Koch Lab:Publications - Revision history

Steven J. Koch at 17:47, 9 June 2011

Steven J. Koch — Thu, 09 Jun 2011 17:47:09 GMT

←Older revision		Revision as of 17:47, 9 June 2011
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	<br style="clear:both;"/>		<br style="clear:both;"/>
		+
		+	==Book Chapters==
		+	===Collaboration Using Open Notebook Science in Academia===
		+	Bradley J-C, Lang A SID, Koch SJ, Neylon C, "Collaboration Using Open Notebook Science in Academia" (2011). Chapter in Collaborative Computational Technologies for Biomedical Research, edited by Ekins, Hupcey, Williams, Bingham. Wiley. ISBN 0470638036

	==[[/Drafts\|Paper Drafts]]==		==[[/Drafts\|Paper Drafts]]==
		+	Also, see our posters, talks, and preprints on Nature Precedings: http://precedings.nature.com/account/submissions

	<br>		<br>

Steven J. Koch at 17:24, 9 June 2011

Steven J. Koch — Thu, 09 Jun 2011 17:24:01 GMT

←Older revision		Revision as of 17:24, 9 June 2011
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	{{Koch_Lab}}		{{Koch_Lab}}
		+	<div style="padding: 10px; width: 720px; border: 5px solid #008;">

	==Kinesin / Microtubule Molecular Motor System==		==Kinesin / Microtubule Molecular Motor System==
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	==Probing Protein-DNA Interactions by Unzipping DNA with Optical Tweezers==		==Probing Protein-DNA Interactions by Unzipping DNA with Optical Tweezers==
	{{DNA Unzipping}}{{OT}}		{{DNA Unzipping}}{{OT}}
-	~~<div style="padding: 10px; width: 720px; border: 5px solid #008;">~~
	===[[Koch Lab:Publications/Proof of principle for shotgun DNA mapping by unzipping\|Proof of principle for shotgun DNA mapping by unzipping]]===		===[[Koch Lab:Publications/Proof of principle for shotgun DNA mapping by unzipping\|Proof of principle for shotgun DNA mapping by unzipping]]===
	[[Image:1. Methods, Applications Flow Chart.PNG\|right\|thumb\|Overview of the shotgun DNA mapping method. We'll have to get rid of the beer can for the final publication.]]		[[Image:1. Methods, Applications Flow Chart.PNG\|right\|thumb\|Overview of the shotgun DNA mapping method. We'll have to get rid of the beer can for the final publication.]]

Steven J. Koch: /* Probing Protein-DNA Interactions by Unzipping DNA with Optical Tweezers */

Steven J. Koch — Thu, 09 Jun 2011 17:23:11 GMT

Probing Protein-DNA Interactions by Unzipping DNA with Optical Tweezers

←Older revision		Revision as of 17:23, 9 June 2011
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	{{DNA Unzipping}}{{OT}}		{{DNA Unzipping}}{{OT}}
	<div style="padding: 10px; width: 720px; border: 5px solid #008;">		<div style="padding: 10px; width: 720px; border: 5px solid #008;">
		+	===[[Koch Lab:Publications/Proof of principle for shotgun DNA mapping by unzipping\|Proof of principle for shotgun DNA mapping by unzipping]]===
	[[Image:1. Methods, Applications Flow Chart.PNG\|right\|thumb\|Overview of the shotgun DNA mapping method. We'll have to get rid of the beer can for the final publication.]]		[[Image:1. Methods, Applications Flow Chart.PNG\|right\|thumb\|Overview of the shotgun DNA mapping method. We'll have to get rid of the beer can for the final publication.]]
-	~~[[Koch Lab:Publications/Proof of principle for shotgun DNA mapping by unzipping\|Proof of principle for shotgun DNA mapping by unzipping]]~~	+
	<br style="clear:both;"/>		<br style="clear:both;"/>
	===Our initial proof-of-principle publication in the Wang Lab at Cornell===		===Our initial proof-of-principle publication in the Wang Lab at Cornell===

