Tag Archives: Caltech

Grand Challenges, point-of-care diagnostics, and a note on proliferating bureaucracies

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Last week, the Bill & Melinda Gates Foundation announced a $21.1 M grant over three years for research into point-of-care diagnostic tools for developing nations. A Canadian nongovermental organization (NGO) will be supplementing this amount with $10.8 M for a total of $31.9 M. (source: Dec. 16, 2011 AFP news item [Agence France-Presse] on MedicalXpress.com)

At this point, things get a little confusing. The Bill & Melinda Gates Foundation has a specific program called Grand Challenges in Global Health and this grant is part of that program. Plus, the Canadian NGO is called Grand Challenges Canada (couldn’t they have found a more distinctive name?), which is funded by a federal Canadian government initiative known as the Development Innovation Fund (DIF). Here’s a little more from the Who We Are page,

In the 2008 Federal Budget the Government of Canada announced the creation of the Development Innovation Fund (DIF) to “support the best minds in the world as they search for breakthroughs in global health and other areas that have the potential to bring about enduring changes in the lives of the millions of people in poor countries.” The Government of Canada is committing $225 million over five years to the Development Innovation Fund.

The Development Innovation Fund will be delivered by Grand Challenges Canada working with the International Development Research Centre (IDRC) and the Canadian Institutes of Health Research (CIHR). As the Government of Canada’s lead on the Development Innovation Fund, the International Development Research Centre will draw on decades of experience managing research projects and ensure that developing country researchers and concerns are front and centre in this exciting new initiative. The initial activities of the Development Innovation Fund will be in global health.

Grand Challenges Canada is a unique and independent not-for-profit organization dedicated to improving the health and well-being of people in developing countries by integrating scientific, technological, business and social innovation both in Canada and in the developing world. Grand Challenges Canada works with the International Development Research Centre, Canadian Institutes of Health Research, and other global health foundations and organizations committed to discovering sustainable solutions to the world’s most pressing health challenges. Grand Challenges Canada is hosted by the McLaughlin-Rotman Centre for Global Health, University Health Network and University of Toronto.

So if I understand this rightly, the Canadian federal government created a new fund and then created a new NGO to administer that fund. I wonder how much money is required administratively for this NGO which exists solely to distribute DIF. I’m glad to see that someone is getting some money for research out of this but it does seem labyrinthine at best.

On a happier, more productive now, here’s the type of research this money will be used for (from the MedicalXpress.com news item),

“Imagine a hand-held, battery-powered device that can take a drop of blood and, within minutes, tell a healthcare worker in a remote village whether a feverish child has malaria, dengue or a bacterial infection,” said Peter Singer, head of Grand Challenges Canada which is partnering with the Microsoft founder Bill Gates’s charitable organization on the project.

In this last year I have posted a few times about similar projects for handheld diagnostic devices, in my Aug. 4, 2011 posting ‘Diagnostics on a credit card‘ and in my Feb. 15, 2011 posting ‘Argento, nano, and PROOF‘. There’s a lot of interest in these devices whether they’re intended for use in developing countries or not.

I have tracked down the Dec. 15, 2011 news release from the Bill & Melinda Gates Foundation to get more details about this specific project,

The grants announced today are part of the Point-of-Care Diagnostics (POC Dx) Initiative, a research and development program with the goal of creating new diagnostic platforms that enable high-quality, low-cost diagnosis of disease, and also facilitate sustainable markets for diagnostic products, a key challenge in the developing world. This first phase of the POC Dx Initiative is focused on developing new technologies and identifying implementation issues to address the key barriers for clinical diagnostics in the developing world.

They also give some examples of projects that will be receiving funding from this grant,

Examples of projects receiving funding:

  • Seventh Sense Biosystems, a company located in Cambridge MA, is developing TAP—a painless, low-cost blood collection device which aims to allow easy, push-button sampling of blood. This simple collection process would reduce training requirements and enable diagnostics closer to the point of need.
  • David Beebe and researchers at the University of Wisconsin are developing a sample purification system that seeks to better filter and concentrate biomarkers from patient samples. This system will be designed for use in impoverished settings.
  • Axel Scherer of the California Institute of Technology, along with collaborators at Dartmouth College, will develop a prototype quantitative PCR (qPCR) amplification/detection component module—a low cost, easy-to-use technology that can rapidly detect a wide range of diseases.

