ReDiClus Empirical Basis - Revision history

Bradley Monk: Redirected page to Neural Anatomy

2013-10-09T00:37:34Z

← Older revision		Revision as of 17:37, 8 October 2013
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	~~==Quantitative Review==~~		#REDIRECT [[Neural Anatomy]]

	[[~~File:Dendrite 3D.png\|thumb\|left\|400px\|[http://synapses.clm.utexas.edu/anatomy/dendrite/tables/table1.stm Harris Website]]]~~

	~~{{Box\|font=120%\|width=45%\|float=left\|text=12px\|The Size of Dendrites\|~~
	~~;adapted from [http://www.ncbi.nlm.nih.gov/pubmed/17243894 Sheng and Hoogenraad (2007)] {{Fig\|[[File:Spine.png\|1000px]]}}<br>~~
	* Dendrite: 1–10 spines per 10 μm <br>
	* Spines: 0.5–2 μm in length <br>
	* PSD: 100 - 300 nm diameter<br>
	* PSD95: within 12 nm of surface <br>

	~~;adapted from [http://synapses.clm.utexas.edu/anatomy/dendrite/tables/table1.stm Harris] {{Fig\|[[File:Dendrite Table.png]]}}<br>~~
	* proximal dendrite diameter: 1 - 3 µm
	* distal dendrite diameter: 0.2 - 2 µm
	* dendrite length: 2000 - 9000 µm
	* dendrite tip to soma: 100 - 200 µm
	* dendrites at soma: 1 - 5
	* dendrite branches (granual): 10 - 30
	* dendrite branches (purkinje): 400-500

	}}

	~~{{Box\|font=120%\|width=43%\|float=left\|text=12px\|Particle Counts\|~~
	~~;adapted from [http://www.ncbi.nlm.nih.gov/pubmed/17243894 Sheng and Hoogenraad (2007)] {{Fig\|[[File:Spine.png\|1000px]]}}<br>~~
	* PSD: 10,000 proteins (or 100 copies of 100 proteins)<br>
	* CaMKIIα: 7.4% <br>
	* CaMKIIβ: 1.3%<br>
	* SynGap: 2.1 pmol/20 μg<br>
	* NMDAR: 20 proteins<br>
	* AMPAR: 15 proteins<br>
	* GluR: 60 subunits, 15 tetramers, 80% or 12 GluR1/GluR2 heteromers<br>
	* PSD95: within 12 nm of surface <br>

	}}

	~~{{Box\|font=120%\|width=43%\|float=left\|text=12px\|Diffusion Rates\|~~
	~~; from Choquet 2010 {{Fig\|[[File:ChoquetDiffusionRate1.png]]}}<br>~~
	* extrasynaptic: 0.1 µm<sup>2</sup>&frasl;s
	* synaptic: 0.05 µm<sup>2</sup>&frasl;s
	* synaptic after glu/gly: 0.01 µm<sup>2</sup>&frasl;s

	}}

	~~{{Box\|font=120%\|width=43%\|float=left\|text=12px\|Images\|~~
	~~; From [http://www.ncbi.nlm.nih.gov/pubmed/17243894 Sheng and Hoogenraad 2007]~~
	* Spine morphology {{Fig\|[[File:Spine.png\|1000px]]}}

	~~; From [http://www.ncbi.nlm.nih.gov/pubmed/22357909 Harris KM and Weinberg 2012]~~
	* Spine morphology {{Fig\|[[File:Synaptic Buton.png]]\|3D reconstruction of a proximal CA3 pyramidal cell dendrite (blue) and a large mossy fiber bouton (translucent yellow). The cut-away in C2 shows synapses (red) onto multiple dendritic spines, some of which are highly branched. The bouton also forms nonsynaptic cell adhesion junctions (fuchsia).}}
	* Hippocampal dendrite {{Fig\|[[ File:Hippocampal Neuron.jpg]]}}

	}}




	~~{{Box\|font=120%\|width=43%\|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.

