Optogenetics Lecture/ Paper 1

Question 1

What are the benefits of optogenetics compared to other brain imaging techniques?

Answer 1

Recording neural activity can most of the times only provide correlations between neural activity and certain phenomena (e.g. neural correlates of attention). However, we are usually interested in finding causal effects, and one possible solution is to manipulate neuronal activity and verify the effects of such manipulations.

Question 2

What is the advantage of optogenetics over methods such as electrical and pharmacological stimulation?

Answer 2

Electrical and pharmacological stimulation are highly effective, but also quite brute, as they lack spatial and cell-type specificity

Question 3

List five further advantages of optogenetics

Answer 3

• Reversible
• Graded (not all-or-none)
• Cell and/or cell-type specific
• Both positive and negative
• High temporal and spatial specificity

Question 4

How do researchers get the light receptive channels into neurons (where from)

Answer 4

They take the channels from algae which use these opsins and use DNA methods to insert them into the neuron membrane

Question 5

Describe the ‘six steps to optogenetics’

Answer 5

Step 1: Piece together the genetic construct (A promotor to drive expression and a gene encoding opsin: light sensitive ion channel)

Step 2: Insert construct into virus

Step 3: Inject virus into animal brain; opsin is expressed in targeted neurons.

Step 4: Insert ‘optrode’, fibre-optic cable plus electrode

Step 5: Laster light of specific wavelength opens ion channel in neurons

Step 6: Record electrophysiological and behavioural results

Question 6

How are target neurons verified?

Answer 6

Using post-mortem histology

Question 7

Why does the experiment have to be timed well?

Answer 7

The virus usually infects the whole brain after a month or so (unless the virus is specifically made to target one type of cell)

Question 8

Describe the properties of the following four opsins:
OptoXR
ChR
HR
BR / PR

Answer 8

ChR is the most widely applied opsin activated by blue light and facilitates the influx of positively charged ions (Na+, Ca 2+, H+) into the membrane through a channel. Thus it causes depolarisation.

HR is activated by yellow/ orange light and allows the influx of negative ions (Cl- etc) into the cell through a pump, therefore aiding hyperpolarisation.

BR/ PR: Is activated by yellow/ orange light and removes photons (H+) from inside the membrane using a pump. This can change the Ph which can cause damage to the cell.

OptoXR: Membrane protein which modulates excitability; not super important to know rn.

Question 9

What is the difference in using an ion channel or pump?

Answer 9

Channel is better because it has a faster current and goes with gradient. Channel pump is more difficult as it requires more energy as it goes against the gradient. You can’t simply use more light as this can cause photobleaching and increase the temperature which can damage and kill cells.§

Question 10

What is the point of using different lights

Answer 10

You can selectively activate different circuits etc

Question 11

What happens generally when the light is turned off?

Answer 11

They are not light switches; it takes some time for the channels to close

Question 12

What three properties should you consider when deciding on an opsin?

Answer 12

• Ionic selectivity / mechanism of action
• Temporal dynamics
• Absorption spectrum

Question 13

Temporally, how should you apply light to the neuron?

Answer 13

It depends; If you don’t care about closing time you can apply continuous polarisation(light being shown contiuously), Pulsed illumination (Light applied for very short time periods repeatedly) can be applied if precise time points are required.

Question 14

When are fast opsins a good option and when are slow opsins a good option

Answer 14

Ultra-fast opsins can go up to 200 Hz and they close very fast. The extent to which opsins are effective is dependent on the Hz; Most opsins are more effective at lower Hz and taper off at higher but ultra-fast opsins are more effective at high Hz.

Slower opsins can be useful for practical reasons in study or to avoid damage to tissue due to light.

Question 15

If you are trying to silence the activity of a single brain area but are not able to utilise hyperpolarising opsins, how could you go about this? (4)

Answer 15

You could stimulate excitatory interneurons which inhibit the neurons of interest. You could also utilise transgenic strategies in order to ensure that it is only expressed in that brain region. You could also decide whether you illuminate somatas or processes and utilise localised injections or precise illumination strategies.

Question 16

A diagram is shown in which a segmented cylinder is shown, with some segments being colour coded and labelled as follows (respectively):

ITR; hSyn; eNpHR 3.0-EYFP; P2A; hChR2-mCherry; WPRE; hGH polyA; ITR

What is this depicting and what do these segments represent?

Answer 16

It is depicting an Opsin being paired with a promoter and fluorescent reporter.

