Malinow - Revision history

Bradley Monk at 00:35, 26 August 2013

2013-08-26T00:35:43Z

← Older revision		Revision as of 17:35, 25 August 2013
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	{{PageHead\|[[Malinow]]\|[[~~Molecular Methods~~]]\|[[Quantum Dots]]\|[[Choquet]]\|[[AMPAR]]}}		{{PageHead\|[[Malinow]]\|[[ReDiClus]]\|[[Quantum Dots]]\|[[Choquet]]\|[[AMPAR]]}}
	[[:Category:Malinow]]		[[:Category:Malinow]][[:Category:ReDiClus]]

	~~{{:ReDiClus}}~~

	==Experiment Notes==		==Experiment Notes==

Bradley Monk: /* 2009 */

2013-08-20T22:26:37Z

2009

← Older revision		Revision as of 15:26, 20 August 2013
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	==2009==		==2009==
			{{Article\|Makino Malinow\|2009\|Cell - [http://www.ncbi.nlm.nih.gov/pubmed/19914186 PDF]\|19914186\|AMPA receptor incorporation into synapses during LTP: the role of lateral movement and exocytosis}}{{ExpandBox\|Expand to view experiment summary\|

			;Abstract
			The regulated trafficking of AMPA receptors (AMPARs) to synapses is thought to underlie the enhanced transmission in long-term potentiation (LTP), a cellular model of memory. However, there is controversy regarding the nonsynaptic site, either on the surface or intracellularly, from which AMPARs move into synapses during LTP. Using recombinant surface-fluorescent receptors in organotypic rat hippocampal slices, we show that the majority of AMPARs incorporated into synapses during LTP is from lateral diffusion of spine surface receptors containing GluR1, anAMPARsubunit. Following synaptic potentiation, AMPARs in intracellular pools containing GluR1 are driven to the surface primarily on dendrites. These exocytosed receptors likely serve to replenish the local extrasynaptic pool available for subsequent bouts of plasticity. These results clarify the role of intracellular and surface AMPARs during synaptic plasticity.



			}}<!-- END ARTICLE -->




	{{Article\|Kessels, Kopec, Klein, Malinow\|2009\|Nat Neurosci. - [http://www.nature.com/neuro/journal/v12/n7/pdf/nn.2340.pdf PDF]\|19543281\|Roles of stargazin and phosphorylation in the control of AMPA receptor subcellular distribution}}{{ExpandBox\|Expand to view experiment summary\|		{{Article\|Kessels, Kopec, Klein, Malinow\|2009\|Nat Neurosci. - [http://www.nature.com/neuro/journal/v12/n7/pdf/nn.2340.pdf PDF]\|19543281\|Roles of stargazin and phosphorylation in the control of AMPA receptor subcellular distribution}}{{ExpandBox\|Expand to view experiment summary\|

Bradley Monk at 02:36, 5 August 2013

2013-08-05T02:36:06Z

← Older revision		Revision as of 19:36, 4 August 2013
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	[[Category:Malinow]]		[[Category:Malinow]] [[Category:ReDiClus]]
	__NOTOC__		__NOTOC__

Bradley Monk: /* Diffusion and Cluster Model of LTP */

2013-07-30T05:03:12Z

Diffusion and Cluster Model of LTP

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 [[:Category:Malinow]]
-==Diffusion and Cluster Model of LTP==
+{{:ReDiClus}}
 ==Experiment Notes==

Bradley Monk: /* Diffusion and Cluster Model of LTP */

2013-07-29T01:11:36Z

Diffusion and Cluster Model of LTP

← Older revision		Revision as of 18:11, 28 July 2013
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	*** where R<sub>step</sub> is the baseline Red dot step size		*** where R<sub>step</sub> is the baseline Red dot step size
	*** where B<sub>n</sub> is number of Blue dots currently expressed at the PSD surface		*** where B<sub>n</sub> is number of Blue dots currently expressed at the PSD surface
	}}

	{{~~Box\|font=120%\|width=95%\|float=left\|text=12px\|Visual Representations~~\|		; Several screen shots of the dynamic graphs in the model
	[[File:Matlab Sim3.png~~\|500px~~]][[File:Matlab Sim2.png~~\|500px~~]]		: {{Fig\|[[File:Matlab Sim3.png]]}}
			: {{Fig\|[[File:Matlab Sim2.png]]}}
	}}		}}


