Molecular Biology of Development

Possible exam questions based on the course content

Development - Argenton
Explain the signi cance of the maternal to zygotic transition (MZT) in early
embryonic development. What changes occur in cell division patterns during this
transition?
The maternal to zygotic transition marks a pivotal shift from maternal to embryonic control
over development. Initially, cell divisions are rapid and synchronous, operating without the
G1 and G2 phases, relying on maternal determinants. Following the MZT, cell proliferation
rates become variable, and cells start to exhibit unique biological characteristics as control
shifts to zygotic DNA, indicating the embryo's increasing autonom .
Describe the role of apoptosis in developmental processes. Provide examples of its
importance in both embryonic and larval stage transformations.
Apoptosis is generally crucial for developmental processes such as tissue sculpting,
removing unnecessary cells, and shaping organs. Examples in development include the
formation of ngers and toes (by eliminating the webbing between them), it is also involved
in the clearance of embryonic and larval sca olds and the proper structuring of the
nervous system.
Discuss the molecular mechanisms underlying the Spemann and Mangold
Organizer's function in dorsal-ventral axis formation. How do morphogens contribute to this
process?
When the organizer activity was observed by Spemann, it was suggested that this activity
changes the fate of ventral tissues. Generally, the Organizer functions by secreting
morphogens (molecules able to establish a gradient of concentration that when
binded to receptors on competent target cells induce a speci c fate depending on
the morphogen concentration) that establish the dorsal-ventral axis, with molecules like
Noggin, Chordin, and Follistatin inhibiting BMP signaling to promote dorsal cell fates.
Detail the experimental evidence supporting the concepts of mosaic vs. regulative
development. How do these concepts di er in explaining cell fate determination?
Mosaic development suggests that each cell's fate is determined early and independently,
while regulative development indicates that cell fates are exible and in uenced by their
environment and interactions with other cells. There were 2 di erent experiments done
with the the goal of discovering if the devolpment was mosaic or regulative, the rst one
was made by Roux where he killed one blastomere of a 2 cell stage xenopus ambryo using
a hot needle and analysed if the embryo were able to continue with the development, only
half embryo developed and he concluded that the development was mosaic however his
conclusion was false due to the fact that if he had separated the dead blastomere from the
other living one, a full complete embryo would have developed from the living blastomere.
The second experiment was made by Driesch where he separated 4 blastomeres of a 4
stage sea urchin and analysed the development of each single blastomere and he found
out that the 4 blastomeres developed well, meaning that the development observed was
regulative. However, to say if development is mosaic or regulative we have to take a look
at the species analised, insects have mosaic development while amphibians for examples
have a regulative development.
Explore the roles of integrins in mediating cell-extracellular matrix (ECM)
interactions. How do these interactions in uence cell behavior during development?
Integrins play a critical role in development by mediating cell-ECM interactions.They
in uence cell adhesion, migration, and di erentiation, essential for tissue morphogenesis
and organ formation. As an example integring make up the Fibronectins that are larger
glycoproteins that acts as an adhesive molecule paving the road for cells migration
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 De ne and compare instructive and permissive induction in the context of cell fate
determination. How does competence a ect a cell's response to inductive signals?
Instructive induction involves signaling where the inducing cell actively directs the
receiving cell towards a speci c fate (the induced cells can have di erent potential fates),
while permissive induction occurs when the receiving cell has the inherent potential to
di erentiate along a particular pathway, given the appropriate conditions. Competence
refers to the receiving cell's ability to respond to inductive signals, a crucial factor
determining the outcome of these interactions.
Describe the process of lateral inhibition and its signi cance in generating cellular
diversity within a developing organism. What role does the Delta-Notch signaling pathway
play in this process?
