STARShiP - Revision history

Bradley Monk at 04:13, 24 July 2014

2014-07-24T04:13:02Z

← Older revision		Revision as of 21:13, 23 July 2014
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			==Quantitative Review==

			[[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>

	[[Category:ReDiClus]]		}}

			{{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\|[[STARShiP]]\|[[Molecular Methods]]\|[[Quantum Dots]]\|[[AMPAR]]\|[[Brownian Motion]]}}

			[[Category:ReDiClus]] [[Category:Neurobiology]]

Bradley Monk at 01:43, 17 July 2014

2014-07-17T01:43:11Z

← Older revision		Revision as of 18:43, 16 July 2014
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	~~http://gfycat.com/GloriousSnarlingBabirusa~~

	<syntaxhighlight lang="matlab" line start="1" highlight="1" enclose="div">		<syntaxhighlight lang="matlab" line start="1" highlight="1" enclose="div">
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	% SPINE RADIAL DISTANCE		% SPINE RADIAL DISTANCE
	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
	~~%SGr={ G1P1r, G1P2r, G2P1r, G2P2r,~~
	~~% G1inP1, G1inP2, G2inP1, G2inP2,~~
	~~% G1xyP1, G1xyP2, G2xyP1, G2xyP2 };~~
	~~doRadDist = 1;~~
	~~doRadDistDPlots=1;~~
	~~if doRadDist~~



	%=================================================		%=================================================
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	yL = sqrt(Qhr.^2 - QxL.^2);		yL = sqrt(Qhr.^2 - QxL.^2);
	Qr = sqrt(Qx.^2 + yL.^2); % Concentric circles		Qr = sqrt(Qx.^2 + yL.^2); % Concentric circles



	</syntaxhighlight>		</syntaxhighlight>




	~~{{ExpandBox\|Expand to view experiment summary\|~~
	~~;Introduction~~
	*The cellular traffic of neurotransmitter receptors has
	~~}}<!-- END ExpandBox -->~~

Bradley Monk at 01:41, 17 July 2014

2014-07-17T01:41:47Z

← Older revision		Revision as of 18:41, 16 July 2014
Line 1:		Line 1:

			{{ExpandBox\|Expand to view experiment animation\|
			<html><iframe src="http://gfycat.com/ifr/GloriousSnarlingBabirusa" frameborder="0" scrolling="no" width="756" height="428" style="-webkit-backface-visibility: hidden;-webkit-transform: scale(1);" ></iframe></html>
			}}<!-- END ExpandBox -->

	~~{{Popup\|<html><iframe src="http://gfycat.com/ifr/GloriousSnarlingBabirusa"~~
	~~frameborder="0" scrolling="no" width="756" height="428" ></iframe></html>}}~~


			http://gfycat.com/GloriousSnarlingBabirusa

	<syntaxhighlight lang="matlab" line start="1" highlight="1" enclose="div">		<syntaxhighlight lang="matlab" line start="1" highlight="1" enclose="div">

Bradley Monk at 00:51, 17 July 2014

2014-07-17T00:51:26Z

← Older revision		Revision as of 17:51, 16 July 2014
Line 1:		Line 1:


			{{Popup\|<html><iframe src="http://gfycat.com/ifr/GloriousSnarlingBabirusa"
	{{Popup\|<html><iframe src="http://gfycat.com/ifr/GloriousSnarlingBabirusa" frameborder="0" scrolling="no" width="756" height="428~~" style="-webkit-backface-visibility: hidden;-webkit-transform: scale(1);~~" ></iframe></html>}}		frameborder="0" scrolling="no" width="756" height="428" ></iframe></html>}}


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


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			{{ExpandBox\|Expand to view experiment summary\|

	{{Article\|Groc, et-al, Choquet, Cognet\|2007\|J Neuro - [http://bradleymonk.com/media/Choquet2007A.pdf PDF]\|18003820\|Surface trafficking of neurotransmitter receptor: comparison between single-molecule/quantum dot strategies}}{{ExpandBox\|Expand to view experiment summary\|
	;Introduction		;Introduction
	*The cellular traffic of neurotransmitter receptors has captured a lot of attention over the last decade, mostly because synaptic receptor number is adjusted during synaptic development and plasticity. Although each neurotransmitter receptor family has its own trafficking characteristics, two main modes of receptor delivery to the synapse have emerged: endo-exocytotic cycling and surface diffusion [e.g., for glutamatergic receptors, see Bredt and Nicoll (2003) and Groc and Choquet (2006)]. Receptor cycling through endo-exocytotic processes can be measured by several experimental means, from biochemical to imaging assays. The use of fluorescent protein (XFP)-tag imaging provides a powerful approach to investigate the trafficking of receptor clusters between neuronal compartments (e.g., soma, dendrite, spine) (Kennedy and Ehlers, 2006). A disadvantage of the XFP-tag approach in live experiment is extreme difficulty in detecting XFP fluorescence signals from small nonclustered receptor pool (Cognet et al., 2002; Lippincott-Schwartz and Patterson, 2003). XFP-tagged neurotransmitter receptors are often present in several cellular compartments from the endoplasmic reticulum to the plasma membrane with various relative contents. For instance, surface XFP-tagged neurotransmitter receptors represent only a minor fraction of the total receptor population, precluding their specific detection. Alternative live-cell imaging approaches were thus required to specifically isolate surface receptors. Interestingly, a variant of the green fluorescent protein (GFP), ecliptic pHluorin, shows a reversible excitation ratio change between pH 7.5 and 5.5, and its absorbance decreases as the pH is lowered. Most neurotransmitter receptors, including the ionotropic glutamate ones, display an extracellular N-terminal region, implying that the N terminus will always be in an acidic environment inside the cell, whereas it will be exposed to a neutral pH after insertion into the plasma membrane. By this means, surface receptors can be specifically detected and tracked with live-imaging approaches (Ashby et al., 2004). Alternatively, surface receptors can be labeled and detected by immunocytochemical approaches using antibodies directed against receptor extracellular epitopes. The purpose of this Toolbox is to outline currently available approaches to measure the surface trafficking of receptor in neurons, with a special emphasis on single-molecule (organic dye) and quantum dot ([[Qdot\|QDot]]) detection for neurotransmitter receptor tracking.		*The cellular traffic of neurotransmitter receptors has
	}}<!-- END ~~ARTICLE~~ -->		}}<!-- END ExpandBox -->

