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NHGRI/NIH awards team $6.5M to advance DNA sequencing using Nanopores

The National Human Genome Research Institute (NHGRI), part of the National Institutes of Health
(NIH), awarded a $6.5 (over 4 years) grant to a team of Harvard University researchers to further develop electronic sequencing in nanopores. The grant is part of more than $20 million in total funding
given by NHGRI/NIH to spur innovative sequencing technologies inexpensive and efficient enough to sequence a person’s DNA as a routine part of biomedical research and health care.

Daniel Branton, Higgins Professor of Biology, Emeritus, in the Faculty of Arts and Sciences (FAS) and Professor Jene Golovchenko, Rumford Professor of Physics and Gordon McKay Professor of Applied Physics, in the School of Engineering and Applied Sciences (SEAS) and Department of Physics (FAS), who lead the Nanopore group at Harvard, will oversee the research.

The team is among several grant winners who are developing nanopores (holes about two nanometers in diameter) that may be able to recognize individual DNA bases by their electrical or ionic signals to achieve
high-accuracy sequencing of individual DNA molecules. The goal of the Harvard scientists is to design and optimize nanopore technology using novel electronic control and sensing methods to create a nanopore
detector chip capable of sequencing a mammalian genome within a day on a single instrument.

In fact, for the past decade, the lab has been investigating electronic methods of rapidly detecting, characterizing and sequencing single molecules of DNA. The group’s research has lead to the development of the first solid–state nanopore structures through which individual DNA molecules could be passed and electronically detected. Recently they have shown that a single DNA molecule can be made to pass back and forth
through, and electronically interrogated, many times, by the same nanopore.

Branton, Golovchenko, and colleagues are now advancing the understanding of the physical properties of these nanopores and the DNA polymers confined in them. They are using and developing advanced physics and
material science tools to fabricate sophisticated nanopore devices needed to better understand the molecular interactions, transport, and electronic, and signal processing mechanisms needed for sequencing.

The NHGRI/NIH award comes on the heels of a recent agreement for the Nanopore Group to work with UK-based Oxford Nanopore Technologies to integrate discoveries and research aimed at advancing the broader field of nanopore science. Harvard University’s Office of Technology Development (OTD) came to a formal licensing and funding agreement with the UK-based firm on August 5th.

Oxford Nanopore has exclusive rights to support and commercialise a number of nanopore technological breakthroughs developed by Branton, Golovchenko, and co-collaborator George Church, Professor of Genetics at
Harvard Medical School, as well as related technologies developed with the Harvard team’s research partners at the University of California Santa Cruz (UCSC) and the National Institute of Standards and Technology


October 23, 2008 Posted by | Uncategorized | Leave a comment

MIT research bringing ‘smart bikes’ to Denmark

Project aims to match sustainability, interactivity

October 10, 2008

MIT researchers unveiled a major new project on Oct. 10 in Copenhagen aimed at transforming bicycle use in Denmark’s largest city, promoting urban sustainability and building new connections between the city’s cyclists.

The project, called SmartBiking, will utilize a novel self-organizing smart-tag system that will allow the city’s residents to exchange basic information and share their relative positioning with each other. The project will be implemented citywide in time for the November 2009 U.N. Climate Change Conference, which Copenhagen will host.

“One of the most striking aspects of Copenhagen is that it is already a very sustainable city,” said Carlo Ratti, Director of MIT’s SENSEable City Lab, which is overseeing the Smart Biking project. “A considerable fraction of its energy comes from renewable sources and, unlike a few decades ago, 30 to 40 percent of its citizens use bicycles as their primary method of transportation.

“So our challenge was, ‘How can we enhance these dynamics of sustainability? And how can we use technology to make them more widespread?'”

Beyond encouraging Copenhagen’s citizens to ride more often, the program aims to help them interact as well.

“We have developed a Facebook application called ‘I crossed your path,’ which creates a social network for cyclists, allowing them to link up with people they may have ridden past during the day and potentially establish new connections,” explained Christine Outram, the principal research assistant on the project.

The smart tags will also allow individuals to monitor the distance they travel while cycling as part of a citywide “green mileage” initiative, which is similar to a frequent-flyer program.

What will the reward for green miles be? “A year of free Muesli,” mused SENSEable City Lab’s Associate Director Assaf Biderman. “The very act of sharing this information and showing individuals the environmental impact of their actions could be very powerful. Research has shown that behavioral change is one of the most powerful forces to tackle climate change and the reduction of carbon emissions.”

