Harvard faculty elected to American Academy of Arts and Sciences

April 12, 2017, Harvard Gazette

Those elected from Harvard include Alan M. Garber, provost of Harvard University and the Mallinckrodt Professor of Health Care Policy at Harvard Medical School; John A. Quelch, Charles Edward Wilson Professor of Business Administration; Jonathan L. Zittrain, George Bemis Professor of International Law; David Charbonneau, professor of astronomy; Pamela A. Silver, Elliot T. and Onie H. Adams Professor of Biochemistry and Systems Biology at Harvard Medical School (HMS); Hopi E. Hoekstra, Alexander Agassiz Professor of Zoology and curator of mammals in the Museum of Comparative Zoology; Myles A. Brown, professor of medicine at HMS; Marc J. Melitz, David A. Wells Professor of Political Economy; Torben Iversen, Harold Hitchings Burbank Professor of Political Economy; Janet Gyatso, Hershey Professor of Buddhist Studies; Naomi Oreskes, professor of the history of science; David Damrosch, Ernest Bernbaum Professor of Literature; Alina Payne, Alexander P. Misheff Professor of History of Art and Architecture. Gerald L. Chan, S.M. ’75, S.D. ’79, and his brother Ronnie C. Chan, sons of the late T.H. Chan and benefactors to the Harvard School of Public Health, were also named fellows.

 

 

The bionic leaf seems poised to lead a fertilizer revolution

5 April 2017, Popular Science

A bionic leaf created by Harvard professors Daniel Nocera and Pamela Silver keeps proving itself to be as cool as—and maybe even cooler than—its natural counterpart.

7 projects win funding for climate change solutions

6 March 2017, Harvard Gazette

The bionic leaf, a proof-of-concept platform pioneered by Harvard scientists, makes possible a cheap, nontoxic, portable device to create value-added products such as bioplastics for accelerating widespread adoption of solar and other renewable technologies, while simultaneously reducing CO2 emissions. This project will support work toward constructing a deployable bionic leaf that could provide a blueprint for bringing this technology to scale.

Synthetic biology to help colonize Mars

1 March 2017, PLoS blogs

Shannon Nangle finished her PhD ready to take on a new challenge and set her sights on research to help make Mars colonization possible. But she isn’t pursuing research on rocket fuels or space suits. She’s using synthetic biology to improve biomanufacturing of needed resources using simple inputs like sunlight, water, and CO2.

   

Compartmentalized life

6 March 2017, Wyss Institute

“Within their new hosts, these encapsulin systems could form capsids with very defined sizes on the nanoscale. These artificially expressed systems were able to protect the cells from high doses of different stressors that are also produced as byproducts of their normal metabolism. Some systems were also able to mineralize and store otherwise toxic iron, while still others may be involved in the so-called anammox process, which generates free dinitrogen from ammonium and nitrite with the rocket fuel hydrazine being an intermediate,” said Giessen, who is working with Silver at the Wyss Institute and HMS as a Postdoctoral Fellow.

 

 

 

India Headed For A Green Energy Revolution: Harvard Scientist

22 Jan 2017, NDTV

Harvard chemist and energy innovator Daniel G. Nocera is a man on a “renewable” mission. The inventor of the artificial leaf and co-creator of its bionic version plans to launch a pilot of the advanced technology in India with the assertion that a “renewable energy revolution will take place” in the country.

 

 

Featured Scientist: Pamela Silver

16 Dec 2016, Aldo Leopold Nature Center

Although a great deal of Silver’s work is with novel therapies for humans and livestock, she can’t ignore concerns about our planet’s need to adapt to bionic_leafincreasing amounts of carbon in the atmosphere. Using her knowledge in synthetic biology, Silver partnered with Daniel Nocera, a leading Harvard researcher in renewable energy and biological systems, to see if they could re-program cells to increase efficiency of photosynthetic rates and carbon fixation in plants. Out of this collaboration came what they call the ‘bionic leaf.’

 

Winners Selected in 2016 Faces of Biology Photo Contest

16 Dec 2016, American Institute of Biological Sciences

Alina Chan, a postdoctoral fellow at Harvard Medical School, won Second Place. Her photo depicts scientists Tami Lieberman and Michael Baym setting up for an experiment on bacterial evolution of antibiotic resistance. The researchers pour media infused with black ink for the the bacteria to grow on. A camera is used to document the movement and survival of the bacteria for two weeks.

