And We're Off!

We apologize for the extremely long hiatus. With classes and preparations it was difficult to keep this blog going.

In just a few hours, the University of Calgary iGEM team will be heading off to MIT to celebrate our hard work over the summer with 112 other teams around the world. How exciting!

Photos of our events will be uploaded on our Picasa album. Check it out!

Democratic Biology

A group called DIY (do-it-yourself) biology relies on development of open source synthetic biology. DIY supports amateur and underfunded labs. Although, due to the fear of biohackers and synthetic biology misuse, the development of DIY biology has been limited.

Can this company and iGEM go and revolutionize biology to the extent it is available to amateurs? Or will this technology stop its development due to the fear of biohackers and synthetic pathogenic genomes?

Find out more here

Himika

Drug-resistant Superbug

One of the main fears of synthetic biology is that a mutant drug-resistant "superbug" will be accidentially synthesized and there will be no way for humans to combat it. There have been incidents of this forming without the aid of humans with the spread of Methicillin-Resistant Staphylococcus aureus (MRSA) in hospitals all over the world.

Now, a gene has been found that is capable of making any bacteria resistant to almost all antibiotics used today. Worse yet, the gene has been found in patients in both Canadian and American hospitals. The Canadian cases were specifically found in Alberta and British Columbia. How this bug will change the public's opinion of genetic research with bacteria remains to be seen.

Read more about this superbug here

Chris

Still Cautious Around Synthetic Biology

A recent news article in Medical News Today talks about a survey of 1000 U.S. adults and their opinions of synthetic biology. The survey was conducted by Hart Research Associates and the Synthetic Biology Project at the Woodrow Wilson Center.

Two thirds of those surveyed believe that synthetic biology should be a field that moves forward, while the remaining third believe we should put a ban on research until the implications and risks are fully assessed.

"The survey shows that attitudes about synthetic biology are not clear-cut and that its application is an important factor in shaping public attitudes towards it," said Geoff Garin, President of Hart Research.

Read the full article here.

Patrick

We're Off to aGEM!

We're all really excited to be heading off to the Alberta Genetically Engineered Machines (aGEM) competition. It's a conference similar to iGEM, but held in Edmonton. The Calgary team, as well as the iGEM teams from the University of Alberta and the University of Lethbridge, give a presentation to a panel of judges, much like what we'll be experiencing at iGEM. We'll be there this coming weekend.

Stay tuned to this blog and our wiki for photos!

Patrick

Over-regulation of Synthetic Biology?

Almost everyone agrees that regulation is needed to keep synthetic biology safe. This is the general consensus from both the public, researchers, and experts in the field. However, how much is too much? Is there the possibility that there can be too much regulation which curbs creativity? This is always the problem. Where do you draw the line? Is there even a too far? Some questions to ponder.

Ethel Machi and Jena Baker McNeill bring up this question briefly as they discuss the endless possibilities of the rapidly expanding field. The title speaks for itself in that the field has the potential to go from one end of the spectrum (Biotechnology advances) to the other (bioterrorism) in its effects.

You can read more about their perspectives here

- Chris

Altruism in bacteria

Dr. Collins from Harvard found that bacteria tend to show altruistic behaviours. Some bacteria can give up their own survival for the better survival of the group, which is termed altruism. This kind of behaviour was only found in mammals but now is found in bacteria. Research shows that a bacterium with antibiotic resistance can
"donate" its plasmid to the other bacteria to create an antibiotic resistant population.
This has medical implications says Dr. Collins. It could mean that, "We'll know that even an isolate that shows no resistance can put up a stronger battle against antibiotics thanks to its buddies." For more information click here.
Synthetic biology could be used to study this altruistic behaviour further and explore its implication more so.

Himika

Synthetic Biology: The Card Game

The ESRC Genomics Forum has developed a version of the dialogue game Democs. In this game, participants will learn about, dicuss, and give thier views on issues in synthetic biology. An example of one card is: "We think it’s OK for humans to make all kinds of inanimate machines. But should we also design and make new living organisms that can reproduce themselves?". If your interested in playing the game, instructions and cards are available on www.genomicsnetwork.ac.uk.

