Impressions from iGEM 2014 Giant Jamboree

The International Genetically Engineered Machine Competition, or iGEM, is an annual event in which teams, mostly comprised of undergraduates, will compete against one another to design and create novel applications in the field of synthetic biology. The atmosphere surrounding the competition and the projects is a refreshing one: they offer enticing visions of how the field of synthetic biology can grow, and how the science can be communicated in an exciting, approachable and often colorful way. Furthermore, the iGEM teams are often highly interdisciplinary, featuring biologists, programmers, mathematics, and even artists (for communication and design).

Below are my impressions from the annual end of the year jamboree in which teams present their work. Last year, iGEM was organized into regional jamborees, with the finalists from each regional group being allowed to participate in the championship jamboree in the Stata Center at MIT. In an earlier post at this blog, you can find my impressions of the 2013 championship jamboree. This year, all teams participated in one giant jamboree, held in the Hynes Convention Center in Boston, MA. This jamboree was very well organized and was a very enjoyable event to attend, a testament to the efforts of the iGEM staff and volunteers. 

Although every team and project is unique, many share similar themes. The jamboree this year was organized into several tracks, such as Energy or Health and Medicine. Within each track (or even across tracks), several teams had similar projects. Some of the more common themes this year included:

• Modification of Bacillus subtilis to detect and/or eliminate pathogens (plant or human pathogens, usually fungal in nature)
• Engineering strains of bacteria (typically E. coli) for bioremediation or biofuel production
• Creation of packing material, patterned paper, and even clothing out of bacterially derived cellulose (or other microbe-derived products)

In the remainder of this post, I discuss some of the iGEM team projects in detail, and some other impressions of the event. Please select 'Read More' to see the rest of this article. I also attended the 'Funders Panel' session. This panel featured leaders of community labs, members of large budget teams, and even a science minister / official for Slovenia and Canada (the former featuring a perspective on funding science and iGEM teams with a limited budget). Even representatives from business and capital investment firms were present.

What was your favorite iGEM team or project this year? Please feel free to share your thoughts and comments below!

Bacteria learn how to take a pulse: programming microbes to convert digital light signals to analog gene expression.

What do telecommunications, power delivery, and your audio system* all have in common? For starters, their underlying electrical systems use digital pulses, alternating ON and OFF states over time. These pulse patterns and the way they change, known as pulse width modulation or PWM, can encode and transmit information. Now, research from a team of British and American scientists have made a surprising addition to the list of systems that can decode information in pulse widths: Escherichica coli (E. coli), a bacteria normally found in our gut. 

In an article recently published in the Journal of Molecular Biology, the research team describes genetic modifications to E. coli that enable it to read the pulse width modulation of alternating green and red lights. The gene expression of a reporter protein represented an analog output in response to this digital pattern of light color. In essence, scientists have been able to replicate in bacteria a process important in electrical engineering.

The creation of a system in E. coli capable of decoding PWM information is a significant step forward in the field of synthetic biology. This field, which sits at the intersection between biology and engineering, attempts to design artificial sensing and gene regulatory networks in bacteria. Perhaps most exciting, however, is the potential to use microbes like this one described in this study as an interface between digital signals from machines and the biological activity of cells.

For more detail and commentary about this study, please select 'Read More'. Which ways do you think PWM sensing in E. coli should be used? How would you continue this study? Comments are welcome below!

*not all audio systems utilize PWM, if I am not mistaken

Impressions from iGEM WCJ 2013

The International Genetically Engineered Machine competition, or iGEM, is an annual event in which teams of undergraduates compete to develop the best synthetic biology project. Their results are presented, and prizes awarded, at conference events dubbed iGEM jamborees. 

The iGEM 2013 event featured hundreds of teams. After qualifying at regional jamborees in North America, Asia, Latin America, and Europe, many teams converged at the Stata Center in MIT between November 1st and November 4th for the World Championship Jamboree.

I attended (as a volunteer) the Championship Jamboree this year. It was a great experience, and is something I recommend to anybody that is interested in the field of synthetic biology but cannot themselves join an iGEM team. In the rest of this post, I will share my impressions of the Jamboree and highlight some of my favorite teams and projects from this year.