There’s additional detail about grantees in the Grand Challenges Canada Dec. 16, 2011 news release,

One grantee, Bigtec Labs in Bangalore, India, has already developed a handheld analyser called a mini-PCR (Polymerase Chain Reaction) machine capable of identifying malaria from a DNA fingerprint.

―A colleague here one day was ill with what he thought was food poisoning,” said

B. Chandrasekhar Nair, Director of Bigtec Labs. “We ran a blood sample through our mini-PCR and it turned out to be malaria.‖ Immediately treated, the colleague returned to health within a week.

With its CAD $1.3 million grant, Bigtec will use nano-materials to develop a sophisticated filter to concentrate pathogen DNA from samples of blood, sputum, urine, or nasal and throat swabs. Once concentrated, the DNA can be processed and illnesses identified in the mini-PCR.

The innovative projects receiving funding include:

 Dr. Dhananjaya Dendukuri from Achira Labs in Bangalore India, and Dr. Nandini Dendukuri from McGill University in Montreal are developing a piece of silk that can be used as a cost-effective and simple diagnostic for blood and urine samples. Called Fabchips (Fabric Chips) the woven diagnostic has the added benefit of providing jobs to local artisans and being environmentally friendly.

 Dr. David Goldfarb, a Canadian working in Botswana, is testing a simple, rapid, easy-to-use swab for the detection of diarrheal disease in the developing world.

 Dr. Wendy Stevens from the University of Witwatersrand in South Africa is testing new point-of-care technologies for the integrated management of HIV and TB treatment to encourage equity, affordability and accessibility to treatment.

 Dr. Patricia Garcia at the Universidad Peruana Cayetano Heredia in Peru will look at ways to overcome social and commercial barriers to delivering point-of-care diagnostic tests aimed at improving maternal and child health – two of the UN‘s Millennium Development goals for 2015.

There’s a full list of all the grantees (Grand Challenges Canada and the Bill & Melinda Gates Foundation) and links to videos here.

Here’s a sample video of Dr. Dhananjaya Dendukuri to get you started,

Congratulations to the researchers!

Viruses as manufacturing plants

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In her January 2011 TEDx talk at Caltech (California Institute of Technology), MIT (Massachusetts Institute of Technology) Professor Angela Belcher talks about using viruses to grow batteries that don’t require toxic materials for their production or produce toxic materials themselves. It’s similar to biomimicry in that the reference point is nature but rather than trying to simulate nature using synthetic materials this work focuses on tweaking nature so that something like a virus can be used to create something new, e.g., a battery, a solar cell, etc.

 

A Sept. 25, 2011 article by Karen Weintraub on the BBC News website offers further insight into Belcher’s work,

Prof Belcher’s work unites the inanimate world of simple chemicals with proteins made by living creatures, a mash-up of the living and the lifeless.

She is motivated, she says, by a simple question: “How do you give life to non-living things?”

Like the abalone collecting its materials in shallow water and then laying them down like bricks in a wall, Belcher takes basic chemical elements from the natural world: carbon, calcium, silicon, zinc. Then she mixes them with simple, harmless viruses whose genes have been reprogrammed to promote random variations.

The resulting new materials just might address some of our most vexing problems.

…

The distinctiveness of Prof Belcher’s work, colleagues say, lies in her use of biology to synthesise new materials for such a wide range of uses, to develop an entirely new method for producing entirely novel materials.

“Her methodologies for directing and assembling materials I think will be unique,” says Yet-Ming Chiang, an MIT professor who collaborates with Prof Belcher on battery research. “I think 50 years from now, we’ll look back on biology as an important part of the toolkit in manufacturing… we’ll look back and say this is one of the fundamental tools we developed in this century.”

As I’ve been thinking about life/nonlife (in the context of human enhancement and memristors), this works offers me additional food for thought. Meanwhile, the TEDx talk and the Weintraub article point to some of the vast difference between scientists and lay people (general public). Belcher references life/nonlife quite casually, almost in passing. This could be quite disturbing to folks who believe there’s a distinct difference. The disturbances don’t stop there.

