Technology Trends

We’re all getting older, and many of us will suffer from some alteration of our sense of vision. We might be one day affected by age-related macular degeneration (AMD), which causes blindness to 700,000 people in the Western world every year. But now, ophthalmologists and physicists at Stanford University have teamed up to design a ‘bionic eye’. This system works like some ‘virtual reality’ devices. A little video camera is mounted on transparent goggles allowing for simultaneous use of remaining natural vision. Images from the camera are processed by a microcomputer and projected on the retina. The ‘bionic eye’ which also includes a solar-powered battery implanted in the iris, is currently tested with rats, but human testing could start within three years. Read more…

Here is an excerpt from the introduction of this news release.

[These researchers have designed] an optoelectronic retinal prosthesis system that can stimulate the retina with resolution corresponding to a visual acuity of 20/80 — sharp enough to orient yourself toward objects, recognize faces, read large fonts, watch TV and, perhaps most important, lead an independent life. The researchers hope their device may someday bring artificial vision to those blind due to retinal degeneration.

And here is a description of the problem.

Worldwide, 1.5 million people suffer from retinitis pigmentosa (RP), the leading cause of inherited blindness. In the Western world, age-related macular degeneration (AMD) is the major cause of vision loss in people over age 65, and the issue is becoming more critical as the population ages. Each year, 700,000 people are diagnosed with AMD, with 10 percent becoming legally blind, defined by 20/400 vision. Many AMD patients retain some degree of peripheral vision.

As there is no effective treatment for most patients with AMD and RP, the researchers tried to directly stimulate the inner retina with visual signals.

To that end, the researchers plan to directly stimulate the layer underneath the dead photoreceptors using a system that looks like a cousin of the high-tech visor blind engineer Lt. Geordi La Forge wore in Star Trek: The Next Generation. It consists of a tiny video camera mounted on transparent “virtual reality” style goggles. There’s also a wallet-sized computer processor, a solar-powered battery implanted in the iris and a light-sensing chip implanted in the retina.

The system has been designed by Daniel Palanker and his colleagues of the Group of BioMedical Physics and Ophthalmic Technologies. Here is how it works.

The chip is the size of half a rice grain — 3 millimeters — and allows users to perceive 10 degrees of visual field at a time. It’s a flat rectangle of plastic (eventually a silicon version will be developed) with one corner snipped off to create asymmetry so surgeons can orient it properly during implantation.

The research work has been published by the Journal of Neural Engineering on February 22, 2005 (Volume 2, Number 1, March 2005) under the name “Design of a high-resolution optoelectronic retinal prosthesis.” Here is the end of the abstract, which summarizes how the system works.

To provide for natural eye scanning of the scene, rather than scanning with a head-mounted camera, the system operates similar to ‘virtual reality’ devices. An image from a video camera is projected by a goggle-mounted collimated infrared LED-LCD display onto the retina, activating an array of powered photodiodes in the retinal implant. The goggles are transparent to visible light, thus allowing for the simultaneous use of remaining natural vision along with prosthetic stimulation. Optical delivery of visual information to the implant allows for real-time image processing adjustable to retinal architecture, as well as flexible control of image processing algorithms and stimulation parameters.

And if you need more information, please read the whole well-written news release.

Sources: Dawn Levy, Stanford University News Service, March 30, 2005; and various websites

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Researchers from the Lawrence Berkeley National Laboratory (LBL) have developed fluorescent and stable nano-probes which can stay inside a cell’s nucleus for hours or even days. According to this LBL news release, this will help biologists to better understand nuclear processes that evolve slowly, such as DNA replication, genomic alterations, and cell cycle control. This research was partially based on previous investigations about quantum dots. Now, the researchers want to tailor their quantum dots, which emit different colors depending on their sizes, to check specific chemical reactions inside nuclei, such as how proteins help repair DNA after irradiation. Read more…

Here is a short description of what the researchers achieved.

“Our work represents the first time a biologist can image long-term phenomena within the nuclei of living cells,” says Fanqing Chen of Berkeley Lab’s Life Sciences Division, who developed the technique with Daniele Gerion of Lawrence Livermore National Laboratory.

Their success lies in specially prepared crystalline semiconductors composed of a few hundred or thousand atoms that emit different colors of light when illuminated by a laser. Because these fluorescent probes are stable and nontoxic, they have the ability to remain in a cell’s nucleus — without harming the cell or fading out — much longer than conventional fluorescent labels.

This could give biologists a ringside seat to nuclear processes that span several hours or days, such as DNA replication, genomic alterations, and cell cycle control. The long-lived probes may also allow researchers to track the effectiveness of disease-fighting drugs that target these processes.

The two researchers closely collaborated with Paul Alivisatos, director of the Materials Sciences Division at LBNL, who’s working on quantum dots for several years now. Here are two links to previous entries about Alivisatos research, “Nano Tetrapods With Tunable ‘Legs’,” and “Nanotech solar cells: Portable Plastic Power.”

So, Chen and Gerion thought it was possible to introduce these quantum dots inside a cell’s nucleus. And they did it.

First, they had to breach the nuclear membrane, which has pores that are only about 20 nanometers wide. To fit through these tiny slits, Chen and Gerion used an especially compact cadmium selenide/zinc sulfide quantum dot coated with silica. Next, they stole a trick from a virus’s playbook to smuggle this nanocrystal past the highly selective membrane that guards the entrance into the nucleus.