Steven J. Koch at 17:20, 9 June 2011

Steven J. Koch — Thu, 09 Jun 2011 17:20:35 GMT

Steven J. Koch: /* Kinesin / Microtubule Molecular Motor System */

Steven J. Koch — Thu, 09 Jun 2011 17:19:07 GMT

Kinesin / Microtubule Molecular Motor System

←Older revision		Revision as of 17:19, 9 June 2011
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	===A discrete-state model for kinesin-1 with rate constants modulated by neck linker tension (under review, PLoS ONE)===		===A discrete-state model for kinesin-1 with rate constants modulated by neck linker tension (under review, PLoS ONE)===
	Koch, Steven and Herskowitz, Lawrence. A Discrete State Model for Kinesin-1 with Rate Constants Modulated by Neck Linker Tension. Available from Nature Precedings http://hdl.handle.net/10101/npre.2010.5038.1 (2010)		Koch, Steven and Herskowitz, Lawrence. A Discrete State Model for Kinesin-1 with Rate Constants Modulated by Neck Linker Tension. Available from Nature Precedings http://hdl.handle.net/10101/npre.2010.5038.1 (2010)
		+
		+	===Effect of water isotope (deuterium or oxygen-18) on the kinesin-1 gliding motility assay (in preparation)===
		+	[[Image:AM D2O.jpg\|left\|thumb\|D2O decreases speed by 20%]][[Image:AM H218O.jpg\|right\|thumb\|Oxygen-18 water decreases speed by 5%]]
		+	Andy Maloney took painstakingly clean data on how D2O and oxygen-18 water affect the gliding speed in the kinesin-1 gliding motility assay. We are preparing this data for submission to PLoS ONE. We are doing further investigation to understand what the mechanism is and whether it is an interesting way to probe this and other biomolecular systems. The effect is strikingly similar to the change in viscosity of the solvents, but we have not yet proven that is the mechanism.
		+	See Andy Maloney's dissertation: http://www.openwetware.org/wiki/User:Andy_Maloney/Water_isotope_effects_on_kinesin_and_microtubules
		+
		+	===Open Source Kinesin-1 Stochastic Simulation and Gliding Assay Tracking Software (pre-print only)===
		+	Herskowitz, Lawrence, Salvagno, Anthony, Josey, Brian, Maloney, Andy, and Koch, Steven. Open Source Kinesin-1 Stochastic Simulation and Gliding Assay Tracking Software. Available from Nature Precedings http://dx.doi.org/10.1038/npre.2010.4468.1 (2010)<br>
		+	Larry Herskowitz wrote this software to test his microtubule image tracking. It's a nice LabVIEW application for generating a series of images that simulate microtubules fractionally-labeled with dye molecules. You can design a route for the microtubules to follow. We are happy to provide the source code and help you get it running on your own system. We decided that it was not worth peer reviewers' time to submit this for formal publication, as we did not anticipate any benefits besides padding our resumes. So, we will leave it at the preprint stage on Nature Precedings.

	===In George Bachand's lab with Susan Rivera, fungal kinesin from Thermomyces lanuginosus===		===In George Bachand's lab with Susan Rivera, fungal kinesin from Thermomyces lanuginosus===

