all 1-2 weeks Flashcards
(111 cards)
1
Q
A
2
Q
Structural and functional. Structural used for brain anatomy, functional for living, functioning, dynamic brain imaging.
A
Two types of neuroimaging?Used for?
3
Q
seconds or fraction of a second High temporal resolution Low spatial resolution
A
structural imaging high/low
4
Q
minutes Low temporal resolution. High spatial resolution.
A
functional imaging high/low
5
Q
Lesional study
A
Phileas Cage
6
Q
Lack of contarast inside the scull.
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Wilhelm Röntgen
7
Q
radiography of the ventricles of the brain with the cerebral fluid replaced by air or radiopaque material or labelled with a radionuclide.
Used until 1970s
Risky!!
A
Walter Dandy
8
Q
EEG
Electroencephalogrphy
Hans Berger (DE)
1924
A
EEG
9
Q
1934 Epileptic spikes
1953 different stages of sleep
Combined with fMRI to be able to identify whole networks and brain regions involved.
A
Milestones of EEG
10
Q
CT - computer tomography
[tomos: slice, section]
A
CT
11
Q
CAT - computer axial tomography
X-ray CT
X-rays from many directions to reconstruct the volume of interest in slices
A
CAT, x-ray CT
12
Q
Positron Emission Tomography PET
GAMMA rays.
Needs a cyclotron close by making the radioactive molecules. (Radioactivity lasts only for ~30 sec.)
A
PET
13
Q
Magnetic Resonance Imaging MRI
DTI type of MRI, looking at microstructural changes
A
MRI
14
Q
functional MRI
resting state fMRI / task-based fMRI
A
MRI
15
Q
Multimodulling imaging
Often includes several MRI and a few fMRI
A
multimoduling imaging
16
Q
EEG
Activity measured on a millisecond scale on the surface of the scalp.
Non-invasive
multiple electrodes
Portable and cheap (hat&gel&computer)
A
EEG
17
Q
MEG - Magnetoencephalography
Measures magnetic fields
Head in a MEG helmet
Low spatial resolution-doesn’t reach to deep brain areas
High temporal, millisecond-level
tolerance, sticking ones head to a massive helmet-like machine, don’t move
A
MEG
18
Q
PET - Positron Emission Tomography
Measures glucose metabolism
Glucose tagged using radiopharmaceuticals (tolerance highest)
fluorine - 18 (F-18)
fluorodeoxyglucose (FDG)
10-20 sec, mid temporal
whole brain mm scan good spatial
A
PET
19
Q
functional near-infrared spectoscopy
BOLD
Difference between oxy-deoxyhaemoglobin (in colour)
Measures both oxygenation level and blood volume (excess of oxygenated blood after use/brain activity)
Spatial resolution: 2/4 low (surface 5 cm, small amount of sensors)
Temporal resolution: 3/4 high
Tolerance needed: low, suitable for babys
Works well for babies with their thin scull
A
fNIRS
20
Q
Blood
Level
Oxygenation
A
BLOOD?Used in which techniques?Based on what?
21
Q
fMRI - functional magnetic resonance image
Difference between oxy-deoxyhaemoglobin (in colour)
Measures both oxygenation level and blood volume (excess of oxygenated blood after use/brain activity)
Gives very detailed image
every few seconds, low temporal
tolerance needed medium, noisy
A
fMRI
22
Q
Indirect:
fMRI - based on BOLD, magnetic differences between oxy-deoxyhaemoglobin. Oxygenated blood flooding after use.
fNIRS - also based on BOLD colour difference
Direct:
EEG
A
indirect-direct imaging
23
Q
strong magnetic field:
deoxyhaemoglobin (Hhb) - paramagnetic
close to nothing magnetic field:
oxyhaemoglobin (O2Hb) - diamagnetic
A
magnetic
24
Q
fMRI
30 000 (strong enough to lift up a car)
A
What technique:1.5 or 3 Tesla [machine]
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MR - magnetic resonance
Wearing no metal in clothing or body.
Magnetic used in MRI scan is 30 000 stronger than earth's magnetic field.
To check that someone is MR compatible?Why is this important
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Comparing different stimuli -\> activation in different brain areas.
Based on BOLD.
What is typically tested using fMRI?
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Darker.