Lateral inhibition, facilitated by the Delta-Notch signaling pathway, is essential for creating
cellular diversity. An equivalence group makes up the sibling cells, the lateral inhibition
process promotes a signal within an equivalence group causing one cell to adopt a
primary fate, while the others in the group are inhibited from doing so, this ensures that
neighboring cells adopt di erent fates through inhibitory signals, preventing them from
di erentiating into the same cell type. This mechanism is pivotal in patterning tissues such
as the nervous system trough the Delta-notch system.
Explain the concept of reaction-di usion systems as proposed by Alan Turing and its
application in pattern formation during development. How do activator and inhibitor
dynamics generate spatial patterns?
The Turing model explains how interactions between activators and inhibitors can lead to
spontaneous pattern formation in biological systems. Activators (Component A) promote
the production of certain substances (including themselves), while inhibitors (Component
B) suppress it. The di erential di usion rates of activators and inhibitors lead to the
emergence of stable patterns, crucial for processes like limb development and fur
patterning.
Outline the molecular pathway by which Wnt signaling a ects cell fate decisions and
tissue patterning. Include the roles of β-catenin and Frizzled receptors in the pathway.
Wnt signaling plays a critical role in cell fate decisions and tissue patterning by regulating
gene expression through β-catenin's stabilization and translocation into the nucleus.
Frizzled receptors mediate Wnt signal transduction, activating downstream pathways that
in uence development and cell di erentiatio .
Discuss the experimental approaches and ndings that led to the discovery of the
mesoderm induction and the role of Nodal signaling in this process. How does the
Nieuwkoop center contribute to axis formation?
Generally, mesoderm induction involves signals like Nodal, which are crucial for specifying
mesodermal fate during gastrulation. The Nieuwkoop center, located at the embryo's
vegetal pole, secretes factors that induce the adjacent cells to become the dorsal
mesoderm, initiating axis formation.

Stem cells - Martello

Self-Renewal and Di erentiation
Q: Discuss the dual capacity of stem cells for self-renewal and di erentiation. How does this
duality contribute to tissue regeneration and maintenance throughout an organism's life?
A: The document highlights stem cells' unique ability to both replicate themselves (self-renewal)
and di erentiate into various specialized cell types. This duality is crucial for the repair and
renewal of tissues, ensuring an organism's regenerative capability and maintaining homeostasis
over its lifetime.
Stem Cell Potency
Q: Explain the di erences between unipotent, multipotent, pluripotent, and totipotent stem cells.
Provide examples of each type and discuss their signi cance in developmental biology and
regenerative medicine.
A: It discusses the spectrum of stem cell potency, from totipotent cells capable of giving rise to an
entire organism, pluripotent cells that can give rise to any cell type from all somatic adult cells to
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 germ lines, to multipotent that can form multiple lineages however tissue restricted and unipotent
cells with more limited di erentiation potential to a single lineage. These distinctions underline the
diverse applications of stem cells, from basic research to potential therapeutic uses.
Embryonic vs. Adult Stem Cells
Q: Compare and contrast embryonic and adult stem cells in terms of their potency, proliferation
capacity in vitro, and potential applications in therapy.
A: The document compares embryonic stem cells (ESCs), which are pluripotent and derived from
the early embryo, with adult (or somatic) stem cells, which are typically multipotent and found in
speci c tissues. While ESCs have a broader potential for di erentiation and therapy, adult stem
cells are pivotal for tissue repair and regeneration, with fewer ethical concerns.
Clonality in Stem Cells
Q: What does clonality mean in the context of stem cells, and why is clonal analysis crucial for
proving a cell's stemness?
A: Clonality, or the ability of a single stem cell to give rise to a clone of cells through self-renewal
and di erentiation, serves as a fundamental proof of stemness. The document likely emphasizes
clonal analysis as a key method for identifying and validating stem cell properties, It can be a
qualitative and quantitative method.
Stem Cell Niches
Q: Describe the concept of the stem cell niche. How does the niche regulate stem cell function,
and what happens when stem cells are removed from their niche?