	~~[[File:Spine.png~~\|~~thumb~~\|left\|~~1000px~~\|		{{Box\|font=120%\|width=95%\|float=left\|text=12px\|The Size of Dendrites\|
	• Dendrite: 1–10 spines per μm <br>		• Dendrite: 1–10 spines per μm <br>
	• Spines: 0.5–2 μm in length <br>		• Spines: 0.5–2 μm in length <br>
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	• PSD95: within 12 nm of surface <br><br>		• PSD95: within 12 nm of surface <br><br>
	• adapted from: [http://www.ncbi.nlm.nih.gov/pubmed/17243894 Sheng and Hoogenraad (2007) The postsynaptic architecture of excitatory synapses: a more quantitative view. Annu Rev Biochem, 76:823-47.]		• adapted from: [http://www.ncbi.nlm.nih.gov/pubmed/17243894 Sheng and Hoogenraad (2007) The postsynaptic architecture of excitatory synapses: a more quantitative view. Annu Rev Biochem, 76:823-47.]
	]]

			<big>Mouse over to see the visual: {{Fig\|[[File:Spine.png\|1000px]]}}</big>

			}}



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	]]		]]

	{{Box\|font=120%\|width=60%\|float=left\|text=12px\|Choquet 2007 Real Time Receptor Diffusion\|		{{Box\|font=120%\|width=45%\|float=left\|text=12px\|Choquet 2007 Real Time Receptor Diffusion\|
	[http://bradleymonk.com/media/QdotsRealTime.mov This link is to a video] of an optimized version from [http://www.cell.com/neuron/supplemental/S0896-6273%2807%2900289-9 Choquet 2007] (seen below). The dimensions in both 10 x 10 µm. The original version below is run at 4x real-time. The linked video above is slowed to 1x real-time, and all analysis is done at 1:1 video to real-time speed.		[http://bradleymonk.com/media/QdotsRealTime.mov This link is to a video] of an optimized version from [http://www.cell.com/neuron/supplemental/S0896-6273%2807%2900289-9 Choquet 2007] (seen below). The dimensions in both 10 x 10 µm. The original version below is run at 4x real-time. The linked video above is slowed to 1x real-time, and all analysis is done at 1:1 video to real-time speed.

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	}}		}}

	{{Box\|font=120%\|width=95%\|float=left\|text=12px\|Choquet 2007 Real Time Receptor Diffusion Analysis\|		{{Box\|font=120%\|width=45%\|float=left\|text=12px\|Choquet 2007 Real Time Receptor Diffusion Analysis\|

	* The video represents a 10µm × 10µm section scaled to a 535px × 535px video.		* The video represents a 10µm × 10µm section scaled to a 535px × 535px video.
	** {{Button\|1<sub>'''µm'''</sub> : 53.5<sub>'''px'''</sub>}}		** {{Button\|1<sub>'''µm'''</sub> : 53.5<sub>'''px'''</sub>}}
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	** That is a distance of 52.2px in 200ms		** That is a distance of 52.2px in 200ms
	** Qdot velocity: {{Button\|Q<sub><var>v</var></sub> ≈ 1<sub>'''µm'''</sub> &frasl; 200<sub>'''ms'''</sub>}}		** Qdot velocity: {{Button\|Q<sub><var>v</var></sub> ≈ 1<sub>'''µm'''</sub> &frasl; 200<sub>'''ms'''</sub>}}
			** Note this diffusion rate of 5µm/s is 10-fold higher than the median diffusion rate reported above.
			** An upper bound of 5µm/s means that receptors can move between synapses in fractions of a second.

			<big>Figures:
			:{{Fig\|[[File:Choquet Diffusion Rate Analysis1.png]]}}
			:{{Fig\|[[File:Choquet Diffusion Rate Analysis2.png]]}}
			:{{Fig\|[[File:Choquet RT1.png]]}}
			:{{Fig\|[[File:Choquet RT2.png]]}}
			</big>

			}}


	~~[[File:Choquet~~ Diffusion Rate ~~Analysis1.png~~\|~~500px]][[File~~:~~Choquet Diffusion Rate Analysis2~~.~~png~~\|~~500px]]~~		{{Box\|font=120%\|width=95%\|float=left\|text=12px\|Receptor Diffusion Rate Best Estimates\|
	[[File:~~Choquet RT1~~.png]][~~[File~~:Choquet ~~RT2.png]~~]		* GABAA: .01 - .05 µm<sup>2</sup>/s {{Fig\|[[File:Choquet1 2010.png]]\|[http://www.sciencedirect.com/science/article/pii/S0896627310004654 Choquet 2010]}}

	}}		}}

Bradley Monk: /* Diffusion and Cluster Model of LTP */

2013-07-29T00:25:14Z

Diffusion and Cluster Model of LTP

← Older revision		Revision as of 17:25, 28 July 2013
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	{{Box\|font=120%\|width=95%\|float=left\|text=12px\|Choquet 2007 Real Time Receptor Diffusion Analysis\|		{{Box\|font=120%\|width=95%\|float=left\|text=12px\|Choquet 2007 Real Time Receptor Diffusion Analysis\|