-Alex

Genetically Engineering Farmed Animals

    Since the introduction of genetic engineering techniques, people have been very polarized about the whole concept. Some see solutions to global problems, while others see naught but a Brave New World in the future. Regardless of your viewpoint, practical genetic manipulation is getting closer and closer to impacting everyday life. A few major projects involving farm animals have been completed (read the details here), and are currently in the federal approval process.
    Projects like the Enviropig (I love that name); a type of pig that needs to eat less to maintain the same health and body weight while producing less, and less environmentally-damaging, waste. Another is also using pigs, causing them to change much of the fat in their bodies (and so in our pork and bacon) from omega-6 into omega-3, which is much healthier for us.
   Both have the possibility of seeing the market in just a few years, so the public reaction can't be far off. Should be interesting to see the outcome of this sure-to-be lively debate!

Dave

Biofilms for the Future

Synthetic biology isn't always a "Frankenstein-sounding" field of science, like one Los Angeles Times article puts it. While some labs like the Venter lab have synthesized and inserted a complete bacterial genome, most other labs, including those from iGEM, have much more modest and practical goals.

For example, the Groningen team is designing a way to use bacteria to create self-assembling film that repels water. By integrating a gene that produces hydrophobic proteins into bacteria, a new strain can be developed that can produce rigid biofilm. The process can be stopped with exposure to UV light.

This project can potentially be cheaper and less toxic than the expensive chemicals used to waterproof materials currently. Repelling water is an effective way to reduce bacterial and fungal growth on surfaces, as well as resisting corrosion because it keeps the surface clean and dry. Imagine: maybe in the future we can rustproof our car parts by letting bacteria do all the work for us.

Now isn't that neat?


Patrick

Revolutionary Biology

When you think of the words "biohackers" and "biopunks"its easy to think of some renegade biologist using his biological knowledge to rebel against society. However biopunk ideologies are actually quite similar to iGEM's. "A Biopunk Manifesto" advocates a necessity for more people to be "scientifically literate" and to understand biology such that they can be contributors to improving the world they live in in areas like healthcare, water quality, etc. The Biopunk Movement represents the ideological view of true open source biology. Supported with a strong community of individuals interested in biology for the sake of unraveling the secrets of biology. Aimed at making practicing biology cheaper and deinstitutionalizing biology. However promising these words sound do not reflect a plan for incorporating these ideas into regular life. 

Note: Biopunks are not associated with bioterrorism, however in an ethical stand point rising popularity of biopunks could increase the amount of bioterrorism.

If your interested in reading "A Biopunk Manifesto" click here or an article about biopunk genetic engineering

Jeremy

Synthetic Immune System?

Imagine taking a drop of your blood, dripping it into a bowl and having it travel through a network of vessels to different colonies of yeast. Each colony would act as an external biosensor for your body detecting a variety of deficiencies and possible anomalies that could be present. It is personalized medicine to the extreme, customized to your body and lifestyle. For example, if you had anaemia the yeast would monitor your iron levels in your blood and alert you if they got low. A different colony of yeast could even synthesize the needed iron for you, which would be sent back to you through the network of vessels, to be absorbed through a mouthpiece. Sound fictitious? Well that’s probably because it is. But Tuur van Balen, a designer in London has just this vision. He calls it the Synthetic Immune System. He imagines that in the future, synthetic biology could lead to a more personalized approach to medicine where we might even outsource our own metabolic actions to engineered organisms such as Yeast. He displayed his model and vision at an exhibition at the Royal College of Art in March. For more information, check out this link to his website.

Emily

Evolution in 3 days!

One of Craig Venter's competitors, Harvard's Dr. Church, made a significant announcement in the field of synthetic biology yesterday. For months now, they have been racing against the J. Craig Venter Institute to be the first to complete the project and allow it to be sold on the market. Even though the Venter Institute brought their news first, Dr. Church still believes that his product can be marketed to drug companies and sold for profit. 

The product that he has designed is a table-top mutagenesis kit able to induce up to 50 DNA sequence changes at once. This kit is similar to the standard site-directed mutagenesis kit but on a much larger scale.

More information can be found here


-Chris

Bio-Art by Osaka

In 2009, the Osaka iGEM team developed a set of "bio-art" tools. They created colour palettes and a signalling system between bacterial cells that produced some pretty awesome artwork when plated on soft agar.

There was a wide array of colours produced, ranging from red, green, cyan, yellow, and orange fluorescent proteins, as well as red, orange, yellow, black, brown, and purple pigments. With this, they created flower-patterned petri dishes, glowing cocktail glasses, and even an 8-bit Mario replica!