Brain activity sips first oxygen in from the nearby environment -\> lots of deoxyhaemoglobing, more magnetic perturbation -\> initial dip (dark picture)
Followed by overflow of diamagnetic oxyhaemoglobin --\> less deoxyhaemoglobin than at rest -\> less magnetic perturbation than at rest --\> bright colour than t rest
BOLD
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**raw data**
**preprocessing**
('clean up': remove head movements, breathing, cardiac pulsation etc. increase the signal to noise to ratio)
**single subject analysis**
(general linear model GLM, fix head size etc to the template, where is the individual brain activity compared to experiment model)
**group-level analysis**
(compare groups, patients/healthy controls)
processing data
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- A g**ene** and its **encoded protein** (and different isoforms)
- how specific genes and proteins **interact**
- the **signalling pathway** and how it works
- the formation/ specification of **cell types, tissues and organs**
- the **circuits and networks** in the nervous system
- the above in **relation to disease**
What is studied with animal models? (
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CHORDATA: animals in this category have ***notochords*** (not always a vertebrate). Frogs etc. also humans
ARTHROPODA: insects
HUMAN:
Kingdom: Animalia
Phylum: Chordata
Class: Mammalia
Order: Primates
Suborder: Haplorhini
Infraorder: Simiiformes
Family: Hominidae
Subfamily: Homininae
Tribe: Hominini
Genus: Homo
Linnaeus, 1758
Chordata?Arthropoda?
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500 million years
500 milj
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Main reason:
understand causes, mechanisms, pathways from **molecule to mind**
Why study animals?
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Homology
Homology
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Homologous genes/proteins
Sequence identity between orthologous genes/proteins from different species
Genes homology
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- **mutating, inactivating** or **overexpressing** a gene/protein
- finding **interacting/ binding partners**
- screening for **enhancers/ suppressors**
of ‘disease gene/protein’
- **e**pistasis tests and manipulation of a **signalling pathway**
- targeted activation/ inactivation of **neural circuits**
- the regulation and function of **behaviour**
Methods
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Genetic similarities between fly and mouse (and human)
Hirth & Reichert 1999
genetic similarities
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Baker’s yeast has been used to discover genes and their function in the regulation of the cell cycle/cell division.
bakers/brewers yeast
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eukaryotic cell
eukaryotic cell
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cell division of bakers yeast
cell division yeast
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TDP-43 and FUS genes has been discovered to be involved in the formation of motor neuron disease.
TDP-43 and FUS inhibit the growth of yeast cultures, they build aggregates = they are toxic.
Glucose = gene has been turned off
Galactose = gene has been turned on
TDP-43 and FUS
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Form aggregates, means they are toxic.
## Footnote
Couthouis et al. (2011)
In human postmortem samples it is visible that human homolog of TAF 15 also forms aggregates in ALS cases, which stands for **amyotrophic lateral sclerosis.**
Couthouis et al. (2011)
TAF-15 and ALS
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C. elegans
C. elegans
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John Sulton 2002
Nobel Prize, C. Elegance
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L1 - L4
a stage where larva can survive for 4 months, doesn't mature into an adult.
larva, Dauer
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daf-2 and daf-16 define **lifespan** in C. elegans
Kenyon et al. (1993)
High levels of daf-2 causes the suppression of daf-16, which therefore are low, which leads to a normal lifespan, around 25 days.
daf-2 is low, it leads to the derepression of daf-16, which then leads to high levels of this protein, and that extends the lifespan. See image!!
daf-2 and daf-16 define .... in C. elegans
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daf-2 /IGF1 is insulin receptor in humans!
(Affects life span)
Gems & Partridge (2013)
daf-2 / IGF1, insulin receptor
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Drosophila melanogaster
Drosophila melanogaster
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Fruit fly, drosophila melanogaster
fully mapped genome
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1912
Thomas Hunt Morgan
Columbia University
Hunt Morgan
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10-12 days
egg - larva - adult
Drosophila melanogaster life cycle?
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Enhancer in generating transgenic flies.
For example, as an enhancer that is specific for all the dopaminergic neurons.
When all the dopaminergic neurons are active, enhancer is transcriptionally active. It recognises the abstract activating sequence of a second set. That could for example be a green fluorescent protein.
Muqit & Feany (2002)
GAL4/UAS system
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Dopaminergic pathway
Voluntary movement.
