Video games and experiments

Performing a biology experiment is somewhat like playing a role playing video game (RPG). You need to pile a series of success to reach the goal. There are two types of the RPGs. One is the Final Fantasy/Dragonquest- type games, and the other is the Zelda/Metroid-type games.

In the Final Fantasy/Dragonquest-type, all you need to do is to give commands to your character to defeat the enemies and to make him/her stronger and stronger. Tactics and strategies are important. The character will gather a lot of weapons and armors, potions, and dozens of other items in the inventory. The inventory has to be well organized by the player.

On the other hand, games like the Zelda series and Metroid, a player needs to develop his/her own skill and technique to control the character. The player needs to learn how to precisely attack enemies and maneuver quickly from their attacks. Very challenging and even stoic.

I assume those who live on biochemistry and molecular biology may prefer the Final Fantasy/Dragonquest type rather than the Zelda/Metroid type.
I prefer Zelda and Metroid. There I could even feel dopamine being gushed out inside my brain when I defeat the final opponent. I feel similarly when I am having a good result from the electrophysiological experiment.

AxoClamp 900A problems

After using the new amplifier in several experiments, I decided not to use AxoClamp 900A any more. The reasons are as follows:

1) I could never get used to control the amplifier with mouse and keyboard. Especially when I needed to push and buzz at the same time. I often "clear" the electrode by giving a long buzz, but this cannot be done quickly in the new amplifier.

2) The bath-ground of AxoClamp 900A and that of AxoClamp 2B don't like each other, when they share the same bath ground. When 900A ground was used, then 2B shows 60Hz hum, and vice versa. This is a critical problem. I contacted the customer service and this is what they said:

I am not sure I can give you a solution to this. But perhaps it is how the two instruments are plugged into the wall socket. Try keeping a single headstage grounded, but vary the way the instruments are plugged into their power sockets on the wall or power strip.

Who could provide two different AC sources for a rig? I cannot believe they did not even consider for those who use two amplifies at the same time for one dish.

3) The software (or my PC) has some problem. Something in the USB system in my PC reset periodically. When it happens, the Ch1 tab comes to the top even when I am working with Ch2 tab. I often buzzed Ch1 electrode by accident when trying to buzz Ch2. Those tabs are small and I have to really gaze at the monitor to check which one is in front.

Well, it should work fine if you use it alone by itself and know what cell you are poking. Good enough for doing e-phys while imaging. I installed my old 2B amplifier back to my rig.

AxoClamp 900A

This week I installed a brand new Axoclamp 900A (Molecular Devices) in my rig.
The new amplifier has several neat features. One can save the setting of the amplifier as a configuration. This may be good for doing different kinds of experiments routinely in one rig.

They changed the headstages. This is really annoying.
The new headstage somewhat resembles that of Axopatch, but shorter. There is no rod and it is designed to be attached directly onto the manipulator. And, of course, it won’t fit on our manipulator. We use Siskyou’s micromanipulator. Siskyou provides a “dove-tail” headstage connector, which costs like $175 for each. This is a rip off.
So, I constructed two headstage holders by myself from scratch.


Photo: The old headstage (blue) and the new headstage (black).
The “dovetail” slide connectors were made from plastic plates cut out from the microelectrode box (Sutter). A wooden rod ($0.87) was bought at Home Depot. It was cut, carved, grooved, and epoxy-glued upon the dovetail plate. The tightness of the dove tail can be adusted by putting something under the headstage. I use a small amount of dental wax. The total cost is less than a dollar + my labor.

Another feature I don't like is that there are no knobs on the front face of the amplifier. You need to control the capacitance compensation using mouse, or type in, like 8 μF through your computer. It has to be all controlled by PC. Bridge balancing is automatic. This sounds good, but actually it is not. In a real E-phys experiment, you don't really balance the bridge that accurately, because I don't trust bridge at all for measuring input resistances. I mostly use the bridge to keep the output within the voltage range of your AD converter.

This was my first day of using it. I might change my mind after getting used to this machine. I don't like it so far, though.

Enhancing circuit perfomance in injured spinal cord

Dr. Lorne Mendell's talk at Emory, May 21, 2009

Smashed spinal cord
- cell death
- activity-based therapy
Encouraging functional recovery
- reducing cell death
- replace absent cells
- enhancing performance of sensory circuit
a) training
b) neurotrophine-induced synaptic potentiation

Neonatal transection: Step training can enhance stepping performance
- trained animals can walk when they grew up
- shape of the movement is slightly different (less force?)
- ankle angle

Recovery reverses transection-induced changes in monosynaptic EPSPs and AHP
- Change in population of EPSP size and AHP
a) transection reduced the overall size of EPSPs (more small EPSPs than large EPSPs)
b) shift of EPSP population to have more large EPSPs
c) much more large EPSPs than control
d) AHP became larger, but became smaller after training.

