Download Week 7 Pre-Lecture Slides

Monday February 13th, 2017
Class 24 Learning Goals
Differentiation and Organogenesis
(case study: Drosophila)
• After this class, you should be able to:
• Identify cases of cellular differentiation and explain the evidence
that supports this conclusion
• Develop a narrative to explain the molecular mechanisms of
differentiation in a particular cell or small group of cells
• Evaluate the likelihood of molecular and cellular events in different
parts of organogenesis
Peer Instruction
All fates possible
No structures built
Differentiation
Role determined
Mitosis, signaling, construction, etc
1 fate possible
Specific structures
1) Where are the cells that are most differentiated?
2) Which cells have the
most possible fates?
3) Do these cells
have the same DNA?
4) How are differentiated
cells different?
Peer Instruction
A zygote
Stage 1
Does this cell have all possible DNA?
Are all possible genes being expressed?
Is this cell playing a final functional role or fate?
An adult
Does this cell have all possible DNA?
Are all possible genes being expressed?
Is this cell playing a final functional role or fate?
Analyze this 8-cell organism.
How are different cell fates determined?
Peer Instruction
gib2
Stage 1
Stage 9
Peer Instruction
Arrows indicate directional mitosis.
Letters are example genes turned on in this cell.
gib2
gib2
Stage 1
gib2
gib2
gib2 gib2 gib2
tgg3 tgg3
Stage 2
Stage 3
zzk1 plub8
tgg3
tgg3
ipl6
ipl6
gib2
ipl6 ipl6
gib2
hr9
Stage 4
ipl6
thh4 thh4
hr9
ipl6 gib2
gib2
Stage 5
zzk1
Stage 6
s2cc zzk1
zzk1
plub8
thh4
thh4
thh4
hr9
hr9 hr9
Stage 7
thh4
hr9
Stage 8
Stage 9
Peer Instruction
Between which stages is mitosis occurring?
gib2
gib2
Stage 1
gib2
gib2
gib2 gib2 gib2
tgg3 tgg3
Stage 2
Stage 3
zzk1 plub8
tgg3
tgg3
ipl6
ipl6
gib2
ipl6 ipl6
gib2
hr9
Stage 4
ipl6
thh4 thh4
hr9
ipl6 gib2
gib2
Stage 5
zzk1
Stage 6
s2cc zzk1
zzk1
plub8
thh4
thh4
thh4
hr9
hr9 hr9
Stage 7
thh4
hr9
Stage 8
Stage 9
Peer Instruction
The cells in stage 3 are all the same
size and shape. How are they different?
gib2
gib2
Stage 1
gib2
gib2
gib2 gib2 gib2
tgg3 tgg3
Stage 2
Stage 3
zzk1 plub8
tgg3
tgg3
ipl6
ipl6
gib2
ipl6 ipl6
gib2
hr9
Stage 4
ipl6
thh4 thh4
hr9
ipl6 gib2
gib2
Stage 5
zzk1
Stage 6
s2cc zzk1
zzk1
plub8
thh4
thh4
thh4
hr9
hr9 hr9
Stage 7
thh4
hr9
Stage 8
Stage 9
Peer Instruction
There are many Hox genes that act
as transcription factors for
particular organs.
FRUIT FLY
Is it unusual to see great
similarity in protein sequence
between similar Hox genes
in different species?
Is it surprising to see Hox
genes lined up in spatial order
on a single chromosome?
Head
Thorax
Abdomen
MOUSE
Peer Instruction
Explain how gene expression changes the results of
organogenesis in this region of the chicken embryo.
Forelimb
Chick
embryo
Forelimb
In the areas where Hoxc6 and Hoxc8
are expressed together, ribs form
Hoxc8
Hoxc6
Tuesday February 14th, 2017
Class 25 Learning Goals
Cellular Signaling
• After this class, you should be able to:
• Propose an appropriate method of cell signaling for use
by a given organism and situation
• Describe the protein-protein interactions needed within a
signaling system and predict the effects of stronger or
weaker binding based on system details
• Predict the source of and reason for a maternal
determinant
Peer Instruction
1) Explain how lipid soluble signals work.
Steroid
hormone
Plasma
membrane
2) Why is this
‘the easy way’?
2) What is a downside
of using a signal that
can enter any cell?