If you are interested in learning more about all of this year's projects, and see their presentations from the World Championship Jamboree, you can visit the iGEM 2013 livestream channel for archived videos. HD videos and other files (including photos) should be or will be available on the main iGEM website. (For example, the finalists and medalists presentations are available, both video and poster files).

What do you think about iGEM, and which team or project was your favorite? Please share your thoughts in a comment below!

Note: I do not own, or claim any rights to, the official iGEM logo shown above; it was taken from igem.org

Paper of the Week at JBC

A stalled ribosome (Dark Blue) is rescued through translation of the tmRNA ORF (Magenta). Proper positioning of this region of tmRNA in the A-site is achieved by the C-terminal tail of SmpB (Yellow) which is connected to the body of the SmpB protein (Orange) by a flexible glycine residue (Yellow gymnast). Generated with PDB files 4ABR, 4ABS, and 3J18.

Although I usually don't use this blog to herald my own accomplishments (i.e. I didn't mention successfully earning my doctorate earlier in the year), I cannot hide my excitement that my first author article, "Active and Accurate trans-Translation Requires Distinct Determinants in the C-terminal Tail of SmpB Protein and the mRNA-like Domain of Transfer Messenger RNA (tmRNA)", has been selected for paper of the week.

As a paper of the week (an honor bestowed on less than 5% of all JBC articles, I am told), there is a neat summary of the article on the JBC site. The summary / synopsis piece is entitled "How Two Molecules Keep Ribosomes Moving". Along with this preview, there is also short profile about me.

Unfortunately, reading the actual, finished article requires a subscription to the Journal of Biological Chemistry. A word of caution to interested readers: it is written for an expert scientific audience (as almost all research articles for scientific journals are). However, it is possible to view the earlier, 'online' version of the article; in addition, the JBC capsule provides a bite-sized summary of the work.

The below is copied from the article page at the JBC website. Although I wrote most of it, I claim no copyright. You can find the original text at http://www.jbc.org/content/early/2013/08/28/jbc.M113.503896

Capsule

Background: tmRNA and small protein B (SmpB) rescue stalled ribosomes through a template switching mechanism.

Results: Changes to the SmpB hinge, SmpB C-terminus, or tmRNA ORF affect ribosome rescue activity and accuracy.

Conclusion: Proper positioning of SmpB and tmRNA make distinct and supplementary contributions to ribosome rescue.

Significance: Template switching requires concerted action of distinct SmpB, tmRNA, and ribosomal determinants.

E. coli Biosensors: Going for the Gold

All that glitters is not gold, and the shine of most modern gold deposits are hidden underneath layers of dirt, soil and sand. Finding these deposits usually requires expensive and time-consuming chemical analysis of soil samples. Recently, an international team of reseachers met this challenge of gold exploration and prospecting by turning a common gut microbe, Escherichia coli (E. coli), into a miniature gold detection device.

In a recent paper published in PLoS One, researchers from the University of Nebraska and their collaborators in Australia detail how they have genetically modified E. coli to act as a gold biosensor by borrowing the golTSB genes from a closely related microbe, Salmonella typhimurium. By pairing these gold recognition genes to a known enzymatic activity, researchers can detect and quantify small amounts of gold by simply measuring a change in the color of the bacteria-containing solution. The gold detection limit for this biosensor is on par with that of the chemical analysis currently used in the industry, which is slower and involves much more expensive instruments.

These proof-of-concept studies, which were partly funded by both Newmont Exploration Proprietary Limited and Barrick Gold of Australia Limited, are the latest step towards the development of a quick, accurate and specific biosensor that will make examining potential gold mining sites easier and faster. The authors of the study demonstrate that their biosensor can be used to determine the concentration of gold in a soil sample or a sample containing multiple metals. This is an improvement over earlier research of prototype biosensors, which only demonstrated detection in relatively pure samples.

For more detail and commentary about this study, please select 'Read More'. Do you think cell based biosensors will revolutionize gold exploration? Comments are welcome below!