Chen and Gerion obtained a portion of this protein and attached it to the quantum dot. The result is a hybrid quantum dot, part biological molecule and part nano-sized semiconductor, that is small enough to slide through the nuclear membrane’s pores and believable enough to slip past the membrane’s barriers.

And what are they working on now?

In the future, they hope to tailor quantum dots to track specific chemical reactions inside nuclei, such as how proteins help repair DNA after irradiation.

They also hope to target other cellular organelles besides the nucleus, such as mitochondria and Golgi bodies. And because quantum dots emit different colors of light based on their size, they can be used to observe the transfer of material between cells.

However, with their current nano-probes, they’re already able to know if “a drug has arrived where it is supposed to, and if it is having the desired impact.”

The research work has been published by Nano Letters on September 9, 2004 (Volume 4, Issue 10, Pages 1827 -1832). Here is a link to the abstract of this paper named “Fluorescent CdSe/ZnS Nanocrystal-Peptide Conjugates for Long-term, Nontoxic Imaging and Nuclear Targeting in Living Cells.”

Sources: Lawrence Berkeley National Laboratory news release, March 18, 2005; and various websites

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In “Lobster colour has quantum cause,” Nature writes that Dutch researchers have found why lobsters change colors when they are cooked. According to Nature, “a lobster’s colour is due to a pigment molecule called astaxanthin, which is attached to a protein called crustacyanin.” The Dutch team, using nuclear magnetic resonance spectroscopy and computer simulations, showed that these astaxanthin molecules, grouped in pairs, are interfering with one another. As a result, it shifts their quantum energy states, altering the wavelength of light they can absorb, thus turning black when cooked. The article doesn’t say how many lobsters the researchers used — and ate — for their experiments, but read more…

First, Nature describes the problem — or the situation.

Chemists know that a lobster’s colour is due to a pigment molecule called astaxanthin, which is attached to a protein called crustacyanin. Astaxanthin is one of the carotenoid pigments responsible for the bright red colours of many animals and plants, including those of oranges, tomatoes and some birds’ feathers.

When a lobster is boiled, its crustacyanin proteins unwind in the heat and the astaxanthin pigment falls off. This ‘free’ astaxanthin is red, just like most other carotenoids, and gives the lobster its freshly-cooked colour. But chemists were mystified as to why live lobsters are blue-black.

Then, Nature describes the Dutch team’s experiments.

The team followed up on the discovery in 2002 that astaxanthin molecules in the crustacyanin proteins are grouped in pairs that cross each other in an X-shape.

This pairing, the researchers’ calculations show, means that the two molecules interfere with one another, like cross-talk between electrical signals in neighbouring wires, and this shifts their quantum energy states. That in turn alters the wavelength of light that they absorb, accounting for most of the blackness.

And here is the conclusion of Francesco Buda of Leiden University in the Netherlands, one of the researchers involved in the project.

“It’s surprising that it took such a long time to solve this problem,” says Buda. But he admits it is only in the past five to ten years that computers have been able to handle the demanding quantum-mechanical calculations involved.

The research work has been published by the Journal of the American Chemical Society under the title “Spectroscopy and Quantum Chemical Modeling Reveal a Predominant Contribution of Excitonic Interactions to the Bathochromic Shift in -Crustacyanin, the Blue Carotenoprotein in the Carapace of the Lobster Homarus gammarus.” Here is a link to the abstract.

And if you want to know more about lobsters, but in plain English, you can read this page at Wikipedia. Or you can check Lobster Facts, written by Alan M. Stewart. It features a picture of a two-color lobster named the Joker, introduced by these words: “The odd thing about this animal is that the cephalothorax is all one [natural] color while the rest of the animal is symmetrically different. Even its mouth parts were normal-colored on the right, and orange on the left.” Is this a real lobster or a PhotoShop joke? You’ll tell me.

Sources: Philip Ball, Nature, February 15, 2005; and various websites

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In “Life on the Scales,” Science News recently wrote that some simple mathematical equations, known as quarter-power scaling laws, can explain the metabolic rates of living organisms. For example, “an animal’s metabolic rate appears to be proportional to mass to the 3/4 power.” And this “3/4-power law appears to hold sway from microbes to whales, creatures of sizes ranging over a mind-boggling 21 orders of magnitude.” The ecologists, physicists and chemists behind this research are now successfully applying this equation to plants, fish, full ecosystems and even biology and genetics, by adding a new key parameter: temperature. Please read this fascinating article for many more details and references. But save some time to read another long article, “Ecology’s Big, Hot Idea,” published by PLoS Biology, which states that “the way life uses energy is a unifying principle for ecology in the same way that genetics underpins evolutionary biology.” Read more…

The Science News article starts with a simple observation. Although a mouse has a shorter life than an elephant, both clock approximately the same number of heartbeats during their lives. Simply, their metabolisms are different. Now, let’s go back several decades ago.

Scientists have long known that most biological rates appear to bear a simple mathematical relationship to an animal’s size: They are proportional to the animal’s mass raised to a power that is a multiple of 1/4. These relationships are known as quarter-power scaling laws. For instance, an animal’s metabolic rate appears to be proportional to mass to the 3/4 power, and its heart rate is proportional to mass to the –1/4 power.

In subsequent decades, biologists have found that the 3/4-power law appears to hold sway from microbes to whales, creatures of sizes ranging over a mind-boggling 21 orders of magnitude.

But nobody had an explanation for this scaling law – until 1997.

