Category Archives: Research

Remove the Identical Stretches of DNA Found in Mice, Rats, and Humans and What Happens?

A Real Genetic Headscratcher by Derek Lowe:

As you root through genomic sequences – and there are more and more of them to root through these days – you come across some stretches of DNA that hardly seem to vary at all. The hard-core “ultraconserved” parts, first identified in 2004, are absolutely identical between mice, rats, and humans.
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Even important enzyme sequences vary a bit among the three species, so what could these pristine stretches (some of which are hundreds of base pairs long) be used for? The assumption, naturally, has been that whatever it is, it must be mighty important, but if we’re going to be scientists, we can’t just go around assuming that what we think must be right. A team at Lawrence Berkeley and the DOE put things to the test recently by identifying four of the ultraconserved elements that all seem to be located next to critical genes – and deleting them.

The knockout mice turned out to do something very surprising indeed. They were born normally, but then they grew up normally. When they reached adulthood, though, they were completely normal. Exhaustive biochemical and behavioral tests finally uncovered the truth: they’re basically indistinguishable from the wild type. Hey, I told you it was surprising. This must have been the last thing that the researchers expected.

What a great example of scientists at work. It will be interesting to see where this goes.

Sandwich Brick – Reusing Waste Material

A brick-through, Malaysia

at the British Invention Show 2007 held in London recently, waste material bagged Universiti Malaya (UM) researcher Asrul Mahjuddin Ressang Aminuddin a Diamond (Special Award for Earth Science). The lecturer, from UM’s Built Environment faculty, designed a “sandwich brick” that incorporated unwanted plastic, wood particles and other waste material at its core. Helping to save about 26% to 30% on construction costs, the sandwich brick promotes green architecture in the built environment.

“I first came up with the idea when I was assisting the tsunami victims in Thailand and Indonesia,” said Asrul Mahjuddin Ressang. “There was a lot of debris lying around and I wondered how if any could be used for rebuilding purposes.” The brick design has been well received by British construction companies as it is not only environmental friendly but is also entitled to tax incentives across Europe.

It also provides a solution to Britain’s hard-pressed construction industry following the ban on sand mining from riverbeds and waste accumulation that stands at 15 million tonnes in 2007 alone. The innovation impressed judges as it had better heat insulation compared to ordinary bricks and encouraged industries to rethink recycling at minimal costs.
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Meanwhile, engineering faculty senior lecturer Dr Mohd Hamdi Abd Shukor received a Double Gold (Special Award for Industry) – for his work on tough synthetic bio-ceramic for bone implant technology and a minimal cutting fluid application in a pulse jet form.

New and Old Ways to Make Flu Vaccines

New and Old Ways to Make Flu Vaccines by Nell Greenfieldboyce, NPR:

Standard Practice
Pros: Millions of Americans receive this [standard] vaccine every year. It’s safe and well tolerated. Its production begins in hens’ eggs — a tried and true technology for 50 years.
Cons: Eggs must be ordered many months in advance, and millions of doses require millions of eggs.

Live-Attenuated Vaccine
Pros: This newer method of production results in a vaccine that has a flu virus that is crippled, so it can’t cause disease. But the virus is not killed, as is the case in the standard vaccine. The vaccine also can be given as a nasal spray.
Cons: More expensive than standard vaccine, and also produced in eggs. Not approved for young children or older people.

Cell-Based Vaccine
Pros: This vaccine can be produced in giant vats of living cells. Such a production method means it can be scaled up much faster than egg-based vaccines, making it more useful in a pandemic. Several versions have been tested successfully in people.
Cons: Won’t be widely available for a few years. Clinical trials are under way, but no flu vaccine made this way is currently approved by the Food and Drug Administration.

CMU Wins $2 million in Urban Robot Auto Race

CMU wins $2 million in urban robot race

Carnegie Mellon University won the $2 million first place prize in DARPA’s urban robot race this weekend, stealing the thunder from 2005’s Grand Challenge leader, Stanford University. The Defense Advanced Research Projects Agency (DARPA) Urban Challenge awarded a total of $3.5 million in prizes on Sunday, a day after the race. Stanford University took second place, with a $1 million cash prize, and Virginia Tech won $500,000 for third place.

The Urban Challenge was a six-hour test of driverless vehicles on the suburban roads of the former George Air Force Base in Oro Grande, Calif., where the robotic cars were required to complete three missions while obeying traffic laws and avoiding obstacles and collisions with other driverless vehicles. The challenge was the first ever to test robots driving among other robots, and it was significantly harder than DARPA’s 2005 desert Grand Challenge because of that interplay and the urban setting, according to race officials.

Reusable Paper

Xerox’s Reusable Paper

Almost half of the paper used in American offices is for daily use. It is for display, not storage and, at the end of the day, it’s in the trash can. All of the energy that was put into harvesting, processing, and shipping that paper was, in the end, for less than a day’s use. A number of companies are working on alternatives to this procedure.
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The system is based on ‘paper’ that contains light sensitive materials. When exposed to certain wavelengths of light, the paper changes to a darker that then slowly fades. Neither the light-sensitive paper, nor the light printers are ready for consumers

Interesting. It is great to see all the efforts undertaken by scientists and engineers to improve. The more we can have working everywhere in the world the better off we will be.