Steven J. Koch: /* Kinesin / Microtubule Molecular Motor System */

Steven J. Koch — Thu, 09 Jun 2011 17:08:36 GMT

Kinesin / Microtubule Molecular Motor System

←Older revision		Revision as of 17:08, 9 June 2011
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	[[Image:Journal.pone.0019522.g003.png\|right\|thumb]]		[[Image:Journal.pone.0019522.g003.png\|right\|thumb]]
	Maloney A, Herskowitz LJ, Koch SJ (2011) Effects of Surface Passivation on Gliding Motility Assays. PLoS ONE 6(6): e19522. http://dx.doi.org/10.1371/journal.pone.0019522<br>		Maloney A, Herskowitz LJ, Koch SJ (2011) Effects of Surface Passivation on Gliding Motility Assays. PLoS ONE 6(6): e19522. http://dx.doi.org/10.1371/journal.pone.0019522<br>
-	<br>Black circles are alpha casein passivation, red squares are beta casein passivation, green up pointing triangles are whole casein passivation, and blue down pointing triangles are mixed casein passivation. Each data point is the mean from three different samples, taken at approximately the same assay time. Error bars represent the standard error of the mean. Alpha casein had the most consistent average speed measurements at 949±4 nm/s. Whole casein and mixed casein averaged to 966±7 nm/s and 966±6 nm/s respectively. Beta casein averaged to 870±30 nm/s.	+	<br>Andy Maloney studies the effects of alpha, beta, kappa, and whole casein in the kinesin-1 gliding motility assay. Automated speed analysis software by Larry Herskowitz.
		+	<br>Figure: Black circles are alpha casein passivation, red squares are beta casein passivation, green up pointing triangles are whole casein passivation, and blue down pointing triangles are mixed casein passivation. Each data point is the mean from three different samples, taken at approximately the same assay time. Error bars represent the standard error of the mean. Alpha casein had the most consistent average speed measurements at 949±4 nm/s. Whole casein and mixed casein averaged to 966±7 nm/s and 966±6 nm/s respectively. Beta casein averaged to 870±30 nm/s.
	<br style="clear:both;"/>		<br style="clear:both;"/>
		+
		+	===A discrete-state model for kinesin-1 with rate constants modulated by neck linker tension (under review, PLoS ONE)===
		+	Koch, Steven and Herskowitz, Lawrence. A Discrete State Model for Kinesin-1 with Rate Constants Modulated by Neck Linker Tension. Available from Nature Precedings http://hdl.handle.net/10101/npre.2010.5038.1 (2010)
		+
	===In George Bachand's lab with Susan Rivera, fungal kinesin from Thermomyces lanuginosus===		===In George Bachand's lab with Susan Rivera, fungal kinesin from Thermomyces lanuginosus===
	[[Image:ATP inhibition of kinesin aggregation.jpg\|right\|thumb]]		[[Image:ATP inhibition of kinesin aggregation.jpg\|right\|thumb]]
	Rivera SB, Koch SJ, Bauer JM, Edwards JM, Bachand GD. 2007. "Temperature dependent properties of a kinesin-3 motor protein from Thermomyces lanuginosus." Fungal Genetics and Biology 44:1170-1179. PMID 17398126		Rivera SB, Koch SJ, Bauer JM, Edwards JM, Bachand GD. 2007. "Temperature dependent properties of a kinesin-3 motor protein from Thermomyces lanuginosus." Fungal Genetics and Biology 44:1170-1179. PMID 17398126
-	<br>Dynamic light scattering data showing the inhibition by ATP of heat-induced aggregation of kinesin from Thermomyces lanuginosus.	+	<br>Figure: Dynamic light scattering data showing the inhibition by ATP of heat-induced aggregation of kinesin from Thermomyces lanuginosus.

	[[User:Steven J. Koch/Kinesin Aggregation\|More on kinesin aggregation]]		[[User:Steven J. Koch/Kinesin Aggregation\|More on kinesin aggregation]]

Steven J. Koch: /* Kinesin / Microtubule Molecular Motor System */

Steven J. Koch — Thu, 09 Jun 2011 17:03:55 GMT

Kinesin / Microtubule Molecular Motor System

←Older revision		Revision as of 17:03, 9 June 2011
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	===Effects of casein surface passivation in kinesin-1 gliding motility assay===		===Effects of casein surface passivation in kinesin-1 gliding motility assay===
	[[Image:Journal.pone.0019522.g003.png\|right\|thumb]]		[[Image:Journal.pone.0019522.g003.png\|right\|thumb]]
-	Maloney A, Herskowitz LJ, Koch SJ (2011) Effects of Surface Passivation on Gliding Motility Assays. PLoS ONE 6(6): e19522. ~~doi~~:10.1371/journal.pone.0019522	+	Maloney A, Herskowitz LJ, Koch SJ (2011) Effects of Surface Passivation on Gliding Motility Assays. PLoS ONE 6(6): e19522. http://dx.doi.org/10.1371/journal.pone.0019522<br>
	<br>Black circles are alpha casein passivation, red squares are beta casein passivation, green up pointing triangles are whole casein passivation, and blue down pointing triangles are mixed casein passivation. Each data point is the mean from three different samples, taken at approximately the same assay time. Error bars represent the standard error of the mean. Alpha casein had the most consistent average speed measurements at 949±4 nm/s. Whole casein and mixed casein averaged to 966±7 nm/s and 966±6 nm/s respectively. Beta casein averaged to 870±30 nm/s.		<br>Black circles are alpha casein passivation, red squares are beta casein passivation, green up pointing triangles are whole casein passivation, and blue down pointing triangles are mixed casein passivation. Each data point is the mean from three different samples, taken at approximately the same assay time. Error bars represent the standard error of the mean. Alpha casein had the most consistent average speed measurements at 949±4 nm/s. Whole casein and mixed casein averaged to 966±7 nm/s and 966±6 nm/s respectively. Beta casein averaged to 870±30 nm/s.
	<br style="clear:both;"/>		<br style="clear:both;"/>

