Saturday, November 24, 2012

Shift in focus to genetic engineering and synthetic biology

I've been working as a genetic engineer slash yeast geneticist at a small start-up biotech in the Bay Area for over a year, and because of the progress we've made in that short time, I've become more interested in the overall fields of genetic engineering and synthetic biology. I also read the book Biopunk, which I didn't like much but got me thinking about biological hackers and DIY bio. Because that's what I'm thinking about more and more these days, I'm shifting the focus of this blog from general biology and biology-tinged science to these more specific topics.

As a preview to this new focus, I'm linking to my company's major paper, published in Science in January 2012. Our work has grown and expanded since this paper was written, but the paper provides the framework and motivation for our current efforts in the biofuels industry.

An engineered microbial platform for direct biofuel production from brown macroalgae.

Sunday, April 22, 2012

Crowdfunding science

Crowdfunding scientific research. This is a crazy idea to people who know how research funding normally works. Large grants are given to researchers who are associated with established universities, research institutions or government departments. Researchers need to prove to funding agencies that their grant proposals are worthy. Popular projects, established projects and projects that align with funding agencies' goals and agendas are more likely to be funded than those that carry higher risks of failure or are more experimental (incredibly). Those scientists who don't want to participate in this funding process need to fund themselves through personal money or a business; the current explosion of scientific start-ups speaks to the popularity of this path.

In addition to putting increasing pressure on traditional scientific research (see this recent NYT article for a related issue), the current system places the power of funding in the hands of a few. Now, for some projects, the power of funding can be placed in the hands of the many. Some new major scientific crowdfunding websites are up and running, including the ones featured here, and They are slick and colorful and mirror the structure of Kickstarter's crowdfunding site. Researchers prepare proposals and provide the dollar amount required to carry out their projects. Those scientists who meet their funding goals by the deadline have their research projects funded.

The parallels to Kickstarter are obvious, making these sites at first seem unoriginal, but the parallels help to make crowdfunded science accessible because people who are familiar with Kickstarter know exactly how it works. Secure payment systems, regular project updates. The companies are for-profit institutions, and they take a transaction fee from each funded project. One significant difference between the two sites is that PetriDish, like Kickstarter, has tangible rewards for different levels of backing (including videos, photographs and T-shirts), while Microryza specifically does not offer tangible rewards. Maybe because of the tangible reward requirement at PetriDish, this site is attracting more visually impactful projects (animals, ecology, geology etc.), while Microryza has a wider range of scientific projects, including computational projects where there's not much to see or print on a poster.

The research projects that are seeking crowdfunding are relatively small in scope, with researchers requesting in the range of $1,000-14,000. This is also a departure from the traditional system of research funding in that small projects are often not considered by major funding agencies unless they are bundled as part of a much larger grant proposal.

I have no personal affiliation with either site, but I am interested in seeing how both of them move forward. I've donated to several Kickstarter campaigns in the past year, and I'll be keeping a close eye on these scientific projects to find some that I'd like to support.

A brief search brought up other science crowdfunding sites to check out:, (cancer-specific projects), and scifundchallenge. It will be interesting to see if one or two crowdfunding sites pulls ahead and becomes dominant in this niche or if the sites will become specialized to avoid competing with each other for projects and donations.

Monday, September 12, 2011

ARPA-E is not your average ARPA

DARPA is the well-known Defense Advanced Research Projects Agency of the U.S. Department of Defense. It conducts top-secret defense research projects, like X, Y and Z. The "advanced research projects" model seems to be working because the government recently launched another Advanced Research Projects Agency, ARPA-E. The E is for energy. It's probably not as stealthy as DARPA, but it's potentially much more important.

ARPA-E operates under the Department of Energy and is responsible for funding research projects that aim to improve our use of energy resources or develop new energy resources. Some of the funded projects are or will be very experimental, not falling in line with previous or even current energy research. All of this funding and research will help us to reduce or eliminate our dependence on fossil fuels.... hopefully.

ARPA-E states that it funds research projects in six major categories of energy technology advancement, plus one category of "other projects." They give their major categories catchy names, which I guess the goal is to help people to remember them better:

BEEST (better batteries)
IMPACCT (reduced carbon dioxide emissions)
GRIDS (grid-scale energy storage)
ADEPT (soft magnetics, high-voltage switches, high-density charge storage)
Electrofuels (microorganism-based biofuel production)
BEETIT (energy-efficient building cooling technology)
Other Projects

It seems that the research programs that are funded by ARPA-E are lines of research that are proposed or maybe already underway at universities, research institutions and private companies. I think in a way, it's good to have these major funding categories to help focus research efforts to accelerate innovation and progress. It might also encourage collaboration among the different groups that are working in the same area of research. I think, though, that the "other projects" category will become ever larger, possibly overtaking all of the other categories in number. ARPA-E will probably need to expand its core research categories as projects in the "other projects" category are funded.

My personal favorite is the Electrofuels category because it acknowledges that people with my basic science training in yeast (the best model organism, but sometimes difficult to translate into real-world applications) have an important role to play in improving our energy outlook.

Friday, August 26, 2011

The missing lager yeast strain has been found!

You probably know that beer is alcoholic because of yeast. Yeast grow and divide in sugary starting solutions, and the byproducts of their metabolism (or fermentation) include ethanol.

If you make beer yourself, you also know that the two major categories, ale and lager, are fermented at very different temperatures. Ales are fermented at room temperature (68-72 degrees Fahrenheit), while lagers are fermented at much cooler temperatures (45-55 degrees). This difference is because the yeast "like" to grow and ferment at different temperatures, but why? A research group thinks they figured it out, and they're publishing their findings next week in the journal PNAS (Proceedings of the National Academy of Sciences).

Ale yeast is the species known as Saccharomyces cerevisiae (the same yeast that people use to make bread). Lager yeast is slightly different. It's a hybrid species that came about because S. cerevisiae mated and hybridized with another species. This hybridization allowed the lager yeast (known as Saccharomyces pastorianus) to ferment at much cooler temperatures than would be possible with S. cerevisiae alone.

The problem was, the other contributing yeast species was unknown. People tried looking at the genome of S. pastorianus to figure out the identity of the other species, but because many yeast species are closely related and have similar gene sequences, these efforts were not conclusive. It was thought that the other strain was Saccharomyces bayanus because this yeast grows much better than S. cerevisiae at lower temperatures. However, S. bayanus is also a hybrid species, which complicates the analysis. Based on gene sequence similarities, it was also proposed that the other strain is Saccharomyces monacensis, but this identification is also controversial because S. monacensis might also be a hybrid species.

Researchers from Argentina, the US and Portugal seem to have finally identified the mystery lager yeast. This species, named Saccharomyces eubayanus, was found on large nodules (galls) that grow on beech trees in Patagonia (southern South America). Tree galls are full of sugary compounds that the yeast like to feast on, so the researchers collected galls from different tree species in different locations. When they isolated the yeast from these Patagonian beech trees, they discovered that this yeast's genome was 99.5% identical to the non-cerevisiae portion of the S. pastorianus genome. The most interesting piece of evidence supporting the true identification of S. eubayanus as the "lager" portion of the hybrid yeast species is that these beech forests exist in an Alpine environment with consistently low temperatures, and they seem to be the yeasts' preferred habitat.

A yeast species that is 99.5% identical to a large portion of the S. pastorianus genome and naturally grows at lager temperatures seems like pretty convincing evidence. There's one giant question remaining, though: how did a yeast species from Patagonia make it to Germany, where lagers were born, in the 1400s? The prevailing thought is that lagers have been made in Germany since the early 1400s, which is long before Patagonia was explored by Europeans. There are several possible explanations...

First, maybe the Germans got their dates wrong. It's possible that lagers were not produced in Germany until after South America was explored by Europeans.

Second, Patagonia might have been explored by other groups before the Columbian era. There is some evidence that Vikings and other seafaring groups found parts of North and South America a long time before the Western Europeans. That alone doesn't explain why lagers were first made in certain regions of Germany. You'd expect Viking lagers if this were true, right?

Third, and the most likely possibility in my mind, S. eubayanus might not be specific to Patagonian forests. There are plenty of Alpine environments in Europe, particularly regions of Europe that are easily accessible to Germans. Now that people know to look at tree galls in cold climates, we may discover that S. eubayanus is common to all forests in cool climates.

Cited paper:

Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast

Monday, August 8, 2011

The buckyball traps a single water molecule!

I thought this was sort of a cute story.

Researchers at Kyoto University in Japan published an article in Science in which they determined that a fullerene C60 (buckminsterfullerene, buckyball, etc.) carbon cage molecule can trap a single water molecule. So what? Well, water molecules are notoriously difficult to separate (maybe impossible using other isolation methods?). This capture in a fullerene cage may be a way to study water molecules without the influence of the ever-present effects of hydrogen bonding. I'm not sure if this is going to be a successful way to study the properties of individual molecules of water, but it's a great start.

Literature cited:

Kurotobi K and Murata Y. A single molecule of water encapsulated in fullerene C60. Science. 2011 Jul 29;333(6042):613-6.

Monday, August 1, 2011

Zinc Finger Nucleases, TALENs and Genesis: the future of human gene manipulation

A major problem in treating genetic disorders is the inability to precisely target and remove or change the offending genes, known as gene therapy. If you can take a person's problem cells out of his or her body, modify the dysfunctional genes, and put the modified cells back into the person's body, then you can most likely treat/cure the disorder. All of the steps in this process are complicated, though, and it's been extremely difficult to "cure" a genetic disorder in this way. First, due to the lack of homologous recombination, it's not easy to target genes in somatic cells, so tricks need to be used to modify the genes of interest. Second, most of the targeted cells would not be "fixed" due to the low efficiency of successful modification. Third, it's extremely challenging, maybe impossible, to modify cells in organs or other solid tissues because they can't be manipulated in a lab or efficiently exposed to the therapy, so gene therapy has generally been restricted to blood disorders, where a person's blood cells can be removed and modified in a lab setting, while all residual dysfunctional blood cells in the body are killed through radiation.

Early ideas of gene therapy involved the use of viruses that could modify or introduce DNA into human cells, theoretically removing the dysfunctional genes or introducing helpful genes to cells that could be re-introduced into the patient's body. However, there were problems with these early trials, mainly that they sometimes caused these cells to grow out of control, like a cancer. It was too high a risk to take with human lives, so this research has not moved forward as much as people would have liked.

A new group of tools has been developed in the last few years that might now allow researchers to use gene therapy to treat or cure genetic disorders. These tools help with the first (and to a lesser extent, the second) problem: they can specifically target genes of interest inside cells, allowing specific mutations or deletions to be made in dysfunctional genes, possibly at a higher efficiency than was possible with the older virus-based tools.

The first tool is known as the ZFN, or zinc finger nuclease, developed by Sangamo BioSciences in Richmond, CA (disclosure: members of my lab are collaborating with Sangamo to test ZFNs in human cell lines and recently published an article on their research). This is a combination of two different proteins, the zinc finger transcription factor and a DNA-modifying endonuclease. The zinc finger is what targets a specific three-letter DNA sequence (codon) in the genome, and the endonuclease makes a cut at that specific region. This can be used to both disrupt a gene and add to a gene. Sangamo has licensed its technology to Sigma-Aldrich, which sells ZFN constructs for $25,000 apiece.

