Transcript Genomics of sensory systems - University of Maryland

Genomics of sensory systems
BSCI 338c / BIOL 708c
M + W 2-3
Bio/Psych Rm. 1230
Karen Carleton
 Email
: [email protected]
 Phone: 301-405-6929
 Office: 2130 Biosciences Research Bldg
2nd floor - if door doesn’t open
PUSH BAR HARDER / FASTER
Office hours - After class or by appointment
Today
 Student
survey
 Introduction
 How
to the senses
class will work
Students on waitlist
I
will email Cecilia Jordan about adding
up to 10 students. She may need you
to go see her
2227 Bio/Psych
[email protected]
 Make
sure I have your email today
The senses
 “There
is nothing in the intellect that was not
before in the senses”
-Aristotle (384-322 BC)
The senses
 “There
is nothing in the intellect that was not
before in the senses”
-Aristotle (384-322 BC)
 “Everything
we know about the world comes to
us through our senses”
- Fain 2003
What are senses good for?
 Survival
- predators
 Sense external environment - find food
 Find mates
 Safety - don’t fall off a cliff
How do senses shape our
perception?
 Limit
it
Breadth of stimuli - wavelengths can see
Intensity of stimuli - minimum detectable
signal
How are senses shaped by
environment?
Influences where signal comes from
Fit the environment - adapt to it
Nocturnal vs diurnal
Shape senses - optimize and select senses
that are key
The “five” senses
Sense
Touch
Mechanosensation
Hearing
Audition
Smell
Olfaction
Taste
Gustation
Vision
Photoreception
Detect different aspects of
environment
Sense
Detects
Touch
Pressure
Hearing
Pressure
Smell
Chemicals
Taste
Chemicals (for food)
Vision
Light
Detect different aspects of
environment
Sense
Detects
Touch
Force / area = pressure
Hearing
Sound = pressure
Smell
Detect chemicals
Taste
Detect chemicals for food
Vision
Light
Early ideas of how sense organs
worked
Herophilus 3rd cent BC via Galen 3rd
cent AD
Descartes 1637
Sensory organs
R
e
c
e
p
t
o
r
s
Detecting stimuli

Receptor is
activated

Causes ion channel
to open / close

Changes voltage
across membrane

Causes change in
synapse release
What determines cell specificity?
Receptor sets
specificity
 If change receptor,
modify what cell
responds to

Electrophysiology

Measure cellular
response
Intracellular recording
Suction electrode
Can follow how
voltage across cell
changes with a
given stimulus
 Measure ion
current

Electrophysiology of rod
Increase stimulus
and see how cell
responds
 Find polarity of
response
 See if cell saturates
as apply more
stimulus

Evolution
 Novelty
problem -
Life originated from common ancestor
Currently there is amazing diversity
How did so much novelty arise?
Plachetzki and Oakley 2007
Francois Jacob
Work on bacterial
genetics including
conjugation, mRNA,
operons, gene
regulation
 “Sexuality and the
Genetics of
Bacteria” 1961

Francois Jacob
Paper on class website
Two design strategies
 Engineering
- theory guides design
Can use any parts that can imagine
 Tinkering
- design by trial and error
Start with parts have on hand
All organisms use same building blocks
DNA, AA
Organization of these parts that matter
Junk Yard Wars
Junk Yard Wars
Junk Yard Wars
Evolution
 All
organisms are built on
Same genetic code
Same 20 AA building blocks
Use similar enzymes
Same cellular structures and replicating
mechanisms
 Organism
alter these, tinkering to make
them work better in their environment
Tinkering with sensory systems
 How
does evolution shape sensory
systems?
 What processes are important?
 How
does diversity increase?
Does diversity ever decrease?
Is there a cost to diversity?
Genome revolution
 Huge
explosion of genomic information
>60 vertebrate genomes in the pipeline
 What
can this information tell us about
the sensory capabilities of animals
Sensory systems in the context of genomes
Information we might get from genomes
about sensory systems
 Similarity
of organisms
 How many receptors are there
 How many have been lost
Structure of DNA Watson and Crick 1953
Molecular basis of vision - 1984
Molecular basis of olfaction - 1991
Molecular basis of taste - 2000
Molecular basis of taste - 2006
Molecular basis of hearing - 2007
So much still to learn about
senses
 What
are receptors?
 How are receptors tuned?
 How are genes turned on in right cells?
 How are they neurally wired?
 How does brain process information?
Goal #1. Learn about the senses
 Sensory
receptors
Morphology
Molecular mechanisms
 Compare
senses
Similarities
Differences / specialities
Goal #2. Learn about genomes
 Learn
a few simple tools to carry out
gene comparisons
Finding and comparing genes
Evolutionary history of genes
 Evolution
of regions
Synteny of regions
 Use
web based resources
Goal #3. Read primary literature
 Learn
about recent studies and results
Methods being used
Science in action
 Find
limits of current scientific
knowledge
Nobel prizes in the senses
Year
Who
Discovery
1920
Nernst
1961
Von Bekesy
Electrochemistry - membrane
potential
Cochlea stimulation
1967
Granit, Hartline
& Wald
Gilman and
Rodbell
Chemical basis of vision
2003
MacKinnon
Ion channels
2004
Axel and Buck
Odorant receptors
1994
G proteins
Goals - 4. Explore sensory
interactions
 Are
there ways in which the senses
work together?
 Are
there trade offs where if one sense
is strong, another is weaker?
Sensory Transduction

Gordon Fain,
Professor of
Physiological Science
at UCLA

Electrophysiology of
visual system

On reserve in Chem
library (won’t use for
first few weeks)
Class philosophy
 Learning
is a collaborative activity
Active learning
“Sage on the stage” vs “Guide on the side”
 Learning
goes both ways
 Communication is key
Ask questions
Send email
Syllabus
 Syllabus
is dynamic
It will be updated and reposted as we add
assignments
 Course
layout
Intro to genes, genomics
Molecular evolution
Cover the senses one by one
Molecular mechanisms
Communication
 Blackboard
- link to class web site
Post assignments
Post lectures (after they are given)
 Email
 Office
hours / appointments
 Individual meetings about projects
Course assessment
 10%
class participation
 30% homework
 20% midterm project
 40% class project
Tailored to your interests
Molecular aspect of the senses
Write as 5 pg research paper
Short class presentation
Homework
 Homework
will be weekly
Get familiar with tools to explore genomes so
you can learn about the senses
 Midterm
project
Class will be analyzing a channel in many
genomes and unraveling its evolutionary
history
Part of a research project by Richard Payne
Final project
 Pick
a topic of your choosing
Related to molecular basis of senses
Write short (5 pg) report or make video or
write a News and Views article
Make a 5-8 min presentation to class