Ultimately, fine-grained monitoring of urban activities could allow cities such as Copenhagen to enter carbon-trading schemes. Cities could obtain funding for sustainable city services in exchange for their efforts to cut carbon dioxide emissions. The impact could be considerable, as cities account for approximately half of the world population, but are responsible for a much larger share of carbon emissions.

Finally, as part of the project, a prototype of a smart bicycle is being developed in collaboration with the MIT Media Lab’s Smart Cities Group at the MIT Media Lab, directed by William J. Mitchell, the Alexander W Dreyfoos (1954) Professor of Architecture and Media Arts and Sciences. This hybrid bicycle uses a regenerative motor to harvest the energy created when braking and release it while cycling, in a manner similar to hybrid cars. Everything, including the battery, is packed in the rear wheel, which becomes a self-contained element that could be retrofitted on most existing bicycles.

The Smart Biking Project is developed by the SENSEable City Laboratory, an MIT research group focused on technology and urban planning that is a part of the MIT Department of Urban Studies and Planning, together with the MIT Design Lab. In addition to professors Ratti and Mitchell, the team comprises Assaf Biderman, Francesco Calabrese, Michael Lin, Mauro Martino and Outram.

Visualization of bicycle paths

October 23, 2008 Posted by | Uncategorized | Leave a comment

MIT Museum glows with promise of future energy

Energy Night brings together campus efforts at innovation

David Chandler, MIT News Office
October 14, 2008

More than 1,200 people showed up Friday night at the MIT Museum to learn about the latest developments, and the most promising new research efforts, in creating new energy technologies and improving the established ones.

Energy Night, organized by the student-run MIT Energy Club and Sloan Energy and Environment Club, showcased more than 40 different projects, clubs and businesses that are pushing the frontiers of research on energy in and around the campus. In addition to posters, displays and demonstrations of energy technologies, the social event featured drinks, hors d’ouevres and a live jazz band.

“Energy Night was fantastic,” said Energy Club co-president Lara Pierpoint. “There was a lot of student excitement, a record number of nuclear-related posters, and the usual great music and food. I know that the Energy Conference team was highly successful in recruiting volunteers, and that the electric vehicle team got a lot of attention.”

Outside the museum’s doors, visitors were treated to inside-and-out views of three electric vehicles: A new fuel-cell car from Honda called FCX Clarity, which is being sold only in California, along with two different versions of custom cars built by the MIT Solar Electric Vehicle team. The team’s original solar car has competed in past solar car races, and a newer version is in the process of being finished in preparation for a trans-Australia solar race next year.

Other groups highlighted a range of research projects being carried out now at MIT, including ongoing development of a new type of concentrating solar cell based on coatings that can be applied to existing windows to redirect much of the light to the edges of the glass, where small solar cells can be installed to harness it. Another group is doing research on a proposal, first advanced two years ago by Department of Mechanical Engineering Professor Paul Sclavounos, for developing offshore wind turbines, mounted using technology derived from offshore drilling platforms. Within a few weeks, they plan to begin testing scale models of a few different versions of the design.

“Although MIT has a wealth and breadth of activity in energy, we each typically spend our time in a very small portion of it,” said event co-organizer and Sloan graduate student Melissa Webster. “Energy Night provides an opportunity to both see across the rich landscape as well as celebrate it.”

While most of the projects showcased at the event are designed to change the world, some are focused closer to home, aiming to begin by transforming MIT itself in order to set an example. Sloan graduate student Jialan Wang presented a poster detailing efforts to save energy within the campus, for example by changing lights to more-efficient compact fluorescents and by reminding students, staff and faculty alike how much of a difference can be made by simply turning off lights, computers and other equipment when they are not in use. “We’re looking for the best opportunities, for what has the biggest impact” on energy use, she said. One way to encourage such savings, she said, is to provide real-time feedback to enable people to see how changes they make actually affect their energy use.

“In every building, there are people doing things” to conserve energy, Wang said, “but people just don’t know about it. We want to make people aware” by highlighting the best practices and the ways people have succeeded in making a difference.

Shuguang Zhang, associate director of MIT’s Center for Biomedical Engineering, agreed, pointing out that right now, “other campuses are ahead of us” in implementing energy conservation measures. “We want to be the best! If you want to change all the people, change yourself first.”

A version of this article appeared in MIT Tech Talk on October 22, 2008 (download PDF).

