Tag Archives: university research

Engineering: Cellphone Microscope

UCLA Professor Aydogan Ozcan‘s invention (LUCAS) enables rapid counting and imaging of cells without using any lenses even within a working cell phone device. He placed cells directly on the imaging sensor of a cell phone. The imaging sensor captures a holographic image of the cells containing more information than a conventional microscope. The CelloPhone received a Wireless Innovations Award from Vodafone

a wireless health monitoring technology that runs on a regular cell-phone would significantly impact the global fight against infectious diseases in resource poor settings such as in Africa, parts of India, South-East Asia and South America.

The CelloPhone Project aims to develop a transformative solution to these global challenges by providing a revolutionary optical imaging platform that will be used to specifically analyze bodily fluids within a regular cell phone. Through wide-spread use of this innovative technology, the health care services in the developing countries will significantly be improved making a real impact in the life quality and life expectancy of millions.
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For most bio-medical imaging applications, directly seeing the structure of the object is of paramount importance. This conventional way of thinking has been the driving motivation for the last few decades to build better microscopes with more powerful lenses or other advanced imaging apparatus. However, for imaging and monitoring of discrete particles such as cells or bacteria, there is a much better way of imaging that relies on detection of their shadow signatures. Technically, the shadow of a micro-object can be thought as a hologram that is based on interference of diffracted beams interacting with each cell. Quite contrary to the dark shadows that we are used to seeing in the macro-world (such as our own shadow on the wall), micro-scale shadows (or transmission holograms) contain an extremely rich source of quantified information regarding the spatial features of the micro-object of interest.

By making use of this new way of thinking, unlike conventional lens based imaging approaches, LUCAS does not utilize any lenses, microscope-objectives or other bulk optical components, and it can immediately monitor an ultra-large field of view by detecting the holographic shadow of cells or bacteria of interest on a chip. The holographic diffraction pattern of each cell, when imaged under special conditions, is extremely rich in terms of spatial information related to the state of the cell or bacteria. Through advanced signal processing tools that are running at a central computer station, the unique texture of these cell/bacteria holograms will enable highly specific and accurate medical diagnostics to be performed even in resource poor settings by utilizing the existing wireless networks.

This is another great example of engineers creating technologically appropriate solutions.

The Only Known Cancerless Animal

Unlike any other mammal, naked mole rate communities consist of queens and workers more reminiscent of bees than rodents. Naked mole rats can live up to 30 years, which is exceptionally long for a small rodent. Despite large numbers of naked mole-rats under observation, there has never been a single recorded case of a mole rat contracting cancer, says Gorbunova. Adding to their mystery is the fact that mole rats appear to age very little until the very end of their lives.

The mole rat’s cells express p16, a gene that makes the cells “claustrophobic,” stopping the cells’ proliferation when too many of them crowd together, cutting off runaway growth before it can start. The effect of p16 is so pronounced that when researchers mutated the cells to induce a tumor, the cells’ growth barely changed, whereas regular mouse cells became fully cancerous.

“It’s very early to speculate about the implications, but if the effect of p16 can be simulated in humans we might have a way to halt cancer before it starts.” says Vera Gorbunova, associate professor of biology at the University of Rochester and lead investigator on the discovery.

In 2006, Gorbunova discovered that telomerase—an enzyme that can lengthen the lives of cells, but can also increase the rate of cancer—is highly active in small rodents, but not in large ones.

Until Gorbunova and Seluanov’s research, the prevailing wisdom had assumed that an animal that lived as long as we humans do needed to suppress telomerase activity to guard against cancer. Telomerase helps cells reproduce, and cancer is essentially runaway cellular reproduction, so an animal living for 70 years has a lot of chances for its cells to mutate into cancer, says Gorbunova. A mouse’s life expectancy is shortened by other factors in nature, such as predation, so it was thought the mouse could afford the slim cancer risk to benefit from telomerase’s ability to speed healing.

While the findings were a surprise, they revealed another question: What about small animals like the common grey squirrel that live for 24 years or more? With telomerase fully active over such a long period, why isn’t cancer rampant in these creatures?

Researching Direct Brain Interfaces for Text Entry

Adam Wilson posted a status update on the social networking Web site Twitter — just by thinking about it. A UW-Madison biomedical engineering doctoral student, Wilson is among a growing group of researchers worldwide who aim to perfect a communication system for users whose bodies do not work, but whose brains function normally. Among those are people who have amyotrophic lateral sclerosis (ALS), brain-stem stroke or high spinal cord injury.

