Developmental Biology
MCDB 4650
– Fall 2023

DEVO@CU provides an introduction to key observations, principes, methods, and systems used to study socio-cellular interactions & developing systems

 
face development

 

Date / Session Topics
 

Useful resources: SDB Collaborative Resourses for Learning Developmental Biologythe hierarchy of alienness
+ biofundamentals (for review)


 

WEEK 1 – Tuesday 29 August

1. How the course works & what you can expect – reviewing ideas we will be using, repeatedly  + signing up & using beSocratic

slides also posted on nota bene - NB tutorial

elephants child
optional: Hossenfelder Heisenberg's microscope 

 

Portfolio questions:
1.1 What was Socrates attempting to achieve?
1.2 What is surprising about the cellular/molecular mechanisms
that underlie biological processes and diversity?
1.3 How is it possible to make plausible predictions about the effects of specific mutations? What limits such predictions?

 worth watching: Feynmann Understanding magnetic attraction

on nota bene and down-loadable here: pre-Devo refresher
Making mechanistic sense

optional stuff: How would Socrates teach science?
+ The surprising conservation of cellular processe


 

Thursday 31 August

2. Reviewing molecluar & cellular level basics – lessons from the lac operon (noise)  slides

elephants child
 

reviewemo 1 beSocratic 1


Portfolio questions:
2.1 What are the sources of noise in the lac operon (and other biological systems)?
2.2 How might changes in gene expression become (effectively) irreversible?
2.3 How is that cells with the same genotype develop different phenotypes?


 

WEEK 2Tuesday 5 September

3. Some technological caveats +  Signaling systems, gradients, thresholds, and modeling – lessons from Saka & Smith   slides

 

 

reviewemo 1 beSocratic 2


Portfolio questions:
3.1 What are the common features of signaling systems?
3.2 Why are dose-response curves typically sigmoidal, not linear?
3.3 How might the response to a signal lead to cells that are unresponssive to that signal?


 

Thursday 7 September

4. Origins of cellular asymmetries and differences (e.g. Caulobacter slides

 

review emo 1beSocratic 3


Portfolio questions:
4.1 How might asymmetries arise at the cellular level?
4.2 How can one DNA strand be older than the other? how might impact cell behavior?
4.3 Where might the handedness of a cell / organism come from?


 

WEEK 3Tuesday 12 September

5.Social systems, quorum sensing & transient metazoans: decision making & differentiation – Dictyostelium

slides    after class zoom video

 

reviewemo 1 beSocratic 4


Portfolio questions:
5.1 How is quorum sensing used by unicellular organisms?
5.2 In a transient (social) metaozoan, why would cell fate choice be likely to be determined stochastically?
5.3 What types of behavior would be considered "cheating" in a transient metazoan?


 

Thursday, 14 September

6.Clonal metazoans & their evolutionary origins

slides after class zoom video

elephants child
 

review emo 1beSocratic 5


Portfolio questions:
6.1 What factors may have driven the evolution of clonal multicellular organisms (animals)?
6.2 Why might you want to distinguish the soma and the germ line?
6.3 What types of behavior would be considered "cheating" in a clonal metazoan?


 

WEEK 4Tuesday 19 September

7. Evolutionary relationships & model systems
slides

elephants child
 

reviewemo 1 beSocratic 6


Portfolio questions:
7.1 What makes for a good model system and what limits their relevance to humans?
7.2 What does it mean that a trait is homologous rather than analogous?
7.3 How do evolutionary adaptations influence development processes, such as the speed and mechanisms behind early embryonic development?


 

Thursday 21 September

8. Being bilateral: A-P axis & HOX clusters slides

elephants child
 

reviewemo 1 beSocratic 7


Portfolio questions:
8.1 How do reproducible developmental phenotypes facilitate "forward" genetic studies?
8.2 How does the stereotyped embryonic lineage in C. elegans make possible studies of cell death during development?
8.3 How is a homeobox-containing gene different from a Hox gene?


 


WEEK 5 – Tuesday, 26 September

9. Finish axes/HOX - Learning from (clawed) frogs

slides

elephants child For the curious: Harrison 2020. The difference between "homeobox" and HOX genes.



