How do cells and tissues organize themselves spatially?
Lecture 1: Membrane trafficking
Basic Principles of the Biosynthetic-Secretory and Endocytic Pathways
o Polarized trafficking routes (proteins travel directly from one place to next)
Start at the same place, materials being continuously budding off
from the vesicle
Regulated secretary pathway
The vesicles are regulated, the cells tells the vesicle when to
o Sorting stations (bus stations of the cells)
o Retrieval mechanism and general balance among routes (buses need to route
The concentration of cargo increases as it being budding off
o Polarized transport route with the retrieval route
Some components are taken back to the Golgi.
o Cells collect resources by endocytosis (e.g. cholesterol)
Cholesterol in the fluid outside the cell is bound to LDL, cells have LDL
receptors. Once grabbed on, placed into endocytosis pits and get
internalized inside the cell, it targets to the sorting station. (receptors are
recycled, but the cholesterol are targeted to the lysosome)
o Cells down regulate cell surface signaling by endocytosis
The cell can pull the entire receptor complex inside the cell, after
endocytosis, thru specific soring; it can be converted to a multi-vesicular
body. And the vesicle inside the vesicle is targeted by lysosome.
Local membrane changes occur during this trafficking
o Fusionvesicles fusing with the membrane
v-SNAREs and t-SNAREs bring the two membranes together.
Forced the membrane so close so there’s no water in between.
o Invaginationmembrane bending in, towards the cytosol.
Clathrin & Dyamin
Clatherin forms a rounded coat, this drives the vesicles inward.
Dynamin curl around the neck of the protein, forces them, exclude
the water, and promote the cells separate. Act similar to SNAREs.
COPI and COPII
o Budding moving from one cytoplasmic space to another
Push the local plasma membrane outwards and then pinch it off to
release the virus outside the cell. Membrane invagination, fusion and budding events occur at specific sites in the system to
control polarized trafficking and retrieval
Control of specificity in polarized trafficking
o Inositol phospholipids
inositol sugar head group can be phosphorylated at the hydroxyl group
Kinase add phosphate group
Phosphatasesremove phosphate group
Each phosphoinositide species binds to specific proteins
o Rab GTPase
GEFexchange GDP to GTP
GAPexchange GTP to GDP
Rab5Aplasma membrane, clathrin-coated vesicles, early
Rab7 late endosomes
Rabs are recruited to specific membranes by RabGEFs, their activation promotes
Lecture 2: Cytoskeletal networks
o Each protofilament is made up of β-tubulin, α-tubulin
o γ-tubulin, complexes nucleate microtubules
Minus end connect γ -tubulin, and the plus end grow outside
cap of GTP-bound tubulin
o Forms like a tubes, 13 filaments, dynamic instability
o Coordinate system
A purified centrosome was mixed with purified tubulin subunits in an
artificial membrane-bound container. It moves to the centre of the
container as microtubule plus ends push on the outer membraneminus
ends central/plus ends outwards
Motor move cargo through the microtubule networks
o Dyneinminus end directed (move towards centre)
o Kinesinplus end directed (move outside) o The microtubule network is very dynamic and can be reorganized
The actin cytoskeleton is inherently polarized (Subunitfilamentsnetwork)
o Monomers, binds to ATP, there are enzymes hydrolysis ATP when it enters the
o Asymmetric (structurally different). Forming helical structure, head to tail.
o Polarized assembly and disassembly leads to treadmilling
Treadmilling actin networks need traction to drive cells forward
A stationary anchor binds one part of the filament.
o The ARP complex nucleates actin filaments and branches actin filaments to form
polarized 2-D networks.
In animals, cells migrate on (and through) the extracellular matrix, a non-cellular material
made of proteins and polysaccharide
o Integrins connect the actin cytoskeleton to extracellular matrix molecules
Subunits of integrins liked to the actin cytoskeleton via adaptor
o Chemoattractant receptors orient the actin networks
Extracellular signal control the behavior of the cell. Chasing the cells,
the bacterium emits small molecule, and host (immune cells) has
receptors to recognize them. A gradient of chemotractin created,
activated the receptors. Activated the ARP complex. turn on the actin
Actin networks can undergo other large scale rearrangements
o Localized assembly of the contractile ring that divides daughter cells after mitosis.
Lecture 3: Cell adhesion
Cells are organized into one of two main tissue categories
o Epithelial tissuedirect connected with minimal extracellular matrix beneath
More than 60% of the cell types in the vertebrate body are epithelial.
