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1
Last
lect
ure
toda
y !
Fina
l due
toda
y in
cla
ss o
r 13-
2042
(< 3
PM
)
2
I Sys
tem
s M
icro
biol
ogy
(13
Lect
ures
)
‘The
cel
l as
a w
ell-s
tirre
d bi
oche
mic
al re
acto
r’
L1In
trodu
ctio
nL2
Che
mic
al k
inet
ics,
Equ
ilibr
ium
bin
ding
, coo
pera
tivity
L3La
mbd
a ph
age
L4S
tabi
lity
anal
ysis
L5-6
Gen
etic
sw
itche
sL7
-9E
. col
i che
mot
axis
L10-
11G
enet
ic o
scill
ator
sL1
2-13
Sto
chas
tic c
hem
ical
kin
etic
s
3
II S
yste
ms
Cel
l Bio
logy
(9 L
ectu
res)
‘The
cel
l as
a co
mpa
rtmen
taliz
ed s
yste
m w
ithco
ncen
tratio
n gr
adie
nts’
L15
Diff
usio
n, F
ick’
s eq
uatio
ns, b
ound
ary
and
initi
al c
ondi
tions
L16-
17Lo
cal e
xcita
tion,
glo
bal i
nhib
ition
theo
ryL1
8-19
Mod
els
for e
ukar
yotic
gra
dien
t sen
sing
L20-
21C
ente
r fin
ding
alg
orith
ms
L22-
23 M
odel
ing
cyto
skel
eton
dyn
amic
s
4
III S
yste
ms
Dev
elop
men
tal B
iolo
gy (2
Lec
ture
s)
‘The
cel
l in
a so
cial
con
text
com
mun
icat
ing
with
neig
hbor
ing
cells
’
L23
Quo
rum
sen
sing
L25
Dro
soph
ila d
evel
opm
ent
5
Mai
n ta
ke h
ome
mes
sage
s fro
m th
is c
ours
e:
1. tr
ansl
ate
the
biol
ogy
into
a q
uant
itativ
e m
odel
:gi
ven
the
biol
ogy
set u
p th
e co
uple
d di
ffere
ntia
leq
uatio
ns th
at c
aptu
re th
e es
senc
e of
the
biol
ogic
al p
heno
men
a
(not
triv
ial s
ince
4 p
aper
s ca
me
up w
ith a
diff
eren
tm
odel
giv
en th
e sa
me
biol
ogic
al p
heno
men
on,
whi
ch a
ssum
ptio
ns to
mak
e is
crit
ical
)2.
ana
lysi
s of
the
syst
em o
f diff
eren
tial e
quat
ions
stab
ility
ana
lysi
s (b
oth
in s
pace
and
tim
e)3.
inte
rpre
tatio
n of
the
mat
hem
atic
al a
naly
sis,
wha
t are
the
biol
ogic
al c
oncl
usio
ns ?
e.g.
if th
e im
agin
ary
part
of th
e ei
genv
alue
is n
on
zero
, wha
t doe
s th
is m
ean
for t
he u
nder
lyin
g bi
olog
y?
4. d
evel
op a
tast
e fo
r the
pot
entia
l of t
hese
sys
tem
s ap
proa
ches
for b
iolo
gica
l pro
blem
s th
at y
ou m
ay
enco
unte
r in
the
futu
re6
Dev
elop
men
tal S
yste
ms
Bio
logy
‘Bui
ldin
g an
org
anis
m s
tarti
ng fr
om a
sin
gle
cell’
Intro
duci
ng: D
roso
phila
mel
anog
aste
r(o
r the
frui
tfly)
Gre
at b
ook:
‘The
mak
ing
of th
e fly
’ by
Pet
er L
awre
nce
78
9
maj
or a
dvan
tage
of
Dro
sphi
la:
each
stri
pe in
the
embr
yo c
orre
spon
dsto
cer
tain
bod
y pa
rtsin
adu
lt fly
10
egg
(con
tain
s m
ater
nal c
ompo
nent
s,m
ater
nal e
ffect
s, o
nly
dete
rmin
ed b
y m
othe
r, R
NA
, pro
tein
s)
zygo
te (c
onta
ins
DN
Afro
m fa
ther
and
mot
her,
zygo
tic e
ffect
s)
11ea
rly d
evel
opm
ent
nucl
ei fo
rmpl
asm
a m
embr
ane
MO
VIE
!ht
tp://
flym
ove.
