User:Janet B. Matsen

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Tools to Share)
(Publications)
(14 intermediate revisions not shown.)
Line 5: Line 5:
|-valign="top"
|-valign="top"
|style="background:#ffffff"|
|style="background:#ffffff"|
-
[[Image:Janet_Matsen.png]]
+
[[Image:Janet_Matsen_2013_bench_photo.png|250px]]
|style="background:#ffffff"|
|style="background:#ffffff"|
Line 19: Line 19:
|}
|}
-
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.  
-
 
+
   
-
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.
+
[[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.
== Research Interests ==
== Research Interests ==
Line 35: Line 36:
== Education==
== Education==
-
<blockquote>PhD University of Washington, Seattle <br>
+
<blockquote>PhD (in progress) University of Washington, Seattle <br>
*Chemical Engineering, expected graduation: 2015
*Chemical Engineering, expected graduation: 2015
*[[Lidstrom| Lidstrom Lab]]
*[[Lidstrom| Lidstrom Lab]]
Line 43: Line 44:
<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
 +
# 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 ==
Line 65: Line 70:
== Tools to Share ==
== Tools to Share ==
-
*[https://www.dropbox.com/s/c1477nbi55d8aad/APE_AnnotationFeatureLibraryCreator.R Ape Annotation Feature Library Creator]  
+
*[https://www.dropbox.com/s/3p5bnfip4ks8daa/APE_AnnotationFeatureLibraryCreator.R Ape Annotation Feature Library Creator]  
** This is an R script that converts the info in [https://docs.google.com/spreadsheet/ccc?key=0AlVxrZi130nMdHlsaml2OGFDUW9zRlVBdkRKaXVEbkE#gid=22 my list of primers] into a file that I can use to annotate DNA files in APE with.  It:  
** This is an R script that converts the info in [https://docs.google.com/spreadsheet/ccc?key=0AlVxrZi130nMdHlsaml2OGFDUW9zRlVBdkRKaXVEbkE#gid=22 my list of primers] into a file that I can use to annotate DNA files in APE with.  It:  
***trims out sequences not intended for sequencing such as Gibson assembly primers
***trims out sequences not intended for sequencing such as Gibson assembly primers
-
***makes a label that combines the unique primer number, the melting temperature, and the letter F or R for forward or reverse
+
***makes a label that combines the unique primer number, the melting temperature, and the letter F or R for forward or reverse, and an asterisk if you should consult the primer spreadsheet comments before using it
***assigns colors in APE that communicate whether it primers in the forward direction or the reverse direction.   
***assigns colors in APE that communicate whether it primers in the forward direction or the reverse direction.   
***saves the info in the format APE needs, with the date it was generated in the title.
***saves the info in the format APE needs, with the date it was generated in the title.
** This allows me to instantly see where all of the primers I own bind to a DNA sequence for a given project I am working on.  It also allows me to share these primers very easily; by sharing the file it outputs allows my lab mates to instantly see if I have any primers that can be used in their project.  It has been very handy for them!  
** This allows me to instantly see where all of the primers I own bind to a DNA sequence for a given project I am working on.  It also allows me to share these primers very easily; by sharing the file it outputs allows my lab mates to instantly see if I have any primers that can be used in their project.  It has been very handy for them!  
** I am happy to help friends modify this script to be useful with their own primer libraries!  No R experience is necessary.
** I am happy to help friends modify this script to be useful with their own primer libraries!  No R experience is necessary.
 +
** Anyone can access my most current primer "Annotation Feature Library" [https://www.dropbox.com/sh/5w53jl3jhbdddvp/iW7cOtZ2Wd here].  You can also see the files used to generate it there.
 +
=== Use notes ===
 +
*If the primer binds in the forward direction, the primer will be light 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.
 +
[[image:2013_05_08_demo_of_APE_primer_library_tool.jpg|thumb|center|demo of APE primer library tool]]
 +
* 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. 
 +
** 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 ==

Revision as of 22:15, 14 May 2013



Janet B. Matsen

Department of Chemical Engineering
Seattle, Washington

jmatsen@uw.edu

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 CO2 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.

Image:Janet_Matsen.png

I started the Lidstrom Lab OWW wiki and am addicted to posting what I learn! 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.

Contents

Research Interests

  • metabolic engineering
  • synthetic biology
  • transcriptomics
  • chemical engineering

Education

PhD (in progress) University of Washington, Seattle
B.S. University of California, Berkeley
  • Chemical Engineering, 2010

Publications

  1. Matsen, Yang, Stein, Beck, & Kalyuzhnaya. Global molecular analyses of methane metabolism in methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: transcriptomic study. Frontiers in Microbiology (open access), 2013
  2. Yang, Matsen, Konopka, Green-Saxena, Clubb, Sadilek, Orphan, Beck, & Kalyuzhnaya. 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

My Personal Pages


Tools to Share

  • Ape Annotation Feature Library Creator
    • This is an R script that converts the info in my list of primers into a file that I can use to annotate DNA files in APE with. It:
      • trims out sequences not intended for sequencing such as Gibson assembly primers
      • makes a label that combines the unique primer number, the melting temperature, and the letter F or R for forward or reverse, and an asterisk if you should consult the primer spreadsheet comments before using it
      • assigns colors in APE that communicate whether it primers in the forward direction or the reverse direction.
      • saves the info in the format APE needs, with the date it was generated in the title.
    • This allows me to instantly see where all of the primers I own bind to a DNA sequence for a given project I am working on. It also allows me to share these primers very easily; by sharing the file it outputs allows my lab mates to instantly see if I have any primers that can be used in their project. It has been very handy for them!
    • I am happy to help friends modify this script to be useful with their own primer libraries! No R experience is necessary.
    • Anyone can access my most current primer "Annotation Feature Library" here. You can also see the files used to generate it there.

Use notes

  • If the primer binds in the forward direction, the primer will be light 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.
demo of APE primer library tool
demo of APE primer library tool
  • 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.
    • 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.
      Kan primers binding in the opposite direction relative to my database appear red
      Kan primers binding in the opposite direction relative to my database appear red

Skills I'm developing

  • molecular biology
  • mass spectrometry based metabolomics
  • R & ggplot2
  • Inkscape
  • Gibson cloning
Personal tools