Lumen of gut
o Connective tissuedispersed with extracellular matrix providing overall structure
o From apical to basal
Tight junctionadherens junctiondesmosomegap junction
Adherens junction structure
o Adherines junctions form strong continuous adhesion belts
o Cadherin clusters mediate the adhesion
Hemophiliac interaction between cadherin receptors
Links to actin cytoskeleton
o Tissue maintenance during development
Sheet of cells flowing around, they can adhere together and also allow
rearrangement to occur
o Tumour suppression
The loss of epithelial structure is a hallmark of cancer
Cadherins are tumour suppressors
Tight junctions enclose the apical end of each cell in an epithelial sheet
4-pass transmembrane protein
Tight junction formation, assembles the structure but leaky
4-pass transmembrane receptor
Required for barrier function
Importance of epithelial structure
o Epithelial polarity controls solute diffusion between our body compartments
Cell Polarity is Fundamental to Cell and Developmental Biology
Sperm entry provides the landmark of the cell, cue to break symmetry, the
flow of cytoskeleton from the cell.
Different anterior posterior cues, different side of the cell determines
different functions of the cell, one side destined to become one sets of
o Adherens junctions (AJs) are important landmarks for epithelial polarity
More polarities form downstream of it, cue apical cues. Mutually
antagonist relationship with the basal lateral domains
How do multicellular organisms develop?
Lecture 4: Tissue morphogenesis
o Surface cells are continuously flakes off, and replaces.
Mammary gland epithelia
o Mammary gland develops alveoli; these ducts are simple epithelial sacs.
o Begin with blastocyst (simple, hollow cell).
o Trophectoderm: outside, not embryonic, supply tissue for placenta
Internalization of cells
Ectodermepidermis/nervous system (outside)
Mesodermmuscles/connective tissue/blood vessels (middle) Endodermgut/lung/liver (inside)
Mechanisms of cell internalization
Epithelial-to-mesenchymal transitions the epithelium are breaking off
and migrating inside,
Epithelial-to-mesenchymal transitions are tightly regulated during
normal developmentQuail/chick cells
Polarity direct actin and myosin to the top. Constrict the top of the
cellSeries of rectangular cells becoming more pyramidal. Bend the
Neural tube development
ventral expression of a transcription factor called Twist specifies
the cells to undergo mesoderm internalization in Drosophila
Elongation of the embryo
Mechanisms of embryo elongation
o Convergent extension
Cells converging toward the midline, as the cells converging. The
overall structure is extended.
o Cell division and cell shape change
At the tip of the root, there is a zone of cell division, dividing
rapidly, there are nowhere the daughter cells forms, and it will be
The orientation of cell elongation is regulated by the orientation of
cellulose microfibrils and driven by driven by turgor pressure
Elongation of gut villi
Fine repositioning of cells
o Cell sorting
Germ cell layers
Take three early germ layer, and randomly mix them. Leave them
they will sort out back.
Differential cadherin expression and cell sorting and the patterning of the
The homophilic adhesion between cadherins may group specific
o Directed cell migration
Cell migration in the cerebral cortex
The neuron migrates to the midline, and move in a highway to the
brain thru floor plate. Creating the spinal cord.
o The growth cone at the tip of the axon. Similar to immune
cell chasing bacterium. Secretion of chemical from the
midline, where the embryo is directing the cell to go.
Forming a gradient, growth cone has receptors to receive signal, forming actin framework of chemical from the
Lecture 5: Tissue patterning
o Asymmetric cell division
Sister cells are born different, a polarity is gained. When this cell
divide, one cell gains material different from the other cell.
Requires cortical polarity & proper spindle alignment
o Direct lateral inhibition
Lateral inhibition by Notch signaling
Mechanisms involve interaction between 2 trans-membrane
proteins, one being the ligand (Delta). They are both connected
to plasma membrane, hence local interaction. Only cell in
direct contact can be affect. Start with low differentiated state.
The ligand Delta binds to Notch receptors, this inhibit the cell
from differentiating, also inhibits the inhibitory signal being
sent back to the other cell. Both protein in expressed. Low
level inhibition across the field.
When one of the gain an advantage (increase slightly activity).