ITR; hSyn; Represents the promoter: a region of DNA upstream of a gene where relevant proteins (such as RNA polymerase and transcription factors) bind to initiate transcription of that gene. The resulting transcription produces an RNA molecule (such as mRNA).,
hSyn stands for human synaptic promoter

eNpHR 3.0-EYFP; P2A; hChR2-mCherry; Is the cleavage site, it contains the opsin and fluorescent reporter.
eNpHR 3.0-EYFP Is the opsin used
P2A are self-cleaving peptides which can induce ribosomal skipping during translation of a protein in a cell
hChR2-mCherry is the fluorescent reporter used to give the infected neurons a red colour

Question 17

It was said that ITR; hSyn; represents the promoter and hSyn stands for the human synaptic promotoer, but what does ITR stand for, what is it and what role does it play?

Answer 17

An inverted repeat (or IR) is a single stranded sequence of nucleotides followed downstream by its reverse complement (e.g 5’—TTACGnnnnnnCGTAA—3’). Inverted repeats have a number of important biological functions. They define the boundaries in transposons (a DNA sequence that can change its position within a genome) and indicate regions capable of self-complementary base pairing (regions within a single sequence which can base pair with each other).

In regards to genetic engineering, inverted DNA repeats stimulate gene editing via double-strand break repair in an episomal context and allude to efficient gene editing of the human chromosome using fragile DNA sequences (Episomes, in eukaryotes, are extrachromosomal, closed circular DNA molecules of a plasmid or a viral genome origin, that are replicated autonomously in the host cell).

In essence, the ITR junction can serve as an origin of viral DNA replication with the Ad genomic plasmid providing all the trans-acting viral factors essential for viral DNA replication.

Question 18

Once this genetic construct is completed, what is next to do in order to insert it into the mouse nerve cells?

Answer 18

First we must introduce it to a viral vector, aka a virus and then inject the viral vector into the area of interest.

Question 19

Describe the following process of using optogenetics in local somata to investigate brain area A, B and C with B being the main area of interest

Answer 19

A virally encoded opsin is injected into the local somata of a neuron in B through a single viral injection. There is then opsin expression throughout B as the virus spreads. Light delivery can then be utilised to activate B cell bodies and observations can be made about the effects and their projections to areas A and C.

Question 20

How can we limit viral expression to specific neuronal subpopulations (e.g. pyramidal cells or interneurons?) (2)

Answer 20

1. Use of cell-type specific promoters
   • Promoter functionality is highly context dependent, as exemplified by gene-specific expression profiles across different tissues and cell types. Cell type-specific promoter regulation is a function of each cell’s unique complement of transcriptional machinery components. Using specific promoters means the injected genes are only expressed in specific cell types
2. Use of cre-lox recombinatrion:
   •Cross two transgenic mouse lines
   •Induce cre-dependent opsin expression in a Cre mouse line

Question 21

Give an example of a cell-type specific promoter and its effect

Answer 21

PAAV-CamKII-ArchT-GFP; PAAV-GFP is the plasmid; -CamKII- is the protein kinase only found in certain cells, -ArchT- is the opsin. It will infect all neurons but will only be expressed in those which contain -CamKII; i.e pyramidal neurons

Question 22

Name five ways of using producing transgenic animals for cell type specific manipulations

Answer 22

In utero electroporation
Viral vectors
Simple transgenic animals
Cre-loxP system: Indicator and driver mice
Comining Cre-driver mice and viral vectors

Question 23

Describe the process of In utero electroporation

Answer 23

In utero electroporation (IUE) is a technique developed to introduce plasmid DNA into embryonic mouse brains, while the animals are still alive in the uterus. First of all the genetic construction is inserted into the expression plasmid. The anaesthetised mouse is opeed to expose the uterine horns (mouse foetuses). The plasmid is then injected into the target neurons of a f via a pressure injection and electroporation (a physical transfection method that uses an electrical pulse to create temporary pores in cell membranes through which substances like nucleic acids can pass into cells). The incision is then closed.

Two days later the suture is reopened and the uterine horns are again exposed, plasmid DNA injection and electroporation is carried out again and autowould clips are placed.

Question 24

Describe the process of viral vectors

Answer 24

The modified vector plasmid is placed in cultured cells with the virus plasmids (e.g AAV-helper). Since viruses have evolved specialised molecular mechanisms to efficiently transport their genomes inside the cells they infect, they can be used to transport the targeted genes into the areas of the mouse nervous system we’re interested in.