The beginnings of an explanation came in 1997, when ecologist James Brown of the University of New Mexico in Albuquerque, physicist Geoffrey West of Los Alamos (N.M.) National Laboratory, and Brian Enquist, an ecologist at the University of Arizona in Tucson, described metabolic scaling in mammals and birds in terms of the geometry of their circulatory systems. It turns out, West says, that Rubner was on the right track in comparing surface area with volume, but that an animal’s metabolic rate is determined not by how efficiently it dissipates heat through its skin but by how efficiently it delivers fuel to its cells.

The idea, West says, is that a space-filling surface scales as if it were a volume, not an area. If you double each of the dimensions of your laundry machine, he observes, then the amount of linens you can fit into it scales up by 2³, not 2². Thus, an animal’s effective surface area scales as if it were a three-dimensional, not a two-dimensional, structure.

This law also can be applied to plants, fish, or even cancer growth rates — providing you add a new parameter: temperature.

In 2001, after James Gillooly, a specialist in body temperature, joined Brown at the University of New Mexico, the researchers and their collaborators presented their master equation, which incorporates the effects of size and temperature. An organism’s metabolism, they proposed, is proportional to its mass to the 3/4 power times a function in which body temperature appears in the exponent.

When the researchers filter out the effects of body temperature, most species adhere closely to quarter-power laws for a wide range of properties, including not only life span but also population growth rates. The team is now applying its master equation to more life processes — such as cancer growth rates and the amount of time animals sleep.

Now, it’s time for two key quotes [which don't appear in bold characters in the original article.]

“We’ve found that despite the incredible diversity of life, from a tomato plant to an amoeba to a salmon, once you correct for size and temperature, many of these rates and times are remarkably similar,” says Gillooly.

“Metabolic rate is, in our view, the fundamental biological rate,” Gillooly says. There is a universal biological clock, he says, “but it ticks in units of energy, not units of time.”

Then the researchers applied their master equation to ecosystems such as forests, and even to evolutionary biology, trying to answer this question: “Why do the fossil record and genetic data often give different estimates of when certain species diverged?”

When the researchers use their master equation to correct for the effects of size and temperature, the genetic estimates of divergence times — including those of rats and mice — line up well with the fossil record, says Allen, one of the paper’s coauthors.

As I wrote in the introduction, don’t miss this other paper by John Whitfield in PLoS Biology on a similar subject, “Ecology’s Big, Hot Idea.” Here are the two first paragraphs.

Life is complicated. It comes in all sorts of shapes, sizes, places, and combinations, and has evolved a dizzying variety of solutions to the problem of carrying on living. Yet look inside a cell and life takes on, if not simplicity, then at least a certain uniformity — a genetic system based around nucleic acids, for example, and a common set of chemical reactions for turning food into fuel. And looked at in broad swathes, life shows striking generalities and patterns. Every mammal’s heart will beat about one billion times in its lifetime. Both within and between species, the density of a population declines in a regular way as the size of individuals increases. And the number of species in all environments declines as you move from the equator towards the poles.

Wouldn’t it be good if there were a simple theory that used life’s shared fundamentals to explain its large-scale regularities, via its diversity of individuals? In the past few years, a team of ecologists and physicists have come up with just such a theory. At its heart is metabolism: the way life uses energy is, they claim, a unifying principle for ecology in the same way that genetics underpins evolutionary biology. They believe that energy use, in the form of metabolic rate, can be understood from the first principles of physics, and that metabolic rate can explain growth, development, population dynamics, molecular evolution, the flux of chemicals through the environment, and patterns of species diversity — to name a few.

If you don’t have enough time today, print the two articles I mentioned and read them next weekend. I promise you will not waste your time.

Sources: Erica Klarreich, Science News, Vol. 167, No. 7, p. 106, February 12, 2005; John Whitfield, PLoS Biology, Vol. 2, Issue 12, December 14, 2004

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In this short article, eWEEK writes that the next generation of biosensors will consist of small holograms costing only fractions of a cent. Prototypes developed by a U.K. company, aptly named Smart Holograms, include contact lenses that monitor glucose levels or thin badges that detect alcohol levels. Not only these holograms used as sensors will be cheap to produce, they’ll also require less training for nurses or police officers. This is because these holograms can be designed to show results graphically, such as morphing into an image of a green car if someone subjected to breath analysis is sober and can drive. Read more…

Here are selected quotes from the eWEEK article.

Prototypes have already been made for contact lenses that monitor glucose levels, thin badges that detect alcohol levels, and sticks that can tell, instantly, if milk has spoiled or become contaminated. The technology promises to be quicker and cheaper than tests used today. It will also require less training, because the hologram itself can be designed to show results graphically.

A test showing that fuel has been contaminated with trace amounts of water reads “dry” or “wet.” In a breath alcohol test intended for police offices, suspects breathe onto tiny cards that either show a green automobile or a red X, establishing whether a person is sober enough to drive.

This technology looks cheap and promising, according to Chris Lowe, a professor at Cambridge University, and co-founder of Smart Holograms.

One advantage of the technology is that each hologram costs only a fraction of a cent to produce. Another is the wide applicability. The holograms can detect pH to four decimal places and chemical concentrations of hormones and other biologically important substances. The samples tested do not need to be pure: The holograms can work in milk or even in stool samples from newborns, said Lowe.

Now, let’s turn to the company itself to see how holograms can be turned into biosensors. Here are some explanations provided on this page whose title is “Creating a Sensor Hologram.”

Sensors that rely on the ability of “smart” polymers to swell or contract when in contact with specific biological reagents, chemicals or physical forces, sometimes called volume holograms, are of significant interest. For example, bright wavelength changes produced by holograms fabricated in hydrophilic polymers offer immediate advantages as a facile and reliable means of measuring volume changes. Hologram gratings capable of exhibiting spectral effects from volume changes need to be of the so-called “Denisyuk” type.