Steven J. Koch at 17:01, 9 June 2011

Steven J. Koch — Thu, 09 Jun 2011 17:01:36 GMT

←Older revision		Revision as of 17:01, 9 June 2011
Line 10:		Line 10:
	[[Image:ATP inhibition of kinesin aggregation.jpg\|right\|thumb]]		[[Image:ATP inhibition of kinesin aggregation.jpg\|right\|thumb]]
	Rivera SB, Koch SJ, Bauer JM, Edwards JM, Bachand GD. 2007. "Temperature dependent properties of a kinesin-3 motor protein from Thermomyces lanuginosus." Fungal Genetics and Biology 44:1170-1179. PMID 17398126		Rivera SB, Koch SJ, Bauer JM, Edwards JM, Bachand GD. 2007. "Temperature dependent properties of a kinesin-3 motor protein from Thermomyces lanuginosus." Fungal Genetics and Biology 44:1170-1179. PMID 17398126
-	<br>\|Dynamic light scattering data showing the inhibition by ATP of heat-induced aggregation of kinesin from Thermomyces lanuginosus.	+	<br>Dynamic light scattering data showing the inhibition by ATP of heat-induced aggregation of kinesin from Thermomyces lanuginosus.
-	~~<br style="clear:both;"/>~~	+

	[[User:Steven J. Koch/Kinesin Aggregation\|More on kinesin aggregation]]		[[User:Steven J. Koch/Kinesin Aggregation\|More on kinesin aggregation]]
		+	<br style="clear:both;"/>

	==Probing Protein-DNA Interactions by Unzipping DNA with Optical Tweezers==		==Probing Protein-DNA Interactions by Unzipping DNA with Optical Tweezers==