Question 25

Describe the process of simple transgenetic animals

Answer 25

The genetic construction can be inserted into the pronuclei (the nucleus of a sperm or egg cell during the process of fertilisation) of a fertilised egg. This egg can then be implanted in the uterus of a ‘foster mother’. The offspring (first generation; F1) should hopefully contain a mouse or mice which express this gene. These mice can then be breed to have more mice which express this gene (second generation; F2)

Question 26

Describe the process of cre-loxP system

Answer 26

The cre-loxP system involves the crossing of Indicator and driver mice. Indicator mice carry an indicator gene in a cre-dependent configuration. This means that the gene is only expressed in the presence of Cre-recombinase. When cre-recominase is not present, genes with stop functions (e.g loxP) prevent the target gene from being expressed and the original gene function is untouched. When cre-recombinase is present, it interacts with the loxP, the original gene function is disrupted and the reporter gene is transcribed instead. The driver mice then carry the Cre only in the target cells in which we want the gene to be expressed. In this way the gene is only expressed in these target cells where both components are present.

Question 27

Describe the process of combining Cre-driver mice and viral vectors

Answer 27

The gene costruction with the lox ‘stop’ genes are combined with virus (e.g AAV) plasmids and these are injected into the target brain regions of cre-driver mice who express cre in target cell types.

Question 28

WHat is an advantage and disadvantage of Cre-loxP?

Answer 28

More flexible and precise but more time consuming

Question 29

For each of the following, indicate the cell expression typically observed if injected into cerebral cortex

In utero electroporation
Viral vectors
Simple transgenic animals
Cre-loxP system: Indicator and driver mice
Comining Cre-driver mice and viral vectors

Answer 29

In utero electroporation: Broad vector of cerebral cortex

Viral vectors: More narrow portion of CC (but spreads)

Simple transgenic animals: All of cerebral cortex (And more?)

Cre-loxP system: Indicator and driver mice: Groups of individual neurons

Comining Cre-driver mice and viral vectors: Groups of individual neurons

Question 30

Describe the following process of recombinase or promoter dependent viral injections to investigate brain area A, B and C with B being the main area of interest

Answer 30

Virally encoded recombinase- or promoter- dependent opsins are inserted into a mixed population of neurons in area B via a single viral injection. Opsin expression is only in neurons expressing recombinase or with an active promoter in B. The illumination of B cell bodies and modulation of recombinase- or promoter expressing cells can then be carried out.

Question 31

Name four properties relevant to the classification of viral vectors for genetic manipulation purposes

Answer 31

•Replicating vs non-replicating
•Anterograde vs. Retrograde
•Tran-synaptic (yes or no)
•Capsid size (∝plasmid length)

Question 32

Would you prefer viruses that replicate or do not replicate? Why?

Answer 32

Viruses which don’t replicate are more safe and usable. Replicating viruses can require bio-safety precautions

Question 33

Why might you be concerned whether the virus travels in the antrograde direction or retrograde?

Answer 33

If you want to investigate connections

Question 34

Why might you want to use transynaptic viruses? Why not?

Answer 34

They can be used to investigate circuits but are the ‘nastiest’ to deal with (rabies; herpes)

Question 35

Give three examples of viral vectors and their properties

Answer 35

•PRV (pseudo-rabies): replicating, anterograde trans-synaptic

•AAV (adeno-associated virus): small, non-replicating, non-trans-synaptic, available in many serotypes (some travel anterogradely, others retrogradely)

•Herpes: mostly retrograde, both replicating and non-replicating, can be trans-synaptic.

Question 36

Describe the following process of projection termination following viral injection to investigate brain area A, B and C with B being the main area of interest

Answer 36

A virally encoded opsin is injected into area B in a single viral injection. This results in opsin expression throughout B. The virus then spreads and opsin is expressed throughout B where neurons project to A and C. Illumination of B axons in A but not C may result in cell bodies in B being activated.

Question 37

Describe the following process of recombinase or promoter dependent viral injections to investigate brain area A, B and C with B being the main area of interest

Answer 37

A virally encoded recombinase-dependent opsin is injected into area B, a second viral injection is then made in A but with a virally encoded lectin-recombinase fusion. The recombinase expressed in A moves transcellularly to cells in B. Opsin expression in B neurons project to A. Illumination of B cell bodies or B axons in A result in activation of the neurons projecting to A without modulation of C.

Question 38

Describe a study which employed a single-cell tracing strategy

Answer 38

(A) Neuron is electroporated with plasmids
(colored circles) coding for a fluorescent marker (e.g., pCAG-mCherry), the TVA receptor (pCMMP.TVA800), and the rabies glycoprotein (pHCMV-RabiesG).