For more information about Yuri Denisyuk, you can read this brief history of the holography.

[The figure above] illustrates the experimental set-up used to create Denisyuk-type holograms. Laser light returning from a plane mirror creates a classical standing wave pattern of nodes and antinodes or interference fringes spaced half a wavelength apart. The standing wave pattern is recorded in the polymer matrix that has been coated on a plastic substrate or glass microscope slide. After a conventional photographic development step, the fringe pattern is represented as a distribution of ultrafine (<20 nm diameter) grains of silver.

Is this technology as accurate as told by its promoters? We’ll see. However, it really seems it has a serious cost advantage over current technologies, so it has the potential to become widely used in a few years.

Sources: M.L. Baker, eWEEK, February 19, 2005; Smart Holograms website

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• Holograms
  
  
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I’m often impressed by some scientists’ ideas. But today, I’m a little bit worried, as researchers have genetically modified a common plant, the Indian mustard, to absorb more selenium, a toxic heavy metal found in soils polluted by irrigation wastewater. The transgenic plants were four times more efficient at swallowing selenium than natural ones in a contaminated area of California’s Central Valley, according to articles from Nature and Wired News. These field tests are only experiments, but the researchers also want to add genes to other plants to remove different toxic materials from soils, such as mercury. What would happen if such transgenic plants filled with dangerous chemicals start to crossbreed with natural ones? Or if an insect eats these plants before being eaten itself in the natural food chain, leading to some selenium in our food? Read more and tell me what you think…

Let’s start with the good news from the Nature article.

Genetically modified Indian mustard plants have successfully cleaned up excessive selenium in a California field. This is the first field trial for a pollution-busting transgenic plant, and it proves that the technology can work outside the laboratory, say the researchers who carried out the test.

Farmland in certain parts of California is heavily irrigated, and the water dissolves selenium in shale found in the region. As the water evaporates on the surface soil, selenium is concentrated to levels that are toxic to plants. But Indian mustard (Brassica juncea) has a natural resistance to the element, and absorbs it as it takes in water through its roots.

To increase the level of absorption of selenium by the Indian mustard plants, the researchers, led by Norman Terry, a plant biologist at the University of California, Berkeley, added extra genes to the plant. And here are the first field test results.

The researchers created three different strains of the transgenic mustard plants, each producing different enzymes to soak up selenium, and tested them in selenium-contaminated soils alongside wild-type Indian mustard. [And] hey found that the transgenic plants could accumulate up to 4.3 times as much selenium as conventional, wild-type Indian mustard.

The transgenic plants showed up to 80% of the growth expected in uncontaminated soil, whereas the wild-type plants had their growth halved by the selenium. They were harvested after 45 days in the field, but the researchers expect that longer growth periods could remove more selenium, and estimate that the most effective plants removed about 4.4% of the element in the top 25 centimetres of soil.

The process known as phytoremediation, which uses natural plants to remove toxic materials from soil, is not new, and is cheaper than traditional methods, which imply to remove polluted soil some place before burying it elsewhere. But it takes a long time, so adding genes to speed the process is an attractive solution. But what about the long term ecological impact?

The possibility of the transgenic plants crossbreeding with food crops is a worry, admits Clayton Rugh, a plant biologist at Michigan State University in East Lansing. “If you’re going to engineer a plant to take up high quantities of metals, you must ensure it doesn’t get into food crops,” he says. “They would have to be carefully contained with measures above and beyond those for genetically modified food crops,” he says.

Another source mentioned by Wired News also admits there are some dangers.

“We don’t know enough about the unintended effects of genetic engineering,” said Gurian-Sherman, senior scientist with the Center for Food Safety. The toxicity of plants can change, or a modified plant could interbreed with wild plants, he said. “What happens when an insect eats one of these plants, and then something else eats that insect?

On the contrary, Terry doesn’t seem concerned by the consequences of such experiments. Read carefully this quote from Nature.

In a useful spin-off, the Indian mustard plants could eventually be used as feed for cattle with insufficient selenium in their diet, says Terry. The team is now trying to boost the plants’ power even more. “We’d like to see increases in accumulation of 10 to 100 times that possible with wild-type plants,” says Terry. “This research is a great start.”

Let me summarize this. First, you add genes to a plant which will then easily absorb dangerous and toxic chemicals. Then you use these plants to feed cows. But why on earth a cow would need to ingest more selenium? And are you sure that you want this selenium in your plate?

I’m not an expert in this field, but these experiments look quite dangerous to me in the long term, especially if they become widespread.

By the way, the research work has been published by Environmental Science & Technology on February 1, 2005. Here is a link to the abstract of the paper called “Field Trial of Transgenic Indian Mustard Plants Shows Enhanced Phytoremediation of Selenium-Contaminated Sediment.”

Can we benefit from this or not? Please post your comments and tell me what you think.

