Integrated Quantitative Science 2. Signaling

lovethreewayAI and Robotics

Oct 20, 2013 (3 years and 5 months ago)

72 views

I
ntegrated Quantitative Science 2
. Signaling



Meeting times: Lecture (MWF 10:20, TTh 9:45), Lab (Th 1:30
-
4:30
; physics and bio
space), Precept (T 1:30
-
2:30; physics space)


Text: Custom publish (math, physics, chemistry, biology: Cengage) and CS text


Time: 9 hours/week in class/lab/precept; 1.5 hours outside of class for each meeting
(class/precept/lab)


Evaluation

(note: this is a rough estimate of what both semesters have agreed upon)
:

1000
total points:

i.

Lab: 250 points (x points on big presentations
, rest broken down into y

points/week)

ii.

Exams: 5;
1
st

4 are 100 points, the final
is 125
;
exams can be part in

class/part take home
-

schedule 4 x 75 minute slots

iii.

Other a
ctivities (not lab): 225 points (15 pts/wk for 15 weeks)
;
activities
can be take hom
e or in class
-

instructor dependent

(homework, quizzes,
etc)



Lecture Schedule

(OL: Ovidiu Lipan, KS: Krista Stenger, MK: Mike Kerckhove, DS: Doug Szajda, LG:
Lisa Gentile)

Date

Topic

Jan 11

Bridge to IQS
-
1,
big picture
-
signaling.
I
ntro to signaling,
examples of
communications
, set vocabulary.

Set discussion in the context of:
w
ay to
generate a signal, receive
a signal, propa
gate a signal, signal/noise ratio.


Lecture
s

1
-
2

(all): examples of signaling from each discipline

(including
,
but not limited
to,

immunology from bio)
.

Lectures 3
-
5 (KS
)
:
include
description of

where in pathways
all
disciplines

are going to be important
).

Jan 18

Lectures 1
-
2 (KS):
Strategies pat
hways use (p
aper: 3 habits of highly
effective signal transduction pathways as well as paper on discovery of
G
-
proteins and how they are part of pathways),
i
dea of modularity of
proteins, genes, pathways (7
-
8 “fundamental pathways?), i
n瑲漠瑯tty灥猠
潦⁲ece灴潲猻⁩湣汵
摥⁥x灥物浥湴慬⁥癩摥vce

iec瑵牥 ㌠⡋p 潲oi䜩㨠
䥮瑲漠瑯te湺ymes
-

reg畬慴潲y 獴sa瑥g楥猺i
(
c潶a汥湴l
ca瑡ty獩sⰠ䝁⽇B⁣a瑡tys楳Ⱐ
zy浯ge湳Ⱐn獯sy浥猬m浥瑡氠l潮⁣a瑡ty獩s
)

iec瑵牥⁰e物潤‴㨠䕸am
-
ㄠ⡦畬u爠灡牴楡氠數a洿⤠

iec瑵牥‵ ⡍(⤺)
Ba獩挠sa汣畬畳
-
ty灥‱⁩湴e杲g瑩潮㨠o湴牯⁡湤n
灲pc瑩ce㨠

Jan 25

Lectures 1
-
3 (MK):
Basic calculus
-
type 1 integration: intro and practice
,
con’t
.

Lecture

4 (MK)
: Equilibrium/math for reactions that push towards
completion

Lecture

period

5 (MK):
Integration
jeopardy

(problem
-
solving session)

Feb 1

Lectures 1
-
3

(LG): Catalytic strategies
(kinetics
-
differential versions)
:
rate laws (0, 1, 2 order)
, activation energy (temp dependence, Arrhenius),
reaction mechanisms
, con’t.

Lecture 4

(and part of 5
): (KS or LG
)
: Michaelis
-
Menten

Lecture 5

(2
nd

part of
): (MK):
equilibrium


Feb 8

Lectures 1
-
5

(LG):
equilibrium constants, relationship between kinetics
and equilibrium, factors affecting equilibrium (conc, vol, P, T,
LeChatelier, catalyst)
, acids and b
ases (Ka, Kb:
types of acids and bases:
Bronsted, Lewis, Arrhenius, strong vs weak, mono/diprotic, pKas/aa side
chains), buffers, titrations

Feb 15

Lecture 1

(DS)

Lecture period 2
: Exam
-
2

Lectures
3
-
5

(MK, OL): Brownian motion

Feb 22


Lecture
s

1
-
2

(MK): line integrals (tied into thermodynamics)

Lectures 3
-
5

(LG): thermo
dynamics: enthalpy, first law, work, heat,
calorimetry, heat capacity, enthalpies of reaction and formation second
law, entropy, spontaneity, free energy

March 1

Lecture
s

1
-
2

(LG): thermo
dynamics, con’t: enthalpy, first law, work,
heat, calorimetry, heat capacity, enthalpies of reaction and formation
second law, entropy, spontaneity, free energy

Lecture

period

3

(LG, MK, OL)
:
Problem solving session

Lecture 4

(LG and MK): e
xample from protein folding of
polynomial
approximation. (The heat capacity function is an example of this
-
quadratic approximations only)

