Paul Jaschke

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[[Image:Pjaschke2.jpg|thumb|right|Paul Jaschke]]
[[Image:Pjaschke2.jpg|thumb|right|Paul Jaschke]]
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==Personal==
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==Bio==
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===Bio===
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I have been a post-doc in Drew Endy's lab at Stanford University since Nov 2010. The focus of my project is to redesign phage using both rational and combinatorial methods in order to finish the genetics of a simple system.  
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I have been a post-doc in Drew Endy's lab at Stanford University since Nov 2010. The focus of my project is to redesign phage using both rational and combinatorial methods in order to finish the genetics of a simple system. In December 2012 we published the first report of a [http://www.ncbi.nlm.nih.gov/pubmed/23079106 fully decompressed genome], using the [http://en.wikipedia.org/wiki/Phi_X_174 bacteriophage øX174] as a model. This virus has shared many other firsts in the world of genomics and synthetic biology from being the [http://en.wikipedia.org/wiki/Frederick_Sanger#Sequencing_DNA first DNA genome sequenced] by Frederick Sanger to the subject of claims of creating life in a test tube by watchers of [http://profiles.nlm.nih.gov/ps/retrieve/Narrative/WH/p-nid/209 Arthur Kornberg] and [http://www.economist.com/node/2224008 Craig Venter ''et al''].
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My current work is focused on using øX174 to pioneer a new method of simplifying synthetic genomes, a process I call 'negative genomics'.
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I started off my science career at the University of Alberta (Canada), working in the Casey and Michalak labs. Summer student work in the Casey Lab on the human sodium-bicarbonate co-transporter protein resulted in an authorship in a peer-reviewed publication. My honors project in the Michalak Lab had me determining the role of calcium signalling and calreticulin on murine embryonic stem cell differentiation. After achieving a B.Sc. (Honors) in Biochemistry in 2003 I went to the Beatty Lab at the University of British Columbia to start my Ph.D. While at UBC I discovered that a photosynthetic organism called ''Rhodobacter sphaeroides'' was capable of re-routing its chlorophyll biosynthetic machinery around a blockage to generate a new type of chlorophyll. November 2010 I was conferred a Ph.D in Microbiology and Immunology from UBC.
I started off my science career at the University of Alberta (Canada), working in the Casey and Michalak labs. Summer student work in the Casey Lab on the human sodium-bicarbonate co-transporter protein resulted in an authorship in a peer-reviewed publication. My honors project in the Michalak Lab had me determining the role of calcium signalling and calreticulin on murine embryonic stem cell differentiation. After achieving a B.Sc. (Honors) in Biochemistry in 2003 I went to the Beatty Lab at the University of British Columbia to start my Ph.D. While at UBC I discovered that a photosynthetic organism called ''Rhodobacter sphaeroides'' was capable of re-routing its chlorophyll biosynthetic machinery around a blockage to generate a new type of chlorophyll. November 2010 I was conferred a Ph.D in Microbiology and Immunology from UBC.
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*Stanford, California, USA
*Stanford, California, USA
*pjaschke 'AT' stanford.edu
*pjaschke 'AT' stanford.edu
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*skype: pjaschke
*[[Special:Emailuser/Paul R Jaschke|Email me through OpenWetWare]]
*[[Special:Emailuser/Paul R Jaschke|Email me through OpenWetWare]]
*[[Media:Paul_Jaschke_v-card.vcf|v-card]]
*[[Media:Paul_Jaschke_v-card.vcf|v-card]]
I work in the [[Endy Lab]] in the Department of Bioengineering
I work in the [[Endy Lab]] in the Department of Bioengineering
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==Work==
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In the Endy Lab I am using synthetic biology methods to design and build new virus genomes to explore minimal genomic space and understand how viruses work. The future applications of the methods I am developing range from better vaccine development to smarter engineering of microbe metabolic pathways for production of pharmaceuticals and industrial chemicals.
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In December 2012 we published the first report of a [http://www.ncbi.nlm.nih.gov/pubmed/23079106 fully decompressed genome], using the [http://en.wikipedia.org/wiki/Phi_X_174 bacteriophage øX174] as a model. This virus has shared many other firsts in the world of genomics and synthetic biology from being the [http://en.wikipedia.org/wiki/Frederick_Sanger#Sequencing_DNA first DNA genome sequenced] by Frederick Sanger to the subject of claims of creating life in a test tube by watchers of [http://profiles.nlm.nih.gov/ps/retrieve/Narrative/WH/p-nid/209 Arthur Kornberg] and [http://www.economist.com/node/2224008 Craig Venter ''et al''].
==Education==
==Education==
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====Stanford====
====Stanford====
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Kay Hung
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Kay Hung -> 3rd year Bioengineering undergrad at Stanford University
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Erica Lieberman -> Bioengineering undergrad at Stanford University
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Diane Liu
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Diane Liu -> 1st year Bioengineering undergrad at Northwestern University
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Jon Rodriguez
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Jon Rodriguez -> Chief Scientist for Epiphany Eyewear (http://www.epiphanyeyewear.com/)
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Adrian Sierra
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Adrian Sierra -> Computer Science undergrad at Stanford University
====University of British Columbia====
====University of British Columbia====
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Amelia Hardjasa
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Amelia Hardjasa -> Data Analyst at Pulse Energy
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Tobie Patterson
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Tobie Patterson -> Analyst, Public Health Initiatives at Fraser Health Authority, Vancouver, BC, Canada
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Elizabeth Digby
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Elizabeth Digby -> Medical School at the University of Calgary, Canada
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Connie Lee
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Connie Lee -> Physiotherapy in Victoria, BC, Canada
==Professional Activities==
==Professional Activities==

