title graphic

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

<a href="thoughts">https://bioliteracy.blog/2016/10/30/biology-education-in-the-light-of-single-cellmolecule-studies/</a>

The syllabus adapts to our pace, so stay tuned in.  

 

overview


Date / Topic                            

 

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

beSocraticWhat 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: Stochastic gene expresssion

class 3 slides

 

read/review BEFORE class:
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: Gradients ...

class 4 slides

 

look at 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


 

WEEK 3:
Tuesday 28 Jan.

Clonal multicellularity

beSocratic: Multicellularity

class 5 slides

 

look at 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:  Emerging cellular polarities

class 6 slides

 

look at 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.

L-R asymmetries / overview of signaling systems

beSocratic: polarity and & left-right asymmetries

class 7 slides

 

look at 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
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

 

look at before class: 
Communication codes in developmental signaling pathways
- Li & Elowitz 2019.


totally optional (supporting):
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

 

look at before class
Constrained architecture of mammalian Hox gene clusters
- Darbelley et al 2019.


introduction to nota bene

totally optional (supporting):

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
REVIEW - CATCH UP

 

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


 

Week 6:
Tuesday, 18 Feb.
MIDTERM #1

 
MIDTERM #1  First midterm exam 2020 answer key 

 

Thursday, 20 Feb.

Model systems and their uses

class 10 slides

 

look at 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.

Learning from the frog & the fish (Exams returned)

beSocratic: Model systems

class 11 slides

 

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

optional: Cellular basis of gastrulation: part 2
Spemann organizaton (twins): part 3


totally optional (supporting):
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


 

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


totally optional (supporting):  
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


 

WEEK 8:
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
Levin: Transcriptional Precision: Enhancers
Patel: Anterior-Posterior Axis Patterning: Homeotic (Hox) Genes
also ↓ very good
Wieschaus - Patterning development in the embryo


totally optional (supporting):
How the dorsal gradient works: insights from postgenome
technologies
- 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

 

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


totally optional (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


 

WEEK 9:
Tues, 10 March

Learning from worm: lineages & cell death

beSocratic: reviewing the fly

class 15

 

look at before class:: Nobel lectures
Sydney Brener | John Sulston | Robert Horowitz

A transparent window into biology: 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

Considering mammals

beSocratic: reflecting on the worm

class 16

 

look at before class
Polarity and cell division orientationin the cleavage embryo: from worm
to human
- Ajduk & Zernicka-Goetz 2016


totally optional (supporting):
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
MIDTERM #2 on
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 17   [video]

 

watch through [link] to ~12:30
Xenopus:
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  [video]

 

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


 

Thurs, 9 April

Neural tube patterning

beSocratic: somites

→class 19   [video]

 

read / review before class
Establishing neuronal diversity in the spinal cord - Sagner & Briscoe 2019


totally optional (supporting):
  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 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


 

Thurs, 16 April

Limb formation

beSocratic: neural crest

→class 21 slides

 

read / review before class
On the formation of digits and joints during 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
A regulatory archipelago controls Hox genes transcription in digits - Montave et al 2011


 

WEEK 14:
Tues, 21 April

Stem cells and organoids

beSocratic: limb fiormation

→class 22 slides

 

read / review before class
Brain organoids: advances, applications and challenges - Qian et al 2019


totally optional (supporting):
The transcriptional legacy of developmental stochasticity - Ballouz et al 2020
Cell types of the human retina and its organoids at single-cell resolution: developmental convergence, transcriptomic identity, and disease map
- Cowan et al 2019


 

Thurs, 23 April

Environmental  effects on
development

→class 23 slides

 

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

- Caputo et al 2016


totally optional (supporting):
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
 Using brain organoids to understand Zika virus-induced microcephaly - Qian et al 2017


 

WEEK 15:
Tues,  28 April

human / primate
organoids - gene editing

→class 24 slides

 

read / review before class
watch: Gene editing is here. It’s an enormous threat. - Thiessen 2018


totally optional (supporting):
What are the Ethical Concerns of Genome Editing?
The transcriptional legacy of developmental stochasticity - Ballouz1 et al 2019
Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution - Pollan et al 2019


 

Thurs, 30 April
Catch up +
REVIEW

 

REVIEW for third midterm & comprehensive exam
Course review questions - part 1 + Course review questions - part 2 - last year's answer key


 

FINAL EXAM
3rd May 2020

 
Exam on beSocratic
Due at 10 PM on Sunday the 3rd of May 2020.


  cell and molecular and developmental
education


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