 

 

Illuminating the dark corners of nature’s nitrogen cycle by mimicking rocket-fuel-producing bacteria

20 Dec 2016, Wyss Institute

“The ultimate example of systems biology is the interactions that happen between the earth and atmosphere that fuel our entire biosphere and world,” said Silver. “We hope to illuminate an until-now dark corner of the nitrogen cycle that could have broad implications for the earth as a whole.”

 

 

Shaping the future of science

5 Dec 2016, Menzies Foundation

Imagine reducing the need for invasive gut tests like colonoscopies or developing bacteria in your gut which could help manage your own inflammatory conditions.

These are some of the potential futures for patients with inflammatory bowel disease being explored in Dr David Riglar’s research at Harvard Medical School and the Wyss Institute for Biologically Inspired Engineering.

Will the artificial leaf sprout to combat climate change? in c&en

21 Nov 2016, Katherine Bourzac

To get around the problem of efficiently making more valuable chemicals at higher purity, some researchers are turning back to the original inspiration: biology. Harvard University synthetic biologist Pamela Silver doesn’t think it’s necessary for chemists to twist themselves into knots trying to mimic biology. The question for her is how to use what biology has already given us. “Plants are the best chemists there are,” she says. “Trying to supplant that with pure chemistry” may be making things unnecessarily difficult. “How is this going to work if we don’t use biology?” she asks.

 

     

Training microbes to hunt out cancer and pollutants in WIRED

7 Oct 2016, Emma Bryce

Silver is working on “programming microbes that could sense and remember” environment information, and has found that bacteria can be engineered to detect a specific antibiotic inside mice and, when excreted, change colour to indicate its presence.

 

 

Outstanding Postdoc Service Award Recipient: David Riglar, PhD, Systems Biology

In conjunction with the 2016 National Postdoc Appreciation Week, the Office for Postdoctoral Fellows is partnering with the HMS/HSDM basic science departments to honor the achievements of some of our exceptional postdoctoral research fellows for their research accomplishments, while also considering all around scientific service.

 

New “Bionic” Leaf Is Roughly 10 Times More Efficient Than Natural Photosynthesis

in the Scientific American, 1 August 2016

Chemist Daniel Nocera of Harvard University and his team joined forces with synthetic biologist Pamela Silver of Harvard Medical School and her team to craft a kind of living battery, which they call a bionic leaf for its melding of biology and technology.

 

Engineered microbes make silver nanoparticles

in c&en, 5 July 2016

To make these minuscule metal globs, Pamela A. Silver and Tobias W. Giessen of Harvard University turned to a 20-sided capsulelike structure in bacteria known as encapsulin, which holds iron-storing proteins that pack the capsule full of iron. The researchers removed the gene that encodes encapsulin’s iron-storing protein from Thermotoga maritima bacteria and replaced it with the sequence for a short protein that precipitates elemental silver instead. Then they transferred the entire genetic piece into an easy-to-grow laboratory strain of Escherichia coli. As a result, these structures in the engineered E. coli stuffed themselves with silver from their growth medium, forming symmetrical nanoparticles about 13 to 15 nm in diameter. The team broke open the cells to isolate and purify the nanoparticles.

Nanoparticle Niche

in the Harvard News, 17 June 2016

“Traditionally, synthetic biology has been very good at making organics—either protein drugs or small organic molecules like antibiotics,” said first author Tobias Giessen, research fellow in systems biology in the Silver lab. “Now the field is starting to be capable of using biology to make functional inorganic materials, such as these nanoparticles that can fight infection.”

Featured publication: Converting a natural protein compartment into a nanofactory for the size-constrained synthesis of antimicrobial silver nanoparticles. Giessen T, Silver PA. ACS Synthetic Biology. In press.

Facets of Discovery: Talks@12

23 June 2016

Three leading Harvard Medical School researchers share their discoveries and innovative approaches to complex scientific questions.