Receptor
in cytosol
Nuclear
membrane
Nucleus
Target gene DNA
Peer Instruction
Intercellular
signal
1) How do membrane signal
receptors work?
Outside of cell
Receptor protein
in membrane
Inside of cell
2) What is signal
amplification?
Second messengers
Intracellular
signals
Peer
Peer
Instruction
Instruction
1) Does a single cell
have just one type
of receptor?
2) What do all signal
pathways share in
common?
Peer Instruction
What is a
‘ligand?’
Peer Instruction
What other signal-sending mechanisms do plants have?
Smooth
endoplasmic
reticulum
Tubule of ER passing through
“plasmodesmata”
Gap
junctions
Membrane proteins
from adjacent cells
line up to form
a channel
Peer Instruction
Why is it advantageous for sea
urchin eggs to release a signal
for sperm to follow?
Is this signal molecule likely to
be a small or large molecule?
Egg
What happens at the sperm
when a ligand is received?
What happens to the sperm after it binds
to the outer jelly coat layer of the oocyte?
Y
Peer Instruction
Peer Instruction
How does the oocyte protect itself against polyspermy?
Vesicles full of carbohydrates
Vesicles moved
towards membrane
High
osmotic
gradient
Peer Instruction
How does the oocyte protect itself against polyspermy?
You may observe this in next week’s lab.
Gene Mutated
Normal location of
the protein
Fertilzation rate
of mutant
Other phenotype?
Small protein from
oocytes
Released from
oocyte
21.3%
Fertilization in test
tube is 100%
“Bindin” receptor
protein
Exterior of sperm
membrane
4.4%
Sperm can pass jelly
coat layer easily
“Resact” receptor
protein
Exterior of sperm
membrane
21.3%
Fertilization in test
tube is 100%
Sperm-specific
receptor protein
Exterior of sperm
membrane
8.5%
Sperm on vitelline
envelope fertilize well
Fertilizin receptor
protein
Exterior of oocyte
vitelline envelope
4.4%
Sperm reach vitelline
layer easily
Jelly coat proteins
Forming jelly coat
layer on oocyte
8.5%
No visible difference in
oocyte layers
Wild-type sperm
and oocytes
n/a
100%
Sperm find oocyte and
reach vitelline
envelope layer quickly
Peer Instruction
Analyze this data.
Blocking polyspermy, The Calcium Wave
Blocking polyspermy, Fertilization Membrane Pulls Away
This clears other sperm away from the plasma
membrane by ~6 seconds after sperm entry
Blocking polyspermy, the Fast block
• The egg is still vulnerable to polyspermy in
the first few seconds
– Especially problematic with many sperm
reaching the jelly coat at nearly the same time
• The ‘Fast Block’ system uses the change
in membrane potential in the egg to help
protect against a second sperm
– Change in membrane potential rapidly and
temporarily distorts fertilizin structure
– This inactivates all fertilizin molecules for ~6
seconds
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Cell-to-Cell Signaling
• We’ve already talked about cell-to-cell
signaling several contexts,
– Growth factors, hormones, secreted proteins, etc
• There is a vast array of cell signaling methods,
which include
–
–
–
–
–
Lipid-soluble signals
Cell-to-cell contact mediated by receptors
Signal receptors
Second messengers and enzymes
Direct cytoplasmic contact
–A quick tour is in order…
Wednesday February 15th,
2017
Class 26 Learning Goals
Determinants (case study: fruit fly ovary)
Proliferation (case study: cleavage)
Apoptosis (case study: caspase)
Migration (case study: gastrulation)
• After this class, you should be able to:
• Propose several potential uses for cell proliferation,
apoptosis or cellular migration in a developing organism
• Predict a likely cleavage pattern based on adult body plan
• Connect logical reasons for apoptosis to potential chemical
cues by a cellular signaling pathway
• Describe a gastrulating embryo in terms of movements of
large numbers of cells
Follicle cell
Oocyte
Nurse cell
This is a confocal microscope image of an ovary
inside of a female fruit fly.
The oocyte, like a human oocyte, is supported
as it grows by a number of surrounding cells.
Peer Instruction
Why is it advantageous for a mother’s cells to provide
extra nutrients for an oocyte?
How can this maternal determinant molecule give
information to the new zygote that isn’t in the zygote DNA?
When are maternally-provided molecules most useful?