October 23, 2008 Posted by | Uncategorized | Leave a comment

Recent research developments in the greater Boston area

I recently posted about three research developments at various Boston schools. They show the existence of brilliant researchers and research money at these schools.

The first story, “Mass Researchers Win ‘American Nobel Prize’ is a testament to the excellence at Mass. General Hospital and Harvard Medical School. One of the researchers said “we like to think of ourselves as the center of the universe as far as RNA biology.” This is a claim that reflects the great research and academic culture of the city. Boston was also referred to as a “global leader in scientific inquiry”.

The second story is most notable for the Personal Genome Project, which is attempting to find a way to decode human DNA at a reasonable cost with an increase in quality of service. This is a continuation of the worldwide, $3 billion Human Genome Project, which first decoded human DNA about five years ago. The ability of a Boston school to host such a significant project is important to the city. These are revolutionary genetics projects that are taking place in Boston academia.

The third story is about the MIT biological engineer’s breakthrough in mass-producing smell receptors in a lab setting. This is a major development in an area that had struggled to produce the receptors in recent years. The MIT engineers will “work with researchers worldwide” to advance the project and create practical uses for the smell receptors. The research funding came from organizations in Japan, Sweden, and the Netherlands. The pouring in of research funds shows that Boston is a major player in medical research and can attract money from global sources.

October 13, 2008 Posted by | Uncategorized | Leave a comment

Biological Engineering Research at Massachusetts Institute of Technology

Sniffing out success

MIT engineers mass-produce smell receptors in lab; ‘artificial noses’ to follow?

Anne Trafton, News Office
September 29, 2008

MIT biological engineers have found a way to mass-produce smell receptors in the laboratory, an advance that paves the way for “artificial noses” to be created and used in a variety of settings.

The work could also allow scientists to unlock the mystery of how the sense of smell can recognize a seemingly infinite range of odors.

“Smell is perhaps one of the oldest and most primitive senses, but nobody really understands how it works. It still remains a tantalizing enigma,” said Shuguang Zhang, associate director of MIT’s Center for Biomedical Engineering and senior author of a paper on the work appearing online this week in the Proceedings of the National Academy of Sciences (PNAS).

Artificial noses could one day replace drug- and explosive-sniffing dogs, and could have numerous medical applications, according to Zhang and his colleagues. DARPA recently approved funding for the team’s MIT (microfluidic-integrated transduction) RealNose project.

Until now, efforts to understand the molecular basis of smell have been stymied by the difficulty in working with the proteins that detect odors, known as olfactory receptors.

“The main barrier to studying smell is that we haven’t been able to make enough receptors and purify them to homogeneity. Now, it’s finally available as a raw material for people to utilize, and should enable many new studies into smell research,” said Brian Cook, who just defended his MIT PhD thesis based on this work.

Smell is one of the most complex and least-understood senses. Humans have a vast olfactory system that includes close to 400 functional genes, more than are dedicated to any other function. Animals such as dogs and mice have around 1,000 functional olfactory receptor genes.

That variety of receptors allows humans and animals to discern tens of thousands of distinct odors. Each odor activates multiple receptors and this pattern of activation creates a signature that the brain can recognize as a particular scent.

The olfactory receptors that bind to odor molecules are membrane proteins, which span the cell surface. Since cell membranes are composed of a bilayer of fatty lipid molecules, the receptor proteins are highly hydrophobic (water-fearing).

When such proteins are removed from the cell and placed in water-based solutions, they clump up and lose their structure, said Liselotte Kaiser, lead author of the PNAS paper. That makes it very difficult to isolate the proteins in quantities large enough to study them in detail.

Kaiser and others spent several years developing a method to isolate and purify the proteins by performing each step in a hydrophobic detergent solution, which allows the proteins to maintain their structure and function.

The technique reported this week in PNAS involves a cell-free synthesis using commercially available wheat germ extract to produce a particular receptor, then isolating the protein through several purification steps. The method can rapidly produce large amounts of protein — enough to start structural and functional studies.

The team has also demonstrated a similar method that uses engineered mammalian cells to produce the receptors. That method, reported in PLoS One in August, takes more time and labor than the cell-free approach, but could have advantages in that the receptor is processed more naturally.

In future work, the team plans to work with researchers worldwide, including MIT’s Media Lab and Department of Biology, to develop a portable microfluidic device that can identify an array of different odors. Such a device could be used in medicine for the early diagnosis of certain diseases that produce distinctive odors, such as diabetes and lung, bladder and skin cancers, Zhang said. There are also a wide range of industrial applications for such a smell-based biosensing device, he said.