Bradley Monk: Protected "STARShiP" (‎[edit=sysop] (indefinite) ‎[move=sysop] (indefinite) ‎[read=sysop] (indefinite))

2014-07-17T00:44:14Z

Protected "STARShiP" (‎[edit=sysop] (indefinite) ‎[move=sysop] (indefinite) ‎[read=sysop] (indefinite))

← Older revision	Revision as of 17:44, 16 July 2014
(No difference)

Bradley Monk at 00:43, 17 July 2014

2014-07-17T00:43:15Z

← Older revision	Revision as of 17:43, 16 July 2014
Line 2:	Line 2:


		{{Popup\|<html><iframe src="http://gfycat.com/ifr/GloriousSnarlingBabirusa" frameborder="0" scrolling="no" width="756" height="428" style="-webkit-backface-visibility: hidden;-webkit-transform: scale(1);" ></iframe></html>}}


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



		<syntaxhighlight lang="matlab" line start="1" highlight="1" enclose="div">

		%%
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% SPINE RADIAL DISTANCE
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		%SGr={ G1P1r, G1P2r, G2P1r, G2P2r,
		% G1inP1, G1inP2, G2inP1, G2inP2,
		% G1xyP1, G1xyP2, G2xyP1, G2xyP2 };
		doRadDist = 1;
		doRadDistDPlots=1;
		if doRadDist



		%=================================================
		for reN = 1:loops
		%=================================================

		SGr = reSGr{reN};

		%--------------------------------------
		% Make concentric circle annulus
		%--------------------------------------
		S1r = round(S1rad);
		Qhr = S1r/2;
		Qx = linspace(0,S1r,6);
		QxL = Qx - Qhr;
		yL = sqrt(Qhr.^2 - QxL.^2);
		Qr = sqrt(Qx.^2 + yL.^2); % Concentric circles



		</syntaxhighlight>






		{{Article\|Groc, et-al, Choquet, Cognet\|2007\|J Neuro - [http://bradleymonk.com/media/Choquet2007A.pdf PDF]\|18003820\|Surface trafficking of neurotransmitter receptor: comparison between single-molecule/quantum dot strategies}}{{ExpandBox\|Expand to view experiment summary\|
		;Introduction
		*The cellular traffic of neurotransmitter receptors has captured a lot of attention over the last decade, mostly because synaptic receptor number is adjusted during synaptic development and plasticity. Although each neurotransmitter receptor family has its own trafficking characteristics, two main modes of receptor delivery to the synapse have emerged: endo-exocytotic cycling and surface diffusion [e.g., for glutamatergic receptors, see Bredt and Nicoll (2003) and Groc and Choquet (2006)]. Receptor cycling through endo-exocytotic processes can be measured by several experimental means, from biochemical to imaging assays. The use of fluorescent protein (XFP)-tag imaging provides a powerful approach to investigate the trafficking of receptor clusters between neuronal compartments (e.g., soma, dendrite, spine) (Kennedy and Ehlers, 2006). A disadvantage of the XFP-tag approach in live experiment is extreme difficulty in detecting XFP fluorescence signals from small nonclustered receptor pool (Cognet et al., 2002; Lippincott-Schwartz and Patterson, 2003). XFP-tagged neurotransmitter receptors are often present in several cellular compartments from the endoplasmic reticulum to the plasma membrane with various relative contents. For instance, surface XFP-tagged neurotransmitter receptors represent only a minor fraction of the total receptor population, precluding their specific detection. Alternative live-cell imaging approaches were thus required to specifically isolate surface receptors. Interestingly, a variant of the green fluorescent protein (GFP), ecliptic pHluorin, shows a reversible excitation ratio change between pH 7.5 and 5.5, and its absorbance decreases as the pH is lowered. Most neurotransmitter receptors, including the ionotropic glutamate ones, display an extracellular N-terminal region, implying that the N terminus will always be in an acidic environment inside the cell, whereas it will be exposed to a neutral pH after insertion into the plasma membrane. By this means, surface receptors can be specifically detected and tracked with live-imaging approaches (Ashby et al., 2004). Alternatively, surface receptors can be labeled and detected by immunocytochemical approaches using antibodies directed against receptor extracellular epitopes. The purpose of this Toolbox is to outline currently available approaches to measure the surface trafficking of receptor in neurons, with a special emphasis on single-molecule (organic dye) and quantum dot ([[Qdot\|QDot]]) detection for neurotransmitter receptor tracking.
		}}<!-- END ARTICLE -->

Bradley Monk: Created page with " Category:ReDiClus"

2014-07-17T00:07:41Z

Created page with " Category:ReDiClus"

New page

[[Category:ReDiClus]]