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By mrriley, November 15, 2011 8:49 pm

Interesting story on a new robot developed to automate the process of harvesting crops on a farm. Story appeared in Wired Science

Manual labor on farm has become a mounting problem in recent years. On the one hand new immigration laws (post 9/11) have made it much more difficult for growers to be able to bring in the help that they need at harvest time. At the same time, food safety guidelines lead to increased regulation on training of on farm help. Despite the high unemployment rate, many crops are spending more time in the field than ideal.

So – how do we solve all these challenges at once? AUTOMATE

Automation and robotics have been used in a number of ag harvesting areas for many years. New tractors with autoguidance, GPS, A/C, etc. have made in field work much more pleasant and safe. Automation has become a major part of greenhouse operations especially in Japan.

Joe Jones, a co-inventor of iRobot’s Roomba vacuum cleaning robot has had interest in horticulture which could use their small, relatively inexpensive, mobile material handling robot. Their venture-backed company has been field testing robots at nurseries around the U.S. Harvest Automation bootstrapped the development of prototype robots using funding from a number of sources.

Small mobile robots that tend crops are just emerging, and most of the action is in produce. Row crops provide a semi-structured environment, and several companies are marketing four-wheeled robots with computer vision systems that monitor and in some cases tend to crops.

For more info on ag automation, see:

http://azstarnet.com/business/local/article_464ed1c7-637f-525f-84dc-8059a1c36e1f.html

or

http://westernfarmpress.com/vegetables/automated-lettuce-thinning-machine-prototype-photos

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By mrriley, October 13, 2011 5:58 pm

Great event this week in Indy for the 2011 iGEM Americas judging. Lot’s of fantastic projects shown by the students and a lot of enthusiasm and energy all around.

In addition to the overall winner (Univ of Washington), there were a number of special awards:
Best Human Practice Advance                            NYC Wetware
Best BioBrick Measurement Approach             Calgary
Best Model                                            British Columbia and Northwestern (shared award)
Best New BioBrick Part, Natural                         Yale
Best New BioBrick Part, Engineered                  Washington

Best Wiki                                                                   Calgary
Best Poster                                                                Berkeley
Best Presentation                                                    Brown-Stanford
Special Safety Commendation                             Gaston Day School

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By mrriley, October 10, 2011 5:48 pm

iGEM 2011 Americas region was a great experience. Hopefully all that participated felt that they learned a lot from the process.

When you get to the point of publishing your work, consider sending it to JBE (J of Biological Engineering), jbioleng.org. This is an open access journal which covers the broad areas of biological engineering. Synthetic biology is well represented and the two most downloaded articles (each with more than 30,000 views) started as iGEM projects.

Also consider joining IBE (Institute of Biological Engineering) ibe.org, as your professional organization. IBE members delve into all sorts of projects which include and connect with iGEM activities.

Oh yeah, the winner is:
University of Washington
Congrats!!!!

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By mrriley, October 10, 2011 3:46 pm

Antifreeze proteins
The Yale team took a unique path to characterize and improve proteins which help organisms avoid the formation of ice crystals through freezing.

Organisms in addition to Yale students have developed ways to avoid freezing effects of cold environments. Antifreeze proteins bind to other proteins (TxTxTx repeats play a large role). Believed to impact the freezing point depression. Two companies put moderately-active fish antifreeze proteins into commercial ice cream products. Stronger activity proteins (from insects) tend to be much harder to produce and haven’t made their way into commercial products.

Antifreeze proteins could have impact on food, agriculture, medicine, and certainly for de-icing airplanes. Ragium inquisitor AFP can survive temps of -30F. Thee RiAFP protein properties has few disulfides and no homology to other antifreeze proteins. It also has fewer sequence repeats and so could be more easily produced in e coli.
The team has evaluated expression and purification of RiAFP, structural and function characterization and then directed evolution. They cloned three new antifreeze proteins which led to 12 total BioBricks. They also improved a previous BioBrick (TmAFP antifreeze protein) from Tokyo Tech 2009. Their submission had an internal EcoRI site and so the Yale team redesigned this. The TmAFP remains insoluble and challenging to characterize.

The Yale team could generate 150 mg / L production of RiAFP (the insect derived AFP). Only one tryptophan in the protein and so its absorbance is weak. When working with a new protein you are expected to crystallize it. Crystallography could be challenging since there are no known homologues.

Functionally the team tested the ability to avoid freezing and crystallization of solutions with BSA.
There is a dose-dependent effect on recrystallization. In survival assays, RiAFP improved freezing tolerance in e coli and c elegans. Huge positive effect when used in concert with glycerol. They are also looking at using this for mammalian cells and looks successful in improving freezing tolerance.

Accelerating engineering through evolution. This team used MAGE (multiplex automated genome engineering) to continually evolve cell populations. The Tx region is hypothesized as the ice binding domain. The team developed various mismatch mutations to see if they could enhance activity. 434 million variants generated in half a day. They will next apply freeze-thaw pressures and analyze mutants.