A: The niche concept is detailed as a specialized microenvironment that maintains and regulates
stem cell behavior, it is composed by TF, proteins and cells. Niches provide critical signals that
govern stem cell self-renewal, di erentiation, and quiescence. The disruption or alteration of these
niches can lead to diseases, including cancer.
Stem Cell Hierarchy
Q: Discuss the hierarchy observed in stem cell populations within tissues. How do transient
amplifying cells/progenitors t into this hierarchy, and what role do they play in tissue physiology?
A: It explains the organizational structure of stem cells within tissues, where stem cells at the top
of the hierarchy give rise to transient amplifying cells with limited self-renewal capacity, these
population of cells can be viewed as an intermediate population that are undi erentiated,
commited to di erentiation, have high proliferation rate but with limited lifespan because their
capacity of self renewal is limited. These progenitors then di erentiate into the mature cells of the
tissue, playing a key role in its function and regeneration. The stem cells hierarchy is
adavantageous because the presence of transient amplfying cells avoids the accumulation of
mutations in stem cells and makes the production of di erentiated cells more e cient.
Stem Cell Identi cation
Q: Detail the experimental approaches used to identify stem cells within a given tissue. How do
these techniques reveal the functional properties of stem cells?
A: The document outlines methods to identify stem cells, emphasizing functional characteristics
like self-renewal and di erentiation potential. Techniques such as uorescence-activated cell
sorting (FACS) and lineage tracing are pivotal for isolating and tracking stem cells within tissues.
Techniques to Identify Stem Cells
Q: Explore the various techniques mentioned for identifying stem cells, including labeling
techniques and surface antigen repertoire. How do these methods contribute to our
understanding of stem cell biology?
A: Techniques include speci c markers and the use of live-cell imaging to follow the behavior of
stem cells over time. These methods enable researchers to distinguish stem cells from
di erentiated cells and study their behavior in real-time.
Functional Analysis of Stem Cells
Q: Explain how in vivo transplantation, in vitro expansion, and di erentiation assays are used to
validate the stemness of putative stem cells. What do these analyses tell us about the cells'
capabilities?
A: By employing in vivo transplantation to assess the ability of stem cells to repopulate and repair
tissues, in vitro expansion to gauge their proliferative capacity, and di erentiation assays to test
their ability to give rise to diverse cell types, the document underscores these analyses as critical
for con rming the functional capabilities of stem cells.
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 Organoids from Stem Cells
Q: Discuss how organoids are generated from stem cells and their signi cance in studying tissue
development and disease. What does the ability to form organoids suggest about the potency
and self-renewal capacity of the originating stem cells?
A: The generation of organoids from stem cells is discussed as a revolutionary technique for
mimicking organ structure and function in vitro. This approach is signi cant for modeling
development and disease, as well as for drug testing and potential organ replacement strategies,
highlighting the vast regenerative potential of stem cells.

Mouse Development - Armadeo

What is somitogenesis, and why is it considered a key process in the transition from
the egg cylinder structure to the actual body plan?
Answer: Somitogenesis is a critical process for transitioning from an egg cylinder structure to a
de nitive body plan, forming repetitive segmented structures like vertebrae, ribs, and associated
muscles, which are substantial for the body plan.
Describe the precursor structures to somites and their signi cance in the mouse embryo.
Answer: In mouse embryos, somites appear as repetitive units along the trunk and developing tail,
emerging from neuro-mesodermal precursors (NMPs) expressing Sox2, Bra, and Cdx1/2/4, located
in the caudal lateral epiblast. These NMPs possess both neural and mesodermal potential, leading
to the formation of neural and mesodermal progenitors contributing to the hindbrain, posterior spinal
cord, and presomitic/paraxial mesoderm.
Explain the role of neuro-mesodermal precursors (NMPs) in somite formation, including the
genes they express and their potential.
