Category Archives: Research

Extinct Ibex is Resurrected by Cloning

The Pyrenean ibex, a form of wild mountain goat, was officially declared extinct in 2000 when the last-known animal of its kind was found dead in northern Spain. Shortly before its death, scientists preserved skin samples of the goat, a subspecies of the Spanish ibex that live in mountain ranges across the country, in liquid nitrogen.

Using DNA taken from these skin samples, the scientists were able to replace the genetic material in eggs from domestic goats, to clone a female Pyrenean ibex, or bucardo as they are known. It is the first time an extinct animal has been cloned.

Sadly, the newborn ibex kid died shortly after birth due to physical defects in its lungs. Other cloned animals, including sheep, have been born with similar lung defects. But the breakthrough has raised hopes that it will be possible to save endangered and newly extinct species by resurrecting them from frozen tissue.

It has also increased the possibility that it will one day be possible to reproduce long-dead species such as woolly mammoths and even dinosaurs.

MRI That Can See Bacteria, Virus and Proteins

IBM team boosts MRI resolution

The researchers demonstrated this imaging at a resolution 100 million times finer than current MRI. The advance could lead to important medical applications and is powerful enough to see bacteria, viruses and proteins, say the researchers.

The researchers said it offered the ability to study complex 3D structures at the “nano” scale. The step forward was made possible by a technique called magnetic resonance force microscopy (MRFM), which relies on detecting very small magnetic forces.

In addition to its high resolution, MRFM has the further advantage that it is chemically specific, can “see” below surfaces and, unlike electron microscopy, does not destroy delicate biological materials.

Now, the IBM-led team has dramatically boosted the sensitivity of MRFM and combined it with an advanced 3D image reconstruction technique. This allowed them to demonstrate, for the first time, MRI on biological objects at the nanometre scale.

That is very cool.

Science Commons: Making Scientific Research Re-useful

Science Commons is a project of Creative Commons. Like other organizations trying to support the advancement of science with open access they deserve to be supported (PLoS and arXiv.org are other great organizations supporting science).

Science Commons has three interlocking initiatives designed to accelerate the research cycle – the continuous production and reuse of knowledge that is at the heart of the scientific method. Together, they form the building blocks of a new collaborative infrastructure to make scientific discovery easier by design.

Making scientific research re-useful, help people and organizations open and mark their research and data for reuse. Learn more.

Enabling one-click access to research materials, streamline the materials-transfer process so researchers can easily replicate, verify and extend research. Learn more.

Integrating fragmented information sources, help researchers find, analyze and use data from disparate sources by marking and integrating the information with a common, computer-readable language. Learn more.

NeuroCommons, is their proof-of-concept project within the field of neuroscience. The NeuroCommons is a beta open source knowledge management system for biomedical research that anyone can use, and anyone can build on.

Fast Fitness Forecast is False, it Takes Time

Fitness Isn’t an Overnight Sensation

“To make a change in how you look, you are talking about a significant period of training,” Dr. Kraemer said. “In our studies it takes six months to a year.” And, he added, that is with regular strength-training workouts, using the appropriate weights and with a carefully designed individualized program. “That is what the reality is,” he said.

And genetic differences among individuals mean some people respond much better to exercise than others
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Now, said Mr. Antane, who runs with a group in Princeton on Thursday nights, “everything changed — my outlook on life, who I hung out with, how I felt about myself.”

Our bodies evolved under conditions with much more exercise than we currently get if we sit in an office all day. And we had less food. It is no surprise with more food and less exercise that we gain weight. And given that the benefit of fat was to help us survive when we had little food out bodies don’t change overnight. If they did then our ancestors would have had much more difficulty surviving – the whole point was to provide a resource to tap in bad times. If that resource dissipated quickly it would not have helped much.

Moving Closer to Robots Swimming Through Bloodsteam

Pretty cool. Tiny motor allows robots to swim through human body

James Friend, of Monash University, said that such devices could enter previously unreachable brain areas, unblocking blood clots, cleaning vessels or sending back images to surgeons. “The first complete device we want to build would have a camera,” Professor Friend said.
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Professor Friend said they had shown the motor, which is a quarter of a millimetre wide, had enough power to navigate this type of nanorobot through the bloodstream of a human artery. Tests of their prototype device in a liquid as viscous as blood were also promising. “It swam.”
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The team plans to conduct animal tests of a nanorobot driven by their motor later this year or early next year. But Professor Friend cautioned that many technical hurdles needed to be overcome.

Their miniature motor was connected to an electricity supply and a way would need to be found to power it remotely. The construction of the flagella also needed refinement.