It’s alive, but is it life: Synthetic biology and the future of creation

at the World Science Festival, 4 June 2016

For decades, biologists have read and edited DNA, the code of life. Revolutionary developments are giving scientists the power to write it. Instead of tinkering with existing life forms, synthetic biologists may be on the verge of writing the DNA of a living organism from scratch. In the next decade, according to some, we may even see the first synthetic human genome. Join a distinguished group of synthetic biologists, geneticists and bioengineers who are edging closer to breathing life into matter.

Scientists say they’ve one-upped photosynthesis with a ‘bionic leaf’

in the Washington Post, by Sarah Kaplan, 2 June 2016

On Thursday, Silver and her colleagues report in the journal Science that they’ve combined solar panels, genetically modified bacteria and a synthetic catalyst to create a system that does exactly what a leaf does — turn sunshine into fuel — but much more efficiently.

A Synthetic Human Genome: Not So Fast

on Science Friday, 20 May 2016

When scientists and entrepreneurs held an invite-only meeting at Harvard last week to discuss the prospect of manufacturing a complete human genome and inserting it into a cell line, ethicists and biologists alike responded with swift and cautionary advice. “The creation of new human life is one of the last human-associated processes that has not yet been industrialised or fully commodified,” wrote Drew Endy and Laurie Zoloth in Cosmos. “Discussions to synthesise, for the first time, a human genome should not occur in closed rooms.”

Aside from the ethical discussions that may ultimately determine the fate of such a project, biologist Jeff Way, who attended the meeting, says building human chromosomes from scratch would be a huge technological leap. “It’s not really feasible. Part of the idea is you have to invent the technology to make it feasible.” Zoloth and Way join Ira to discuss the scientific and ethical challenges that lie ahead for large genome synthesis.

 

Forget the sci-fi horror stories. Here’s what we could really learn from a synthetic genome

in STAT news, by Ike Swetlitz, 18 May 2016

Pamela Silver, a Harvard bioengineer who was invited to but did not attend last Tuesday’s meeting, said that taking the genome apart (with new gene-editing techniques likeCRISPR) and putting it together (through synthesis) are “complementary” methods: “No one is better than the other.”

Alina Chan, a postdoctoral researcher in Silver’s lab who gave a presentation about her work at last week’s meeting, is in the early stages of trying to put all these elements together to build and test human artificial chromosomes, the first step in making the real thing. Chan said that even if scientists were able to build a human genome from the ground up, it would be a far cry from a real person.

“Being able to write a book doesn’t mean the story actually becomes real,” Chan said.

Targeting EPO to Treat Anemia

in Science Signaling, by Annalisa M VanHook, 17 May 2016

Burrill et al. engineered a form of EPO that activates EPO-R specifically on RBC precursors, but not on other cell types. Because many signaling molecules affect multiple types of cells, similar engineering strategies to create forms that are tissue- or cell type–specific may permit the development of therapies that deliver a benefit while reducing or eliminating undesirable side effects.

Featured publication: D. R. Burrill, A. Vernet, J. J. Collins, P. A. Silver, J. C. Way, Targeted erythropoietin selectively stimulates red blood cell expansion in vivo. Proc. Natl. Acad. Sci. U.S.A. 113, 5245–5250 (2016). [PubMed]

 

 

Shapesifter

We have developed Shapesifter, a three-dimensional constrained Brownian dynamics (CBD) simulation system for modeling protein systems at the domain level of detail (“coarse-grained”), and shown its application to quantitatively engineered therapeutic proteins.  The system focuses on a size scale below the resolution of the light microscope, where movement is difficult to observe and human intuition is poor, and above that of single atoms (the domain of more traditional molecular dynamics simulation).  Shapesifter allows the representation and modeling of macromolecular systems including Brownian forces, volume exclusion, linkers of various stiffnesses/material properties, electrostatics, and association/dissociation interactions.  We are interested in applications of this modeling approach to various engineered multidomain protein systems, including therapeutic protein fusions, in order to optimize their geometry and quantitative properties.  Shapesifter is under ongoing development and is available to the synthetic biology community at http://shapesifter.org.

 

 

Grassroots Future of Research group makes it official

4 May 2016

The Future of Research (FoR), which was a network of postdoc volunteers when ScienceCareers named the movement its 2015 People of the Year, is now a full-fledged nonprofit organization complete with a full-time executive director. Gary McDowell, a member of the founding group of Boston-area activists (and a Science Careers Working Life author), will assume the “full-time role assisting junior scientists in grassroots efforts to change science policy” thanks to a 2-year, $300,000 grant from the Open Philanthropy Project, FoR announced on 30 April.”