The interface consists, essentially, of a keyboard displayed on a computer screen. “The way this works is that all the letters come up, and each one of them flashes individually,” says Williams. “And what your brain does is, if you’re looking at the ‘R’ on the screen and all the other letters are flashing, nothing happens. But when the ‘R’ flashes, your brain says, ‘Hey, wait a minute. Something’s different about what I was just paying attention to.’ And you see a momentary change in brain activity.”

The system still is not very quick. However, as with texting, users improve as they practice using the interface. “I’ve seen people do up to eight characters per minute,” says Wilson.

Read full press release

Engineered Circuits That can Count Cellular Events

Engineered circuits can count cellular events by Anne Trafton

MIT and Boston University engineers have designed cells that can count and “remember” cellular events, using simple circuits in which a series of genes are activated in a specific order.
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The first counter, dubbed the RTC (Riboregulated Transcriptional Cascade) Counter, consists of a series of genes, each of which produces a protein that activates the next gene in the sequence.

With the first stimulus — for example, an influx of sugar into the cell — the cell produces the first protein in the sequence, an RNA polymerase (an enzyme that controls transcription of another gene). During the second influx, the first RNA polymerase initiates production of the second protein, a different RNA polymerase.

The number of steps in the sequence is, in theory, limited only by the number of distinct bacterial RNA polymerases. “Our goal is to use a library of these genes to create larger and larger cascades,” said Lu.

The counter’s timescale is minutes or hours, making it suitable for keeping track of cell divisions. Such a counter would be potentially useful in studies of aging.

The RTC Counter can be “reset” to start counting the same series over again, but it has no way to “remember” what it has counted. The team’s second counter, called the DIC (DNA Invertase Cascade) Counter, can encode digital memory, storing a series of “bits” of information.

The process relies on an enzyme known as invertase, which chops out a specific section of double-stranded DNA, flips it over and re-inserts it, altering the sequence in a predictable way.

The DIC Counter consists of a series of DNA sequences. Each sequence includes a gene for a different invertase enzyme. When the first activation occurs, the first invertase gene is transcribed and assembled. It then binds the DNA and flips it over, ending its own transcription and setting up the gene for the second invertase to be transcribed next.

When the second stimulus is received, the cycle repeats: The second invertase is produced, then flips the DNA, setting up the third invertase gene for transcription. The output of the system can be determined when an output gene, such as the gene for green fluorescent protein, is inserted into the cascade and is produced after a certain number of inputs or by sequencing the cell’s DNA.

This circuit could in theory go up to 100 steps (the number of different invertases that have been identified). Because it tracks a specific sequence of stimuli, such a counter could be useful for studying the unfolding of events that occur during embryonic development, said Lu.

Other potential applications include programming cells to act as environmental sensors for pollutants such as arsenic. Engineers would also be able to specify the length of time an input needs to be present to be counted, and the length of time that can fall between two inputs so they are counted as two events instead of one.

Dennis Bray Podcast on Microbes As Computers

Carl Zimmer interviews Dennis Bray in an interesting podcast:

Dennis Bray is an active professor emeritus in both the Department of Physiology and Department of Neuroscience at the University of Cambridge. He studies the behavior of microbes–how they “decide” where to swim, when to divide, and how best to manage the millions of chemical reactions taking place inside their membranes. For Bray, microbes are tiny, living computers, with genes and proteins serving the roles of microprocessors.

Washing Machine Uses 90% Less Water

We wrote about the nearly waterless washing machine from Xeros previously, here are some additional details. The nearly waterless washing machine (which uses 90% less water) was developed by transferring known science to another application. After extensive R&D by University of Leeds scientists a nylon polymer was selected to absorb stains and dirt due to its unique property to become highly absorbent in humid conditions. Better still, it is highly resilient so can be re-used time after time without losing its strength.

The power of polymer cleaning
The nylon polymer has an inherent polarity that attracts stains. Think of how your white nylon garments can get dingy over time as dirt builds up on the surface despite constant washing. However, under humid conditions, the polymer changes and becomes absorbent. Dirt is not just attracted to the surface, it is absorbed into the center.

Such research in university settings, then transferred to products are a great source of economic growth and environmental improvement.

Moth Controlled Robot

Photo of moth controlled robot from Ryohei Kanzaki’s bio-machine page. The moth is on top of the ping pong ball in the middle of the robot.

Japanese scientists to build robot insects

Ryohei Kanzaki, a professor at Tokyo University’s Research Centre for Advanced Science and Technology, has studied insect brains for three decades and become a pioneer in the field of insect-machine hybrids.