Early in development?
Late in development?
Why are paternal determinant molecules relatively rare?
Peer Instruction
In a few words:
What is happening
in this organism?
Why is this early stage called ‘cleavage’?
Besides development, where might
we expect to find cell proliferation?
Explain the mechanism of cleavage in each example.
Radial cleavage:
Example:
Spiral cleavage:
Discoidal cleavage:
Peer Instruction
Example:
Example:
Yolk
Superficial cleavage:
Example:
Cells
Yolk
Un-separated nuclei
Why would an adult multicellular organism
intentionally destroy a few of its own cells?
How does apoptosis help to develop
the structure of this paw?
Peer Instruction
Peer Instruction
Frog Gastrulation
Ectoderm
Mesoderm
Endoderm
Blastocoel
Dorsal lip
Cross section
Blastopore
Pre-Gastrulation
Whole embryo
Explain these cell movements.
Initial Gastrulation
Blastopore
Frog Gastrulation
Ectoderm
Mesoderm
Endoderm
Presumptive gut
Cross
section
Whole
embryo
What is happening here?
Proliferation
Apoptosis
Migration
Differentiation
Signaling
Thursday February 16th, 2017
Class 27 Learning Goals
Abiotic Parasites
• After this class, you should be able to:
• Describe the important roles for genes and mechanisms in
SINES, LINES, viruses and retroviruses
• Predict the effect on viral survival of human mutations
• Compare the timescales of abiotic parasite evolution, viral
evolution, anti-viral human evolution, viral infection and viral
entrance into a host cell
Peer Instruction
Transposons are small regions of a chromosome that happen to code
for proteins that move that DNA to other regions of the chromosome.
A mutation in a transposon causes increased production of similar
transposons. Will evolution select for or against this mutation?
How do transposons increase their population?
Can transposons cause harmful mutations for the host?
Peer Instruction
How do Long Interspersed Nuclear Elements make new copies?
Gene for reverse transcriptase
Gene for integrase
Cytoplasm
“Parent” LINE
Translation
Transcription
LINE
protein
LINE mRNA
RNA polymerase
Ribosome
LINE mRNA and LINE proteins
Reverse transcriptase
Integrase
cDNA
Reverse
transcriptase
mRNA
Integrase
Original “parent” copy
New copy
Insertion of
“Daughter” LINE
How many of them are there?
98% similar
Fraction of the genome made of
transposons (or remnants of them):
• Maize: 49-78%
• Wheat: 68%
90% similar
75% similar
• What does it means to say
that viruses are:
– Acellular
– Obligate parasites
– Diverse
A bacterial cell (E. coli)
How many genes does a circovirus have?
Peer Instruction
Circovirus
ssDNA
genome
(1700 bp)
What does the circovirus capsid gene encode?
This bacteriophage has more genes than a
circovirus. Every virion is heavier and more
expensive. What advantage does this phage
get from these genes?
Peer Instruction
Why is it worth it to the Ebola virus to spend
energy to create envelope, matrix and
nucleocapsid proteins?
What parts of the Ebola virion
give it the ability to specifically
target human cells?
Peer Instruction
Explain how HIV infects a cell.
Viral protein
Enveloped virus
Host protein
Envelope (lipid bilayer)
Genome
(in this case,
RNA)
Capsid (protein)
…about 10 billion virions produced daily
Peer Instruction
HIV has virion proteins that interact specifically with T-cell
membrane proteins. Why is this advantageous for HIV?
HIV increases transcription when
T-cells are most active.
Why is this advantageous for HIV?
T-cell DNA:
Activation TF
P
HIV Genome:
Gag, Pol, Env
P
Viruses: Disease history
• The last 1,000 years:
– Smallpox and measles: High lethality destroyed
colonized native cultures worthwide.
– Influenza and common rhinoviral colds are likely to
have killed more humans than any other cause
• The past 100 years:
– 1906: Viruses can cause cancer?
– 1918: a new strain of influenza
• killed >50 million people
• was the most lethal combatant of WWI
• reached almost every population in the world
•
– 1930s (and again in 2010s): polio outbreaks
– 1970s: HIV
The past 10 years:
– SARS, avian flu and swine flu viruses threaten to make
the jump from animals to humans to pandemic activity
– Ebola
• Current outbreak is largest on record & first North American case