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Fall Science Chat!

Science Chat November 1 in veteran chat

I’m thrilled to announce that the Fall Science Chat will be next week on Wednesday, November 1st at 10:00pm GMT (3:00pm, Pacific Time Zone). If you have questions for our developers/scientists it would be helpful to post them right here so the team can review them in advance. If we aren’t able to answer all your questions in the given time, we will attempt to get a blog post up soon with answers. Despite the fact that this chat will take place in #veteran, it will be accessible to all who want to join via the following link: http://chat.mibbit.com/?channel=%23veteran&server=irc.fold.it. Looking forward to chatting with you all!

Date: Wednesday, November 1st, 2017
Time: 10:00-11:00pm GMT; 3:00-4:00pm Pacific Time Zone
Location: #veteran chat

http://www.thetimezoneconverter.com/

(Thu, 10/26/2017 - 19:15  |  15 comments)

Destroying a Silent Killer in the Food System

We are launching an uncommon collaboration between UC Davis, University of Washington, Northeastern University, Mars Incorporated, Thermo Fisher Scientific, and the global public, to engineer a protein tailor-made for the degradation of aflatoxins.

Imagine a naturally occurring poison – known to cause liver cancer – which 4.5 billion people around the world are chronically exposed to1.

You don’t have to imagine. The poison exists in the form of aflatoxins, which are compounds produced by certain fungi that can grow in or on almost all grains and groundnuts1. Aflatoxins are known hepatocarcinogens, meaning they cause liver cancer, and are considered a Class 1 carcinogen by the International Agency for Research on Cancer, part of the UN World Health Organization. Liver cancer is the third leading cause of cancer death globally, with 83% of cases occurring in East Asia and sub-Saharan Africa2-3.

Beyond liver cancer, aflatoxins are associated with worsened health outcomes in the developing world. These fungal toxins have been shown to negatively impact the immune system, rendering vaccines less effective, and to reduce vitamin absorption and recovery rates from malnutrition4.

Aflatoxin in Our Food System

So how does this potent carcinogen get into – and stay in – our food? In developed countries, laws limit the amount of aflatoxins allowed in food for humans, livestock, and pets. These laws are backed by expensive monitoring and advanced food safety technologies.

In the developing world, aflatoxin limits are set but often unenforced. Under-regulated food manufacturing, subsistence agriculture, small-scale farming, and lower healthcare budgets all contribute to the aflatoxin contamination problem. Over the past 50 years, when food and feed has been sampled in developing countries, the majority has been found to contain aflatoxins well above the legal limits5. A recent study in India found that 100% of collected samples of grain flour were contaminated, with an average aflatoxin concentration three times higher than the limit allowed in the United States6-7.

Aflatoxins affect more than just the plants we eat. When fed to cattle, they transform into a more potent toxin which accumulates in milk. A 2016 study in urban low-income areas in Nairobi found that 100% of the milk tested had detectable levels of aflatoxin, with 63% of the samples above the legal limit8.

This global health issue is also a trade and economic problem. Before scientists understood how harmful aflatoxins can be, Africa accounted for more than three quarters of the global peanut export market. Its current share is about 4%, partly due to its inability to meet aflatoxin standards outside of Africa. This costs Africa $1 billion per year in lost peanut revenue alone. Other African crops are similarly affected.

Climate change may make the world’s aflatoxins problem worse. The fungi which produce aflatoxins thrive in hot and humid conditions. Right now many parts of the world are not well suited for these deadly fungi, but rising temperatures could allow for more growth in more areas, increasing the threat of exposure. In just the last five years, cases of aflatoxin contamination have been increasing in Europe9.

Mitigation of Aflatoxin

How can we tackle aflatoxin? Removing aflatoxins from our food is extremely difficult. To date, there appears to be no ‘best practice’ for minimizing exposure other than strong enforcement of legal limits and systemic use of safe agricultural practices commonly adhered to in developed countries.

Several approaches for managing and degrading aflatoxins are currently in practice, but none are widely considered effective. At present, microbial, enzymatic, and bio-control approaches are preferred. Each has its own complications, ranging from expensive multi-day treatments to low efficacy in certain environments. The underlying issue is that there is no cost-effective and efficient system to remove aflatoxins from our food system5,10.

Our Challenge For You

Through Foldit (run from University of Washington and Northeastern University), anyone in the world can help to optimize an enzyme that we hypothesize could be capable of degrading a susceptible lactone ring in aflatoxin. Chemical degradation of this lactone ring has been demonstrated to decrease aflatoxin toxicity by more than 20-fold11. However, the enzyme in its current state is unable to perform this reaction. We are asking Foldit players to restructure the active site of this enzyme.

The goal is to enable the enzyme to effectively interact with the partially degraded Aflatoxin B1 molecule that we have modeled inside. Once we develop a highly effective enzyme capable of degrading the toxin, enzymes could readily be added to feed and food to remove toxins in real-time, complementing the current techniques for aflatoxin management and control12.

The Siegel Lab at the UC Davis, through the support of Mars, will select the top player designs to experimentally characterize. Thermo Fisher Scientific will donate gene synthesis services, encoding player designs through its proprietary DNA synthesis platforms. Using these genes, researchers in the Siegel Lab will produce the player-designed proteins and determine whether they are capable of degrading Aflatoxin B1, the type of aflatoxin that is most potently carcinogenic.