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By mrriley, October 10, 2011 3:23 pm

Make it or break it: diesel production and gluten destruction

Goal is to close the gap in fuels production through use of biofuels which can recycle CO2 and make this a renewable cycle. FAMEs and alcohols have lower fuel densities than their hydrocarbon counterparts. We need higher energy density renewable fuels. Need 2 enzymes added to be able to accomplish this using acyl acp reductase and aldehyde decarbonylase to act on fatty acids.
Alkane production leads to what they call petro bricks (Bba_K590025). Cells were grown up in a minimal media to produce alkanes which are excreted and then extracted into an organic layer and analyze by CG-MS. Production of a C14 (even # of C’s) are consistent with full function. They also see some C17, C15, and C13 (odd # of C’s) decarbamylation process appears to be working. Sugar is converted into a reasonable equivalent of diesel. Initial results had 2 mg / L – a moderate level of production. However, they were able to get above 170 mg / L after optimization of production.
The team also worked on the destruction of gluten, an issue for individuals with coeliac disease (a digestive problem which afflicts many). Gluten is commonly found in wheat products. PQLP amino acid motif is the primary mutagenic component. This team is developing a protein based theory which would break down the PQLP amino acid sequence using a protease which would remain active in the acidic gut. Their approach uses kumamolisin which is optimal at low pH. Its activity on gluten was unknown. The team used computational tools to redesign kumamolisin using “fold it” software (http://Fold.it). They tested their designs using a whole cell lysate assay. They tested over 100 mutants to kumamolisin. One had an 11-fold increase in activity. A second round of improvement led to a 118-fold improvement which is 784-fold more active than a commercial product.
The team also developed iGEM toolkits to improve cloning efficiencies. They also looked at making a magnetosome toolkit (magnetic bacteria). They were able to clone out 18 genes and place into BioBricks.
Wow – seems like three separate, fairly large projects which were done very well.
Love their outreach activities in which kids use balloons and ribbons placed inside a balloon which they blow up. Very graphic and hands on.

65 total BioBricks submitted.
Large team, but boy did they get a lot done.

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By mrriley, October 10, 2011 3:03 pm

Second up is the Lethbridge team from Alberta, Canada. The project was a tailings pond clean up kit.

A cool pic at: www.flutrackers.com/forum/showthread.php

Alberta has the second largest oil reserves in the world. Bitumin = oil + fine clay particles. The particles can settle and deposit but due to their small size this can take decades. PAH’s are present in the tailing ponds. The team developed biological machinery to address multiple aspects of this problem. They utilized a kill switch to generate “Death e. coli” using a BamHI endonuclease based off of the work of the 2007 Berkeley iGEM team. Induction stops replication after about 120 minutes and leading to substantially fewer colonies.
E coli bind to clay particles and then aggregating to each other, leading to an increase in particle size and hence sedimentation. This utilizes Antigen43 as a cell surface protein to interact with the clay. Experiments demonstrate good functionality and increased clay particle sedimentation. E coli growth in the presence of tailings pond LB broth grew nearly as well as in LB broth alone. PAH degradation was addressed by investing the catechol breakdown pathway. A likely slow step was identified by flux analysis and found to be the xylF catalyzed conversion. The team co-localized the enzymes within microcompartments using lumazine synthase which self assembles into closed compartment. Positively-charged proteins were co-localized inside the negatively charged capsule. Electron microscopy and fluorescence microscopy demonstrated success. Hollow icosahedral capsules are observed by TEM. For outreach they filmed a short movie called bioSpirits which addressed many of the ethical challenges with companies competing over the production of genetically engineered trees which produce beer.

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By mrriley, October 10, 2011 2:59 pm

The Brown-Stanford team was first up for final presentations. Their work was called the “Power cell project” and has great elements across all of the important levels of synthetic biology.

Anabaena cyanobacteria cells capture sunlight and produce sucrose. E coli W then utilizes the sucrose and could generate bioplastics using D lactate, or L-alanine. Then they modulariezed biocementation – this forms bricks out of Martian regolith. Uses Sporosarcina pasteurii, a spore forming bacteria that generate urease to generate ammonia to raise the pH and generate calcium carbonate. They made a microbrick with this technique. Produced a urease BioBrick, starting from a 10.6 kB cassette with no sequence data. This was successfully transformed into E. coli. 9 team members gave the presentation. Uploading their urease sequence not only to the registry but also to NCBI. The team sent balloons into the stratosphere (110,000 feet (~30 km)) ideally with their bacteria. Ran tests on urease activity at altitude. First attempts appeared to fail spectacularly, but the second trial went well. They recovered bacteria and demonstrated ureatic activity. Strong outreach activities to educate the public on synthetic biology and even reached NASA administrators. They also built the web site for AlumniGEM. Developing CommunityBricks to document outreach activities of multiple teams which were successful. This includes instructions in how to manufacture an open source gel electrophoresis box.

Off to a great start.

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By mrriley, October 10, 2011 2:54 pm

Congrats to the 2011 iGEM Americas regional finalists:
Brown-Stanford
Lethbridge
Washington (Univ of, in Seattle)
Yale
Each team will have 20 minutes to present their projects to the audience and for the second round of judging.

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By mrriley, October 10, 2011 12:41 pm

Awards will be announced for the Americas region for 2011 iGEM in a couple of hours. The top four teams will be givig a second presentation this morning in front of the entire group. Teams don’t know who will have this opportunity. The short list is a tight secret so that no team gets an unfair advantage.

Medal breakdown has:
18 bronze
8 silver
23 gold
Excellent work by teams this year.

I suspect that there will be good representation for the special awards from the environment section. Some of the best presentations I saw yesterday were from this area.

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By mrriley, October 10, 2011 3:18 am

Long evening of discussion by the judges for 2011 iGEM. We discussed first on the medals (bronze, silver, and gold) to be award to teams based on meeting the specific criteria of meeting. Bronze requires registering the team, developing the wiki, and creating a new biobrick which is sent to and annotated in the registry. Some teams did a good job in the research but did not send DNA to the registry. Some others had only rudimentary characterizations of their parts. The teams that appeared best were the ones that also performed extensive functional tests of their constructs. Some of the best characterizations brought in techniques beyond the molecular biology and used GC-MS, chemotaxis, or electrical responses.

Judges took their roles seriously and spent much time discussing and debating the awards. The longest discussions were on which of 25 teams would have an opportunity to move on the world competition to be held in November in Boston.