Hirth (2010); Strausfeld & Hirth (2013)
dopaminergic pathway
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**Forward genetics:**
## Footnote
Starting with a mutant phenotype, then identify the protein and the gene (Thomas Hunt Morgan)
**Reverse genetics:**
Knowing the (human) gene, then going to Drosophila, looked whether it has a human homolog, or a fly homolog in this case, and then we started to manipulate that gene, and then, we could look, how does that relate to the disease.
(picture on the slide wrong?)
genetic string
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Parkinson's disease, introduced mitochondrial dysfunction in cholinergic, dopaminergic; and serotonergic neurons.
behaviour
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Only affected dopaminergic.
Parkinsons, dopamin
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All cells derive from one.
J. Sutton was able to trace this tree in C. Elegance, got a Nobel Price for it.
cell lineage
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It's vertebrate!
Behaviour
The zebrafish: Danio rerio, vertebrate
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Orger & de Polavieja (2017)
Advantages:
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Transparent embryo
transparent embryo
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72h
3 months
72h, 3 months
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yes
live brain imaging
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Autism
Hyperactivity (night time activity)
Hoffman et al. 2016
cntnap2a - autism
63
Estrogenic phenotypic suppressors were able to suppress hyperactivity.
Biran & Levkowitz (2016)
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Mouse
Is a mammal with social behaviour.
90%
Mus musculus
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loss of nigrostriatal pathway
degenerative loss of dopaminergic neurons in the SNpc
(substantia nigra pars compacta)
Parkinson's
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D1 and D2 affected, Gpi/SNr not inhibited, messages don't get to thalamus
What condition typically follows:
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Modified with channelrhopsin ChR2-YFP
Channelropsin is a protein that can be activated by light pulse --\> over activation of a neuron.
Kreitzer's lab San Francisco
68
Switching neurons on/off by light (for example D1 or D2 neurons in striatum)
optogenic activation
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Enzyme leading to dopamine production
tyrosine hydrolaxe
70
It is antagonist of dopamine.
Used to create Parkinson's model in mice.
6-OHDA
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6-OHDA (dopamin antagonist) blocked the effect of dopamin --\> PD model
ChR2 possible to activate with laser (light pulse). When D1 activated mice ran.
When D2 activated mice stopped.
Shows that D1 activation can overcome Parkinsonian phenotype.
Friend&Kravits 2014
D1, D2 Parkinson's, Kreitzer
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Voltage difference across the membrane of a neuron when it is at rest (non-signalling)
Intracellular -70 mVs, (compared to extracellular 0mV)
Resting membrane potential
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Positive or negative ions is higher/lower in one area than another.
Concentration gradient:
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A change in a neurons membrane potential that makes it more positive (less negative).
Depolarisation:
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A change in a neurons membrane potential that makes it more negative. It is the opposite of depolarization.
Hyperplarisation:
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Transmembrane proteins that form a channel allowing ions to travel in/out of a cell.
These channels are opened when the receptor binds a **ligand**, like a **neurotransmitter.**
**Glutamate** receptors and **GABA** A receptors are examples of ionotropic receptors.
Ionotropic receptors:
77
Transmembrane proteins that form ion channels whose opening and closing is regulated by the **membrane potential** near the channel.
Voltage-gated ion channels:
78
**Large voltages generated by animals**
(electric eels or rays: electroplaque)
**Negative resting membrane potential**
(most neurons)
**Postsynaptic potentials**
(small variable changes in membrane potential)
**Action potentials**
(large, fast, all or none fashion)
types of electric activity
79
An electroplaque has Na/K pump maintaining membrane potential, operates on ATP.
When **acetylcholine binds** (ionotropic ligand gated) to nicotinic Ach receptor nAchR, sodium (Na+) flows in. depolarisation 120 mV.
Has electroplaques piled up, can create a shock up to 700V (volts)
Electroplaque
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EPSPs are generated by activation of ion channels that let positive ions into the cell --\> depolarise neurons.
IPSPs are generated by activation of ion channels that let negative ions into the cell --\> hyperpolarise neurons.
EPSP-IPSP
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**concentration and length of time** the neurotransmitter is in the synaptic cleft
## Footnote
**amplitude**
EPSPs and IPSPs are:• graded in amplitude due to the ..... o
82
**Nav and Kv**
a) closed, closed
b) open, closed
c) closed inactive, starts open
d) closed inactive, open
e) closed, closed
action potential
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Electric potential in the extracellular space around neurons.
field potential
84
Nerve: a bundle of axons.
Nerve
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Compound axon potential: the sum of the activity in a number of nerve fibers [axons].