Coiled proteins puncture membranes in response to pH cue

28 April 2016

Jane Coffin Childs Fellow Jessica Polka demonstrates the engineering potential of a unique protein polymer.

“There’s so much unique biology in non-model organisms, some of which is beautifully described by older literature,” she explains. “With DNA sequencing and synthesis technologies becoming more readily available, we can revisit these phenomena with modern tools. Perhaps these edge cases are the best systems to use to understand what biology is really capable of.”

Featured publication: A tunable protein piston that breaks membranes to release encapsulated cargo. Polka J, Silver PA. ACS Synthetic Biology. PMID: 26814170.

Fusion Protein Technique Shows Promise for Safer Cell-Targeted Therapeutics

26 April 2016

“Compared to currently available EPO drugs, our molecule is engineered to prevent EPO from binding to and activating cells that promote side effects such as blood clotting or tumor growth,” said Jeffrey Way, Ph.D., Wyss Institute Senior Staff Scientist and the senior author on the study. “This cell-targeted EPO approach demonstrates a new theoretical basis for the rational design of engineered protein fusion drugs.”

 

Brendan Colón on the Stuff You Should Know podcast

Starting at 2:12 from the end, released 3 March 2016

In response to The Future of Renewable Energy podcast

Renewable energy could be the key to ensuring the future prosperity and health of Planet Earth and humankind. In this very special episode, we sit down and discuss the possibilities with Bill Gates.

R bodies

Biologists steal nanospear technology from bacteria in The Atlantic

Ed Yong, 17 Feb 2016

Billions of years before hominids sharpened sticks into stabbing weapons, bacteria invented spears. Specifically, they invented transforming spears—structures that could almost instantly unfold from flat, coiled ribbons into long, pointed cylinders. They use these weapons to wage war on other microbes. And now, scientists—descendants of those early stick-sharpening hominids—are planning to tweak these bacterial javelins, and deploy them as tools for research, medicine, and more.

Breaking cell barriers with retractable protein nanoneedles in the Wyss Press Release

11 Feb 2016

Described in the American Chemical Society Synthetic Biology journal, the team describes using protein polymers known as “R bodies”, which are found in certain bacteria, as retractable nanoneedles that can extend to puncture cellular membranes and release molecules on command.

Featured publication: A tunable protein piston that breaks membranes to release encapsulated cargo. Polka J, Silver PA. ACS Synthetic Biology. PMID: 26814170.

Diatom

Tapping the Marine Microbiome in the Wyss Press Release

22 Dec 2015

“The realization that we know so little about the Earth’s oceans, along with the advent of modern experimental techniques such as next generation sequencing and advanced microscopy methods, prompts me to believe that some of the major advances in the fields ranging from basic biochemistry, enzymology, metabolism, signaling, microbial interactions, and ecology, to medicinal natural products discovery, biomaterials, biogeochemistry, and origins of life will come from the oceans over the next few decades,” said Turnsek.

People of the Year: Future of Research’s Postdoc Activists in Science Careers

by Beryl Lieff Benderly, 22 December 2015

Each December, Science Careers names a “Person of the Year” to recognize those who have made especially significant and sustained contributions to improving the lot of early-career scientists. Up to now, each year’s honoree has been a senior academic figure occupying a prestigious post. This year’s choice, by contrast, is plural; of a different generation; and at the opposite end of the academic status ladder. For their dedicated, creative, and expanding efforts to empower early-career and aspiring scientists with knowledge and awareness so that they can take control of their futures and help bring needed change to the scientific enterprise, we are delighted to name the activists of the Future of Research (FOR) movement as the 2015 Science Careers People of the Year.

How microbes in your gut today hold clues to tomorrow’s medicines in STAT

9 December 2015

Silver, a biologist at the Wyss Institute for Biologically Inspired Engineering in Cambridge, Mass., wants to try to improve on nature. By altering the DNA of gut-dwelling microbes, she and her colleagues are designing organisms that can monitor the body and produce drugs on demand. Someday, Silver’s research could lead to a new way to treat our diseases: with living medicine.