In the first place, viruses do not have a good reputation. When you add in the problems with calling your work biotechnology (as Belcher does in her TEDx talk), the stage is set for some interesting possibilities. If that isn’t enough, Belcher’s work comes perilously close to Eric Drexler’s self-assembling nano entities and the spectre of ‘grey’ or ‘green’ goo. It’s been a while since the big scares over genetically modified organisms (GMO), I wonder if scientists have forgotten or perhaps they don’t realize just how much conflicting (and often frightening) information is still being pushed at the general public. As for breaching the life/nonlife boundaries, that could be a whole other mess.

Folding, origami, and shapeshifting and an article with over 50,000 authors

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I’m on a metaphor kick these days so here goes, origami (Japanese paper folding), and shapeshifting are metaphors used to describe a certain biological process that nanoscientists from fields not necessarily associated with biology find fascinating, protein folding.

Origami

Take for example a research team at the California Institute of Technology (Caltech) working to exploit the electronic properties of carbon nanotubes (mentioned in a Nov. 9, 2010 news item on Nanowerk). One of the big issues is that since all of the tubes in a sample are made of carbon getting one tube to react on its own without activating the others is quite challenging when you’re trying to create nanoelectronic circuits. The research team decided to use a technique developed in a bioengineering lab (from the news item),

DNA origami is a type of self-assembled structure made from DNA that can be programmed to form nearly limitless shapes and patterns (such as smiley faces or maps of the Western Hemisphere or even electrical diagrams). Exploiting the sequence-recognition properties of DNA base paring, DNA origami are created from a long single strand of viral DNA and a mixture of different short synthetic DNA strands that bind to and “staple” the viral DNA into the desired shape, typically about 100 nanometers (nm) on a side.

Single-wall carbon nanotubes are molecular tubes composed of rolled-up hexagonal mesh of carbon atoms. With diameters measuring less than 2 nm and yet with lengths of many microns, they have a reputation as some of the strongest, most heat-conductive, and most electronically interesting materials that are known. For years, researchers have been trying to harness their unique properties in nanoscale devices, but precisely arranging them into desirable geometric patterns has been a major stumbling block.

…

… To integrate the carbon nanotubes into this system, the scientists colored some of those pixels anti-red, and others anti-blue, effectively marking the positions where they wanted the color-matched nanotubes to stick. They then designed the origami so that the red-labeled nanotubes would cross perpendicular to the blue nanotubes, making what is known as a field-effect transistor (FET), one of the most basic devices for building semiconductor circuits.

Although their process is conceptually simple, the researchers had to work out many kinks, such as separating the bundles of carbon nanotubes into individual molecules and attaching the single-stranded DNA; finding the right protection for these DNA strands so they remained able to recognize their partners on the origami; and finding the right chemical conditions for self-assembly.

After about a year, the team had successfully placed crossed nanotubes on the origami; they were able to see the crossing via atomic force microscopy. These systems were removed from solution and placed on a surface, after which leads were attached to measure the device’s electrical properties. When the team’s simple device was wired up to electrodes, it indeed behaved like a field-effect transistor

Shapeshifting

For another more recent example (from an August 5, 2010 article on physorg.com by Larry Hardesty,  Shape-shifting robots),

By combining origami and electrical engineering, researchers at MIT and Harvard are working to develop the ultimate reconfigurable robot — one that can turn into absolutely anything. The researchers have developed algorithms that, given a three-dimensional shape, can determine how to reproduce it by folding a sheet of semi-rigid material with a distinctive pattern of flexible creases. To test out their theories, they built a prototype that can automatically assume the shape of either an origami boat or a paper airplane when it receives different electrical signals. The researchers reported their results in the July 13 issue of the Proceedings of the National Academy of Sciences.

As director of the Distributed Robotics Laboratory at the Computer Science and Artificial Intelligence Laboratory (CSAIL), Professor Daniela Rus researches systems of robots that can work together to tackle complicated tasks. One of the big research areas in distributed robotics is what’s called “programmable matter,” the idea that small, uniform robots could snap together like intelligent Legos to create larger, more versatile robots.

Here’s a video from this site at MIT (Massachusetts Institute of Technology) describing the process,

Folding and over 50, 000 authors

With all this I’ve been leading up to a fascinating project, a game called Foldit, that a team from the University of Washington has published results from in the journal Nature (Predicting protein structures with a multiplayer online game), Aug. 5, 2010.