Improved stepping performance correlated with change in motoneuron
- Change in AHP depth indicates the ability to fire at high frequency
- Change in EPSP amplitude indicate changes in the sensory feedback from muscle spindle (ankle)

NT-3 (&BNDF)
- motor improvement
= both mimicked by NT-3?
- electrophysiological changes (EPSP, AHP)

NT-3 is required for motoneuronal projections to muscle spindle
Acute sensitization by NTs
- neurotrophic factor (NT-3) sensitize motoneurons.
- for example, it sensitize GluR

Chronic effects of NT-3 on the strength of the mo...

NT-3 strengthen projections of injured & developing spindle afferent to motoneurons
- intraneural NT-3 enhance synapses for axotmized neurons.

Substitute NT-3 for training
- virus that has NT-3 is injected into muscle

Delivery of neurotrophines to intact preparations without trauma: Viral vectors
- AAV/NT-3; expression, 150 days

NT-3 expression profiles differ according to the preparation, and physiological effects differ accordingly
- Cord NT-3 was plotted against DRG NT-3.
- In spinal cord, NT-3 expression is larger in the intact than transected animal.
- In the intact prep, EPSPs became smaller after transection (probably by increase of the motoneuron's size).
- Appearance of large EPSPs for transected animals (by sprouting by presynaptic afferent neurons = DRG neuron)

Input resistance of motor neuron was reduced
- by increase of the motoneuron's size
- contribute to the reduction of the EPSP size

AAV/NT-3 decreases motoneuronal input resistance
- in intact animal, it reduced both EPSP size and Rm
- in transected animal, it only reduced Rm size, but increased the EPSP size.

Ventrolateral white matter (VLF?) synapses persist on motoneurons in chronically transected preparation

Changes after AAV/NT-3 in intact preparations
- the change in EPSP size was synapse specific

Trained animals are different from AAV/NT-3 treated
- Trained animal shows both increase in Rm and EPSP size in the motoneurons.
- c-fos

AVV/NT-3 enhances the stretch-reflex by increased performance in stepping

NT-3 strengthens MG strech pathway by increased EPSP size.

- K. Pearson Exp Br Res (2003)

- Chen Y et al., 2006, JNsc26: 12537.

- Modeling stepping function by a model: Yakovenko et al., (2004)
Stretch reflex enhances stability of CPG circuit

Neurotropin treatment of adult transected preparations (preliminary results).

Homeostatic synapse-driven membrane plasticity in nucleus accumbens neurons

By Ishikawa,M.; Mu,P.; Moyer,J.T.; Wolf,J.A.; Quock,R.M.; Davies,N.M.; Hu,X.T.; Schluter,O.M.; Dong,Y.


Abstract:
- Homeostatic mechanisms balances the input-output/synapse-membrane interaction at nucleus accumbens neurons.
- Studies on nucleus accumbens (NAc) neurons revealed a novel form of synapse-to-membrane homeostatic regulation (hSMP), homeostatic synapse-driven membrane plasticity (hSMP).
- Through hSMP, NAc neurons adjusted their membrane excitability to functionally compensate for basal shifts in excitatory synaptic input.
- hSMP is triggered by synaptic NMDA receptors.

Introduction:- Homeostatic plasticity is an important cellular mechanism through which neurons use the neuroplasticity mechinery to maintain stable functional output in an ever-changing internal and external environment (Turrigiano and Nelson, 2004).
- The functional output of a neuron relies on dynamic integration of synaptic inputs and intrinsic membrane excitability.
- It has long been known that homeostatic plasticity can occur independently at either synapses (Turrigiano and Nelson, 2004) or the membrane excitability (Zhang and Linden, 2003).

Results:
- hSMP in NAc slice cultures: NAc mediam spiny neuron (MSNs) increased excitability in slice culture.
- NMDA receptor mediates hSMP. DCS (D-cycloserine).
- hSMP in acute brain slices.
- Synapse-specific hSMP.
- SK channels mediate the expression of hSMP.
- Implication of hSMP in cocaine -induced membrane adaptation.