User:Janet B. Matsen - Revision history

Janet B. Matsen: /* Publications */

Janet B. Matsen — Wed, 15 May 2013 02:15:23 GMT

Publications

←Older revision		Revision as of 02:15, 15 May 2013
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	== Publications ==		== Publications ==
-	* Matsen, Yang, Stein, Beck, & Kalyuzhnaya. [http://www.frontiersin.org/Microbiological_Chemistry/10.3389/fmicb.2013.00040/abstract Global molecular analyses of methane metabolism in methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b]. Part I: transcriptomic study. Frontiers in Microbiology (open access), 2013	+	# Matsen, Yang, Stein, Beck, & Kalyuzhnaya. [http://www.frontiersin.org/Microbiological_Chemistry/10.3389/fmicb.2013.00040/abstract Global molecular analyses of methane metabolism in methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b]. Part I: transcriptomic study. Frontiers in Microbiology (open access), 2013
		+	# Yang, Matsen, Konopka, Green-Saxena, Clubb, Sadilek, Orphan, Beck, & Kalyuzhnaya. [http://www.frontiersin.org/microbiological_chemistry/10.3389/fmicb.2013.00070/abstract Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. metabolomics and 13C-labeling study]. Frontiers in Microbiology (open access), 2013

	== Awards & Activities ==		== Awards & Activities ==

Janet B. Matsen: /* Education */

Janet B. Matsen — Wed, 15 May 2013 02:13:51 GMT

Education

←Older revision		Revision as of 02:13, 15 May 2013
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	<br>		<br>
	</blockquote>		</blockquote>
		+
		+	== Publications ==
		+	* Matsen, Yang, Stein, Beck, & Kalyuzhnaya. [http://www.frontiersin.org/Microbiological_Chemistry/10.3389/fmicb.2013.00040/abstract Global molecular analyses of methane metabolism in methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b]. Part I: transcriptomic study. Frontiers in Microbiology (open access), 2013

	== Awards & Activities ==		== Awards & Activities ==

Janet B. Matsen: /* Use notes */

Janet B. Matsen — Mon, 13 May 2013 01:48:29 GMT

Use notes

←Older revision		Revision as of 01:48, 13 May 2013
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	* Examples:		* Examples:
	** Primer 7 is VF2 in BioBricks. Primer 60 is its reverse compliment. In a biobrick vector, it appears light gray for 7 and dark gray for 60. pCM66 happens to have this same sequence in the region upstream from the multiple cloning site, except it is REVERSED. Both primers will appear red as they bind in the opposite direction expected.		** Primer 7 is VF2 in BioBricks. Primer 60 is its reverse compliment. In a biobrick vector, it appears light gray for 7 and dark gray for 60. pCM66 happens to have this same sequence in the region upstream from the multiple cloning site, except it is REVERSED. Both primers will appear red as they bind in the opposite direction expected.
-	** I designed some primers for a Kan casette. The Kan casette in pCM66 is read in the reverse direction, so all the primers built for a forward Kan casette appear red. [[image:2013_05_08_Kan_casette.jpg\|\|thumb\|center\|Kan primers binding in the ~~reverse~~ direction ~~intended~~ appear red]]	+	** I designed some primers for a Kan casette. The Kan casette in pCM66 is read in the reverse direction, so all the primers built for a forward Kan casette appear red. [[image:2013_05_08_Kan_casette.jpg\|\|thumb\|center\|Kan primers binding in the opposite direction relative to my database appear red]]

	== Skills I'm developing ==		== Skills I'm developing ==

Janet B. Matsen at 15:23, 12 May 2013

Janet B. Matsen — Sun, 12 May 2013 15:23:16 GMT

←Older revision		Revision as of 15:23, 12 May 2013
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	I am a 3rd year Chemical Engineering PhD student at the University of Washington working in Mary Lidstrom's Lab. We are engineering E. coli to make biofuel precursors from electricity and CO<sub>2</sub> using a metabolic pathway that doesn't exist in nature. The dream is to be able to produce biofuel from renewable energy. Getting the pathway to work in living cells has been challenging. We are combining metabolic engineering, synthetic biology, metabolomics, enzyme engineering, and directed evolution to achieve this goal.		I am a 3rd year Chemical Engineering PhD student at the University of Washington working in Mary Lidstrom's Lab. We are engineering E. coli to make biofuel precursors from electricity and CO<sub>2</sub> using a metabolic pathway that doesn't exist in nature. The dream is to be able to produce biofuel from renewable energy. Getting the pathway to work in living cells has been challenging. We are combining metabolic engineering, synthetic biology, metabolomics, enzyme engineering, and directed evolution to achieve this goal.