Answer: NMPs, positioned at the intersection of the neural plate and future spinal cord, express a
combination of neural and mesodermal genes. They are pivotal for contributing to both neural and
mesodermal tissues, indicating their essential role in somite formation.
Discuss the conservation of somitogenesis across species and how it affects the timing and
number of somite formations.
Answer: The process is highly conserved across species, indicating its fundamental role in
vertebrate development, affecting the timing and number of somites formed, which varies among
species, yet follows a conserved ordered manner.
What is the "determination front" in somitogenesis, and how do FGF and WNT signaling
in uence it?
Answer: The determination front in somitogenesis is where cells transition from an undifferentiated
state in the presomitic mesoderm. FGF and WNT signaling are crucial for positioning this front,
affecting somite formation pace and differentiation.
Explain the concept of the "segmentation clock" and its importance in somite formation.
What factors contribute to its oscillatory expression pattern?
Answer: The segmentation clock, generating oscillatory waves of gene expression in the presomitic
mesoderm, is vital for timing and periodic somite segmentation. Factors like Notch, Wnt, and FGF
pathways contribute to its oscillatory behavior.
How does the interaction between the segmentation clock and the determination front lead to
somite speci cation?
Answer: The interaction between the segmentation clock and the determination front is crucial for
somite speci cation, with the clock determining timing and the front de ning segmentation positions.
Describe the process by which somites differentiate from the presomitic mesoderm (PSM),
including the role of Mesp2 and EPHA4.
Answer: Somites differentiate from the PSM through the regulation of boundary formation by Mesp2
and the segmentation process and anterior-posterior polarity establishment by EPHA4.
How are somites patterned into dermatome, myotome, and sclerotome, and what signaling
molecules in uence this patterning?
Answer: Somites are patterned into dermatome, myotome, and sclerotome in uenced by signaling
molecules such as Sonic hedgehog (Shh) from the notochord and oor plate, and Wnt and BMP
signals from the ectoderm, guiding their differentiation into speci c tissue types.
Discuss the implications of alterations in FGF signaling on the size of somites and how
somitogenesis research has evolved with in vitro models.
Answer: Alterations in FGF signaling can impact somite size and differentiation, leading to potential
developmental issues. In vitro models have advanced somitogenesis research, helping to unravel
the complex signaling interplay that regulates this developmental proces .
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 Stem Cells:
• How do the intrinsic and extrinsic factors interact within the stem cell niche to
in uence stem cell fate decisions, and what implications does this have for
tissue regeneration and repair?
he stem cell niche is a specialized microenvironment that regulates stem cell behavior
through a combination of intrinsic factors (gene expression pro les, epigenetic marks) and
extrinsic factors (cell-cell interactions, signaling molecules). This interaction determines
whether stem cells undergo self-renewal or differentiation, crucial for tissue repair and
regeneration. Manipulating these factors could enhance regenerative therapies by
directing stem cell fate.
• Discuss the role of pluripotency factors (e.g., OCT4, SOX2, NANOG) in
maintaining stem cell identity. How does the manipulation of these factors
contribute to the generation of induced pluripotent stem cells (iPSCs) and
their potential applications in regenerative medicine?
Pluripotency factors such as OCT4, SOX2, and NANOG are essential for maintaining the
undifferentiated state of stem cells. Their manipulation is central to reprogramming somatic
cells into iPSCs, offering a potential unlimited source of patient-speci c cells for
regenerative medicine, disease modeling, and drug screening.
Development:
• In the context of embryonic development, how do morphogen gradients
establish the body axes, and what experiments have elucidated the
mechanisms by which cells interpret these gradients to differentiate into
speci c cell types?
Morphogen gradients provide positional information that cells use to differentiate into
speci c cell types, establishing the body axes during embryonic development. Key
experiments using Drosophila and vertebrate models have shown how cells measure
gradient concentration over distance to make fate decisions, involving gene expression
changes triggered by threshold levels of morphogens.