His original and ultimate goal is to understand human brains and restore connections damaged by diseases and accidents – but to get there he has taken a very close look at insect “micro-brains”.
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Insects’ tiny brains can control complex aerobatics such as catching another bug while flying, proof that they are “an excellent bundle of software” finely honed by hundreds of millions of years of evolution, Prof Kanzaki said.
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In an example of ‘rewriting’ insect brain circuits, Prof Kanzaki’s team has succeeded in genetically modifying a male silkmoth so that it reacts to light instead of smell, or to the odour of a different kind of moth.

Such modifications could pave the way to creating a robo-bug which could in future sense illegal drugs several kilometres away, as well as landmines, people buried under rubble, or toxic gas, the professor said.

It is nice to be reminded of the cool research being done by professors all over the globe.

Algae Farm Aims to Turn Carbon Dioxide Into Fuel

Dow Chemical and Algenol Biofuels, a start-up company, are set to announce Monday that they will build a demonstration plant that, if successful, would use algae to turn carbon dioxide into ethanol as a vehicle fuel or an ingredient in plastics.
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“We give them the oxygen, we get very pure carbon dioxide, and the output is very cheap ethanol,” said Mr. Woods, who said the target price was $1 a gallon.

Algenol grows algae in “bioreactors,” troughs covered with flexible plastic and filled with saltwater. The water is saturated with carbon dioxide, to encourage growth of the algae. “It looks like a long hot dog balloon,” Mr. Woods said.
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The company has 40 bioreactors in Florida, and as part of the demonstration project plans 3,100 of them on a 24-acre site at Dow’s Freeport, Tex., site. Among the steps still being improved is the separation of the oxygen and water from the ethanol. The Georgia Institute of Technology will work on that process, as will Membrane Technology and Research, a company in Menlo Park, Calif. The National Renewable Energy Laboratory, an Energy Department lab, will study carbon dioxide sources and their impact on the algae samples.

Algenol and its partners are planning a demonstration plant that could produce 100,000 gallons a year. The company and its partners were spending more than $50 million, said Mr. Woods, but not all of that was going into the pilot plant.

Initial proof of science was generated by Dr. John Coleman at the University of Toronto between 1989 and 1999. Since then, the process has been refined to allow algae to tolerate high heat, high salinity, and the alcohol levels present in ethanol production. This is another example of the benefit of university research and investing in science and engineering innovation.

Barbara Liskov wins Turing Award

photo of Barbara Liskov by Donna Coveney

Barbara Liskov has won the Association for Computing Machinery’s A.M. Turing Award, one of the highest honors in science and engineering, for her pioneering work in the design of computer programming languages.

Liskov, the first U.S. woman to earn a PhD from a computer science department, was recognized for helping make software more reliable, consistent and resistant to errors and hacking. She is only the second woman to receive the honor, which carries a $250,000 purse and is often described as the “Nobel Prize in computing.”

“Computer science stands squarely at the center of MIT’s identity, and Institute Professor Barbara Liskov’s unparalleled contributions to the field represent an MIT ideal: groundbreaking research with profound benefits for humankind. We take enormous pride that she has received the Turing Award,” said MIT President Susan Hockfield.

“Barbara Liskov pioneered some of the most important advances in fundamental computer science,” said Provost L. Rafael Reif. “Her exceptional achievements have leapt from the halls of academia to transform daily life around the world. Every time you exchange e-mail with a friend, check your bank statement online or run a Google search, you are riding the momentum of her research.”

The Turing Award is given annually by the Association for Computing Machinery and is named for British mathematician Alan M. Turing, who helped the Allies crack the Nazi Enigma cipher during World War II.

Read the full article at MIT.

Great Lake Sinkholes

Grand Valley State University Scientist Discovers Great Lake ‘sinkholes’

Biddanda said the sinkholes are home to “bizarre” ecosystems dominated by brilliant purple mats of cyanobacteria, or blue-green algae, but largely devoid of fish.

“Groundwater from beneath Lake Huron is dissolving minerals from the defunct seabed and carrying them into the lake to form these exotic, extreme environments,” Biddanda said. “Those ecosystems are in a class not only with Antarctic lakes, but also with deep-sea, hydrothermal vents and cold seeps.”
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The Lake Huron sinkholes are dominated by brilliant purple mats of cyanobacteria — cousins of microbes found on the bottom of permanently ice-covered lakes in Antarctica — and pallid, floating pony-tails of other microbial life