Fluorescent-glowing bacteria help scientists see inside the body’s ‘dark places’ in the betaBoston

Shining light on microbial growth and death inside our guts in a Wyss Institute press release

30 November 2015

“The dream in this field is to make cell–based computers, using cells that can remember, count, sense, actuate and complete tasks in a programmable way,” said Pamela Silver, Ph.D., who is senior author on the new study, a Wyss Institute Core Faculty member on the Institute’s Synthetic Biology platform, the Eliot T. and Onie H. Adams Professorship of Biochemistry and Systems Biology at Harvard Medical School (HMS), and a founder of the HMS Department of Systems Biology. “This advance brings us another step closer to making that original dream a reality.”

Featured publication: Myhrvold C, Kotula JW, Hicks WM, Conway NJ, Silver PA. (2015). A distributed cell division counter reveals growth dynamics in the gut microbiota. Nature Communications, 6: 10039. PMID: 26615910

Microbiomes could hold keys to improving life in the Harvard Gazette

by Kat McAlpine, Wyss Institute Communications, 30 October 2015

“Microbes are everywhere. Therefore understanding microbiomes, whether they be the ones that live in and on our bodies or the ones in the environment, is essential to understanding life,” said Pamela Silver, a core faculty member at the Wyss Institute for Biologically Inspired Engineering at Harvard University.

The 2015 Innovation By Design Awards Winners: Fashion 

WANDERERS

Creators: MIT Media Lab Mediated Matter Gorup (Steven Keating, Neri Oxman, Will Patrick and Sunanda Sharma) with Deskriptiv, the Pamela Silver Lab at Harvard Medical School, and Stratasys

Most wearables convey a bit of information and not much more. But Neri Oxman, founder of the Mediated Matter research group at MIT, imagines a future where wearables aren’t just passive lifestyle devices: They could generate the food, energy, light, and oxygen to keep us alive. In a project dubbed Wanderers, Oxman proposes wearable vessels that have photosynthetic bacteria culturing inside, creating the resources that an interplanetary traveler would need to survive in other climates.

Synthetic Biology Needs Robust Safety Mechanisms Before Real World Application in Elsevier

and Is synthetic biology the key to health? in Elsevier Connect

by Lucy Goodchild van Hilten, 16 September 2015

“Historically, molecular biologists engineered microbes as industrial organisms to produce different molecules,” said Dr. Silver. “The more we discovered about microbes, the easier it was to program them. We’ve now reached a very exciting phase in synthetic biology where we’re ready to apply what we’ve developed in the real world, and this is where safety is vital.”

Publication featured: Ford TJ and Silver PA. (2015). Synthetic biology expands control of microorganisms. Current Opinion in Chemical Biology, 28:20-28. PMID: 26056951

 

Synthetic Biology at FAB11, MIT

6 August 2015

Transplanting circadian rhythms from one organism to another in The Boston Globe

by Kevin Hartnett, 1 July 2015

“Anna interfaced the clock with transcription of genes that makes these colored proteins,” says Silver. “You could just look at cells and see that they were keeping time.”

Publication featured: Chen AH, Lubkowicz D, Yeong V, Chang RL and Silver PA. (2015). Transplantability of a circadian clock to a noncircadian organism. Science Advances. 1(5):e1500358.

Re-booting the human gut, a Wyss Institute press release, 16 June 2015

“A new grant awarded by the Defense Advanced Research Projects Agency (DARPA), for up to $4.7 million dollars over the course of the work, will support the efforts of the project’s co–principal investigators Wyss Core Faculty member Pamela Silver, Ph.D., and Wyss Senior Staff Scientist Jeffrey Way, Ph.D., who will team up with Wyss Founding Director Donald Ingber, M.D., Ph.D. The cross–disciplinary Wyss team aims to fight gastrointestinal illness through tactics invisible to the naked eye by developing an army of genetically engineered bacteria designed to sense, report and combat harmful microbial invaders.”

Circadian Clock Transplant in The Scientist

by Ruth Williams, 12 June 2015

“Circadian clock machinery from cyanobacteria has been successfully reconstructed inside Escherichia coli bacteria, which do not have a natural day-night cycle, according to a paper published today (June 12) in Science Advances. The E. coli cells exhibited 24-hour-long repeating oscillations in both transcription of a reporter gene and phosphorylation of a key clock protein. The results serve as a proof of principle that engineering such a synthetic circadian circuit is possible.”