	* The video represents a ~~10x10 µm~~ section scaled to a ~~535x535 px~~ video.		* The video represents a 10µm × 10µm section scaled to a 535px × 535px video.
	** {{Button\|~~1µm~~ : 53.~~5px~~}}		** {{Button\|1<sub>'''µm'''</sub> : 53.5<sub>'''px'''</sub>}}
			* The analysis below documents one instance of Qdot diffusion, between the 6s-7s time points.
			* This instance was chosen because of the clarity of motion and no Qdot flicker.
			* The Qdot (center) moves from pixel location (X:291, Y:302) at 6.78s to (X:319, Y346) at 6.98s
			** That is a distance of 52.2px in 200ms
			** Qdot velocity: {{Button\|Q<sub><var>v</var></sub> ≈ 1<sub>'''µm'''</sub> &frasl; 200<sub>'''ms'''</sub>}}

	[[File:Choquet Diffusion Rate Analysis1.png\|500px]][[File:Choquet Diffusion Rate Analysis2.png\|500px]]		[[File:Choquet Diffusion Rate Analysis1.png\|500px]][[File:Choquet Diffusion Rate Analysis2.png\|500px]]
			[[File:Choquet RT1.png]][[File:Choquet RT2.png]]

	}}		}}

Bradley Monk: /* Diffusion and Cluster Model of LTP */

2013-07-28T23:55:25Z

Diffusion and Cluster Model of LTP

← Older revision		Revision as of 16:55, 28 July 2013
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	}}		}}

	[[File:3D Model.png\|~~400px~~]]		{{Box\|font=120%\|width=95%\|float=left\|text=12px\|Visual Representations\|
			[[File:3D Model.png\|500px]][[File:Model 3d space.png\|500px]]
			}}

	{{Box\|font=120%\|width=60%\|float=left\|text=12px\|two independent processes\|		{{Box\|font=120%\|width=95%\|float=left\|text=12px\|two independent processes\|
	;In this model, there are two independently occurring processes.		; In this model, there are two independently occurring processes.
	* 1. Blue dots can be expressed at the surface or internalized within their PSD area		* 1. Blue dots can be expressed at the surface or internalized within their PSD area
	** The Blue dot internalization/externalization rate properties are set by the Shouval cluster model equations.		** The Blue dot internalization/externalization rate properties are set by the Shouval cluster model equations.
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	;The step size for Red dots is dynamically altered when it's located in a PSD area		; The step size for Red dots is dynamically altered when it's located in a PSD area
	* In a PSD, the step size is reduced by a by some factor based on the number of Blue dots currently expressed at the surface of that PSD		* In a PSD, the step size is reduced by a by some factor based on the number of Blue dots currently expressed at the surface of that PSD
	* The more Blue dots at the surface, the more the step size is reduced		* The more Blue dots at the surface, the more the step size is reduced
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	*** where R<sub>step</sub> is the baseline Red dot step size		*** where R<sub>step</sub> is the baseline Red dot step size
	*** where B<sub>n</sub> is number of Blue dots currently expressed at the PSD surface		*** where B<sub>n</sub> is number of Blue dots currently expressed at the PSD surface
			}}

			{{Box\|font=120%\|width=95%\|float=left\|text=12px\|Visual Representations\|
			[[File:Matlab Sim3.png\|500px]][[File:Matlab Sim2.png\|500px]]
	}}		}}

	~~[[File:Model 3d space.png\|thumb\|500px]]~~
	~~[[File:Matlab Sim3.png\|500px]]~~

	~~[[File:Matlab Sim2.png\|500px]]~~

	[[File:Spine.png\|thumb\|left\|1000px\|		[[File:Spine.png\|thumb\|left\|1000px\|
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	]]		]]

	{{Box\|font=120%\|width=60%\|float=left\|text=12px\|Real Time Receptor Diffusion\|		{{Box\|font=120%\|width=60%\|float=left\|text=12px\|Choquet 2007 Real Time Receptor Diffusion\|
	[http://bradleymonk.com/media/QdotsRealTime.mov This video] is an optimized version from [http://www.cell.com/neuron/supplemental/S0896-6273%2807%2900289-9 Choquet 2007]. The dimensions ~~are~~ 10 x 10 µm.		[http://bradleymonk.com/media/QdotsRealTime.mov This link is to a video] of an optimized version from [http://www.cell.com/neuron/supplemental/S0896-6273%2807%2900289-9 Choquet 2007] (seen below). The dimensions in both 10 x 10 µm. The original version below is run at 4x real-time. The linked video above is slowed to 1x real-time, and all analysis is done at 1:1 video to real-time speed.