Compound axon potential:
86
* field potentials
* whole nerve activity
* multi-unit activity
* single unit activity
* multi-electrode arrays (MEAs)
Extracellular recording (ER)
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* activity within single cells
* sharp electrodes
* patch suction electrodes
Intracellular recording (IR):
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* recording activity of single ion channels
* patch clamp-type electrode
Single channel recording (SCR):
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* the electrode is outside but close to the neurons
* the electrodes pick up only field potentials and low frequency filtered action potentials
* it is not possible to record Vm rest or post-synaptic potentials
Extracellular recording (ER)
90
Stimulating electrode in tissue, Schaffer collaterals.
When stimulus given, activates Sch collaterals --\> release of NT onto purkinje neurons in the area of CA1.
One electrode records the *fEPSP* and another sum of many AP of CA1 neurons = *somatic population spike.*
O'keefe & Nadel (1978); The Scripps Research Institute (2008)
Field potential
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Whole nerve recording
Frog sciatic nerve
Maximum capacity can be recording, adding voltage over hat won't change the curve of an AP.
Mark CNS end, place on a dish over stimulating an recording electrodes. Apply olive oil at the ends, ringer in the middle (ions). Silicon grease between containers [conductance all the way through]
Lilley & Robbins (1998)
Give an example of whole nerve activity
92
Rattus rattus has been used to separate different axons in the vagus nerve by measuring the intensity of the stimulus and their conducting velocity.
separating axons
93
yes
Electrode in rat brain, lateral geniculate nucleus.
Flash of light
Measures the neuron closest by but a neuron further away. Simultaneously measuring two neurons.
Multi-unit extracellular recording
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A human (with DBS electrode) gave consent to a single-unit recording.
Was shown pictures of Halle Berny, neuron showed activity. A picture of Michelle Pfeiffer didn't cause a reaction.
Association neurons
Quiroga et al. 2009
Human single unit recording-
95
64
yes, it doesn't bug them. Cells can happily grow on it. non invasive
Extracellular activity [outside the axons]
Multi-electrode arrays MEA
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current clamps
voltage clamps
sharp electrodes
patch clamps electrodes
Intracellular recording
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potential difference between two points
Voltage
98
1. sharp electrode current clamp
2. Sharp electrode voltage clamp
Perezoso, 2007
Ciona intestinalis
99
**- cell-attached patch recording:**
pipette forms gigasel on the cell membrane, measures *single-cell activity.*
**- whole cell patch:**
inside the cell records all *ion channels*
**- inside out patch, outside out patch:**
possible to record *single* ion channel activity
**- perforated patch:**
using antibiotics to pore wholes
Patch clamp electrode
100
Whole cell patch clamp in current mode.
calcium
intracellular calcium
101
Yes, by using patch clamp electrode
[remember pipette, air pressure etc.]
Can a single ion channel be recorded?
102
yes (as a part of treatment like DBS) / yes (implanted,anaesthetic) / yes
no / yes (anaesthetic=kept still) / yes
no / yes (anaesthetic=kept still) / yes
used in human/animal/in vitro?
103
A
Records activity of the cell in ‘physiological conditions’ Detailed and high resolution recordings of voltages
D
Can't control voltage
advantages / disadvantages current clamp?
104
A
Can control the voltage
Detailed and high resolution recordings of currents
D
unstable
advantages / disadvantages voltage clamp?
105
A
reusable, simple electrode solution
D
High resistance
Can be difficult to make
Some damage to the cell
advantages / disadvantages sharp electrode?
106
A
## Footnote
Low resistance
Relatively easy to make
Less damage to cell
Dialysis of cell contents
D
Not reusable
Dialysis of cell contents
Complex electrode solution
advantages / disadvantages patch electrode?
107
A
## Footnote
Allows the recording in real time of the functional activity of a single protein
Elucidates drug action at molecular level
D
Complex and lengthy analysis
advantages / disadvantages single channel?
108
Electrophysiology can record the electrical activity of whole brain **tissue**, a **single** neuron or a single ion **channel**.
Electrophysiology can record the electrical activity of wholElectrophysiology can
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temporal
Electrophysiology is..
110
vivo
Many electrophysiological approaches can be used in xxxx.
111
Electrophysiology can be used simultaneously or in **conjunction** with optical, molecular, biochemical and pharmacological techniques.
Electrophysiology can be used simultaneously