(B) After 1-3 days, SADAG-XFP(EnvA) virus is
applied to the tissue, and infects only the electroported neuron, because no other cells express the EnvA receptor, TVA (red indicates electroporated marker expression; black symbols, TVA and rabies glycoprotein [G]). As the virus replicates in the host neuron, it expresses XFP from the rabies genome, labelling the neuron (green in C; yellow, merge with electroporated marker).

(C) After 3-6 days, the tissue is fixed with paraformaldehyde after time has elapsed for transsynaptic infection (dotted arrow) and expression of the rabies virus and the tissue is visualised with fluorescence microscopy. The virus only transsynaptically infects and labels direct monosynaptic presynaptic inputs (green) to the original host neuron, and not secondary connections (red crosses) because rabies glycoprotein, which is necessary for transsynaptic spread, is expressed only in the electroporated neuron.

Diagram in docs

Question 39

How dangerous are AAV viruses for humans?

Answer 39

They’re not human viruses (but can infect mammalian cells)

Question 40

Briefly review manually activating or deactivating the axon terminal of neurons

Answer 40

It’s easy for excitation and evoke synaptic transmission however this can cause backpropogation which could act as a confound. Stopping an AP is much more difficult once it has begun (stopping the vesicles from being released) but there has been recent progress on it.

Question 41

What are the two main forms of light source used in optogenetics?

Answer 41

LEDs and lasers

Question 42

Give the pros and cons to both light sources

Answer 42

Lasers have a higher intensity and are more accurate as the light comes out in one cylinder. Lasers also have one single frequency. Lasers can be quite expensive.

LEDs have a conical shape and the light is much more dispersed, light is wasted with LEDs. They also have a relatively broad range of frequencies despite appearing as one colour. LEDs are cheaper however

Question 43

Are there any solutions to the LEDs conical shape?

Answer 43

Yes, their light can be focused using a 100-200um optic fiber (at least in vivo)

Question 44

What two differet strategies can be utilised using lasers?

Answer 44

1-photon vs 2-photon:
1-photon is standard; hits focal point and becomes wider again. When a single photon hits the opsin it opens.

2-photon lasers have double wavelength than 1-photon ones; normal opsins will not be very efficient. Only where photons are super concentrated so that two photons hit an opsin not specific to it at exactly the same time will it open.

Question 45

Give an example of single cell illumination

Answer 45

Two-photon laser

Question 46

Give three examples of multiple cell illumination apart from single photon

Answer 46

a. galvo based scanning
b. Direct projection
c. Holographic projection

Question 47

Give three advantages of optogenetics

Answer 47

•A powerful technique to explore causal links in neural systems
•(Relatively) easy to use

•It can be integrated within most experimental setups: in vitro, slices, in vivo, within behavioural paradigms, imaging and electrophysiology…

Question 48

However, to properly use optogenetics many skills are necessary. What are these?

Answer 48

•Molecular biology
•Optics
•Software and hardware (to integrate light into existing setups and experimental paradigms)
•Physiology (to design meaningful experiments)
•Electrophysiology / imaging / behavior etc. etc.

Question 49

Why use 2-photon holographic optogenetics? Could you use standard (1 photon) illumination via an optic fiber? Why?

Answer 49

The authors used two-photon holographic optogenetics because they wanted to observe the behavioural effects of activating one ensemble neuron, or sets of neurons to activate an ensemble without affecting neighbouring neurons. 2-photon illumination provides higher spatial resolution as compared to 1-photon illumination as an opsin requires two photons from the laser to hit it at the exact same time which only occurs at the extremely small focal point of the lasers light, focused by the holographic projection. This makes it very well suited to activating just one neuron at a time. While the addition of an optic fibre to one-photon excitation does increase the spatial resolution significantly, it is still unreasonable to expect it to activate a single neuron and not those around it due to the efficiency at which it activates the opsins. The large wavelengths of 2-photon lasers only activating the opsins at the focal point are what make them so accurate.

Question 50

You read a paper regarding 2-photon illumination in which the authors use a different opsin than the the typical ChR2. What was this and why?

Answer 50

) The authors used the C1V1 opsin as it is more suited to 2-photo illumination than the more commonly used channelrhodopsin. While ChR2 was initially used in two-photon optogenetics research, studies have since shown that some issues are prevalent with its usage, namely it’s reliance on advanced hardware adaptations and larger focal points which spanned outside the intended boundary as well as it’s off-kinetics and maximal photocurrents of optogenetic tools. Research has shown that with the C1V1 variant, the off-kinetics were two to five times slower than ChR2 (Prakash, 2017), facilitating the temporal precision required for fast spike generation. This is very useful for experimental frameworks such as the no-go task. Additionally single-photon illumination resulted in greater photocurrents. C1V1t for example robust action potential generation with only 20mW of laser power was possible as the C1V1 action spectrum is red shifted and thus long illumination wavelength lasers could be used, preventing tissue damage caused by high power lasers. This also prevented power loss due to divided beams or diffraction gratings previously found to be an issue with ChR2. For these reasons, C1V1 was much better suited to 2-photon illumination and this experimental design than ChR2. Additionally the authors used calcium imaging so it made sense to use a differet wavelength of light so that it would not activate the opsins.