uni-m
uens
ter.d
e
12
Pio
neer
ing
expe
rimen
ts b
y K
laus
San
der (
1958
)on
leaf
-hop
pers
disr
upte
d st
ripes
inta
ct s
tripe
s
13
ligat
ion
and
trans
plan
tatio
nex
perim
ents
indi
cate
the
pres
ence
of m
orph
ogen
s cr
eate
d/de
stro
yed
atth
e po
les
of th
e em
bryo
14
Firs
t mor
phog
en:
bico
id (t
rue
mat
erna
l)
trans
plan
tatio
n of
bic
oid
can
resc
ue c
ells
head
fold
shi
ft to
right
for i
ncre
asin
gnu
mbe
r of g
ene
copi
esin
mot
her
dose increase
15
radi
oact
ive
labe
led
RN
A re
veal
s lo
caliz
atio
nat
pol
e
16
inte
rpre
ting
the
bico
id g
radi
ent (
crea
ted
by m
ater
nal e
ffect
s) b
y zy
gotic
effe
ct(g
ene
expr
essi
on b
y em
bryo
itse
lf)
hunc
hbac
k is
a z
ygot
ic e
ffect
!
17
hunc
hbac
k re
ads
the
bico
id g
radi
ent
18a
lot o
f zyg
otic
gen
e co
ntro
ls fo
rmat
ion
of s
tripe
s
19
rece
nt e
xper
imen
tal p
aper
exp
lore
s re
latio
nbe
twee
n bi
coid
and
hun
chba
ck q
uant
itativ
ely:
Hou
chm
andz
adeh
et a
l. N
atur
e 41
5, 7
98 (2
002)
.
20
2122
23
only
gen
e th
at m
akes
hb
mor
e no
isy
is S
tauf
en24
How
can
you
mak
e a
stee
p st
ep in
hun
chba
ckex
actly
in th
e m
iddl
e of
the
embr
yo fr
oma
nois
y bi
coid
gra
dien
t ?
Nob
ody
know
s ...
Sec
ond
exam
ple:
R
obus
tnes
s of
Dro
soph
ila p
atte
rnin
g
Eld
ar e
t al.,
Nat
ure
419,
304
(200
2)
25
rem
embe
r rob
ustn
ess
of c
hem
otax
is (L
9-10
):
26
expl
ore
robu
stne
ss in
Dro
soph
ila p
atte
rnin
g
27
dorsal
ventral
anterior
posterior
28
mai
n m
olec
ules
of i
nter
est:
Scw
: BM
P (b
one
mor
phog
enic
pro
tein
) lig
and
Sog
: a B
MP
inhi
bito
r
Tld:
pro
teas
e (c
leav
es S
og)
29
(scw
)
periv
itelli
neflu
id
activ
ates
nex
t ste
pin
dev
elop
men
t30
sim
ple
reac
tion-
diffu
sion
mod
el:
]][
[]
[]
][[
][
][
]][
[]
[]
][[
][
][
]][
[]
[]
][[
][
][
2
22
2
2
2
Scw
Sog
Tld
Scw
Sog
kScw
Sog
kxScw
Sog
DtSc
wSog
Scw
Sog
Tld
Scw
Sog
kScw
Sog
kxScw
DtScw
Sog
Tld
Scw
Sog
kScw
Sog
kxSog
DtSog
bb
C
bb
BMP
bb
S
−−
−−
+∂−
∂=
∂−∂
−+
−+
−∂
∂=
∂∂
−−
+−
∂∂
=∂
∂
−
−
−
λ
λ
α
wha
t doe
s th
is m
ean
?
31
robu
stne
ss a
naly
sis
conc
lusi
on: p
ower
n=2
, DBM
P<<D
BMP-
Sog, α
/λ<<
132
]][
[]
[]
][[
][
][
]][
[]
[]
][[
][
][
]][
[]
[]
][[
][
][
2
22
2
2
2
Scw
Sog
Tld
Scw
Sog
kScw
Sog
kxScw
Sog
DtSc
wSog
Scw
Sog
Tld
Scw
Sog
kScw
Sog
kxScw
DtScw
Sog
Tld
Scw
Sog
kScw
Sog
kxSog
DtSog
bb
C
bb
BMP
bb
S
−−
−−
+∂−
∂=
∂−∂
−+
−+
−∂
∂=
∂∂
−−
+−
∂∂
=∂
∂
−
−
−
λ
λ
α
why
robu
st, i
deal
mod
el: D
BMP=
0, α
=0, k
-b=0 ]
][[
]][
[]
[0
]][
[]
][[
00
]][
[]
[0
2
2
2
2
Scw
Sog
Tld
Scw
Sog
kxScw
Sog
D
Scw
Sog
Tld
Scw
Sog
k
Scw
Sog
kxSog
D
bC
b
bS
−−
+∂−
∂=
−+
−=
−∂
∂=
λ
λSb Dk
Scw
x=
∂∂]
[1
22
33
THE
EN
D