• Explain the concept of cellular competence in development. How does a cell's
ability to respond to inductive signals change over time, and what are the
molecular underpinnings that govern these changes?
Cellular competence refers to a cell's ability to respond to developmental cues, which
changes over time due to alterations in receptor expression, signaling pathway
components, and transcriptional regulators. This dynamic capability ensures that cells
follow the appropriate developmental trajectory, responding correctly to inductive signals at
different stages.
Mouse Development and Somitogenesis:
• Describe the process of somitogenesis in mouse development. How does the
segmentation clock contribute to the periodic formation of somites, and what
are the key molecular players involved in this process?
Somitogenesis involves the sequential segmentation of the presomitic mesoderm into
somites, regulated by the segmentation clock—a network of oscillating gene expressions.
This clock ensures the periodic formation of somites, with Notch, Wnt, and FGF pathways
playing crucial roles in maintaining its rhythm and coordinating somite formation and
differentiation.
• Investigate the role of Wnt signaling in mouse embryonic development,
particularly in the formation and differentiation of the mesoderm. How does
Wnt signaling interact with other pathways (e.g., FGF, Notch) to orchestrate
somitogenesis and subsequent tissue patterning?
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 Wnt signaling is pivotal in mesoderm formation and differentiation during mouse
development, interacting with FGF and Notch pathways to regulate somitogenesis. It
in uences cell fate decisions, tissue patterning, and the establishment of the anterior-
posterior body axis, demonstrating its central role in early embryonic development and the
formation of structured tissues.

Signaling Pathways and Their Roles:

Notch Signaling Pathway
Role in Development: Integral for cell fate determination, differentiation, and
maintenance of stem cells. It plays a crucial role in somitogenesis, in uencing the
segmentation and patterning of embryonic development.
Action in Different Species: The Notch pathway's function in somite segmentation
is conserved across vertebrates, affecting the precise timing and formation of
somites in species ranging from sh to mammals, including mice and humans.
Wnt Signaling Pathway
Role in Development: Wnt signaling is essential for stem cell maintenance,
particularly in tissues like the intestinal epithelium, and is crucial for early embryonic
development, including axis patterning and organogenesis.
Action in Different Species: The pathway's role in controlling cell fate and
proliferation is conserved, with its impact seen in diverse organisms, from
Drosophila to humans, indicating its fundamental role in developmental processes.
FGF (Fibroblast Growth Factor) Signaling Pathway
Role in Development: FGF signaling is key for somitogenesis, affecting the
differentiation and proliferation of cells in the presomitic mesoderm. It also plays a
signi cant role in limb development and neural induction.
Action in Different Species: The role of FGF signaling in development is widely
conserved, with its effects on somite formation, neural development, and limb
patterning observed across species, including zebra sh, chicken, and mammals.
Retinoic Acid (RA) Signaling Pathway
Role in Development: RA signaling regulates the anterior-posterior axis,
somitogenesis, and neural differentiation. It antagonizes the action of FGF and Wnt
signaling to ne-tune developmental processes.
Action in Different Species: The role of RA in patterning the vertebrate embryo is
conserved, with its involvement in axis patterning and organogenesis observed in
species from sh to humans, demonstrating its critical role in vertebrate
development.
Precursors and Context:
Neuro-Mesodermal Precursors (NMPs): These cells, expressing genes like Sox2, Bra,
and Cdx1/2/4, are pivotal in somitogenesis, giving rise to the somites and neural
structures. The induction of NMPs and their differentiation is in uenced by FGF and WNT
signaling, highlighting the integrated nature of developmental signaling pathways.
Conservation Across Species: The document emphasizes the conservation of
somitogenesis and the roles of these signaling pathways across species. While speci c
genes and the timing of developmental events may vary, the fundamental processes and
signaling mechanisms are remarkably conserved, underscoring the shared evolutionary
history of vertebrate developmen .
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