Over the next few months, we’ll be releasing a series of puzzles in which Foldit players can manipulate the enzyme model with escalating degrees of control (starting with simple site directed mutagenesis and leading to full redesign with insertion/deletion of protein segments). We will continue to provide feedback on previous rounds of player designs in order to further explore this enzyme’s ability to degrade aflatoxin. The first puzzle of the series, 1440: Aflatoxin Challenge: Round 1, is available now!

By participating in these Aflatoxin Challenge puzzles, the players agree that all player designs will be available permanently in the public domain, and the players will not seek intellectual property protection over the designs created as part of the challenge.

1. Williams, J. H.; Phillips, T. D.; Jolly, P. E.; Stiles, J. K.; Jolly, C. M.; Aggarwal, D., Human aflatoxicosis in developing countries: a review of toxicology, exposure, potential health consequences, and interventions. Am J Clin Nutr 2004, 80 (5), 1106-22.
2. Schatzmayr, G.; Streit, E., Global occurrence of mycotoxins in the food and feed chain: facts and figures. World Mycotoxin Journal 2013, 6 (3), 213-222.
3. Ajani, J.; Chakravarthy, D. V. S.; Tanuja, P.; Pasha, K. V., Aflatoxins - A Review. Indian Journal of Advances in Chemical Science 2014, 3, 49-60.
4. Liu, Y.; Wu, F., Global burden of aflatoxin-induced hepatocellular carcinoma: a risk assessment. Environ Health Perspect 2010, 118 (6), 818-24.
5. Williams, J. H.; Phillips, T. D.; Jolly, P. E.; Stiles, J. K.; Jolly, C. M.; Aggarwal, D., Human aflatoxicosis in developing countries: a review of toxicology, exposure, potential health consequences, and interventions. Am J Clin Nutr 2004, 80 (5), 1106-22.
6. Kumar, P.; Mahato, D. K.; Kamle, M.; Mohanta, T. K.; Kang, S. G., Aflatoxins: A Global Concern for Food Safety, Human Health and Their Management. Front Microbiol 2016, 7, 2170.
7. Ramesh, J.; Sarathchandra, G.; Sureshkumar, V., Survey of market samples of food grains and grain flour for Aflatoxin B1 contamination. Int. J. Curr. Microbiol. Appl. Sci 2013, 2 (5), 184-188.
8. USDA, Mycotoxin Handbook. 2015.
9. Kiarie, G.; Dominguez-Salas, P.; Kang’ethe, S.; Grace, D.; Lindahl, J., Aflatoxin exposure among young children in urban low-income areas of Nairobi and association with child growth. African Journal of Food, Agriculture, Nutrition and Development 2016, 16 (3), 10967-10990.
10. Herrera, M.; Anadón, R.; Iqbal, S. Z.; Bailly, J. D.; Ariño, A., Climate Change and Food Safety. In Food Safety: Basic Concepts, Recent Issues, and Future Challenges, Selamat, J.; Iqbal, S. Z., Eds. Springer International Publishing: Cham, 2016; pp 149-160.
11. Ehrlich, K. C.; Moore, G. G.; Mellon, J. E.; Bhatnagar, D., Challenges facing the biological control strategy for eliminating aflatoxin contamination. World Mycotoxin Journal 2015, 8 (2), 225-233.
12. Lee, L. S.; Dunn, J. J.; DeLucca, A. J.; Ciegler, A., Role of lactone ring of aflatoxin B1 in toxicity and mutagenicity. Experientia 1981, 37 (1), 16-17.
13. Olempska-Beer, Z. S.; Merker, R. I.; Ditto, M. D.; DiNovi, M. J., Food-processing enzymes from recombinant microorganisms—a review. Regulatory Toxicology and Pharmacology 2006, 45 (2), 144-158.

( Posted by 83 2645  |  Fri, 10/13/2017 - 20:57  |  6 comments )
8

New Release!

Hey everyone,

We've just released a small update with the following changes:

General
* Updated the splash screen. The old credits screen was getting crowded, so instead we've listed the contributing institutions and included a link to the website credits page.

Bug Fixes
* Fixed an issue with multistart puzzles not properly handling some setups.

As always, thanks to our devprev players for helping test this release!

(Mon, 10/09/2017 - 23:48  |  0 comments)

New Devprev Puzzle!

Try out the new Multi-start Chaperone puzzle in the Developer Preview release! We've recently corrected some problems with multi-start puzzles, and we'd appreciate if devprev users would briefly try out this puzzle. If you experience any issues with the puzzle, please leave a comment on the puzzle page!

(Thu, 10/05/2017 - 22:19  |  0 comments)

Player Feedback Welcome!

The fantastic Timo Van Der Laan will be offering up his expertise to the Foldit team as he begins his volunteer work with us. He's requested that players give feedback as to their most desired Lua functions. You can find his call for feedback on this post. Thanks in advance for your suggestions!!!

(Thu, 10/05/2017 - 19:48  |  4 comments)
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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons