My current research is inspired by lichen, which is formed by a symbiosis between fungi and algae.

The evolution of eukaryotic cells is widely agreed to have proceeded through a series of endosymbiotic events between larger cells and proteobacteria or cyanobacteria, leading to the formation of mitochondria or chloroplasts, respectively. Engineered endosymbiotic relationships between different species of cells are a valuable tool for synthetic biology, where engineered pathways based on two species could take advantage of the unique abilities of each mutualistic partner. We explored the possibility of using the photosynthetic bacterium Synechococcus elongatus PCC 7942 as a platform for studying evolutionary dynamics and for designing two-species synthetic biological systems. We observed that the cyanobacteria were relatively harmless to eukaryotic host cells compared to Escherichia coli when injected into the embryos of zebrafish, Danio rerio, or taken up by mammalian macrophages. In addition, when engineered with invasin from Yersinia pestis and listeriolysin O from Listeria monocytogenes, S. elongatus was able to invade cultured mammalian cells and divide inside macrophages. Our results show that it is possible to engineer photosynthetic bacteria to invade the cytoplasm of mammalian cells for further engineering and applications in synthetic biology. Engineered invasive but non-pathogenic or immunogenic photosynthetic bacteria have great potential as synthetic biological devices.

Read our paper in PLoS ONE.

“Gutsy” -The Boston Globe

FeFe-hydrogenases are the most active class of H2-producing enzymes known in nature and may have important applications in clean H2 energy production. Many potential uses are currently complicated by a crucial weakness: the active sites of all known FeFe-hydrogenases are irreversibly inactivated by O2. We have developed a synthetic metabolic pathway in E. coli that links FeFe-hydrogenase activity to the production of the essential amino acid cysteine. Our design includes a complementary host strain whose endogenous redox pool is insulated from the synthetic metabolic pathway. Host viability on a selective medium requires hydrogenase expression, and moderate O2 levels eliminate growth. This pathway forms the basis for a genetic selection for O2 tolerance. Genetically selected hydrogenases did not show improved stability in O2 and in many cases had lost H2 production activity. The isolated mutations cluster significantly on charged surface residues, suggesting the evolution of binding surfaces that may accelerate hydrogenase electron transfer. Rational design can optimize a fully heterologous three-component pathway to provide an essential metabolic flux while remaining insulated from the endogenous redox pool. We have developed a number of convenient in vivo assays to aid in the engineering of synthetic H2 metabolism. Our results also indicate a H2- independent redox activity in three different FeFe-hydrogenases, with implications for the future directed evolution of H2-activating catalysts.

Towards a Synthetic Chloroplast in the German Newspaper Frankfurter Allgemeine Sonntagszeitung

The Harvard iGarden is a venture into plant engineering. Our aim is to create a toolkit for the cultivation of a personalized garden containing features introduced through synthetic biology. In addition to a “genetic fence” designed to prevent the spread of introduced genetic material, we have developed three independent features to be included in this toolkit - inclusion of novel flavors, knockdown of plant allergens, and modification of petal color. All parts are BioBrick compatible and introduced into plants through agrobacterium-mediated transformation, using existing plant vectors modified with the BioBrick multiple cloning site. The Harvard iGarden, beyond being an application of the BioBrick system to plant engineering, is an effort to raise public awareness of synthetic biology, production of food, and how the two can intertwine. We envision the iGarden as a medium through which the non-scientist can see the power and potential of synthetic biology and apply it to everyday life.

Modular electron transfer circuits for synthetic biology: insulation of an engineered biohydrogen pathway. Bioengineered Bugs.

NOTHING STINKS ONLY THINKING MAKES IT SO

We live in biological world completely surrounded by rich communities of microorganisms, but often in a cultural world that emphasizes total antisepsis. But “sanitized and pasteurised for your protection” is the antiseptic symbol of sensory death. Because not all smells and bacteria can be pleasant, the consequences of hyper-sanitation could be that we decide to have none at all. Smells, bacteria, and bacteria that produce smells surround us all the time; chemical detection is an ancient biological communication tool used by bacteria and animals alike. Smells and bacteria are a crucial component in defining, understanding of and orienting in any environment.

The intersection of our interests in smell and microbial communities led us to focus on cheese as a “model organism.” Many of the stinkiest cheeses are hosts to species of bacteria closely related to the bacteria responsible for the characteristic smells of human armpits or feet. Can knowledge and tolerance of bacterial cultures in our food improve tolerance of the bacteria on our bodies or in other parts of our life? How do human cultures cultivate and value bacterial cultures on cheeses and fermented foods? How will synthetic biology change with a better understanding of how species of bacteria work together in nature as opposed to the pure cultures of the lab?

Will we be able to re-engineer bacterial communities as readily as we can add or delete genes to and from E. coli? How will synthetic biology change our relationship to the microbial communities that surround us?

SB 5.0 Poster [PDF]

We were fascinated by the similarities between cheese and human microbiodiversity and curious about the historic origin of cheese microflora. Given the physicality of cheesemaking, we speculated on the human origins of many of the unique cheese flavors. To explore this hypothesis and to foreground the microbiology of our food and bodies, we sought out to make cheeses with starter cultures isolated from the human body. Swabs from hands, feet, noses, and armpits were inoculated into fresh, pasteurized, organic whole milk and incubated overnight at 37° Celsius. The milk curds were then strained and pressed, yelding unique smelling fresh cheeses. Eight cheeses were produced in total for further study, with bacterial origins from the bodies of the Synthetic Aesthetics team.

Comparative smell-omics of the cheeses analyzed with headspace technology. The largest difference in odor and bacterial diversity was between Armpit-3 (pink) and Foot-5 (blue). Armpit-3 had the most pleasing, cheese-like smell, and also contains the largest number of ketones previously identified as being involved in cheese odor. For more information, read my thesis chapter on the Synthetic Aesthetics project (PDF).

Harvard iGEM 2008: Our project sought to combine the detecting capabilities of bacteria with the speed and ubiquity of electricity by creating an inducible system in Shewanella oneidensis MR-1 with an electrical output, allowing for the direct integration of this biosensor with electrical circuits via microbial fuel cells.