Unit 3 - Lecture 1 Flashcards
What are some general considerations of using animal models?
- Most knowledge is from animal models
- Idea: similar anatomy = similar physiology (ensure by orthologous genes)
- Animals with similar anatomy should have similar outcomes to humans
- Similar functions are reported among species with similar anatomy/genetics
What are translational issues?
Can animal knowledge really be applied to humans?
Why is human research largely limited?
Human research is largely limited due to ethical reasons.
What animals are typically tested on?
Mice, monkeys are too expensive
What limitations exist with using animal knowledge to study humans?
Difficult to study human specified functions (e.g., speech, language)
2 classification of methods in neuroscience
- Anatomic/ morphological methods
- Functional methods
Anatomic/ morphological methods
On structures from gross to fine, to molecules
What are two types of functional methods?
- Behaviour methods (subjective)
- Objective methods
Functional methods - behaviour methods (subjective)
- Observation (passive, not interference, natural, lack of control)
- Empirical study (stimuli-responses, designed condition)
Functional methods - objective methods
- Evoked response (Electrophysiology/optical/magnetic responses)
- Functional imaging
Methods for anatomy and structures (microstructures)
Microstructures: dissection, staining, microscopy technologies
Explain how staining works
- Staining to show special materials (histochemical staining,
immunohistochemical (IHC): against proteins w/ antibodies) - Staining uses special chemicals and antibodies which specifically target particular proteins (this lets you observe one thin slice)
- We want staining to only stain one particular anti body
- 3D puts the slice information into whole structures
What is a very common chemical to use for staining lipids?
Golgi staining with silver nitrate
How can you track the pathway using a tracer?
- why is it not easy
- It is not easy to track the pathway if the fibers are not distributed in a laminated manner (they are very thin)
- There is a special transportation system to carry the tracer to different places from the site of injection
IHC to identify special protein (calpain)
- Calpain increase in hair cells by noise exposure
- Calpain is a proteinase that is activated by calcium overload in response to noise
- In normal ear, this protein is very low level. If too much calpain, ear can be destroyed.
What 3 things does the nucleobase chain form?
- Genetic code
- Ribonucleic acid
- Deoxyribonucleic acid
What are 4 methods of molecular biology?
- Expression
- Immunohistochemistry
- Structural studies
- Genetic methods
Methods of molecular biology - expression
- Expression: PCR (Polymerase chain reaction) for mRNA (transcription); Western Blotting for proteins (translation)
- Both methdos need to remove tissue and take out cells (therefore cant observe normal structures)
Expression - PCR
Used to identify mRNA for certain protein
Expression - WB
- Method to identify proteins
- The protein contains charge and different sizes
- Spread protein on certain gel, the protein will move in a field of electricity because it contains charge, smaller molecule moves faster, larger moves slowly or not at all)
Methods of molecular biology - Immunohistochemistry
- what does it use
- what does it allow you to observe
- (IHC), with light microscopy and electron microscopy
- Allows you to observe the molecules in the tissue where they are located (used together with dissection, staining, and microscope)
Methods of molecular biology - Structural studies
- What is it good for
- What is a limitation
Xray observation provides a good observation of 3D proteins (but there are more modern methods); limitation is that it can only observe fixed proteins, not living tissues
Methods of molecular biology - Genetic methods
- Gene knockout/in: germ cells and conditional knockout/in somatic cells
- Gene therapy:
- Modulation and editing
- siRNA
- Stem cell transplantation
Genetic methods - what is gene knockout?
- What is the difference between animals with and without the gene?
- Shows the role of the gene, done to eggs so species is born without gene
Genetic methods - what is conditional knockout?
Knock out gene at a particular time
Genetic methods - What is gene therapy? What are two types
- Decrease or increase the expression of certain genes
- Modulation and editing
- Stem cell transplantation
Gene therapy - Modulation and editing
Can correct particular genes for treatment (needs more research)
Gene therapy - Stem cell transplantation
- One cell that can be used with other types of cells
- For regeneration, some cells can be treated in vitro (can be manipulated)
- Has been used with Parkinson’s disease
What are some methods suitable to human subjects? (5)
These are limited by invasiveness
- Behaviour studies
- Evoked potential studies
- Functional imaging
- Neural recording during surgery
- Biopsy
Human subject methods - Behaviour studies
- Subjective
- Give instructions then see human response
- Non-invasive
Human subject methods - Evoked potential studies
- Objective
- Using gross-electrodes that are non-invasive
Human subject methods - Functional imagine
- Can observe the functional change of the brain
- No surgeries so not harmful
Human subject methods - Biopsy
Very popular method, shows if a particular tissue or organ has a disease
____ is the most important single category of functional methods in neuroscience
Electrophysiology
Electrophysiology is an ____ method that can be used in humans
Objective
What are 3 electrophysiology methods?