Here are some of the many art pieces the team has created.

This just goes to show that with enough creativity, the sky really is the limit for synthetic biology. Who knows? Maybe in the future we'll be using bacteria as an art medium.

Patrick

Biobricks = Legos

The “biobrick” concept of iGEM (International Genetically Engineered Machine) give genetic engineering a more playful dimension in an interesting way. For example, undergraduate teams can combine compatible parts to create a useful system. Just as we play with legos and let our imagination take its course, and learn about shapes and compatibility through the project, biobricks let our curiosity become reality, and learn more about the biological systems, compatibility of different genes and much more. iGEM has the potential to teach students molecular biology in a much more interesting and interactive method. An undergraduate student, Dev Vyas, of the University of Calgary says that he likes the biobrick concept of iGEM because it allows him to “understand the biological concepts visually in a way that is more comprehensible and creative.”

Raida

Bacterial Bandage

In 2009, the Denmark team designed E. coli such that it produced a chemical called RIP (RNA III-inhibiting-peptide). This chemical breaks down the ability of S. aureus to communicate with each other. This process is called quorum quenching. The E. coli they designed quenches the communication between S. aureus cells and therefore inhibits them from spreading and also increases the chance of antibiotics working.

For more information click here

Himika

Synthetic Biologist collaborate with Cancer Researchers!

A current article posted on the NCI Cancer suggest that cancer researchers recognize the potential that synthetic biologist. Especially the efforts to engineer bacterial cells that selectively target cancer cells by Dr. Chris Anderson (who is also the supervisor for UC Berkley's team). The interest that the Division of Cancer Biology has with Synthetic Biology is its application through the combination of various fields including biology, engineering, chemistry and physics which they hope will offer new insights into ongoing cancer research.

Heres the video of Dr. Jerry Li the program director in NCI’s Division of Cancer Biology (DCB) and his colleague Dr. Daniel Gallahan discuss the potentials of synthetic biology.



Original article can be found on:
http://www.cancer.gov/ncicancerbulletin/071310/page4

Jeremy

How do you define an organism?

Despite being defined in high school biology textbooks everywhere, this is a question the National Research Council (NRC) is currently asking. They are particularly interested in the context of their Select Agent list, which designates dangerous organisms with the potential to be used as weapons. This was generally clear-cut before; Bacillus anthracis (the cause of anthrax) was Bacillus anthracis, it was dangerous and controlled, and Bacillus subtlis (causes no disease) was different and benign. But these days, where synthesizing DNA is becoming cheaper and widespread, that distinction may not hold. What if someone were to take a non-controlled organism, and give it some toxin genes from a controlled organism? If this organism looks like the benign one, but causes disease like the controlled one, which is it? Should we be defining an organism based on its DNA sequence? Read the full story here.

Genetically Engineered Clock Powered by Quorum Sensing

Researchers at the University of San Diego have been working on the creation of a bacterial clock. Their system relies on the bacterial communication system known as quorum sensing. In nature, microorganisms such as E coli use pheromone-like molecules called autoinducers to communicate and monitor their population density. The researchers made use of the autoinducer AHL and three different engineered circuits using the LuxI promoter.

One circuit consists of the luxI promoter with the luxI gene downtream. The luxI gene product is involved in the synthesis of AHL, which when bound to luxR, which is constitutively produced, activates the lux I promoter. The other two circuits use the same promoter, but with GFP and aiia downstream. Aiia is a molecule that degrades AHL. When a limited number of cells are present, these promoters are not activated. The cells produce AHL naturally, but not enough to cause activation. When the population recahes a certain level, 'quorum', however, there is enough AHL present that all of the luxI promters are activated and there is a burst of GFP expression. This occurs until enough aiia is also produced that it can degrade all fo the AHL. With not enough AHL present, the luxI promoters are all turned off and the cycle can start again. The result of their system is that they have a population of bacteria that glow green at intervals, a type of visual genetically engineered clock. The researchers hope that this will eventually lead the way to genetic sensors able to pulse differently dependent on different environmental conditions such as the presence of certain toxins.