The second tool, called the Genesis system, is based on adeno-associated viruses (AAVs) and has been developed by Horizon Discovery in the UK. Their technology, named Genesis, seems to be more flexible than the ZFNs in that they can add genes as easily as they can delete them. The technology uses AAVs that contain single-stranded DNA sequence that is homologous to the sequence of the target gene. This company has not licensed its technology to a large biotech, but it has collaborated with Novartis on a pilot study and is working with a number of academic institutions (called Centers of Excellence) to use this technology. Horizon Discovery seems to collaborate with these academic institutions free of charge, but it charges industry clients between $20,000 and $50,000 per cell line, depending on the level of customization.

The third tool has been developed by the French company Cellectis. This technology, similar to ZFNs, is called transcription activator-like effector nucleases, or TALENs. They make use of enzymes called meganucleases, which cut at specific DNA regions. The major difference is that TALENs can target individual DNA nucleotides rather than the three-nucleotide codons that are targeted by ZFNs. Cellectis offers TALEN constructs for $5,000 and up.

Together, these new technologies represent the next leap in human genetic disease (and animal model of human disease) research. These technologies could solve some of the problems plaguing gene therapy research, and they could set us forward many years in our ability to precisely modify human and mouse genes for the purposes of treating and curing diseases.

Interesting reading:

Sangamo BioSciences
Horizon Discovery

Sunday, July 3, 2011

Change your diet, change your microbes?

In this week's issue of Science, an interesting article by Faith et al. at Wash U in St. Louis described the effects of dietary changes on the composition of gut microbes in a "human gut" mouse model. Ten strains of human gut bacteria were introduced into mice that had few (or no) gut microbes of their own to mimic the effects of dietary changes on the human gut. The authors could predict the changes that occur in gut microbe compositions after changing the mouse diets in specific ways. Because different microbes play different roles in nutrient utilization and overall health, the results suggest that very real changes in your ability to use the nutrients in your food could be made by changing the composition of your diet.

The researchers changed the proportions of protein, fat, carbohydrate and sugar of the mouse diet and looked at the overall numbers and percentages of the ten human gut species in the mouse guts. Higher levels of protein led to higher overall numbers of microbes. Seven species (including E. coli) had increased numbers with increasing protein percentage, while the other three had decreased numbers. It wasn't clear why these three species had decreased numbers, but the authors suggest that it could be an effect of simple competition for resources. Changing the concentration of fat had no significant effect on any individual species or overall microbe numbers, and carbohydrate and simple sugar concentrations only had effects on one species each. So... the main factor that affects the microbe composition in your gut seems to be the concentration of protein in your diet.

Studies like this could be useful on many levels. Knowledge of how diet can affect normal microbial loads in people's guts can help to develop food programs for poor and undernourished people. It can also help to make specific dietary recommendations for different life stages. Also, and this is my personal speculation, this information could be helpful for people with severe food allergies who want to plan optimal diets but have restricted food choices.

The study has a lot of moving parts and much more information than I have space to talk about, but if you're interested in the topic, the Gordon lab is doing fascinating work on this topic. I don't think any recommendations for human diets can be made yet, but this is an important step toward understanding how diet can relate to and affect gastrointestinal microbial communities.


Faith JJ, McNulty NP, Rey FE, Gordon JI. Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science. 2011 Jul 1;333(6038):101-4.

Gordon Lab at Washington University in St. Louis School of Medicine;

Thursday, June 30, 2011

Welcome to the blog

There's a lot of great science being done out there, and because of vast increases in the number of labs, projects, scientific fields and research journals reporting these discoveries, it's increasingly difficult to sift through everything to focus on the great discoveries that will stop you in your tracks.

I'm a biologist by training, but I'm interested in all aspects of science and how scientific research relates to my life and the world. I'll be posting regularly on new discoveries and revisits of past discoveries that I feel are important to share widely. I hope you enjoy the blog, and I hope it helps you to find fascinating discoveries that you might have otherwise missed.