User:Zach Bjornson



MIT Biology 2010 - S.B. Stanford Microbiology and Immunology - graduate student (Ph.D.)

My primary focus is in virology. I get a kick out of BL4 pathogens, and on the other end of the spectrum, I'm fascinated by rhinoviruses (major cause of the common cold). In both cases, I enjoy studying emerging pathogens and characterizing their differences from already-characterized bugs.

I also have an interest and some experience in mechanical and electrical engineering.

You can contact me at bjornson{at}stanford{.}edu or bjornson{at}broadinstitute{.}org.

Current Research and Biology Projects

 * Identifying causal agents of fevers of unknown origin via Illumina sequencing. (Rubins lab and Sabeti lab)
 * Assorted monkeypox transcriptomics and genomics; Ebola genomics.

Past Research and Biology Projects

 * Research proposal: Antigenic characterization of newly detected rhinovirus variants; vaccination via polyvalent recombinant capsid protein expression. (This is a very detailed proposal about 20 pages in length. Two papers that came out in early 2009 support that this project might even work!)
 * Summer 2008: Developed a protocol to measure radical/reactive oxygen species in Gram-negative bacteria at the royal Chulabhorn Research Institute in Bangkok, Thailand. Also worked on isolating and identifying a compound (suspected to be homogentisic acid) from a Pseudomonas culture in which a certain oxidase was knocked out.
 * 20.109 research proposal assignment: [enhancement of] vasculogenesis with statins and hyaluronan jelly. mock project only (wiki page)
 * Optimization of Expression, Solubilization and Purification of the Membrane Protein HORF17-4 in E. coli Using Fractional Factorial Design (Zhang Lab).
 * Optimization of Cell-Free Expression of Membrane Proteins with Self-Assembling Peptides (Zhang Lab)
 * Cloning and Expression of UGT1A1 in E. coli (project blog)
 * Airplane Drinking Water Testing for Microbial Contaminants
 * The EPA just proposed new regulations to enforce the cleanliness of drinking water served on airplanes!
 * U.S. EPA honors 37 environmental heroes at Earth Day ceremony
 * How Safe Is Airline Water? Bring Your Own Bottle!
 * Edutopia Daring Dozen 2006
 * CNN Transcripts
 * As well as others

Honors and Media

 * Special Congressional Recognition for Environmental Work
 * Environmental Protection Agency environmental service award
 * United Nations Environment Programme youth advisor
 * 2005 International Young Eco-Hero Award
 * June 22, 2006 designated in Moraga, CA as a day of recognition
 * Ready, set, go: Class of 2010 leaps into action. MIT Tech Talk article.
 * A Genius for Leadership: MIT's Amazing Students. MIT Spectrum Summer 2007 article. (Cover page and following pages.)
 * Making their own music. MIT Tech Talk article.
 * See also the links above, in projects.

Lab Skills and Areas of Experience
Analytical
 * General protein work (1D gels, Western blots, dot blots, ELISAs, etc.)
 * Fluorescence microscopy (fixed cells, multicolor)
 * Very extensive flow cytometry (multilaser, multicolor) of mammalian, bacterial and yeast cells
 * UV/Vis spectroscopy (96-well format, for protein and DNA quantification; also in LC detection)
 * Affinity chromatography (for purification of proteins; basic; used His-Trap and His-Spin kit)
 * FPLC (of proteins)
 * HPLC (of organic molecules)
 * Real time PCR
 * Very extensive microarray work
 * RNA analysis (Northerns, qPCR)
 * Ultra-high-throughput sequencing (Illumina platform) for transcriptome profiling and viral sequence recovery

Preparative
 * Nucleic acids (cloning, engineering, extraction, site-directed mutagenesis, RT-PCR, real time PCR, etc.)
 * Bacterial cell culture, including BSL2+ pathogens - micro to macro scale (microwell to bioreactor)
 * Cell-free protein expression (E. coli lysate system)
 * Mammalian cell (tissue) culture (small scale) - 2D (plates/dishes) and 3D (scaffolds)
 * Mammalian cell culture (large scale) - hollow fiber, rocked-bed and stirred-tank bioreactors
 * Mammalian cell culture - metabolite monitoring; scale-up design
 * Extensive membrane protein work (overexpression of membrane proteins; lysing cells and solubilizing membrane proteins while maintaining native conformation)

Bioinformatics
 * Microarray probe design (challenges: minimization of cross-hybridizations and maximization of target alignment)
 * Microarray signal processing and analysis
 * Short-read sequencing processing and analysis
 * Selective/subtractive hybridization bait design
 * Pathogen detection algorithms
 * Fractional factorial and D-optimal design of experiment

Other
 * Computer programming - extensive knowledge of Mathematica. High-performance (parallelized) computing. Knowledge also of R, Visual Basic and Perl (mostly for Web interfaces).
 * Various mechanical engineering skills, including systems automation, robotics and fluids handling.

Other Interests
I play organ.

I'm from the San Francisco Bay Area. I'm a vegetarian, tree-hugger, environmentalist, ... spreading San Francisco values.

And I love to travel.

Personal Sites

 * Harpsichord Project Blog
 * Coming online in September, my main portal site (previously utopia.mit.edu)