For more details, check out this article published in Nature :

http://www.nature.com/nature/journal/v463/n7279/pdf/nature08753.pdf

Emily

Biological and Toxins Weapons Convention Update

Last week the U.S. State Department Released an unclassified version of the report "Adherence to and Compliance with Arms Control, Nonproliferation, and Disarmament Agreements and Committees". The report can be viewed here.

The compliance of certain countries with the Biological and Toxins Weapons Convention (BTWC) is covered in a section of this report. This report addresses the activity of nine state parties of the BTWC, China, Cuba, India, Iran, Iraq, Libya, North Korea, Pakistan, and Russia. Also, biological weapon activity of Egypt, Syria, and Taiwan was evaluated. Egypt and Syria are signed but not ratified members of the treaty.

In this report, Egypt, India, Iraq, Libya, Pakistan, and Taiwan were all found to be in full compliance with the BTWC, although not all of the countries being evaluated were found to be in full compliance. If Syria was ratified, it would be in violation of the treaty as it maintains the stance that Syria is "entitled to defend itself by acquiring its own chemical and biological deterrent". Available information leads to the belief that North Korea may still consider the use of chemical and biological weapon. In previous reports, the U.S. has expressed the worry that North Korea may have biological weapons agents weaponized in violation of the treaty.

China, Cuba, Iran, and Russia were not in violation of the convention, but were found to be engaging in dual-use research initiatives. Although the activities engaged in by these countries are not prohibited by the BTWC, dual-use research by China included "identifying factors that enhance the virulence, toxicity, or antibiotic resistance of pathogens, including through the use of genetic engineering." Iran has failed to address or resolve issues regarding it's compliance with the BTWC, and, according to this report, is "conducting research involving BW-related pathogens and genetic engineering, and developing mechanisms that could be used to deliver biological agents". It is unclear whether Russia has made efforts to change inherited weapons programs from it's time as the Soviet Union, although it recognizes the offensive nature of those programs.

"Playing God", a meaningless phrase?

The recent accomplishments of the Venter lab have caused a lot of controversies in the public eye, one of which is the perspective that humans should not be "playing god" with research pertaining to synthetic life. The Ethical Perspective News at the University of Oxford has an interesting article with a very different viewpoint.

Read the full article here.


Dev

"Impossible? Think Twice!" says Escherichia coli

The process of simple manipulation of genes by Geneticists 40 years ago has gradually evolved into the exciting field of Science known as Synthetic Biology. Just recently, researchers at South San Francisco-based biotech company LS9 Inc. introduced a gene usually found in algea, which naturally produces hydrocarbon, into the genome of E.coli bacteria. Further manipulating its metabolism, the E.coli bacteria was designed to deliver "100 times more fuel than the algae did."

With the vast amount of opportunity that Synthetic Biology delivers, it can now easily be expected, to manipulate the genome of E.coli bacterium to produce a "diesel-like mixture of hydrocarbons" in the future. Does this mean mankind can slowly become less dependent on non-renewable resources like Oil? So far, with the potential of Synthetic Biology, it sure seems so.

Read the full article here.

**Raida

Presidential Panel Update

Two of the leading researchers in the field spoke out, yesterday, on their opinions on the potential for the industry of synthetic biology and how they felt that it should be regulated.

Both Craig Venter (J. Craig Venter Institute) and George Church (Harvard University professor) both believe that government regulation is necessary in order to maintain safety within synthetic biology as it continues to develop. President Obama ordered that a commission be put together to study if there was any need for regulation for the field and to determine the degree of danger the field presented to the public.

“If you have a speed limit but no one enforcing it, you’ll have people speeding. You need to proactively set up a radar system and surveil it.’’ Church said, in a statement encouraging preliminary action that would be preventative in nature. This mentality is similar to that of the medical field where "an ounce of prevention is worth a pound of cure". Allison Snow, a professor from Ohio State University, said that the environmental aspects would have to be monitored as well so accidental releases of toxins and bacteria could be minimized.

The panel was called for after the J. Craig Venter Institute announced that they had "created synthetic life". Yesterday was the first day of two that the panel will convene and discuss the merits and possible dangers of the field.

The article containing more information can be found here.

Chris

iGEM Calgary: Front Page News

The 40 mile County Commentator has published a brief story on iGEM Calgary that appeared on the front page of the latest issue. You can view it here.