	~~<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=43%\|float=left\|text=12px\|Choquet 2007 Real Time Receptor Diffusion Analysis\|~~
	* The video represents a 10µm × 10µm section scaled to a 535px × 535px video.
	** {{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>}}
	** 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>~~

	}}


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






	~~{{PageHead\|[[Malinow]]\|[[Molecular Methods]]\|[[Quantum Dots]]\|[[Choquet]]\|[[AMPAR]]}}~~
	~~[[Category:Malinow]] [[Category:ReDiClus~~]]

Bradley Monk at 23:25, 24 August 2013

2013-08-24T23:25:43Z

← Older revision		Revision as of 16:25, 24 August 2013
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	==Quantitative Review==		==Quantitative Review==

	[[File:Dendrite 3D.png\|thumb\|left\|~~500px~~\|[http://synapses.clm.utexas.edu/anatomy/dendrite/tables/table1.stm Harris Website]]]		[[File:Dendrite 3D.png\|thumb\|left\|400px\|[http://synapses.clm.utexas.edu/anatomy/dendrite/tables/table1.stm Harris Website]]]

	{{Box\|font=120%\|width=45%\|float=left\|text=12px\|The Size of Dendrites\|		{{Box\|font=120%\|width=45%\|float=left\|text=12px\|The Size of Dendrites\|
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	}}		}}

	{{Box\|font=120%\|width=45%\|float=left\|text=12px\|Particle Counts\|		{{Box\|font=120%\|width=43%\|float=left\|text=12px\|Particle Counts\|
	;adapted from [http://www.ncbi.nlm.nih.gov/pubmed/17243894 Sheng and Hoogenraad (2007)] {{Fig\|[[File:Spine.png\|1000px]]}}<br>		;adapted from [http://www.ncbi.nlm.nih.gov/pubmed/17243894 Sheng and Hoogenraad (2007)] {{Fig\|[[File:Spine.png\|1000px]]}}<br>
	* PSD: 10,000 proteins (or 100 copies of 100 proteins)<br>		* PSD: 10,000 proteins (or 100 copies of 100 proteins)<br>
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	}}		}}

	{{Box\|font=120%\|width=45%\|float=left\|text=12px\|Diffusion Rates\|		{{Box\|font=120%\|width=43%\|float=left\|text=12px\|Diffusion Rates\|
	; from Choquet 2010 {{Fig\|[[File:ChoquetDiffusionRate1.png]]}}<br>		; from Choquet 2010 {{Fig\|[[File:ChoquetDiffusionRate1.png]]}}<br>
	* extrasynaptic: 0.1 µm<sup>2</sup>&frasl;s		* extrasynaptic: 0.1 µm<sup>2</sup>&frasl;s
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	}}		}}

	{{Box\|font=120%\|width=45%\|float=left\|text=12px\|Images\|		{{Box\|font=120%\|width=43%\|float=left\|text=12px\|Images\|
	; From [http://www.ncbi.nlm.nih.gov/pubmed/17243894 Sheng and Hoogenraad 2007]		; From [http://www.ncbi.nlm.nih.gov/pubmed/17243894 Sheng and Hoogenraad 2007]
	* Spine morphology {{Fig\|[[File:Spine.png\|1000px]]}}		* Spine morphology {{Fig\|[[File:Spine.png\|1000px]]}}
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	{{Box\|font=120%\|width=45%\|float=left\|text=12px\|Choquet 2007 Real Time Receptor Diffusion\|		{{Box\|font=120%\|width=43%\|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=45%\|float=left\|text=12px\|Choquet 2007 Real Time Receptor Diffusion Analysis\|		{{Box\|font=120%\|width=43%\|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>}}

Bradley Monk: Created page with "==Quantitative Review== [http://synapses.clm.utexas.edu/anatomy/dendrite/tables/table1.stm Harris Website] {{Box|font=120%|width=45..."

2013-08-24T23:21:39Z

Created page with "==Quantitative Review== thumb|left|500px|[http://synapses.clm.utexas.edu/anatomy/dendrite/tables/table1.stm Harris Website] {{Box|font=120%|width=45..."