Sources: Mark Peplow, Nature, February 11, 2005; Stephen Leahy, Wired News, February 12, 2005; and various websites

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Nano-sized particles embedded with bright, light-emitting molecules have enabled researchers to visualize a tumor more than one centimeter below the skin surface using only infrared light. An interdisciplinary team from the Universities of Pennsylvania and Minnesota have imaged tumors within living rats by embedding fluorescent materials into cell-like vesicles called polymersomes, which are composed of two layers of self-assembling copolymers. According to the researchers, this imaging process has the potential to go even deeper. And “it should also be possible to use an emissive polymersome vesicle to transport therapeutics directly to a tumor, enabling us to actually see if chemotherapy is really going to its intended target.” Read more…

“We have shown that the dispersion of thousands of brightly emissive multi-porphyrin fluorophores within the polymersome membrane can be used to optically image tissue structures deep below the skin — with the potential to go even deeper,” said Michael J. Therien, a professor of chemistry at Penn. “It should also be possible to use an emissive polymersome vesicle to transport therapeutics directly to a tumor, enabling us to actually see if chemotherapy is really going to its intended target.”

“These polymers are also larger than phospholipids, so that there is enough space for the fluorophores, which are larger than the average molecule that is found inside cell membranes,” said Daniel Hammer, professor and chair of the Department of Bioengineering at Penn’s School of Engineering and Applied Sciences. “Another feature that makes emissive polymersomes so useful is that they self-assemble. Simply mixing together all component parts gives rise to these functional nanometer-sized, cell-like vesicles.”

Now, what’s next?

According to Therien, there is keen interest in developing new technology that will enable optical imaging of cancer tissue, as such technology will be less costly and more accessible than MRI-based methods and free of the harmful side effects associated with radioactivity. In this imaging system, the fluorophores can also be tuned to respond to different wavelengths of near-infrared light. This sets the stage for using emissive polymersomes to target multiple cancer cell-surface markers in the body simultaneously.

The research work will be published by the Proceedings of the National Academy of Sciences in its online Early Edition. As I’m typing this, the article is not yet online. Be sure to visit the site in a couple of days.

A patent application was filed in February 2004 for this invention named “Polymersomes incorporating highly emissive probes.” You can find technical details on this patent by visiting the United States Patent and Trademark Office and search for it. As the patent is not yet approved, click on the left side of the screen on the “Status & IFW” link. On the next window, enter 10/777,552 as the application number. And in the next window, click on the “Published documents” tab.

Here is a direct link to the patent, but I can’t guarantee it always will work. So use the above method if this direct link leads you to an error. In the mean time, here is the abstract.

The instant invention concerns compositions comprising polymersomes, visible or near infrared emissive agents, and optionally a targeting moiety associated with a surface of the polymersome. The invention also relates to use of these compositions in the treatment of disease and in imaging methodology.

The “Images” section of the patent description contains 16 pages of drawings and pictures, including a black and white version of the photograph shown above.

Sources: University of Pennsylvania news release, via EurekAlert!, and various websites

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Researchers from the Lawrence Berkeley Lab are using nanotechnology to learn how to clean up environmental contaminants like nuclear waste. They are also using supercomputers and state-of-the-art imaging to predict how quickly pollutants react with minerals in soils and aquifers. This article from the Daily Californian says they are studying kinetics, or rates, of reactions which occur at the earth’s surface using a nanoscale approach. They started to look at the reactions that take place at the pore scale and plan to expand their scope from nanometers to meters in the months to come. This research has implications for transport of contaminants, especially of radioactive materials, but also for oil or ore recovery. Read more…

Here is the introduction of the Daily Californian article.

Nanotechnology, normally used for work with the crystal structures of silicone chips and pure oxides, is being used for something a little more dirty at the Lawrence Berkeley Lab, like learning how to clean up environmental contaminants like nuclear waste.

Researchers Glenn Waychunas and Carl Steefel are using techniques that allow them to study the environment at the nanoscale as part of the new Center for Environmental Kinetics Analysis (CEKA) program, based at Pennsylvania State University.

The goal of the program is to gain insight into the kinetics, or rates, of reactions that occur at the earth’s surface using a nanoscale approach that better models what happens in the real world as opposed to in the lab.

The CEKA program uses a multidisciplinary approach and includes chemists, geochemists, biochemists, soil scientists and engineers.

[For their part,] Waychunas and Steefel are working on the reactions that take place on the pore scale, like the flow of water through the minerals in an aquifer.

“What has been left out is determining rates at the pore scale, we’re measuring rates at different scales to see how biogeochemical and microbial reactions scale up,” Steefel said.

What will be the impact of this program, which has received $6.7 million from the NSF?

This can have implications for transport of contaminants, especially of radioactive materials. Researchers seek to determine reaction rates to determine how long it would take for a plume of pollutant to spread through different mineral substrates.

The next scale is supercomputer modeling, according to Waychunas. “This will model chemical reactions and integrate fluid flow through pore structures, using more complicated fluids and soils. Then we’ll apply them to real systems, like the Yucca Mountains, natural aquifers, oil recovery, ore recovery, and natural gas,” Waychunas said.

For more information, you can read “Taking a Peek At Our Environmental Future,” published by Berkeley Lab View, and from which I extracted the above photograph. Here are more details about Steefel’s work.

Steefel, also a geochemist in the Earth Sciences Division, will also start small and then try to go big. First, he wants to gain a mechanistic understanding of the processes that control biogeochemical reaction rates in porous material by focusing on a single pore. In a common scenario, there may be a reactive mineral on one side of a pore and biofilm on the other side. How do they communicate? To answer this question, Steefel and several other scientists will conduct reactive flow experiments using single-pore microfluidic devices. They’ll also monitor how fluid reacts with porous samples using imaging technology with a spatial resolution of about 30 nanometers, such as the Advanced Light Source’s scanning transmission x-ray microscope (STXM). They will probably begin with a calcium carbonate mineral that has been studied extensively — but never at the pore scale — and observe the rate at which a slightly acidic solution reacts with the mineral as it flows through.