Synthetic Biology Awareness

May 27, 2010. Upon Craig Venter's recent announcement that he has successfully inserted the synthetic genome of genitalia mycoplasma into an empty cell, the media has developed huge interest in the matter. This coincided with President Barack Obama's decision earlier to order a six month review of synthetic biology. The panel that is reviewing Obama's request include Venter and several of his synthetic biology colleagues including Jay Keasling and Drew Endy. House committee members lack knowledge regarding synthetic biology. However they were interested in the potential of synthetic biology such as in the areas of synthetic fuels or synthetic compounds. This article also mentions the selling point of this meeting as the commercialization of synthetic biology based on the vested interest of the panel.

http://www.wired.com/wiredscience/2010/05/congress-obama-synthetic-bio/#more-21922

Jeremy

Drew Endy's DNA factory up and running

A project discussed for many years by many scientists, including MIT researcher and facility director Drew Endy, BIOFAB has now been up and running for the last 6 months. The (B+) International Open Facility for Advancing Biotechnology (BIOFAB), the world's first DNA factory, aims to offer scientists and students certain well-characterized pieces of DNA that can be assembled in different ways to carry out various functions. A real-world offshoot from the undergraduate iGEM competition, the BIOFAB is currently carrying out the characterization and standardization necessary to turn past iGEM projects into a true, world-wide synthetic biology registry. Read the full Nature News article, or check out the BIOFAB home page.

Dave

Directed Evolution

Evolution -- A process by which organisms become more suited to their environment. This occurs due to incorporation of random mutations in the genome which makes the particular organism "fitter". -- Darwin

Evolution is due to random mutations that occur in nature...or is it?

In 2009 University of Science and technology China iGEM team designed a system which allows directed evolution. This system allows the incorporation of a mutant gene and gets the desired product as the output. The system is designed such that that if the mutated gene gets expressed then the cell would live by suppressing ccdB and if the mutated gene does not get expressed then the cell would die as a result of ccdB production.

Fun fact: most of the registry reporters (fluorescent proteins such as RFP, GFP etc) are designed via directed evolution. This team just gave a new system which allows directed evolution.

For more information on the design of the system click here.

Himika

Synthetic Biology Matters to the President!

On July 8-9, 2010 Drew Endy and several of his colleagues were invited to the White House to discuss the ethical considerations of synthetic biology. This meeting was more for updating the Obama administration to the development and advances in the field of synthetic biology. The meeting is in response to Craig Venter's current insertion of synthetic genitalia mycoplasma genome. There are videos documenting their discussion here, and an official letter written by Barack Obama to Dr. Amy Gutmann inquiring about the potential effects of synthetically created genome.

Barack Obama's letter about synthetic biology can be found here. (PDF)

This will be covered in more detail soon!

Jeremy

iGEM Team Helps Prevent Rogue Use of Synthetic Biology

Synthetic biology is a constantly developing field. New things are popping up every day. Here's an example, published yesterday in Science Centric:

A team of students from ENSIMAG, an engineering school in Grenoble, France, and Virginia Tech is using bioinformatics to implement federal guidance on synthetic genomics. The students' work will help gene synthesis companies and their customers better detect the possible use of manufactured DNA as harmful agents for bioterrorism.

Kudos to the VT-ENSIMAG_Biosecurity team! We wish you the best of luck.

Read the full article here.


Patrick

Welcome to the iGEM Calgary 2010 Blog!

Thanks for visiting! This is where we'll be keeping you guys updated on everything that the University of Calgary 2010 iGEM team is doing.

For those who are unfamiliar, iGEM stands for the International Genetically Engineered Machines competition. This is an undergraduate-driven event, hosted by MIT, where teams from all over the world come together to show off their work in synthetic biology. As of 2010, there are 118 teams competing.

Synthetic biology is a rapidly expanding field that attempts to apply engineering principles to biology. One major part is the standardization of DNA pieces that can be reassembled like building blocks. Each team is given a starter set of "BioBricks" that can be used to solve many problems in biology.

This year, iGEM Calgary is attempting to build a "troubleshooting kit" for gene expression. Many researchers in biology face problems expression various genes into proteins (which do everything in a cell). We're trying to create a system that will show researchers precisely what is going wrong with their gene and where the problem is happening.

More details can be found on our team wiki at http://2010.igem.org/Team:Calgary, which can also be accessed by the link up on the very top.

Be sure to follow us on our RSS feed and also our Twitter at @iGEMCalgary!