 

reviewemo 1 beSocratic 8


9.1 How did John Gurdon’s experiment help establish that genomic diminution in somatic cells was not happening in Xenopus?
9.2 What factors might contribute to making it more difficult to reprogram a somatic nucleus? 
9.3 Sketch out the stages of the reorientation of the Xenopus egg upon fertilization.


 


Thursday, 28 September

10. Learning from frogs slides


 

reviewemo 1 beSocratic 9


10.1 Describe the events during oogenesis and early development “set up” the embryonic axes.
10.2. What types of evidence lead one to conclude that mRNA (and protein) stability determined by their environment.
10.3 What types of evidence suggest that the Spemann-Mangold organizer is induced by more vegetal regions of the early Xenopus embryo?


 

WEEK 6Tuesday, 3 October

11. review Xenopus - Learning from the Zebrafish
slides

 

reviewemo 1 beSocratic 10


Portfolio questions:
11.1 How did early embryonic asymmetries aid in identifying (natural) inductive molecules in Xenopus?
11.2 What makes zebrafish a good system for studying cellular aspects of development?
11.3 Where are inductive interactions occurring the early zebrafish embryo?


 


Thursday, 5 October

12. complete Zebrafish + consider single cells analyses
slides


 

reviewemo 1 beSocratic 11


Portfolio questions:
12.1 What does single cell RNA sequence data tell you about the process of cell determination (in zebrafish and xenopus)?
12.2 What are the sources of noise in a signaling system (e.g. Wnt)?
12.3 How might cellular noise be suppressed (in zebrafish) and likely elsewhere?


 

Week 7Tuesday, 10 October

13. Exam 1 review exam practice brain

reviewslides

 

reviewemo 1 beSocratic 12


brain Update your portfolios brain
– anything confusing,
let's talk about it.

2022 EXAM 1 review questions 

REVIEW QUESTION NOTES



 

Thursday,  12 October –– EXAM - on beSocratic (opens at 9AM - closes at midnight on Friday)

 


Exam 1 Answer  key– Fall 2023



 

Week 8Tuesday, 17 October

15. Learnin' from the worm and reproducible lineages
slides

elephants child
 

Portfolio questions:
15.1 Why are reverse genetic screens now more common that forward screens?
15.2 How do the details of C. elegans development facilitate studies of development mechanisms?
15.3 How would you (forward) screen for mutations that influence programmed cell death (apoptosis)?

on nota bene and down-loadable here: Predicting mutation outcomes frm early stochastic variation in genetic interaction partners


 


Thursday 19 October 
(midterm exam feedback)

16. Finishing the worm:: discovering the roles of non-coding RNAs in the worm   slides

 

reviewemo 1 beSocratic 15


Portfolio questions:
16.1 How did the nature of C. elegans development facilitate the discovery of miRNAs?
16.2 Describe the types of mutations in the lin4/lin14 system that produce similar phenotypes?


 

Week 9 – Tuesday 24 October

17. Learnin' from fruit fly - stereotyped phenotypes
slides


 

reviewemo 1 beSocratic 16


Portfolio questions:
17.1 How do the features of Drosophila embryogenesis facilitate a forward genetic approaches to identifying the processes involved.
17.2 How might the early syncytial stage of Drosophila development favor maternal mRNA localization and translation (compare to C. elegans)


 



Thursday, 26 October

18. Drosophila continues slides




 

reviewemo 1 beSocratic 17


Portfolio questions:
18.1 How do interactions between maternally encoded proteins influennce axis formation (both a-p and d-v)?
18.2 Which function is likely to be ancestral (for the NFkB system): innate immunity or axis specification in embryos?
18.3 While is likelly to have a more direct impact on HOX expression, segment polarity or a-p axis specification systems?


 

Week 10 – Tuesday, 31 October

19. Drosophila Dorsal-Ventral, segments & HOX
slides

elephants child
background for the curious: Nipam Patel: The role of homeotic genes in development
 

reviewemo 1 beSocratic 18


Portfolio questions:
19.1 What is the role of signaling and feedback in the context of establishing dorsal-ventral patterning (in the fly)?
19.2 How is "posterior prevelence" different between the fly and vertebrates?  (will will review this in class on the 2nd).


 


Thursday, 2 November

20. Early development in the mouse & human slides

elephants child
 

reviewemo 1 beSocratic 19
watch: Imperial College - Human Embryo Development 


Portfolio questions:
20.1 What is meant by "regulative" development?
20.2 How do cell division planes and epithelial behaviors influence blastocyst morphology and cellular lineage decisions?