Next, this pore-by-pore data will be used to develop supercomputer-derived models that depict the rates of these reactions in a much larger sample of porous material.

Here is his conclusion.

“The idea of scaling kinetics is a frontier issue, but that’s what this project is about,” says Steefel. “If we develop a mechanistic understanding of reactive transport at several scales, then we can devise predictive models for bioremediation, chemical weathering, and carbon sequestration. And only through the convergence of modeling, supercomputers, synchrotron techniques, and advanced microfluidic reactors is this possible.”

Sources: Francesca Hopkins, The Daily Californian, January 19, 2005; Dan Krotz, Berkeley Lab View, November 12, 2004; and various websites

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Once again, I’m amazed by the creativity of scientists. Researchers at Cornell University have made a brilliant and environmentally friendly discovery: plastics made from orange peel and a greenhouse gas. By adding a zinc catalyst to a mix of citrus fruits, such as oranges, and carbon dioxide, they found a way to make a new polymer called polylimonene carbonate, very similar to polystyrene, a petroleum-based plastic. This is a double whammy: it will reduce existing carbon dioxide, almost certainly responsible for the global warming effect, while reducing future emissions. Of course, time will pass between this discovery and its practical applications. But ultimately, this will greatly beneficial to all of us. Read more…

A Cornell University research group has made a sweet and environmentally beneficial discovery — how to make plastics from citrus fruits, such as oranges, [which contain limonene oxide ]and carbon dioxide.

Limonene is a carbon-based compound produced in more than 300 plant species. In oranges it makes up about 95 percent of the oil in the peel.

In industry, explains Geoffrey Coates, a Cornell professor of chemistry and chemical biology, the orange peel oil is extracted for various uses, such as giving household cleaners their citrus scent. The oil can be oxidized to create limonene oxide. This is the reactive compound that Coates and his collaborators used as a building block.

The other building block they used was carbon dioxide (CO₂), an atmospheric gas that has been rising steadily over the past century and a half — due largely to the combustion of fossil fuels — becoming an environmentally harmful greenhouse gas.

By using their catalyst to combine the limonene oxide and CO₂, the Coates group produced a novel polymer — called polylimonene carbonate — that has many of the characteristics of polystyrene, a petroleum-based plastic currently used to make many disposable plastic products.

The above diagram shows the very simple process of making polymers by adding a catalyst to a mix of limonene oxide and carbon dioxide (Credit: Cornell University)

And here is Coates’s conclusion.

“Almost every plastic out there, from the polyester in clothing to the plastics used for food packaging and electronics, goes back to the use of petroleum as a building block,” Coates observes. “If you can get away from using oil and instead use readily abundant, renewable and cheap resources, then that’s something we need to investigate. What’s exciting about this work is that from completely renewable resources, we were able to make a plastic with very nice qualities.”

The research work has been published by the Journal of the American Chemical Society (Vol. 126, No. 37, September 22, 2004, Pages 11404-11405, Link).

Here is a direct link to the abstract of this paper called “Alternating Copolymerization of Limonene Oxide and Carbon Dioxide.”

For more information, you can check these pages about Geoffrey Coates and his research group.

Here is what Coates says about his research on polymers created from renewable resources, and more specifically about the copolymerization of CO₂ and epoxides.

Carbon dioxide is an ideal synthetic feedstock since it is abundant, inexpensive, nontoxic, and nonflammable. Although it is estimated that Nature uses CO₂ to make over 200 billion tons of glucose by photosynthesis each year, synthetic chemists have had embarrassing little success in developing efficient catalytic processes that exploit this attractive raw material. There has been considerable recent interest in the development of catalysts for the alternating copolymerization of carbon dioxide with epoxides to produce aliphatic polycarbonates. Due to the low cost and accessibility of the monomers and the attractive properties of polycarbonates, the development of new, efficient initiators for this polymerization process is a significant scientific goal. We have recently discovered a new class of well-defined, highly active zinc-based catalysts that copolymerize carbon dioxide and epoxides under exceptionally mild conditions. These catalysts are remarkable since they are several orders of magnitude more active than the current commercial catalysts.

Let’s hope that this discovery quickly leaves the lab…

Sources: Sarah Davidson, Cornell University news release, January 17, 2005; and various websites

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• Chemistry
  
  
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Even if the Morse code usage has almost disappeared, it was a very efficient communication protocol. Now, researchers from several universities and drug companies in the U.K. have discovered that our cells are also using Morse-like signals to switch genes on and off. In this news release, the Biotechnology and Biological Sciences Research Council (BBSRC) writes that this discovery may have major implications for the pharmaceutical industry. Better and more efficient drugs would only deliver the signals to our cells that will activate a desired behavior. Sounds like science fiction? Read more…

This research is featured as the cover story of the January 2005 issue of Business, the quarterly magazine of the BBSRC. Here is a link to this full issue (PDF format, 32 pages, 1.08 MB). The article about “A Morse code in cells?” appears on pages 16 and 17.

Below is a picture and its legend as they appear in the magazine (Credit: BBSRC)

Composite picture showing a series of timelapse images of a neuroblastoma cell (SK-N-AS) stimulated with TNFalpha continuously for 360 minutes. The images show that in the cell, fluorescent RelA (an NF-kappaB protein) moves into and out of the nucleus three times. Individual pictures of the cell were superimposed over a graph (subsequently removed) that quantified the extent to which the fluorescent protein is localised in the nucleus versus the cytoplasm at different times after stimulation.