Lecture

5

(
DS): Shannon’s law and entropy

March 8

Lecture

1

(DS): Shannon’s law and entropy
, con’t


Lecture period
2: Exam 3


Lectures 3
-
5: Rotational kinematics: (OL, MK)

March 15

Spring break

March 22

Lecture period 1:
problem solving session


Lectures 2
-
5: Rotational kinematics
, con’t
: (OL, MK)

March 29

Lectures 1
-
3
: Rotational kinematics
, con’t
: (OL, MK)

Lecture

period 4
: Exam 4

Lecture 5

(KS):
CXCR4 signaling pathway: chemokine
-

GPCR, HIV

April 5


Lecture 1

(OL):10 minute movie and discussion of what’s happening in
the pathway (just portion of pathway: receptor
-
effector interaction),
lines/arrows

Lec
ture 2

(OL,

MK): writing equations for the pathway

Lecture period 3
: Problem
solving

section

Lecture
s

4
-
5

(OL, DS): simulations, introduction of a delay (need for
numerics), going back to measurements (need to find this in literature)


April 12

Lecture

1

(OL, KS, MK):
Transport/trafficking


Lecture period 2: Exam 5


Lecture

3

(OL, KS, MK):
Transport/trafficking
, con’t


Lectures
4
-
5

(DS):
Anti
-
viral software and resistance to them, lack
diversity that biol. systems have
-

what happens without them? Viruses

that mutate in wild on purpose.


April 19

Keep free for spill
-
over


Precept Schedule


Date

Topic

Jan 12

Intro to pathway for lab
-
1, intro to the first lab module (KS)

Jan 19

Plate cells for week
-
2 lab (KS, LG) plus demonstration of poor/good oral
presentation (DS)

Jan 26

Intro to electrophoresis/Western blots and background for the NO assay
(KS)


Feb 2

Real time q
-
PCR theory (AH), math and curve fitting (MK)

Feb 9

Intro to neural networks (DS)

Feb 16

Con’t of neural network discussion (DS)

ce戠㈳b

䵡瑨⁢慣kg牯畮r 景f⁴桥 B牯r湩慮潴n潮慢
M䬩

March 2

How Brownian motion ties in with transport and trafficking in biology,
osmosis (OL)

March 9

Inheritance
-
1 (DS)

March 16

Spring break

March 23

Intro to AIDS and HIV protease (LG)

March 30

Background into types of inhibitors and K
I
determination (LG)

April 6

Intro to ITC (LG)

April 13

Inheritance
-
2 (DS)

April 20

Intro to signal propagation/waves (OL)







Laboratory Schedule


Date

Topic

Jan 14

(KS) Cell culture technique, start
cultures, immunofluorescence

Jan 21

(KS) Activate cells early, harvest supernatants and lysates, protein assays

Jan 28

(KS) Run gels, set up Western blots (iNOS), real time q
-
PCR

Feb 4

(KS) Western blots (iNOS), real time q
-
PCR

Feb 11

(DS) Neural
networks
-
1: development

Feb 18

(DS) Neural networks
-
2: training plus analysis

Feb 25

(OL, MK, DS) Brownian motion
-
1: movement of fluorescence beads in
cells, collect image in microscopy lab and analyze

March 4

(OL, DS, MK) Brownian motion
-
2: simulation

March 11

Student oral presentations (all groups)

March 18

Spring break

March 25

(LG) HIV
-
1 protease
-
I: kinetics of substrate binding to both wt and
MDR
-
HM (multidrug resistant
-
hexa mutant) protease:

measurement of initial velocity, investigation of how

initial velocity
depends on [E], K
m

determination, V
max

determination. How have
kinetics been affected in the MDR protease?

April 1

(LG) HIV
-
1 protease
-
II: kinetics of inhibition by two anti
-
HIV drugs to
both wt and MDR
-
HM protease: determination of K
I
values. How has
inhibition been affected in the MDR protease?

April 8

(LG) HIV
-
1 protease
-
III: thermodynamics. ITC of both wt and MDR
-
HM protease binding to two anti
-
d
binding been affected in the MDR protease?

Apri
l 15

(LG/CP) HIV
-
1 protease
-
IV: molecular modeling (computation).
Visualization of crystal structure (apo and drug bound), location of
mutants in MDR
-
HM, location of drug binding pockets, prediction of
how mutants confer resistant to these drugs.

April
22

(OL) Signal propagation/waves: NS application (frog hearts?)


Preliminary thoughts on IQS
-
2 lab a
ssessment:


1.

Oral scientific communication: early on, a precept period will be used to
demonstrate aspects of both good and poor oral communication.
Throughout the
semester, students will give one oral presentation communicating the results of
one lab module (HIV
-
protease not included). Done before spring break
-

first half
of lab.


2.

Written scientific communication: a formal written report will be done

for the 4
week HIV protease module. In preparation for this, assessment for other lab
modules will focus on various aspects of a formal written report (ie how to create
figures, present data, write conclusions, etc). Done after spring break
-

2
nd

half of

lab.