Steven J. Koch: /* Kinesin / Microtubule Molecular Motor System */

Steven J. Koch — Thu, 09 Jun 2011 17:01:01 GMT

Kinesin / Microtubule Molecular Motor System

←Older revision		Revision as of 17:01, 9 June 2011
Line 3:		Line 3:
	==Kinesin / Microtubule Molecular Motor System==		==Kinesin / Microtubule Molecular Motor System==
	===Effects of casein surface passivation in kinesin-1 gliding motility assay===		===Effects of casein surface passivation in kinesin-1 gliding motility assay===
-	[[Image:Journal.pone.0019522.g003.png\|right\|thumb\|Black circles are alpha casein passivation, red squares are beta casein passivation, green up pointing triangles are whole casein passivation, and blue down pointing triangles are mixed casein passivation. Each data point is the mean from three different samples, taken at approximately the same assay time. Error bars represent the standard error of the mean. Alpha casein had the most consistent average speed measurements at 949±4 nm/s. Whole casein and mixed casein averaged to 966±7 nm/s and 966±6 nm/s respectively. Beta casein averaged to 870±30 nm/s.]]	+	[[Image:Journal.pone.0019522.g003.png\|right\|thumb]]
		+	Maloney A, Herskowitz LJ, Koch SJ (2011) Effects of Surface Passivation on Gliding Motility Assays. PLoS ONE 6(6): e19522. doi:10.1371/journal.pone.0019522
		+	<br>Black circles are alpha casein passivation, red squares are beta casein passivation, green up pointing triangles are whole casein passivation, and blue down pointing triangles are mixed casein passivation. Each data point is the mean from three different samples, taken at approximately the same assay time. Error bars represent the standard error of the mean. Alpha casein had the most consistent average speed measurements at 949±4 nm/s. Whole casein and mixed casein averaged to 966±7 nm/s and 966±6 nm/s respectively. Beta casein averaged to 870±30 nm/s.
		+	<br style="clear:both;"/>
	===In George Bachand's lab with Susan Rivera, fungal kinesin from Thermomyces lanuginosus===		===In George Bachand's lab with Susan Rivera, fungal kinesin from Thermomyces lanuginosus===
-	[[Image:ATP inhibition of kinesin aggregation.jpg\|right\|thumb~~\|Dynamic light scattering data showing the inhibition by ATP of heat-induced aggregation of kinesin from Thermomyces lanuginosus.~~]]	+	[[Image:ATP inhibition of kinesin aggregation.jpg\|right\|thumb]]
	Rivera SB, Koch SJ, Bauer JM, Edwards JM, Bachand GD. 2007. "Temperature dependent properties of a kinesin-3 motor protein from Thermomyces lanuginosus." Fungal Genetics and Biology 44:1170-1179. PMID 17398126		Rivera SB, Koch SJ, Bauer JM, Edwards JM, Bachand GD. 2007. "Temperature dependent properties of a kinesin-3 motor protein from Thermomyces lanuginosus." Fungal Genetics and Biology 44:1170-1179. PMID 17398126
		+	<br>\|Dynamic light scattering data showing the inhibition by ATP of heat-induced aggregation of kinesin from Thermomyces lanuginosus.
	<br style="clear:both;"/>		<br style="clear:both;"/>

Steven J. Koch at 16:58, 9 June 2011

Steven J. Koch — Thu, 09 Jun 2011 16:58:15 GMT

←Older revision		Revision as of 16:58, 9 June 2011
Line 2:		Line 2:

	==Kinesin / Microtubule Molecular Motor System==		==Kinesin / Microtubule Molecular Motor System==
-	===Effects of casein surface passivation in kinesin-1 gliding motility assay==	+	===Effects of casein surface passivation in kinesin-1 gliding motility assay===
	[[Image:Journal.pone.0019522.g003.png\|right\|thumb\|Black circles are alpha casein passivation, red squares are beta casein passivation, green up pointing triangles are whole casein passivation, and blue down pointing triangles are mixed casein passivation. Each data point is the mean from three different samples, taken at approximately the same assay time. Error bars represent the standard error of the mean. Alpha casein had the most consistent average speed measurements at 949±4 nm/s. Whole casein and mixed casein averaged to 966±7 nm/s and 966±6 nm/s respectively. Beta casein averaged to 870±30 nm/s.]]		[[Image:Journal.pone.0019522.g003.png\|right\|thumb\|Black circles are alpha casein passivation, red squares are beta casein passivation, green up pointing triangles are whole casein passivation, and blue down pointing triangles are mixed casein passivation. Each data point is the mean from three different samples, taken at approximately the same assay time. Error bars represent the standard error of the mean. Alpha casein had the most consistent average speed measurements at 949±4 nm/s. Whole casein and mixed casein averaged to 966±7 nm/s and 966±6 nm/s respectively. Beta casein averaged to 870±30 nm/s.]]
	===In George Bachand's lab with Susan Rivera, fungal kinesin from Thermomyces lanuginosus===		===In George Bachand's lab with Susan Rivera, fungal kinesin from Thermomyces lanuginosus===