New page

==Quantitative Review==

[[File:Dendrite 3D.png|thumb|left|500px|[http://synapses.clm.utexas.edu/anatomy/dendrite/tables/table1.stm Harris Website]]]

{{Box|font=120%|width=45%|float=left|text=12px|The Size of Dendrites|
;adapted from [http://www.ncbi.nlm.nih.gov/pubmed/17243894 Sheng and Hoogenraad (2007)] {{Fig|[[File:Spine.png|1000px]]}} 
* Dendrite: 1–10 spines per 10 μm 
* Spines: 0.5–2 μm in length 
* PSD: 100 - 300 nm diameter 
* PSD95: within 12 nm of surface 

;adapted from [http://synapses.clm.utexas.edu/anatomy/dendrite/tables/table1.stm Harris] {{Fig|[[File:Dendrite Table.png]]}} 
* proximal dendrite diameter: 1 - 3 µm
* distal dendrite diameter: 0.2 - 2 µm
* dendrite length: 2000 - 9000 µm
* dendrite tip to soma: 100 - 200 µm
* dendrites at soma: 1 - 5
* dendrite branches (granual): 10 - 30
* dendrite branches (purkinje): 400-500

}}

{{Box|font=120%|width=45%|float=left|text=12px|Particle Counts|
;adapted from [http://www.ncbi.nlm.nih.gov/pubmed/17243894 Sheng and Hoogenraad (2007)] {{Fig|[[File:Spine.png|1000px]]}} 
* PSD: 10,000 proteins (or 100 copies of 100 proteins) 
* CaMKIIα: 7.4% 
* CaMKIIβ: 1.3% 
* SynGap: 2.1 pmol/20 μg 
* NMDAR: 20 proteins 
* AMPAR: 15 proteins 
* GluR: 60 subunits, 15 tetramers, 80% or 12 GluR1/GluR2 heteromers 
* PSD95: within 12 nm of surface 

}}

{{Box|font=120%|width=45%|float=left|text=12px|Diffusion Rates|
; from Choquet 2010 {{Fig|[[File:ChoquetDiffusionRate1.png]]}} 
* extrasynaptic: 0.1 µm2&frasl;s
* synaptic: 0.05 µm2&frasl;s
* synaptic after glu/gly: 0.01 µm2&frasl;s

}}

{{Box|font=120%|width=45%|float=left|text=12px|Images|
; From [http://www.ncbi.nlm.nih.gov/pubmed/17243894 Sheng and Hoogenraad 2007]
* Spine morphology {{Fig|[[File:Spine.png|1000px]]}}

; From [http://www.ncbi.nlm.nih.gov/pubmed/22357909 Harris KM and Weinberg 2012]
* Spine morphology {{Fig|[[File:Synaptic Buton.png]]|3D reconstruction of a proximal CA3 pyramidal cell dendrite (blue) and a large mossy fiber bouton (translucent yellow). The cut-away in C2 shows synapses (red) onto multiple dendritic spines, some of which are highly branched. The bouton also forms nonsynaptic cell adhesion junctions (fuchsia).}}
* Hippocampal dendrite {{Fig|[[ File:Hippocampal Neuron.jpg]]}}

}}

{{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.

<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=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.
** {{Button|1'''µm''' : 53.5'''px'''}}
* 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<var>v</var> ≈ 1'''µm''' &frasl; 200'''ms'''}}
** 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>

}}

{{Box|font=120%|width=95%|float=left|text=12px|Receptor Diffusion Rate Best Estimates|
* GABAA: .01 - .05 µm2/s {{Fig|[[File:Choquet1 2010.png]]|[http://www.sciencedirect.com/science/article/pii/S0896627310004654 Choquet 2010]}}
}}

{{PageHead|[[Malinow]]|[[Molecular Methods]]|[[Quantum Dots]]|[[Choquet]]|[[AMPAR]]}}
[[Category:Malinow]] [[Category:ReDiClus]]