			<html>
			<iframe src="http://bradleymonk.com/media/QD1/vid1.html"
			height="470" width="470" frameborder="0" seamless="seamless" style="float:left">
			</iframe>
			</html>

			}}

			{{Box\|font=120%\|width=95%\|float=left\|text=12px\|Choquet 2007 Real Time Receptor Diffusion Analysis\|

			* The video represents a 10x10 µm section scaled to a 535x535 px video.
			** {{Button\|1µm : 53.5px}}


			[[File:Choquet Diffusion Rate Analysis1.png\|500px]][[File:Choquet Diffusion Rate Analysis2.png\|500px]]


	}}		}}

Bradley Monk: /* Diffusion and Cluster Model of LTP */

2013-07-28T21:35:28Z

Diffusion and Cluster Model of LTP

← Older revision		Revision as of 14:35, 28 July 2013
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	]]		]]

			{{Box\|font=120%\|width=60%\|float=left\|text=12px\|Real Time Receptor Diffusion\|
			[http://bradleymonk.com/media/QdotsRealTime.mov This video] is an optimized version from [http://www.cell.com/neuron/supplemental/S0896-6273%2807%2900289-9 Choquet 2007]. The dimensions are 10 x 10 µm.
			}}

	}}<!-- END MODEL -->		}}<!-- END MODEL -->

Bradley Monk: /* Diffusion and Cluster Model of LTP */

2013-07-28T01:05:23Z

Diffusion and Cluster Model of LTP

← Older revision		Revision as of 18:05, 27 July 2013
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	• Dendrite: 1–10 spines per μm <br>		• Dendrite: 1–10 spines per μm <br>
	• Spines: 0.5–2 μm in length <br>		• Spines: 0.5–2 μm in length <br>
			• PSD: 100 - 300 nm diameter
	• PSD: 10,000 proteins (or 100 copies of 100 proteins)<br>		• PSD: 10,000 proteins (or 100 copies of 100 proteins)<br>
	• CaMKIIα: 7.4% <br>		• CaMKIIα: 7.4% <br>
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	• SynGap: 2.1 pmol/20 μg<br>		• SynGap: 2.1 pmol/20 μg<br>
	• NMDAR: 20 proteins<br>		• NMDAR: 20 proteins<br>
	• AMPAR: 60 subunits (15 tetramers, 80% or 12 GluR1/GluR2 heteromers)<br>		• AMPAR: 15 proteins
			• GluR: 60 subunits, 15 tetramers, 80% or 12 GluR1/GluR2 heteromers<br>
	• PSD95: within 12 nm of surface <br><br>		• PSD95: within 12 nm of surface <br><br>
	• adapted from: [http://www.ncbi.nlm.nih.gov/pubmed/17243894 Sheng and Hoogenraad (2007) The postsynaptic architecture of excitatory synapses: a more quantitative view. Annu Rev Biochem, 76:823-47.]		• adapted from: [http://www.ncbi.nlm.nih.gov/pubmed/17243894 Sheng and Hoogenraad (2007) The postsynaptic architecture of excitatory synapses: a more quantitative view. Annu Rev Biochem, 76:823-47.]
			]]


			[[File:ChoquetDiffusionRate1.png\|thumb\|left\|700px\|
			• Diffusion rate was measured as µm<sup>2</sup>/s <br>
			• Below are the linearized median diffusion rates <br>
			• Dendrite: 0.8 µm/s <br>
			• PSD: 0.4 - 0.1 µm/s <br>
			• PSDp: 0.1 - 0.01 µm/s <br><br>
			• from: [http://www.ncbi.nlm.nih.gov/pubmed/20670832 Choquet et al (2010) CaMKII triggers the diffusional trapping of surface AMPARs through phosphorylation of stargazin. Neuron]
	]]		]]

Bradley Monk: /* Diffusion and Cluster Model of LTP */

2013-07-28T00:03:48Z

Diffusion and Cluster Model of LTP

← Older revision		Revision as of 17:03, 27 July 2013
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	[[File:Matlab Sim2.png\|500px]]		[[File:Matlab Sim2.png\|500px]]

	[[File:Spine.png\|thumb\|left\|~~800px~~\|		[[File:Spine.png\|thumb\|left\|1000px\|
	• Dendrite: 1–10 spines per μm <br>		• Dendrite: 1–10 spines per μm <br>
	• Spines: 0.5–2 μm in length <br>		• Spines: 0.5–2 μm in length <br>