Now, let’s move to the essential details of the BBSRC news release.

Morse code is a simple, effective and clear method of communication and now scientists believe that cells in our body may also be using patterns of signals to switch genes on and off. The discovery may have major implications for the pharmaceutical industry as the signalling molecules that are targeted by drugs may have more than one purpose. The number of ‘dots and dashes’ being used by each signal could have different purposes, all of which could be modified by a drug.

The researchers, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and working at the Universities of Liverpool and Manchester and the Royal Liverpool Children’s Hospital, in collaboration with scientists at AstraZeneca and Pfizer, have studied transcription factors, the signalling molecules inside cells that activate or deactivate genes. They found that the strength of the signal is less important than the dynamic frequency pattern that is used.

The researchers focused on the response of a transcription factor involved in controlling the crucial processes of cell division and cell death. They found that the dynamics of the signalling molecule resemble the changes in calcium levels that encode other messages in cells. The results suggest how common signalling molecules could convey different messages through different frequencies.

Below is a series of pictures showing the results of an experiment which lasted several hours (Credit: BBSRC)

Neuroblastoma (SK-N-AS) cells, expressing EGFP (green) and RelA-Ds-Red (red), showing repeated movements of RelA-DsRed (RelA/p65 is an NF-êB subunit) between the cytoplasm and nucleus following treatment of the cells with TNFá (Time = minutes)

And here is the conclusion of Professor Julia Goodfellow, BBSRC Chief Executive.

This research is an example of a multi-disciplinary approach producing vitally important results. By combining expertise in cell biology, chemistry, mathematical modelling and bio-imaging the research team have discovered this coded signal that is going to inform the development of better, more effective drugs.

Sources: BBSRC news release, January 10, 2005; BBSRC website

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Happy 2035! Thirty years from now, we’ll use bionic eyes giving us ‘zoom vision’ for faster reactions. Nanobots injected in our bloodstream will complement our immune system. Artificial muscles built with electroactive polymers will help us to be stronger and faster. So you think it’s science fiction? Not at all. Here is my last reading suggestion for 2004, an article from EE Times. You’ll see that some people are so convinced that this kind of human enhancements will happen that they predict than in a few decades, all sporting events ‘will be split up to accommodate enhanced and unenhanced athletes.’ And they will be safer than today’s drugs. Read more and happy 2005!

Here are the opening paragraphs of the EE Times article.

Thirty years from now, the uproar surrounding Barry Bonds’ alleged steroid use might seem quaint by comparison to the human enhancement technologies that could be available then.

In the next few decades, futurists say, athletes and soldiers will call on artificial muscles to lift heavier loads and run faster. Bionic eyes will let them see distant targets, while “nanobots” enhance their cognitive abilities and genetic-engineering techniques boost their performance under pressure.

“The use of anabolic steroids, in retrospect, will seem almost prehistoric — as well as stupid,” said Jerome C. Glenn, executive director of the American Council for the United Nations University (Washington) and co-author of the book 2004 State of the Future. “In the future, we’ll be able to enhance ourselves in other ways that won’t be so dangerous.”

Right now, in 2004, many of these enhancement techniques are already actively being investigated, like artificial muscles or body implants for example.

And of course, the military forces are looking at these new technologies, such as molecular-sized ‘bots,’ put in soldiers’ bloodstream.

Soldiers could use the “bots,” which are molecularly assembled structures that behave much like red blood cells, to combat biological warfare by accelerating the actions of the human immune system, said Glenn. Bots could also be programmed to move to the frontal part of the brain to dispense certain chemicals and hence speed an individual’s anticipation and response time.

At the same time, scientists are said to be examining DNA strings in search of certain behavioral characteristics desirable for elite soldiers. “We’ve heard that researchers have identified a genetic DNA string that makes Navy Seals and other elite soldiers more effective,” said John L. Petersen, founder of the Arlington Institute (Washington). “They’re trying to find a way to take that to the military and make it generally available.”

I guess you can approve such enhancements for a soldier in danger during a war, but what about more ‘pacific’ events, such as the Olympic Games or the World Series?

Because he considers some level of augmentation inevitable, Glenn believes that sporting events will be split up to accommodate enhanced and unenhanced athletes.

“It’s not fair for someone with enhanced vision to compete with someone who doesn’t have that capability,” Glenn said. “You’ll probably need three Olympics — one for those who are enhanced, another for those who are natural and a third for those who are handicapped.”

I might not see 2035 — or even 2005, who knows? — but I would like to know if some of these human enhancements look plausible or desirable for you.

Please post your ideas below and happy new year!

Source: Charles Murray, EE Times, December 17, 2004

Related stories can be found in the following categories.

• Biotechnology
  
  
• DNA
  
  
• Future
  
  
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It’s Sunday, so you have enough time for cooking. Why not trying a Mexican spicy dinner using some super hot jalapeño or habanero peppers? Too strong for you? No problem. Two years after creating mild jalapeño peppers, Texas pepper breeders have created a mild habanero pepper after 5 years of research. The New York Times reports that this mild habanero is available to growers and you’ll soon find it in grocery stores (free registration, but permanent link). As says Dr. Crosby, the plant geneticist who bred this habanero pepper, “It’s a pretty fruit. It’s got the flavor but it doesn’t kill you.” Read more before enjoying your meal…

Before going further, why this need for a mild habanero pepper?

With worldwide pepper consumption on the rise, according to industry experts, the new variety — a heart-shaped nugget bred in benign golden yellow to distinguish it from the alarming orange original, the common Yucatan habanero — is beginning to reach store shelves, to the delight of processors and the research station, which stands to earn unspecified royalties if the new pepper catches on.