Other authors of the PNAS paper are Johanna Graveland-Bikker, a postdoctoral fellow at MIT, visiting graduate students Dirk Steuerwald and Melanie Vanberghem, and Kara Herlihy of GE Healthcare Biacore.

The research was funded by the ROHM Corporation (Japan), the Knut and Alice Wallenberg Foundation (Sweden), the Netherlands Organization for Scientific Research, and a John Simon Guggenheim Fellowship. Joyce and Roger Kiley ’60, MS ’61 provided pure odorants.

A version of this article appeared in MIT Tech Talk on October 1, 2008 (download PDF).

October 13, 2008 Posted by | Uncategorized | Leave a comment

Continuing Genetics Research at Harvard

When genetics gets personal

DNA analysis of individuals promises ethical quandaries

September 12, 2008

Alvin Powell
Harvard News Office

Just five years after the Human Genome Project announced it had decoded the first human DNA, the era of personal genetics is dawning, bringing with it not just the promise of targeted, personalized medicine and a new level of self-knowledge, but also a host of ethical, legal, and practical issues. A new project out of a Harvard Medical School genetics lab is trying to make sure we’re prepared to deal with the potential benefits and pitfalls arising from these issues.

Though just a handful of years have passed since the Human Genome Project’s scientific milestone, technology’s rapid advance has transformed the genetics landscape. While the decoding of the first human genome took 12 years and $3 billion, today companies have opened shop offering personal genome decoding for just a fraction of the cost. Within five years, experts predict, such a service could cost as little as $1,000 and take just days.

While knowing one’s genetic makeup could reveal secrets of ancestry, health, and other characteristics, the access to these secrets raises potentially troubling ethical and legal questions, ranging from control of that information, to health insurance coverage, to job discrimination, to issues of privacy within families whose members share the same genetic background.

That’s where the Personal Genetics Education Project comes in.

The project was founded two years ago by Harvard Medical School Genetics Professor Chao-Ting Wu and Jack Bateman, a former postdoctoral fellow in Wu’s lab and now assistant professor of biology at Bowdoin College. It is headed by Dana Waring, who has developed educational material about personal genetics and who presents that material to schools, colleges, private firms, and even the U.S. Senate office of Democratic Party nominee Barack Obama. Waring advised Obama’s policymakers on ethical issues in their Genomics and Personalized Medicine Act of 2006.

“It’s the old story of technology coming first and everyone else catching up,” Waring said. “We’re talking optimistically and hopefully, but there are risks, many of which are not totally clear.”

Wherever she speaks, Waring said, people are quick to pick up the implications of the sudden availability of such intimate information.

She offered the example of a child who wants to be tested for an inheritable disease even though her parents don’t want to find out. The test comes back positive and it turns out the disease is inherited through the mother. What does the child do? Does she tell her? Does she tell her siblings about her mother or even about herself, since telling people about herself would automatically tell them something about her mother?

New knowledge about a genetic susceptibility for ill health also has implications in areas such as health insurance and employment because an employer may not want to hire someone likely to develop an ailment that could increase the employer’s health insurance costs.

Waring has developed several lessons and made them available to high school and college teachers on the project’s Web site. The classes, she said, are intended to educate students about the science surrounding personal genetics and to foster discussions about its potential benefits — such as improved diagnosis and treatment, early detection of disease, and more effective medicines — as well as its potential pitfalls.

Today’s high school and college students are important audiences, said Wu and Waring, because the personal genetics revolution will be maturing as they do, and as they take the reins of society,  they’ll be the ones making the ethical, moral, and legal decisions about the technology’s use.

“It’s in their hands to guide this world,” Wu said. “We’re not really telling them what to think, just posing these questions.”

Wu said the project has its roots in conversations she’s had over the years with other geneticists, including her husband, Harvard Genetics Professor George Church, who is running the Personal Genome Project, an academic effort to decode the genomes of as many as 100,000 people.

Wu and Church traveled to meet volunteers in that project and Wu said there was universal curiosity about the work. But the curiosity and enthusiasm was almost always tempered by reservations and concern about the use of the information to be derived.

Though companies already exist that will decode a person’s genome and compare it with known markers for genetic diseases and other things, Wu and Waring expect the costs to drop rapidly and the quality of the scans to increase dramatically in the next few years. Though the Personal Genetics Education Project has been up and running for two years, Wu and Waring said they feel like they’re behind, trying to catch up. They already have more requests for speaking engagements than they can fulfill and are talking about seeking new sources of funding and hiring more staff.