Revision as of 12:33, 4 September 2013

Back to Lab Members

Paul Jaschke
Paul Jaschke

Contents

Bio

I have been a post-doc in Drew Endy's lab at Stanford University since Nov 2010. The focus of my project is to redesign phage using both rational and combinatorial methods in order to finish the genetics of a simple system.

I started off my science career at the University of Alberta (Canada), working in the Casey and Michalak labs. Summer student work in the Casey Lab on the human sodium-bicarbonate co-transporter protein resulted in an authorship in a peer-reviewed publication. My honors project in the Michalak Lab had me determining the role of calcium signalling and calreticulin on murine embryonic stem cell differentiation. After achieving a B.Sc. (Honors) in Biochemistry in 2003 I went to the Beatty Lab at the University of British Columbia to start my Ph.D. While at UBC I discovered that a photosynthetic organism called Rhodobacter sphaeroides was capable of re-routing its chlorophyll biosynthetic machinery around a blockage to generate a new type of chlorophyll. November 2010 I was conferred a Ph.D in Microbiology and Immunology from UBC.

Badge graphic for SB5.0 representing my refactoring phage project
Badge graphic for SB5.0 representing my refactoring phage project

Contact Info

Table of contents picture for Biochemistry paper. Shows the change in the central metal bacteriochlorophyll from Mg to Zn, and changes to photosystem proteins in the bchD (Mg-chelatase) mutant.
Table of contents picture for Biochemistry paper. Shows the change in the central metal bacteriochlorophyll from Mg to Zn, and changes to photosystem proteins in the bchD (Mg-chelatase) mutant.

I work in the Endy Lab in the Department of Bioengineering

Work

In the Endy Lab I am using synthetic biology methods to design and build new virus genomes to explore minimal genomic space and understand how viruses work. The future applications of the methods I am developing range from better vaccine development to smarter engineering of microbe metabolic pathways for production of pharmaceuticals and industrial chemicals.

In December 2012 we published the first report of a fully decompressed genome, using the bacteriophage øX174 as a model. This virus has shared many other firsts in the world of genomics and synthetic biology from being the first DNA genome sequenced by Frederick Sanger to the subject of claims of creating life in a test tube by watchers of Arthur Kornberg and Craig Venter et al.

Education

Ph.D. in Microbiology, University of British Columbia, Canada (2010)

B.Sc. in Biochemistry (First-Class Honors), University of Alberta, Canada (2003)

Publications

Paul Jaschke., Ju Lu Ph.D., Widya Mulyasasmita and Luke J. Lee. (2013). Incyte Pharmaceuticals Is Primed For A Run. Seeking Alpha. Link

Jaschke PR, Lieberman EK, Rodriguez J, Sierra A, Endy D. (2012). A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast. Virology (Cover). DOI: 10.1016/j.virol.2012.09.020. Abstract PDF

Supplementary Files: Phage Assembled with Plasmid Sequence: pRS425::phiX174_1f // Redeployed Phage Sequence: phiX174_1f

Neupane B, Jaschke P, Saer R, Beatty JT, Reppert M, Jankowiak R. (2012). Electron Transfer in Rhodobacter sphaeroides Reaction Centers Containing Zn-Bacteriochlorophylls: A Hole-Burning Study. The Journal of Physical Chemistry B. Mar 15; 116(10): 3457-3466. Abstract PDF

Jaschke PR, Hardjasa A, Digby E, Hunter CN, Beatty JT. (2011). A bchD (Mg-chelatase) mutant of Rhodobacter sphaeroides synthesizes zinc-bacteriochlorophyll through a novel zinc-containing intermediates. The Journal of Biological Chemistry Jun 10;286(23):20313-22. Abstract PDF

My unsuccessful cover illustration submission for JBC paper. A novel Zn-bacteriochlorophyll pathway operates in a Mg-chelatase mutant of Rhodobacter sphaeroides. The bchD mutant cannot chelate Mg2+ into protoporphyrin IX, which instead, has both both Fe2+ (red sphere) and Zn2+ (green sphere) inserted by ferrochelatase. Zn-protoporphyrin IX joins the bacteriochlorophyll pathway and is converted to Zn-bacteriochlorophyll.
My unsuccessful cover illustration submission for JBC paper. A novel Zn-bacteriochlorophyll pathway operates in a Mg-chelatase mutant of Rhodobacter sphaeroides. The bchD mutant cannot chelate Mg2+ into protoporphyrin IX, which instead, has both both Fe2+ (red sphere) and Zn2+ (green sphere) inserted by ferrochelatase. Zn-protoporphyrin IX joins the bacteriochlorophyll pathway and is converted to Zn-bacteriochlorophyll.

