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By mrriley, April 14, 2012 5:02 pm

I saw a presentation yesterday by Carolyn Compton, the new head of C-PATH, the critical path institute located in Tucson, AZ. This group has the goal of accelerating the development of new medicines by working at the interface between pharmaceutical companies, academic researchers and clinicians, the FDA, and the public.

Dr. Compton spoke especially on utilization of sequenced genomes of individuals could impact medical diagnostics. The cost and time has dramatically decreased to the point where it is now feasible to sequence an individual’s genome in less than 24 hours at a cost of less than $US 1,000. This information could be used to select patient-specific interventions. For example, breast cancers that are HER2+ should be treated with Herceptin® since this intervention is truly a life saving approach; but if the cancer is HER2- (not having the HER2 mutation), the treatment is not likely to be effective and essentially $US 100k per year for treatment is poorly spent. In this example, having the knowledge of a disease’s genetic fingerprint is crucial in selecting a treatment.

Dr. Compton spoke on identifying many more paths by which a diagnostic physician’s judgement could be better replicated by detailed heuristics based on better diagnostic tools. She referenced the long repeated concept that individuals can consider only 5 inputs when making a decision. What is to be done when there are >5 relevant pieces of information?

We are moving toward greater utilization of computerized expert systems to guide medical diagnostics. How quickly these are implemented depends not only on the development of technology but also on the public acceptance and acceptance by the medical community. Biological engineers are developing tools for rapid detection of SNP’s, of certain microbial components of disease, and in physiological function.  Many of these use lab-on-a chip approaches, microfluidics, nanotech, etc.  Will we every get to the point where medical diagnostics do not require human intervention?

I think that medicine will eventually become fully automated in which an individual who is not feeling well would be able to self collect a relevant sample (perhaps a finger stick) which is inputted to equipment which quickly reports back not only what is the problem but also provides a list of recommended interventions. Certainly many diseases are not driven by host genome but include infections, environment-gene interactions, and physical trauma. My assumption is that deep diagnostic techniques will follow for each of these in the wake of utilizing personalized genetic medicine.

Do we need to rely on the judgement of a physician? Many (most, but certainly not all) have excellent judgement and can see connections and use intuition. Could we some day be able to replicate this intuition (especially an intuition which is developed through varied training and experiences – a sequence which could be replicated digitally)?  If such a path is feasible for medicine, it should also be feasible to address environmental challenges, personalized nutrition, and the like. I do have faith in technology, although we must be cautious to not over hype the coming developments which would raise the public’s expectations unrealistically and too quickly.

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By mrriley, April 8, 2012 5:06 pm

This past spring saw the passing of Renato Dulbecco (1913-2012) who was eulogized by David Baltimore in the March 30 issue of Science. Dulbecco was a pioneer in bacteriophage genetics, cell transformation by viral DNA, and was the earliest proponent of the human genome project. He developed the first method for quantifying viruses in a culture. He won the Nobel prize for demonstrating that viral DNA can be integrated into cellular DNA thus leading to the inescapable conclusion that genes cause cancer. A key enzyme discovered has come to be known as reverse transcriptase. Dulbecco remained active scientifically well into his 90′s.

There is great importance in scientists understanding the history of their field and the brilliant individuals whose keen intuition led to the framework of our understanding of how the world works. A simple way to make this connection is to recognize that many of the tools we use today are named after real people either because they were the first to develop the tool or it was named for them by a colleague paying respect.

Dulbecco’s name is attached to one of the most prevalent mammalian cell culture media: Dulbecco’s Modified Eagle media, or DMEM. This substance contains all of the sugars, amino acids, and small molecules (usually supplemented with serum) to keep mammalian cells alive for many generations. Dulbecco’s work on cellular transformation not only unlocked a key mechanism in the onset of cancer, but also provided the concept for generating immortalized cells as used in numerous laboratories today. One of Dulbecco’s mentors was Luria – whose name has become synonymous with LB (or Luria broth) used to grow many types of bacteria.

What other common laboratory tools have been named after preeminent scientists whose name may not immediately conjure a real individual?

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By mrriley, April 2, 2012 3:54 pm

As any art lover would recognize, Vincent van Gogh’s paintings of sunflowers often depict a variety of flower shapes not commonly seen in nature. These impressionist paintings may be derived from his interpretation of the flower shape or these unusual structures could arise from a very tangible set of unusual genetic variations. A study by John Burke (UGa) recently published in PLoS Genetics addresses sunflower genes that lead to alterations in flower petal symmetry.

The large head of a sunflower is not a single flower, but comprised of many smaller flowers called florets. Burke’s work led to the discovery of two mutations to a single gene (HaCYC2c) that impacts floret symmetry. “Mis-expression of this gene causes a double-flowered phenotype, similar to those captured in Vincent van Gogh’s famous nineteenth-century paintings, whereas loss of gene function causes radialization of the normally bilaterally symmetric ray florets.” It appears that Burke’s group has identified the mutation that caused the double-flowered varieties painted by van Gogh.

Does this new knowledge diminish the aesthetic quality and artistic value of van Gogh’s paintings? We have a small poster replica of one of these paintings in our house and I had always thought that the double headed flowers were flights of fancy rather than an accurate record of plants that once lived. Having evidence that changes in flower shape and structure just like in the painting increases my joy in viewing.

The intersection between art and science will become increasingly well developed as we gain greater depth of understanding in the relationship between gene expression and phenotype. While this removes some of the mystery behind the presence of surprising aspects of our world, to the scientist, this new knowledge increases the beauty. There is much to be gained by having scientists view the world from the perspective of the artist; a much less developed approach is to encourage the artist to view the world through the lens of the scientist.

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By mrriley, February 28, 2012 4:32 pm

The annual international meeting of IBE in 2012 will be held in Indianapolis, IN starting on Th March 1st. There will be talks on a variety of developing areas including synthetic biology, renewable biofuels, microdevices, biomaterials, iGEM, environmental engineering, and bio-nanotech. We’ll also have a new session on “biological engineering basics” for those who may have a narrow background and want to learn more about the breadth of our field.

This year IBE is developing communities, groups centered around specific topical content in Biology, Systems Engineering and Bioenergy; Design and Education in Biological Engineering; Biosensors, BioNano and Biomedical Engineering; and Ecological Engineering. Should be a good way to catalyze further discussion on how to drive the research agenda.

Hope to see you in Indy.

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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.