Question 51

The authors employed optogenetic activation. Could they have achieved the same results using
optogenetic inhibition? Or would have they obtained different results? Why?

Answer 51

You could have drawn conclusions about the essemble being necessary, not just sufficient

Question 52

The authors focused on excitatory neurons in cortical layer 2-3. Could they have targeted other
neuronal subpopulations, such as interneurons and deep layers? How?

Answer 52

The researchers could have targeted other neuronal subpopulations, such as interneurons and deep layers. However this would require an adaptation to their technique such as introducing the Cre-loxP system rather than simply injecting viral vectors into the area of interest. This could have involved first making a gene construct with the C1V1 opsin or another opsin, the cherry indicator they used, loxP and inverted terminal repeats etc. They could then follow their previous method of introducing this gene construct to a viral vector. This could then be introduced into a cre-driver mouse which has Cre present in the neurons of interest (e.g PV-Cre would result in the expression of cre-recombinase in parvalbumin positive interneurons). The Cre protein would then interact with the loxP in cells in which both were present so that the opsin would be expressed in those neurons while neurons in which only the opsin was present the original gene function would be untouched. This makes selective activation of neural assemblies in slightly deeper layers of the cortex possible, however for deeper structures an optic fibre would likely have to be utilised as the depth of two-photon illumination and imaging (in the mouse brain) is quite superficial (Takasaki, Abbasi-Asl & Waters, 2020). For the same reason they would have to employ a different imaging technique than two-photon calcium imaging, perhaps post-mortem imaging. This comes with significant drawbacks to their illumination and imaging accuracy; two distinct advantages of their study. Thus these other neurons could be targeted albeit with negative consequences for other aspects of their methodology.

Question 53

Could the authors achieve the same results without using optogenetics? Motivate your answer.

Answer 53

There are other methods of stimulating neurons and neuron assemblies in the brain such as that of current injection paradigms. This involves the recording of spike patterns of neurons and the utilisation of an electrode to induce changes in their firing rate via the patch clamp method. These techniques come with significant drawbacks that are solved with optogenetics however. One of these drawbacks is how difficult it is to make these injections anywhere in the cell but the soma, which is problematic as the majority of the synaptic input causes changes to the membrane potential at the dendrites. Additionally it is very difficult to maintain this clamp connection with the cell for any significant amount of time given the tiny size of both the neuron and the tip of the pipette. Targeting one specific neuron in a neuron assembly would be very difficult, require careful precision and the connection and influence on the cell would not be maintained for very long. This would make inciting a neuron throughout the course of several trials of a go\ no go task very difficult in comparison to optogenetics. In addition, the behavioural markers in the task are licks; a behaviour which inherently requires movement of the head. This would be virtually impossible while maintaining the clamp with the neuron. For these reasons I believe that the authors could not have utilised methods other than optogenetics for this experimental design.

Another alternative to optogenetics is the utilisation of chemogenetics. The results would be more attainable with this set of techniques than the patch clamp method, however there are also some considerable drawbacks. Chemogenetics do not offer the same temporal resolution as optogenetics. Since chemogenetics relies on chemical activation, the results can take minutes. This is a significant factor in this design due to the inclusion of a go/ no go task. Such a temporal lag would make the current experimental design very difficult and would require a number of significant adaptations in order to carry it out. Receptor activity is also drawn out longer than optogenetics, providing similar problems.

Question 54

Describe three illumination strategies for the targeting of multiple cells

Answer 54

Galvo-based scanning: This technique typically uses a high-powered laser beam. The illumination is restricted to a single spot at a time, and the intensity of the spot follows a Gaussian distribution. Patterns more complex than a single spot are traced out on the sample by illuminating different points sequentially, commonly by raster or spiral scanning, which are each useful for different experimental conditions.

Direct Projection: Use a mask that will create a light pattern e.g grid. Activate multiple neurons at a time according to mask. Mask and activation pattern MUST be decided beforehand

Holographic projection: Precisely activate multiple neurons at a time, with a customised pattern or spacing between them. Can do it while recording (live). You then decide which of the cells you want to activate and how they are dispersed