With over 50,000 authors, this study is a really good example of citizen science (discussed in my May 14, 2010 posting and elsewhere here) and how to use games to solve science problems while exploiting a fascination with folding and origami. From the Aug. 5, 2010 news item on Nanowerk,

The game, Foldit, turns one of the hardest problems in molecular biology into a game a bit reminiscent of Tetris. Thousands of people have now played a game that asks them to fold a protein rather than stack colored blocks or rescue a princess.

…

Scientists know the pieces that make up a protein but cannot predict how those parts fit together into a 3-D structure. And since proteins act like locks and keys, the structure is crucial.

At any moment, thousands of computers are working away at calculating how physical forces would cause a protein to fold. But no computer in the world is big enough, and computers may not take the smartest approach. So the UW team tried to make it into a game that people could play and compete. Foldit turns protein-folding into a game and awards points based on the internal energy of the 3-D protein structure, dictated by the laws of physics.

Tens of thousands of players have taken the challenge. The author list for the paper includes an acknowledgment of more than 57,000 Foldit players, which may be unprecedented on a scientific publication.

…

“It’s a new kind of collective intelligence, as opposed to individual intelligence, that we want to study,”Popoviç [principal investigator Zoran Popoviç, a UW associate professor of computer science and engineering] said. “We’re opening eyes in terms of how people think about human intelligence and group intelligence, and what the possibilities are when you get huge numbers of people together to solve a very hard problem.”

There’s a more at Nanowerk including a video about the gamers and the scientists. I think most of us take folding for granted and yet it stimulates all kinds of research and ideas.

Nanotechnology dieting; snowflakes; nano haiku

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It’s a bit disconcerting to read about a new drug delivery system using silicon, a substance I strongly associate with computers. From the news item on Azonano,

Different types of drug molecules can be bound to the porous structure of silicon, thereby making it possible to alter their properties and control their behaviour within the body.

Porous silicon can be produced as both micro- and nanoparticles, which facilitates the introduction of the material through different dosing routes – orally, as injections or subcutaneous applications. Furthermore, biodegradable nanoparticles can be used for drug targeting.

Scientists in Finland are working on this project and possible applications include dieting. Apparently peptides which control appetite can be targeted with this new delivery system. I suspect that if this is possible there will be a stampede to use silicon drug delivery systems and public concerns about risk will be left far behind as people chase the dream of dieting without effort.

The NISE (Nanoscale Informal Science Education) Network has included some timely information about snowflakes and nanotechnology it its latest newsletter. The downloadable  education programme is here. The snowflake images are supplied by Kenneth Libbrecht, Caltech and you can see more of those here. The haiku in this month’s newsletter is,

Nano, oh nano
With surface area so
Small, but big impact

This week will be short as I’m not sure if I’ll be posting after tomorrow. Changes are afoot.

Maskwriting facilities at 4D Labs and some bottom-up engineering news

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Following up on yesterday’s news from Simon Fraser University (SFU), I gather that maskwriting has to do with fabricating nanoscale materials and the facility they will be building for their 4D Labs will allow them to create nanoscale structures that measure less than 20 nanometres.

“This capability will eventually be as key to nanoscale materials fabrication as the photocopier is to information dissemination,” explains [Byron] Gates, 4D LABS’ director of nanofabrication. “With our new maskwriting facility, we’ll be able to fabricate the next generation of technologies, particularly in the fields of alternative energy and biomedical engineering.”

Local companies will not have send off to Alberta to get this work done and it will give 4D Labs some revenue.  Given that universities are under pressure these days to develop new revenue streams, this has to be good news.

Meanwhile, scientists at the California Institute of Technology (Caltech) have recently published a paper describing their work on bottom-up engineering of DNA ‘seeds’. The two main approaches to engineering in nanotechnology (and this is simplified) are top-down and bottom-up. Traditional enginerring has been top-down; we make things smaller and smaller. The bottom-up approach means taking your cue from biological processes (or nature) and encouraging objects to build themselves or to ‘grow’. There’s more here.

The Project for Emergining Nanotechnologies’ June 17, 2009 event (mentioned in yesterday’s posting) has been rescheduled to Fall 2009.