-	My first year was spent investigating methanotrophic metabolism in pure cultures and a model ecosystem in a team that combined transcriptomics, metabolomics, and single-cell observation.	+	My first year was spent investigating methanotrophic metabolism in pure cultures and a model ecosystem in a team that combined transcriptomics, metabolomics, and single-cell observation.
		+
	[[Image:Janet_Matsen.png]]		[[Image:Janet_Matsen.png]]

Janet B. Matsen at 15:22, 12 May 2013

Janet B. Matsen — Sun, 12 May 2013 15:22:16 GMT

←Older revision		Revision as of 15:22, 12 May 2013
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	\|-valign="top"		\|-valign="top"
	\|style="background:#ffffff"\|		\|style="background:#ffffff"\|
-	[[Image:Janet_Matsen_2013_bench_photo.png]]	+	[[Image:Janet_Matsen_2013_bench_photo.png\|250px]]
	\|style="background:#ffffff"\|		\|style="background:#ffffff"\|

Janet B. Matsen at 15:18, 12 May 2013

Janet B. Matsen — Sun, 12 May 2013 15:18:01 GMT

←Older revision		Revision as of 15:18, 12 May 2013
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	\|-valign="top"		\|-valign="top"
	\|style="background:#ffffff"\|		\|style="background:#ffffff"\|
-	[[Image:~~Janet_Matsen~~.png]]	+	[[Image:Janet_Matsen_2013_bench_photo.png]]
	\|style="background:#ffffff"\|		\|style="background:#ffffff"\|

Janet B. Matsen at 15:17, 12 May 2013

Janet B. Matsen — Sun, 12 May 2013 15:17:37 GMT

←Older revision		Revision as of 15:17, 12 May 2013
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	\|}		\|}

-	I am a 3rd year Chemical Engineering PhD student at the University of Washington working at Mary Lidstrom's Lab and it is ~~so fun!~~	+	I am a 3rd year Chemical Engineering PhD student at the University of Washington working in Mary Lidstrom's Lab. We are engineering E. coli to make biofuel precursors from electricity and CO<sub>2</sub> using a metabolic pathway that doesn't exist in nature. The dream is to be able to produce biofuel from renewable energy. Getting the pathway to work in living cells has been challenging. We are combining metabolic engineering, synthetic biology, metabolomics, enzyme engineering, and directed evolution to achieve this goal.

-	My first year was spent investigating methanotrophic metabolism in pure cultures and a model ecosystem in a team that combined transcriptomics, metabolomics, and single-cell observation. ~~Currently I am helping engineer E~~. ~~coli to make biofuel precursors from electricity and CO<sub>2</sub>.~~	+	My first year was spent investigating methanotrophic metabolism in pure cultures and a model ecosystem in a team that combined transcriptomics, metabolomics, and single-cell observation.
		+	[[Image:Janet_Matsen.png]]

	I started the [[Lidstrom\|Lidstrom Lab OWW wiki]] and am addicted to posting what I learn! [[User:Amanda_L_Smith\|Amanda Smith]] is significant contributor as well. It has been a lot of fun for me to record what I have learned about lab techniques. It is also a fun place me to share tips/tricks and experiments that probe how important variables in a protocol are.		I started the [[Lidstrom\|Lidstrom Lab OWW wiki]] and am addicted to posting what I learn! [[User:Amanda_L_Smith\|Amanda Smith]] is significant contributor as well. It has been a lot of fun for me to record what I have learned about lab techniques. It is also a fun place me to share tips/tricks and experiments that probe how important variables in a protocol are.