“I love it,” said Josh Ruiz, a local farmer whose pickers this week filled some 200 boxes of the peppers to be sold to grocers for about $35 a box. “It yields good and I’m able to eat it.” As for the Yucatan habanero, he said, “My stomach just can’t take it.”

By comparison, if a regular jalapeño scores between 5,000 and 10,000 units on the Scoville scale of pepper hotness based on the amount of the chemical capsaicin (cap-SAY-sin), and a regular habanero averages around 300,000 to 400,000 units, A&M’s mild version registers a tepid 2,300, or barely one-hundredth of its coolest formidable namesake. A bell pepper, by the way, scores zero.

For more information about the Scoville scale, which was devised in 1912, you can read this page from Wikipedia, which tells us more about habanero peppers in this other page.

Now let’s look at how this mild habanero is grown at the Texas A&M Agricultural Experiment Station (TAM).

The process to produce a more palatable habanero, Dr. Crosby said, began with cross-breeding a regular hot variety with germ plasm from a wild heatless pepper from Bolivia. “We took pollen from the hot to pollinate the heatless to create a hybrid,” he said. The hybrid was then self-pollinated, fertilized with its own pollen, to inbreed desired qualities and then, Dr. Crosby said, “backcrossed to the hot to recover more of its genes for flavor.” That was repeated for eight generations, or four years at two growing seasons a year, to produce the TAM Mild Habanero.

And did you know there was an International Pepper Conference? The 17th conference was held last week in Naples, Florida, on November 14-16. And Dr. Crosby animated a discussion about “Breeding Peppers for Enhanced Beneficial Phytochemical Compounds.”

If you want to know more about his work, you can read “Texas plant breeder develops mild habanero pepper” (PDF format, 2 pages, August 2004).

Finally, I cannot conclude this column before giving you a recipe. What about some Habanero Pepper Sauce from Diana’s Kitchen?

Here is what you’ll need.

• 12 habanero peppers, stems removed, finley chopped
  
• 1/2 cup chopped onion
  
• 2 cloves garlic, minced
  
• 1 tablespoon vegetable oil
  
• 1/2 cup chopped carrots
  
• 1/2 cup distilled vinegar
  
• 1/4 cup lime juice

And here is your cooking assignment.

Saute the onion and garlic in oil until soft; add the carrots with a small amount of water. Bring to a boil, reduce heat and simmer until carrots are soft. Place the mixture and raw chiles into a blender and puree until smooth. Don’t cook the peppers, since cooking reduces flavor of the Habaneros. Combine the puree with vinegar and lime juice, then simmer for 5 minutes and seal in sterilized bottles.

But be warned if you’re using hot habanero peppers. This recipe is rated 9 on a scale of 1 to 10 by the author, B. Emert.

And now, bon appétit!

Sources: Ralph Blumenthal, The New York Times, November 21, 2004; and various websites

Related stories can be found in the following categories.

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Biologists and physicists from the University of California, Santa Barbara (UCSB), have discovered living nanoscale ‘necklaces’. They were studying “microtubules from the brain tissue of a cow to understand the mechanisms leading to their assembly and shape.” And unexpectedly, they found that some divalent cations pushed these microtubules, which are nanotubes derived from cell cytoskeleton, to assemble into ‘necklaces’ of different shapes. Now they think their discovery could be used to deliver drugs or genes. These ‘necklaces’ also could be used to build biosensors or new optical nanomaterials. Read more…

Here is the description of the discovery.

The scientists studied microtubules from the brain tissue of a cow to understand the mechanisms leading to their assembly and shape. Microtubules are nanometer-scale hollow cylinders derived from cell cytoskeleton. In an organism, microtubules and their assembled structures are critical components in a broad range of cell functions — from providing tracks for the transport of cargo to forming the spindle structure in cell division. Their functions include the transport of neurotransmitters in neurons. The mechanism of their assembly within an organism has been poorly understood.

the researchers report the discovery of a new type of higher order assembly of microtubules. Positively-charged large, linear molecules (tri-, tetra- and penta-valent cations) resulted in a tightly bundled hexagonal grouping of microtubules — a result that was predicted. But unexpectedly, the scientists found that small, spherical divalent cations caused the microtubules to assemble into a “necklace.” They discovered distinct linear, branched and loop shaped necklaces.

And what can we expect from these living necklaces?

The scientists envision applications based on both the tight bundle and living necklace phases. For example, metallization of necklace bundles with different sizes and shapes would yield nanomaterials with controlled optical properties.

A more original application is in the area of using the assemblies — encased by a lipid bilayer — as drug or gene carriers where each nanotube may contain a distinct chemical, as noted by the team. In delivery applications the shape of the bundle determines its property. For example, the linear necklace phase with its higher surface to volume ratio would have a larger contact area and a faster delivery rate compared to the tight bundle phase.

The research work has been published online by the Proceedings of the National Academy of Sciences under the intriguing title “Higher-order assembly of microtubules by counterions: From hexagonal bundles to living necklaces.” It should appear in the printed version on November 16, 2004. Here is a link to the abstract of the paper.

For more information, you can visit the Materials Research Laboratory website at UCSB, and more specifically, the Biomaterial Microstructures page.

Sources: UCSB news release, via EurekAlert!, November 8, 2004; and various other websites

You also can read previous entries on this blog in the following categories.

• Biotechnology
  
  
• Materials
  
  
• Nanotechnology
  
  
• Physics