Setting the circadian clock, a Wyss Institute press release, 12 June 2015

“Now, scientists led by the pioneering Harvard synthetic biologist Pamela Silver, Ph.D., have harnessed the circadian mechanism found in cyanobacteria to transplant the circadian wiring into a common species of bacteria that is naturally non–circadian. The novel work, which for the first time demonstrates the transplant of a circadian rhythm, is reported in a new study in Science Advances.”

Publication featured: Chen AH, Lubkowicz D, Yeong V, Chang RL and Silver PA. (2015). Transplantability of a circadian clock to a noncircadian organism. Science Advances. 1(5):e1500358.

mushtari

Mushtari by Neri Oxman

14 May 2015

In collaboration with our lab, alongside members of the Mediated Matter research group and Deskriptiv, Oxman unveiled the 3D printed photosynthetic wearable on the TED2015 stage in Vancouver.

This is the first time that 3D printing technology has been used to produce a photosynthetic wearable piece with hollow internal channels designed to house microorganism.” Inspired by the human gastrointestinal tract, Mushtari is designed to host synthetic microorganisms – a co-culture of photosynthetic cyanobacteria and E. coli bacteria – that can fluoresce bright colors in darkness and produce sugar or biofuels when exposed to the sun. Such functions will in the near future augment the wearer by scanning our skins, repairing damaged tissue and sustaining our bodies, an experiment that has never been attempted before.” – Oxman

disruptive

What breakthroughs are possible by modifying an organism’s genome?

The Wyss Institute Disruptive podcast, May 2015

In this inaugural episode, radio host Terrence McNally discusses with Wyss Core Faculty Pam Silver and George Church the high-impact benefits of their synthetic biology work, as well as how they manage potential unintended consequences.

bionicleaf2

 

“Bionic Leaf” Makes Fuel from Sunlight in the Scientific American

by David Biello, 9 February 2015

Bacteria Turn Sunlight to Liquid Fuel in ‘Bionic Leaf’ in NBC News

by Alan Boyle, 9 February 2015

<< Ralstonia eutropha makes fuel using the hydrogen produced via catalysts powered by electric current from a photovoltaic panel.

Publication featured: Torella JP, Gagliardi CJ, Chen JS, Bediako DK, Colón B, Way JC, Silver PA & Nocera DG. (2015). Efficient solar-to-fuels production from a hybrid microbial-water-splitting catalyst system. Proc Natl Acad Sci U S A. 112(8):2337-42. PMID: 25675518

 

paminterview

 

Top 20 Influencers in Synthetic Biology by SynBio 2014

Radcliffe Asks, “What Is Life?” by Harvard Magazine, 3 June 2014

<< Discussing the science and ethics of engineering life are (from left) Eric S. Lander, Linda Griffith, David Liu, Pamela Silver, and I. Glenn Cohen.

 

gut

 

Bacterial reporters that get the scoop

Wyss Institute press release, 17 March 2014

<< Inspired by nature, the team engineered E. coli to sense, record and remember an environmental signal in the gut — and also demonstrated that they can survive and function within the complex environment of the mammalian gut. This work lays the foundation for the use of engineered probiotic bacteria that serve as non-destructive living diagnostics. In this schematic engineered probiotic E. coli have colonized the mammalian intestine and “remember” exposure to an environmental signal, which is indicated by the cells turning blue in color.

Publication featured: Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC and Silver PA. (2014). Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc Natl Acad Sci U S A. 111(13):4838-43. PMID: 24639514

joetyler

High-Octane Bacteria Could Ease Pain at the Pump

Harvard Medical School news, 25 June 2013

<< By rerouting the metabolic pathway that makes fatty acids in E. coli bacteria like these, researchers have devised a new way to produce a gasoline-like biofuel. Image courtesy of Wyss Institute.

Publication featured: Torella JP, Ford TJ, Kim SN, Chen AM, Way JC and Silver PA. (2013). Tailored fatty acid synthesis via dynamic control of fatty acid elongation. Proc Natl Acad Sci U S A. 110(28):11290-5. PMID: 23798438