Janet B. Matsen: /* Use notes */

Janet B. Matsen — Wed, 08 May 2013 13:40:28 GMT

Use notes

←Older revision		Revision as of 13:40, 8 May 2013
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	*If the primer binds in the reverse direction that it was designed for, it will appear red.		*If the primer binds in the reverse direction that it was designed for, it will appear red.
	[[image:2013_05_08_demo_of_APE_primer_library_tool.jpg\|thumb\|center\|demo of APE primer library tool]]		[[image:2013_05_08_demo_of_APE_primer_library_tool.jpg\|thumb\|center\|demo of APE primer library tool]]
-	** Examples:	+	* Examples:
-	*** Primer 7 is VF2 in BioBricks. Primer 60 is its reverse compliment. In a biobrick vector, it appears light gray for 7 and dark gray for 60. pCM66 happens to have this same sequence in the region upstream from the multiple cloning site, except it is REVERSED. Both primers will appear red as they bind in the opposite direction expected.	+	** Primer 7 is VF2 in BioBricks. Primer 60 is its reverse compliment. In a biobrick vector, it appears light gray for 7 and dark gray for 60. pCM66 happens to have this same sequence in the region upstream from the multiple cloning site, except it is REVERSED. Both primers will appear red as they bind in the opposite direction expected.
-	*** I designed some primers for a Kan casette. The Kan casette in pCM66 is read in the reverse direction, so all the primers built for a forward Kan casette appear red. [[image:2013_05_08_Kan_casette.jpg\|\|thumb\|center\|Kan primers binding in the reverse direction intended appear red]]	+	** I designed some primers for a Kan casette. The Kan casette in pCM66 is read in the reverse direction, so all the primers built for a forward Kan casette appear red. [[image:2013_05_08_Kan_casette.jpg\|\|thumb\|center\|Kan primers binding in the reverse direction intended appear red]]

	== Skills I'm developing ==		== Skills I'm developing ==

Janet B. Matsen: /* Use notes */

Janet B. Matsen — Wed, 08 May 2013 13:39:39 GMT

Use notes

←Older revision		Revision as of 13:39, 8 May 2013
Line 77:		Line 77:
	*If the primer binds in the reverse direction, it will be dark gray		*If the primer binds in the reverse direction, it will be dark gray
	*If the primer binds in the reverse direction that it was designed for, it will appear red.		*If the primer binds in the reverse direction that it was designed for, it will appear red.
-	[[image:2013_05_08_demo_of_APE_primer_library_tool.jpg\|\|thumb\|center\|demo of APE primer library tool]]	+	[[image:2013_05_08_demo_of_APE_primer_library_tool.jpg\|thumb\|center\|demo of APE primer library tool]]
	** Examples:		** Examples:
	*** Primer 7 is VF2 in BioBricks. Primer 60 is its reverse compliment. In a biobrick vector, it appears light gray for 7 and dark gray for 60. pCM66 happens to have this same sequence in the region upstream from the multiple cloning site, except it is REVERSED. Both primers will appear red as they bind in the opposite direction expected.		*** Primer 7 is VF2 in BioBricks. Primer 60 is its reverse compliment. In a biobrick vector, it appears light gray for 7 and dark gray for 60. pCM66 happens to have this same sequence in the region upstream from the multiple cloning site, except it is REVERSED. Both primers will appear red as they bind in the opposite direction expected.

Janet B. Matsen: /* Use notes */

Janet B. Matsen — Wed, 08 May 2013 13:39:26 GMT

Use notes

←Older revision		Revision as of 13:39, 8 May 2013
Line 77:		Line 77:
	*If the primer binds in the reverse direction, it will be dark gray		*If the primer binds in the reverse direction, it will be dark gray
	*If the primer binds in the reverse direction that it was designed for, it will appear red.		*If the primer binds in the reverse direction that it was designed for, it will appear red.
		+	[[image:2013_05_08_demo_of_APE_primer_library_tool.jpg\|\|thumb\|center\|demo of APE primer library tool]]
	** Examples:		** Examples:
	*** Primer 7 is VF2 in BioBricks. Primer 60 is its reverse compliment. In a biobrick vector, it appears light gray for 7 and dark gray for 60. pCM66 happens to have this same sequence in the region upstream from the multiple cloning site, except it is REVERSED. Both primers will appear red as they bind in the opposite direction expected.		*** Primer 7 is VF2 in BioBricks. Primer 60 is its reverse compliment. In a biobrick vector, it appears light gray for 7 and dark gray for 60. pCM66 happens to have this same sequence in the region upstream from the multiple cloning site, except it is REVERSED. Both primers will appear red as they bind in the opposite direction expected.
-	*** I designed some primers for a Kan casette. The Kan casette in pCM66 is read in the reverse direction, so all the primers built for a forward Kan casette appear red. [[image:2013_05_08_Kan_casette.jpg\|\|thumb\|Kan primers binding in the reverse direction intended appear red]]	+	*** I designed some primers for a Kan casette. The Kan casette in pCM66 is read in the reverse direction, so all the primers built for a forward Kan casette appear red. [[image:2013_05_08_Kan_casette.jpg\|\|thumb\|center\|Kan primers binding in the reverse direction intended appear red]]

	== Skills I'm developing ==		== Skills I'm developing ==