord - Sagner & Briscoe 2019
  in vitro neural tube patterning with a microfluidic device - Demers etal, 2016
Wnt/β-catenin signaling during early Vertebrate Neural development
- Brafman & Willert 2017


WEEK 13:
Tues,  14 April
Neural crest
beSocratic: in vitro patterning
class 20 ZOOM


supporting: The neural crest migrating into the twenty-first century- Bronner & Simoes-Costa. 2016
What can vertebrates tell us about segmentation? - Graham et al 2014
Neural crest delmination and migration: from epithelium-to-mesenchyme transition to collective cell migration - Theveneau & Mayor 2012.


Thurs, 16 April
Limb formation started
beSocratic: neural crest

class 21 ZOOM


watch : The Evolution of Limbs from Fins - Neil Shubin  2016

supporting: On the formation of digits and joints during limb development - Hiscock et al 2017
A regulatory archipelago controls Hox genes transcription in digits - Montave et al 2011


WEEK 14:
Tues, 21 April
finish limb
beSocratic: limb formation
class 22 ZOOM


On the formation of digits and joints during limb development - Hiscock et al., 2017
Shh and Gli3 are dispensable for limb skeleton formation but regulate digit number and identity – Litingtun et al 2002
Funtions of FGF signaling from the apical ectodermal ridge in limb development - Sun et al 2002.
BMP signals control limb bud interdigital programmed cell death by regulating FGF - Panji-Underwood et al., 2017
Evolution of limb development in cephalopod mollusks - Tarazona et al 2019


Thurs, 23 April
Organoids and the study of
beSocratic: Organoids

class 23 ZOOM


supporting: Brain organoids: advances, applications and challenges- Qian et al 2019
Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in
- Schiebinger, et al 2019
The transcriptional legacy of developmental stochasticity-
Ballouz et al 2020
Cell types of the human retina and its organoids at single-cell resolution: developmental
- Cowan et al 2019
Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids - Beccari et al. 2018.
Embryoids, organoids and gastruloids: new approaches to understanding embryogenesis - Simunovic & Brivanlou 2017
Fetal and neonatal abnormalities due to congenital rubella syndrome: a review of literature - Yazigil et al 2017


WEEK 15:
Tues,  28 April
developmental defects +
beSocratic: Organoids

class 24 ZOOM


watch: Gene editing is here. It’s an enormous threat. - Thiessen 2018

supporting:  Impact of fetal alcohol syndrowm on body systems: a systemtic review
- Caputo et al 2016
What are the Ethical Concerns of Genome Editing?
Did CRISPR help—or harm—the first-ever gene-edited babies? - Cohen 2019
Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution - Pollan et al 2019


Thurs, 30 April
Catch up +


emo 1beSocratic explanations ← emo 2

Course review - part 1 + part 2 - last year's answer key


3rd May 2020

Exam on beSocratic
Available from Saturday 2nd May at noon until
midnight on Sunday the 3rd of May 2020 (but you should limit yourself to 4 hours total)

  cell and molecular and developmental

The original version of DEVO@CU
by M.W. Klymkowsky/virtuallaboratory/beSocratic, llc.| part of the biofundamentals project
Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License
.  2019-2020