- In viva (done on a living organism)
- In vitro (done in a lab dish/test tube)
- Pharmacological methods (in vivo and in vitro can be used in pharmacological studies)
Electrophysiology - In viva
- Gross electrode vs microelectrode (multi units vs single unit)
- Near field vs far field
- Acute vs chronic
Electrophysiology - In vitro
- Patch clamp, whole cell clamp
- Taking out the whole piece of the cell
Electrodes for recording and stimulation
- At least two electrodes are needed to form a circuit for signal recoding and stimulation (the material must be conductive).
- Two electrodes creates a loop to allow the current to pass
- A grounding electrode provides a pathway to reduce noise
- Isolation is needed, only tip is exposed to tissue.
- Also dependent on the diameter (spatial selectivity)
Explain gross electrodes (7)
- Thick, and low impedance
- Tough
- Poor spatial resolution
- Far-field recording
- Noninvasive (but can also be used invasively, but micro electrode cannot be noninvasive)
- Responses from many neurons
- Depends on synchronized activity
Explain microelectrodes (7)
- Thin, high impedance (high level noise)
- Fragile
- Good spatial resolution
- Invasive
- Near-field recording (micro electrode wont work in far-field because of the low impedance that is needed for gross electrodes)
- Single unit responses
- Need surgery to place electrode close to the target,
Voltage clamp: breakthrough for action potential
- Axon from Giant Squid provides the best sample for the study of voltage clamp: to study the feature of ion channels at different membrane potential (axon is 1mm which allows investigation of membrane/action potential)
- In generation of action potential, the permeability of ion channels are changed with both time and membrane potential. In order to identify the contribution of the two factors, voltage clamp fix the membrane potential to see the change with time. (We cannot freeze time!)
Explain the patch clamp
- Patch clamp: voltage clamp on small patch
- Patch is small, allow the study of ion channel properties (single ion channel if patch is really small) cell is sucked into the pipe in order to tear of a small piece.
- This allows us to understand how a particular ion channel works (in vitro study)
Functional Features of Individual Neurons (4)
- Functional units (neurons and circuits)
- Single neuron activities are the foundation of signal coding
- Must be recorded separately (single unit study)
- By microelectrodes
Explain single unit studies
Single unit study forms the foundation of neuroscience (very time consuming, need to repeat hundreds of times)
How are acoustic signals are coded in neural behaviour? (3)
- By rate change
- By phase locking (temporal pattern)
- By place (tonotopic map in auditory pathway)
What are 2 ways to record timeline in experiment?
- Acute
- Chronic
Explain acute recording
- Recording over several hours
- Under anesthesia to make animal stabilized
- Difficulty to hold electrode in position
- Suitable for microelectrode recording of single neurons
Explain chronic recording
- Using implanted electrodes
- Can be gross and microelectrodes
- Can be recorded from awake animals
- Long-lasting, allow more manipulation over time
What are two types of single unit recording?
- Single channels
- Multi-channels
Explain single channel single unit recording
- Recording activities of one neuron at a time
- Very time consuming
- Can be combined with dye injection to verify neurons with certain response pattern
Explain multi-channel single unit recording
- Recoding activities of many neurons that may be connected via circuits
- Allow exploring of neural circuits and the mechanism of signal processing
- Can be done using acute and implantable electrodes.
What are 7 changes from peripheral (low level) to central station (high level, cortex)?
- Increased number of neurons (SGNs increase in the cortex)
- Increased versatility
- Slower working speed (due to synaptic delay, temporal resolution goes down)
- More complicated circuits, allowing detailed processing
- Specified processing combined with high level of integration (seen in high levels)
- More place coding (more functional features are related with place coding)
- Responses are modulated by many factors—inconsistent response to the same stimuli (sleep, attention, activities, etc)
Central neurons and signal processing
- Relay neurons and inter neurons
- Principle pathway and local circuits
- Excitation and inhibition
- Membrane property variation
Excitation and inhibition doesn’t exist in the ____
Peripheral
Relay neurons deliver single across different ____, inter neurons are ____
Stimuli (long distance), local
Integration of Auditory Function (what are the 3 types)
- Integrate information from single unit studies
- Example in intensity coding of auditory nerve
- Longitude integration (along pathway: ascending and descending innervation)
- Transverse integration: ex: integration across different frequency channels for speech coding
- Cross-modality integration
EEG tests ____ brain activity
Spontaneous
Explain EEG
- Electroencephalography: only largely synchronized brain rhythm can be demonstrated
- Spontaneous brain activity
- Can occur with or without stimulation (always brain activity happen)
Evoked potential is ____ to stimuli
Time locked
Explain time locking
- You know when the response will happen after the stimulation
- Due ton consistency of the time lock, the EVPs can be picked up from large noise by time averaging.
- Detection of such small signal depends on phase/time locking
What is time averaging?
- Time averaging = we can do thousands of sweeps so over time
- You are averaging the response (because every sweep you get a response)
- Noise is random at all times, the noise cancels out each sweep (this is why time averaging works)
- Gets the peak to stand out
What does AER stand for?