Sent a stronger signal, it will shut down the inhibitory signal,
inhibited the inhibitory signal, and it gets even stronger. It goes
thru this cycle until it completely shut off.
o Induction by diffusible signals
Morphogens and organizers
Secreted molecules are called morphogens. The morphogens
concentrations dictate cell fate. you can have the same
molecules, but with different gradients, high gradients will
have a different pattern with low gradients
o Organizer function in vertebrate limb development
Mechanism is control by the polarizing
organizer region. The source of the morphogen
is called sonic hedgehog (Shh). The expression
of the gene is expressed and spread as a gradient.
o “Organizer” tissues act as morphogen sources
o Regulatory hierarchies refine patterns of cell differentiation to create
Gap gene: Kruppel
Segment-polarity gene: Gooseberry
HOX genesSpecifies which part develops into what.
o “Antennapedia” (Antp)
the mutated gene cause legs to growing in the position of the antenna o Order of the gene position on the chromosome is the same order they are
expressed on the animal body.
o Hox genes encode transcription factors with different targets in different
Drosophila vs. Dragon fly
Lecture 6: Stem cells
o auditory hair cells
Vibration in the fluid pushes the tectorial membrane, this pushes the
top of the sensory cells, they have the projections called stereocilia,
then tectorial membrane push on them, and they bend. Sound causes
the sterocilia to tilt. When they tilt, this affect one tether, cadherin
adhesion molecules undergoes hemophilic cell-to-cell adhesion.
cadherin pull on the lid of the channel, and opens the lid of the channel,
this allow ions to flow, induced action potentials, then the AP travels
thru the neuron
Stereocilia are filled and supported by actin, the actin undergoes
continually polarized treadmilling.
o photoreceptor cells
The photoreceptors are at the back of the eye, connecting to nerve cells.
Converts photons to nerve impulses.
Cell exposed to radio-labeled leucine for a short time period of
time. Radioactivity that can be detected, because it's leucine, so
it can incorporated into protein. By monitoring the radio
activity, it will either be detect in the cell for a lifetime, or it
will be lost gradually.
o Extracellular example of molecular turnover: bone
Osteoclastcontinuously eating the bone away
o Stem cell dependent
One daughter receives factors promoting “stemness”, and the
other receives factors promoting differentiation
o Problemif stem cells are lost, their original numbers
cannot be restored
The daughter's fate is dependent by the environment they are
born into. One received the environment signal to maintain
stemness. The other is actually pushed to another environment,
received signal promote terminal differentiation.
o Can lose stem cells, and remain them in the stem cell
environment, to have the daughter cell to be stem cells
again Stem cells divide slowly
Cell division can create mutation
Telomere depletion associated with cell division
o Therefore, transit amplifying cells expand cell numbers before final
differentiation, they expand their numbers before they differentiated, so even
when stem cells divide slowly, they can divide rapidly
o basal lamina provides a niche for the stem cells
After detaching from the basal lamina, the cells differentiate through a
linear sequence of cell types and are finally shed from the animal
o Blood stem cells differentiate into various populations creating a branched
pathway to final differentiation
o Blood stem cells and their progeny reside in bone marrow
Homogenize mouse bone are expose to fluorescent antibodies
recognizing specific cell surface molecule, then the labelled cells are
isolated by Fluorescence-Activated Cell Sorting (FACS)
o Blood stem cells are maintained through interactions with stromal cells in the
bone marrow (osteoblast)
Stem cell independent
o liver cells and insulin-secreting cells of the pancreas
Medical uses for stem cells
o Embryonic stem (ES) cells can proliferate indefinitely in culture and have full
Take cells from early embryo, cultured them and add mimicry signals
to make them grow into different cells
This can increase the yield of cells needed for treatments, but ethical
issues, immune rejection and the potential of cancer are still concerns
o Two potential ways to avoid immune rejection of ES cells
Somatic cell nuclear transfer: use a nucleus from one of the patient’s
own cells and transfer it into an unfertilized egg to develop an embryo
from which ES cells can be harvested
Treat some of the patient’s own cells with factor known to specify ES
cell character (e.g. a combination of Oct3/4, Sox2, Myc and Klf4 can
convert differentiated cells into cells with ES cell characteristics) How do cells communicate with each other?
Lecture 7: Principles of cellular signalling
Examples of unicellular communication
o Quorum sensing in bacteria
Many bacterial cells can emit signals into the extracellular space,
coordinates motility, production of antibiotics, sexual relations.
o Mating in budding yeast
o Aggregation of ameboid cells
aggregate together when no food available, form a fruiting body, and
move to a place with food
The basics of sending and receiving signals
o Signaling occurs over short or long distances
signals are retained on the cell surface (Notch-Delta signalling)
Molecules diffuse away to surrounding cells, but only diffuse
in a short distance
o Signaling occurs over short or long distances
Neurons extend ax