Jaschke PR, Saer RG, Noll S, Beatty JT. (2011). Modification of the genome of Rhodobacter sphaeroides and construction of synthetic operons. Methods in Enzymology. 497:519-38. Abstract PDF

Our solution for French Presses that leak.
Our solution for French Presses that leak.

Jaschke PR, Drake I, Beatty JT. (2009). Modification of a French pressure cell to improve microbial cell disruption. Photosynth Res. 102(1): 95-7. Abstract PDF

Jaschke PR. (2010). Discovery and characterization of a new zinc-bacteriochlorophyll biosynthetic pathway and photosystem in a magnesium-chelatase mutant. PhD Thesis. University of British Columbia. Abstract PDF

Lin S,Jaschke PR, Wang H, Paddock M, Tufts A, Allen JP, Rosell FI, Mauk GA, Woodbury NW, Beatty JT. (2009). Electron transfer in the Rhodobacter sphaeroides reaction center assembled with zinc bacteriochlorophyll. Proceedings of the National Academy of Sciences of the USA.106(21): 8537-42. Abstract PDF

Jaschke PR, LeBlanc HN, Lang AS, Beatty JT. (2008). The PucC protein of Rhodobacter capsulatus mitigates an inhibitory effect of light-harvesting 2 alpha and beta proteins on light-harvesting complex 1. Photosynthesis Research. 95(2-3): 279-84. Abstract PDF

Jaschke PR, Beatty JT. (2007). The photosystem of Rhodobacter sphaeroides assembles with zinc bacteriochlorophyll in a bchD (magnesium chelatase) mutant. Biochemistry. 46(43): 12491-500. Abstract PDF

Loiselle FB, Jaschke P, Casey JR. (2003). Structural and functional characterization of the human NBC3 sodium/bicarbonate co-transporter carboxyl-terminal cytoplasmic domain. Molecular Membrane Biology. 20(4): 307-17. Abstract PDF

Presentations

Paul R Jaschke, Jon Rodriguez, Adrian Sierra, Drew Endy. (2012). Redesign and Construction of Bacteriophage Genomes in Yeast. SynBERC Retreat. PDF

Jaschke PR and Beatty JT. (2010). Out of the Blue. In a mutant lacking the magnesium-chelatase complex, we find zinc-bacteriochlorophyll incorporated into the photosystem and a new way to make bacteriochlorophyll. PDF

Jaschke PR and Beatty JT. (2007). Discovery of zinc-bacteriochlorophyll in Rhodobacter sphaeroides. PDF

Mentored Student Alumni

Stanford

Kay Hung -> 3rd year Bioengineering undergrad at Stanford University

Erica Lieberman -> Bioengineering undergrad at Stanford University

Diane Liu -> 1st year Bioengineering undergrad at Northwestern University

Jon Rodriguez -> Chief Scientist for Epiphany Eyewear (http://www.epiphanyeyewear.com/)

Adrian Sierra -> Computer Science undergrad at Stanford University

University of British Columbia

Amelia Hardjasa -> Data Analyst at Pulse Energy

Tobie Patterson -> Analyst, Public Health Initiatives at Fraser Health Authority, Vancouver, BC, Canada

Elizabeth Digby -> Medical School at the University of Calgary, Canada

Connie Lee -> Physiotherapy in Victoria, BC, Canada

Professional Activities

Advisor, Mendeley reference manager software (08/2011 - Current)

Developed and taught classes at BioCurious community DIY bio lab (2011 - 2012)

Mentored inaugural UBC iGEM team and guided to gold medal Press: Students build tiny E.coli ‘traffic light’ (see pg.9) (01/2009 - 11/2009)

'Project Management' & 'Grant Writing for Research and Development' Workshops (10/2009)

Teaching assistant for senior level bioinformatics class at UBC (2005 - 2008)

Reviewer for PLOS ONE and Journal of Proteome Research (2004 - Current)

Elected Biochemistry Student Association executive member (09/2001 - 06/2003)

Useful links

Research Gate Profile

Mendeley Profile

LinkedIn Profile

Google Scholar Profile

Rhodobacter sphaeroides on Wikipedia

Refactored øX174.1f genome sequence JX913857

Other

Teaching

BioCurious

Zamorano University Synthetic Biology Outreach Trip

Hobbies

Beer Making

Snowboarding

Hiking & Camping

Sailing

Personal tools