Auditory evoked response
What are 5 ways to categorize AER?
- Labelled by latency
- Labelled by stimulus
- Labelled as exogenous or endogenous
- Labelled by the distance between the electrode and the generator
- Labelled by generator
- Labelled by latency
- The most common method of categorization
- Early, middle, and later latency
Explain short latency (5)
Shorter the latency…
- Lower the generators in ascending pathway, therefore smaller in amplitude
- Deeper in location
- Smaller in number of neurons
- More transient for synchrony required
- Less influenced by sleep
ABR has ____ latency, which means it is ____.
Short, low in the ascending pathway
Why is the shortest latency response the smallest amplitude? Where is it located?
The shortest latency response is smallest amplitude because the structure is deeply inside the brainstem (far away from the electrode that is bring used to measure)
Long latency = ____. Where does it directly come from?
Bigger amplitude (Directly from the cortex)
Short latency response can also be called a ____.
Transient response
- When something is labelled by stimulus it can either be ____ or ____.
Transient, sustained
Transient: signals vs. response
- Signal: quick change of signal with time, better transient at onset and offset than other signals (transient = quick change)
- Responses: those rely on the transient feature of signals, e.g., CAP in EcochG, ABR etc.
- Example: click evoked ABR (click is the stimuli which is a transient signal, ABR is also transient)
Why do we need transient?
- Smaller amplitude due to deeper location and smaller amount of neurons
- Larger difference between electrode and target, therefore we need the neurons working together
- Short duration resulting in stronger requirement for synchronization
____ is the most transient auditory evoked response
ABR
Only see transient signal at the ____ and ____ of tone burst. Therefore ____ is the most transient.
onset, offset, click
A transient ____ is needed to produce a transient ____.
Signal, response
Why does ABR require a transient stimulus?
- Early response generated from deeper structure (spatial attenuation)
- Early response generated from smaller number of neurons.
- Action potential of early response has shorter duration, therefore require better synchronization.
Transient vs frequency selectivity
- Transient: signal with short duration, sharp on and off
- Abrupt on and off causes frequency splattering, therefore poor frequency selectivity
- The more transient the stimulus is, the less frequency selective you will have (a very quick onset and offset means there is more chance for splattering)
What is a method for compromising splattering?
Short duration tone with time windows
Short duration means ____.
Broad band
____ are more frequency selective than a click because they ____.
Tone bursts, don’t splatter as much
Explain a click
- what is it (range)
- what is below
- where is synchronization best
- Broad spectrum signal, further limited by transducer (speaker or earphone) but still broad, up limit: ~4-5 kHz
- Evoke below 5 kHz, spread at high intensity
- Synchronization better in high F at basal end due to high speed of traveling wave
Why is a click a broadband signal?
- A click is a broadband signal because it is so short in duration and quickly changes with time
- Therefore, a click is going to have poor frequency selectivity
Explain a click by a 0.1ms pulse
- what is the half power point
- what are the main contributors of ABR?
- what intensity is a cochlear excited at below 5 kHz?
- 0.1 ms pulse is the click that we use (the cut off frequency is at 5 kHz = half power point)
- Between 0 – 5 is the main contributors of the ABR (3kHz – 5 Khz) = better synchronization
- At low to moderate intensity, cochlea is excited below 5kHz
Major contributor to ABR is ____ region
2-5 kHz
Using clicks for ABR will give you the best ____.
Frequency region
Sustained response or steady-state response
- Example: 40 Hz response
- Repeated click presented at a rate of 40 Hz (doesn’t depend on transient, but periodicity)
- Or any signal with periodicity of 40 Hz, such as AM
- You can have a signal with a frequency of 4000 Hz, but you can amplitude modulate it so the periodicity is 40 Hz
What are event-related potentials?
Related to the circumstances under which they are elicited rather than to the physical properties of the signals
What is ASSR?
- what frequencies and where is the generator
- Auditory steady state response
- ASSR at higher frequency: generator moves to brainstem
- ASSR = a clinical method to record sustained response
Why does ERP happen?
It is not entirely clear, it may be related to internal brain activities
steady-state potential is not a response to the ____ of the signal, but to ____.
transient feature, periodicity
What is the advantage for a 40 Hz event related response?
Big amplitude, better frequency selectivity (due to long duration of stimuli)
What is the disadvantage for a 40 Hz event related response?
- Unknown generator, not reliable in children, influenced by sleep (consciousness)
How 40 Hz ASR added up?
If stimuli have periodicity of 40 Hz (25 ms interval), the peaks will add up (the stimuli will match the interval and enhance the signal)
ASSR signals
- carriers
- what does it tell us
- what produces periodicity
- signal energy
- Carriers: could be tone, narrow/wide band noise
- ASSR tell the function of region of carrier frequency (CF)
- Amplitude modulation to produce periodicity: modulation frequency (MF)
- Signal energy: mainly at CF, two sidebands: CF+/-MF
For ASSR use a long-lasting signal with a periodicity of ____
40 Hz