←Older revision		Revision as of 17:20, 9 June 2011
Line 11:		Line 11:
	===A discrete-state model for kinesin-1 with rate constants modulated by neck linker tension (under review, PLoS ONE)===		===A discrete-state model for kinesin-1 with rate constants modulated by neck linker tension (under review, PLoS ONE)===
	Koch, Steven and Herskowitz, Lawrence. A Discrete State Model for Kinesin-1 with Rate Constants Modulated by Neck Linker Tension. Available from Nature Precedings http://hdl.handle.net/10101/npre.2010.5038.1 (2010)		Koch, Steven and Herskowitz, Lawrence. A Discrete State Model for Kinesin-1 with Rate Constants Modulated by Neck Linker Tension. Available from Nature Precedings http://hdl.handle.net/10101/npre.2010.5038.1 (2010)
-		+	<br style="clear:both;"/>
	===Effect of water isotope (deuterium or oxygen-18) on the kinesin-1 gliding motility assay (in preparation)===		===Effect of water isotope (deuterium or oxygen-18) on the kinesin-1 gliding motility assay (in preparation)===
	[[Image:AM D2O.jpg\|left\|thumb\|D2O decreases speed by 20%]][[Image:AM H218O.jpg\|right\|thumb\|Oxygen-18 water decreases speed by 5%]]		[[Image:AM D2O.jpg\|left\|thumb\|D2O decreases speed by 20%]][[Image:AM H218O.jpg\|right\|thumb\|Oxygen-18 water decreases speed by 5%]]
	Andy Maloney took painstakingly clean data on how D2O and oxygen-18 water affect the gliding speed in the kinesin-1 gliding motility assay. We are preparing this data for submission to PLoS ONE. We are doing further investigation to understand what the mechanism is and whether it is an interesting way to probe this and other biomolecular systems. The effect is strikingly similar to the change in viscosity of the solvents, but we have not yet proven that is the mechanism.		Andy Maloney took painstakingly clean data on how D2O and oxygen-18 water affect the gliding speed in the kinesin-1 gliding motility assay. We are preparing this data for submission to PLoS ONE. We are doing further investigation to understand what the mechanism is and whether it is an interesting way to probe this and other biomolecular systems. The effect is strikingly similar to the change in viscosity of the solvents, but we have not yet proven that is the mechanism.
	See Andy Maloney's dissertation: http://www.openwetware.org/wiki/User:Andy_Maloney/Water_isotope_effects_on_kinesin_and_microtubules		See Andy Maloney's dissertation: http://www.openwetware.org/wiki/User:Andy_Maloney/Water_isotope_effects_on_kinesin_and_microtubules
-		+	<br style="clear:both;"/>
	===Open Source Kinesin-1 Stochastic Simulation and Gliding Assay Tracking Software (pre-print only)===		===Open Source Kinesin-1 Stochastic Simulation and Gliding Assay Tracking Software (pre-print only)===
	Herskowitz, Lawrence, Salvagno, Anthony, Josey, Brian, Maloney, Andy, and Koch, Steven. Open Source Kinesin-1 Stochastic Simulation and Gliding Assay Tracking Software. Available from Nature Precedings http://dx.doi.org/10.1038/npre.2010.4468.1 (2010)<br>		Herskowitz, Lawrence, Salvagno, Anthony, Josey, Brian, Maloney, Andy, and Koch, Steven. Open Source Kinesin-1 Stochastic Simulation and Gliding Assay Tracking Software. Available from Nature Precedings http://dx.doi.org/10.1038/npre.2010.4468.1 (2010)<br>
	Larry Herskowitz wrote this software to test his microtubule image tracking. It's a nice LabVIEW application for generating a series of images that simulate microtubules fractionally-labeled with dye molecules. You can design a route for the microtubules to follow. We are happy to provide the source code and help you get it running on your own system. We decided that it was not worth peer reviewers' time to submit this for formal publication, as we did not anticipate any benefits besides padding our resumes. So, we will leave it at the preprint stage on Nature Precedings.		Larry Herskowitz wrote this software to test his microtubule image tracking. It's a nice LabVIEW application for generating a series of images that simulate microtubules fractionally-labeled with dye molecules. You can design a route for the microtubules to follow. We are happy to provide the source code and help you get it running on your own system. We decided that it was not worth peer reviewers' time to submit this for formal publication, as we did not anticipate any benefits besides padding our resumes. So, we will leave it at the preprint stage on Nature Precedings.
-		+	<br style="clear:both;"/>
	===In George Bachand's lab with Susan Rivera, fungal kinesin from Thermomyces lanuginosus===		===In George Bachand's lab with Susan Rivera, fungal kinesin from Thermomyces lanuginosus===
	[[Image:ATP inhibition of kinesin aggregation.jpg\|right\|thumb]]		[[Image:ATP inhibition of kinesin aggregation.jpg\|right\|thumb]]