Open Access Legislation May Be Included in HHS Budget Bill

Open Access to Research Funded by U.S. Is at Issue by Rick Weiss:

The idea is that consumers should not have to buy expensive scientific journal subscriptions — or be subject to pricey per-page charges for nonsubscribers — to see the results of research they have already paid for with their taxes. Until now, repeated efforts to legislate such a mandate have failed under pressure from the well-heeled journal publishing industry and some nonprofit scientific societies whose educational activities are supported by the profits from journals that they publish.

But proponents — including patient advocates, who want easy access to the latest biomedical findings, and cash-strapped libraries looking for ways to temper escalating subscription costs — have parlayed their consumer-friendly “public access” message into legislative language that has made it into the Senate and House versions of the new HHS bill.

The opponents of open science are lobbying to keep scientific research funded by taxpayers unavailable to the public. As I have said before it is time to stop supporting those who attempt to stop scientific progress. The out of date thinking behind closed access journals should be discouraged and those journals fighting progress should not be supported. This legislation would bring openness to federal research in a similar manner to the steps taken by Howard Hughes Medical Institute announced for research they fund.

Most Powerful Anti-matter Beam Yet

NC State Nuclear Reactor Program Celebrates Scientific Breakthrough

Success was two years in the making – the positron project began in 2005 as a collaboration between NC State, the University of Michigan and Oak Ridge National Laboratory with the support of the U.S. Department of Energy and the National Science Foundation. “The idea here is that if we create this intense beam of antimatter electrons – the complete opposite of the electron, basically – we can then use them in investigating and understanding the new types of materials being used in many applications,” Hawari said.

Now that the intense beam has been generated, members of NC State’s nuclear engineering program and their collaborators will turn their focus to developing instrumentation such as antimatter spectrometers and potentially long-discussed antimatter microscopes, which would allow for a much more detailed look into materials at the atomic level.

NC State Nuclear Reactor Generates Record Low-Energy Positron Beam

Once the stuff of science fiction, these anti-matter, or positron, beams have a multitude of uses in nanoscience and materials engineering because of the positron’s ability to gravitate toward and trap in defects or pores in a material at sizes as small as a single atom. Positrons are used to detect damage from radiation in nuclear reactors and are impacting the emerging field of nanoengineered materials where nanometer-sized voids control properties such as dielectric constant in microelectronic devices and hydrogen storage in fuel cells.

An intense positron beam means that researchers will have better measurements of a material’s porosity, especially in high-tech thin film applications where traditional techniques falter. This beam will be used in Positron Annihilation Lifetime Spectrometry (PALS) and Doppler Broadening Spectrometry (DBS). Hawari also believes that other positron analysis techniques will become possible. While the spectrometers are not yet built, they are on the books for completion next year.

More Dinosaurs Fighting Against Open Science

Controversy at the American Chemical Society by John Dupuis

So, what’s my take on this? First of all, I’m not surprised. Unfortunately there are some scholarly societies that operate more like for-profits when it comes to their publishing arms and ACS is certainly one of the most notable for that sort of thing. While it should be shocking that ACS is acting more like Elsevier than Elsevier at times, sadly it isn’t.

Secondly, what should we, as librarians do about it? Mostly we need to advocate. We need to push our vendors towards business models that favour open access, we need to reassure them that we’re interested in a sustainable model for scholarly publishing

I agree. It is sad that so many organizations distort behavior though poor management structures but that is the world we live in. My management improvement blog focused on how to manage better. And I have posted several times about the need to shift our support to open access science and away from those who want continue outdated strategies that restrict the advancement of scientific ideas.

Nanoengineers Use Tiny Diamonds for Drug Delivery

Nanoengineers Mine Tiny Diamonds for Drug Delivery

Northwestern University researchers have shown that nanodiamonds — much like the carbon structure as that of a sparkling 14 karat diamond but on a much smaller scale — are very effective at delivering chemotherapy drugs to cells without the negative effects associated with current drug delivery agents.
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To make the material effective, Ho and his colleagues manipulated single nanodiamonds, each only two nanometers in diameter, to form aggregated clusters of nanodiamonds, ranging from 50 to 100 nanometers in diameter. The drug, loaded onto the surface of the individual diamonds, is not active when the nanodiamonds are aggregated; it only becomes active when the cluster reaches its target, breaks apart and slowly releases the drug. (With a diameter of two to eight nanometers, hundreds of thousands of diamonds could fit onto the head of a pin.)

“The nanodiamond cluster provides a powerful release in a localized place — an effective but less toxic delivery method,” said co-author Eric Pierstorff, a molecular biologist and post-doctoral fellow in Ho’s research group. Because of the large amount of available surface area, the clusters can carry a large amount of drug, nearly five times the amount of drug carried by conventional materials.

The Chemistry of Hair Coloring

Scientists Develop the First Significant Advance in Hair Dye in 50 Years by Kristen Philipkoski

Hair color is serious chemistry. Getting color into that hair shaft is no joke. That’s why Procter & Gamble employs 1,800 “beauty scientists” around the globe. I spoke to two of these beauty scientists this week who told me they have invented a kinder hair color, and that it marks the first significant advance in dye jobs in 50 years.
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Small, diffuse color molecules enter the hair, and while they’re inside, they oxidize and form a chemical reaction with a larger color molecule that’s already trapped in there. But the small molecules aren’t all that selective about who they get it on with, and they end up breaking some of the chemical bonds that hold hair together. That releases free radicals that make hair weaker and less able to resist things like aggressive brushing, blow-drying and ironing.
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So the beauty scientists came up with a whole new chemistry for getting the lightening molecules inside the hair. First, the new process works at a much lower pH. That makes it less alkaline, so it strips away much less of the lipid coating.