 

Week 11 Tuesday, 7 November

21. Early mammalian development continues slides

elephants child
background for the curious (good video): Labs growing human embryos for longer than ever before
 

reviewemo 1 beSocratic 20

review: Tarazi et al., 2022. Post-gastrulation synthetic embryos generated ex utero from mouse naive ESCs. Cell. 


Portfolio questions:

21.1 How are eccentric cells recognized in the mammalian embryo
21.2 How do axial asymmetries arise in the mammalian embryo?
21.3 What types of limits (if any) should apply to studies on artificial (stem cell-derived) embryos?


 

Thursday, 9 November

22. Primitive streak and crest slides

elephants child
 

reviewemo 1 beSocratic 21


Portfolio questions:
22.1 How is the patterning of the head region different from that of the trunck (somitic mesoderm)
22.2 What factors influence where a neural crest cell goes and what it differentiates into?
22.3 What defects in cellular behavior could lead to the failure of the neural tube to close


 

Week 12Tuesday, 14 November

23. neural crest & somite formation slides

elephants child
 

reviewemo 1 beSocratic 22


Portfolio questions:
23.1 How might you design a molecular clock to drive somite formation?
23.2 Why does a molecular clock (like the Hes7 loop) need to be reset periodically?
23.2 How do HOX genes influence somite differentiation?



 


Thursday, 16 November

24.Patterning & connecting the nervous system slides

elephants child
 

emo 1
Optional: videos Development of Spinal Nerves
somite (mouse) formation: video 4 & video 11


Portfolio questions:
24.1 How is the system that leads to different neural types (from ventral to dorsal), in the neural tube similar to the activin-Gsc-Xbra system described by Saka and Smith?
24.2 What is the distinction between attractive and repulsive signals in axon growth?
24.3 How could a neuron recognize it target?



 

20-24 Nov '2022 Fall Break & Thanksgiving

 

Fall Break & Thanksgiving


 

Week 13Tuesday, 28 November

25. Limb formation slides

elephants child
 

reviewemo 1 beSocratic 23


Portfolio questions:
25.1 What determines where a limb will form along the body axis?
25.2 How different axes (e.g., A-P axis, D-V axis) are set up in the limb?
25.3 What is the role of regulated apoptosis in limb / autopod formation?


 

Thursday, 30 November

26.Limb development completed slides

 

reviewemo 1 beSocratic 24


Portfolio questions:
26.1 How does the Cre-Lox system work? how can it be turned on in a cell and timing specific manner?
26.2 How might you determine whether expression of Gli3 influences apoptosis?


 

Week 14Tuesday 5 December

27. Making and using induced pluripotent stem cells (iPSCs)  slides

elephants child
 

reviewemo 1 beSocratic 25


Portfolio questions:
27.1 How do stem cells, embryonic, and induced pluripotent stem cells differ?
27.2 Why might the original iPSC protocol not work on all somatic cell types?
27.3 How might you introduce axes within an organoid?


 

Thursday 7 December

28. Organoids and synthetic embryos slides (coming)

elephants child
 

reviewemo 1 beSocratic 26

Portfolio questions:
28.1 How might you identify human specific genetic factors + then study their roles in the development of brains, behavior, and such? 
28.2 What are the ethical limits (if any) of using iPSC-derived organoids for understanding and treatment of human disease?
28.3 In the light of using organoids to study the effects of neanderthal genes in neural development, how might you use organoids to build a "better humans"? what outcomes would you worry about?


 

Week 15Tuesday 12 December

29. Genetic engineering: practical & ethical considerations
slides

elephants child
 

reviewemo 1 beSocratic 27


Portfolio questions:
29.1  Should we recreate Neanderthals (or other "pre-humans")?
29.2 Should engineering for purposes other than avoding genetic diseases be allowed?


 


Thursday 14 December

30. Exam review  slides

 

FINAL EXAM DAY and Time (set by University)

EXAM 2 + GRADING NOTES 2022

Review & submit your portfolios by midnight
-
bring confusions & clarifying questions to class


 


  cell and molecular and developmental
education


The original version of DEVO@CU
by M.W. Klymkowsky/virtuallaboratory + SocraticChat, LLC
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.  2019-2023