“It’s like many other revolutions. [How you handle it depends on] how educated you are and how prepared you are,” Wu said. “It can be fantastic if we’re prepared for it.”

Among their plans is outreach to physicians, a substantial number of whom received their M.D.s before the personal genetics revolution hit. Wu said they’d like to put together an easy-to-read booklet with the basics of what’s going on, so doctors understand what’s happening when a patient walks in with a genome scan and asks for advice. As prices come down, Wu said, it may become standard medical practice for patients to get their genome scanned and kept as part of their medical records.

“We feel it’s important to engage people before it’s pounding on your doorstep,” Waring said.

October 13, 2008 Posted by | Uncategorized | Leave a comment

Boston researchers win “America’s Nobel Prize”

Mass. researchers win ‘America’s Nobel Prize’

Email| Text size + September 13, 2008 05:01 PM

By Carolyn Y. Johnson, Globe Staff

Two Massachusetts researchers who discovered a natural dimmer switch in cells that can turn down the effects of genes are the winners of an Albert Lasker Medical Research Award, an honor sometimes called America’s Nobel Prize.

Victor R. Ambros

Victor R. Ambros of the University of Massachusetts Medical School in Worcester, and Gary B. Ruvkun of Massachusetts General Hospital and Harvard Medical School, shared the $300,000 Lasker Award for Basic Medical Research with David C. Baulcombe, of the University of Cambridge.Ambros, 54, said the award recognizes Massachusetts as a hub of research into RNA, a molecule that was once seen as the workhorse of the cell, translating instructions in the genome into proteins. The Lasker Award recognizes the role that tiny strands of RNA, called microRNA, play in regulating gene expression.

“Out here at UMass, we like to think of ourselves as the center of the universe as far as RNA biology,” Ambros said, “but there is a certain truth to that.”

In a statement, Governor Deval Patrick said, “This very prestigious award illustrates that the University of Massachusetts Medical School has become a global leader in an area of scientific inquiry that has transformed the research landscape and offers so much promise for mankind.”

In 2006, Ambros’s colleague at UMass Medical School, Craig C. Mello, shared the Nobel Prize in Physiology or Medicine for discovering that short, double-stranded RNAs could silence specific genes. But Ambros and Ruvkun discovered a gene in a microscopic roundworm that codes for microRNAs that can turn down gene expression. Baulcombe was studying how plants fight viruses when he discovered that short strands of RNA could shut down genes in plants. Today, microRNAs are thought to regulate one-third of the genes in the human body and have been implicated in numerous diseases.

Ruvkun described the award as an honor and said it has been gratifying to watch their discovery ripple through the field of biology. “Others started to look the same way we have looked in many, many organisms and processes. It went from two people thinking in these terms to hundreds and thousands of scientists over a 10 year period,” he said.

Scientists now study microRNAs to understand everything from normal development to their possible role in diseases such as cancer. MicroRNAs are also being investigated for their potential therapeutic potential at Regulus Therapeutics, a company that is a joint venture between Cambridge’s Alnylam Pharmaceuticals and Isis Pharmaceuticals in Carlsbad, Calif.

“It’s nice to see they’re getting recognition,” said Tyler Jacks, the director of the David H. Koch Institute for Integrative Cancer Research at MIT. “The appreciation of microRNAs, which has really been over the last 10 years, has opened up a whole new vista in our thinking about the regulation of expression of genes.”

Carolyn Y. Johnson can be reached at

October 12, 2008 Posted by | Uncategorized | Leave a comment

Welcome to my Boston Blog

Welcome to my blog about Boston, Massachusetts as a Global City!

Throughout the semester, I will be focusing on the role of educational institutions and all the positive (and maybe negative?) features that they bring to a city such as Boston.

Boston has a huge concentration of higher education institutions in the city. Some of these include Harvard University, Massachusetts Institute of Technology, Boston College, and Boston University, among others. These schools are world-famous and make Boston and important city for higher education.  Along with teaching, research and innovation are important parts of these institutions. They bring brilliant teachers, scholars, researchers, money, and industry from all over the world to Boston.

Throughout the semester, I will be posting news and analysis of different developments at Boston educational institutions. I will reflect on how these developments put Boston on a global scale and influence its connections with the rest of the world.

Stay tuned for more news and info!

October 7, 2008 Posted by | Uncategorized | Leave a comment