New Family of Antibacterial Agents Discovered

Bacteria continue to gain resistance to commonly used antibiotics. In this week’s JBC, one potential new antibotic has been found in the tiny freshwater animal Hydra.

The protein identified by Joachim GrÃ¶tzinger, Thomas Bosch and colleagues at the University of Kiel (Germany), hydramacin-1, is unusual (and also clinically valuable) as it shares virtually no similarity with any other known antibacterial proteins except for two antimicrobials found in another ancient animal, the leech.

Hydramacin proved to be extremely effective though; in a series of laboratory experiments, this protein could kill a wide range of both Gram-positive and Gram-negative bacteria, including clinically-isolated drug-resistant strains like Klebsiella oxytoca (a common cause of nosocomial infections). Hydramacin works by sticking to the bacterial surface, promoting the clumping of nearby bacteria, then disrupting the bacterial membrane.

GrÃ¶tzinger and his team also determined the 3-D shape of hydramacin-1, which revealed that it most closely resembled a superfamily of proteins found in scorpion venom; within this large group, they propose that hydramacin and the two leech proteins are members of a newly designated family called the macins.

Source: American Society for Biochemistry and Molecular Biology

Soil Mineral Degrades the Nearly Indestructible Prion

Warped pathogens that lack both DNA and RNA, prions are believed to cause such fatal brain ailments as chronic wasting disease (CWD) in deer and moose, mad cow disease in cattle, scrapie in sheep and Creutzfeldt-Jakob disease in humans. In addition to being perhaps the weirdest infectious agent know to science, the prion is also the most durable. It resists almost every method of destruction from fire and ionizing radiation to chemical disinfectants and autoclaving, which reduce prion infectivity but fail to completely eliminate it.

Other studies have shown that prions can survive in the soil for at least three years, and that soil is a plausible route of transmission for some animals, says Joel Pedersen, a UW-Madison environmental chemist. “We know that environmental contamination occurs in deer and sheep at least,” he notes.

Prion reservoirs in the soil, Pedersen explains, are likely critical links in the chain of infection because the agent does not appear to depend on vectors — intermediate organisms like mosquitoes or ticks — to spread from animal to animal.

That the birnessite family of minerals possessed the capacity to degrade prions was a surprise, Pedersen says. Manganese oxides like birnessite are commonly used in such things as batteries and are among the most potent oxidants occurring naturally in soils, capable of chemically transforming a substance by adding oxygen atoms and stripping away electrons. The mineral is most abundant in soils that are seasonally waterlogged or poorly drained.

full press release

Data Analysts Captivated by R’s Power

data mining has entered a golden age, whether being used to set ad prices, find new drugs more quickly or fine-tune financial models. Companies as diverse as Google, Pfizer, Merck, Bank of America, the InterContinental Hotels Group and Shell use it.
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Close to 1,600 different packages reside on just one of the many Web sites devoted to R, and the number of packages has grown exponentially. One package, called BiodiversityR, offers a graphical interface aimed at making calculations of environmental trends easier.

Another package, called Emu, analyzes speech patterns, while GenABEL is used to study the human genome. The financial services community has demonstrated a particular affinity for R; dozens of packages exist for derivatives analysis alone. “The great beauty of R is that you can modify it to do all sorts of things,” said Hal Varian, chief economist at Google. “And you have a lot of prepackaged stuff that’s already available, so you’re standing on the shoulders of giants.”

R first appeared in 1996, when the statistics professors Ross Ihaka and Robert Gentleman of the University of Auckland in New Zealand released the code as a free software package. According to them, the notion of devising something like R sprang up during a hallway conversation. They both wanted technology better suited for their statistics students, who needed to analyze data and produce graphical models of the information. Most comparable software had been designed by computer scientists and proved hard to use.

R is another example of great, free, open source software. See R packages for Statistics for Experimenters.

via: R in the news

So What are Genetic Algorithms?

Genetic Algorithms: Cool Name and Damn Simple is a very nice explanation with python code of genetic algorithms.

What Can Genetic Algorithms Do?
In a word, genetic algorithms optimize. They can find better answers to a question, but not solve new questions. Given the definition of a car, they might create a better car, but they’ll never give you an airplane.
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For each generation we’ll take a portion of the best performing individuals as judged by our fitness function. These high-performers will be the parents of the next generation.

We’ll also randomly select some lesser performing individuals to be parents, because we want to promote genetic diversity. Abandoning the metaphor, one of the dangers of optimization algorithms is getting stuck at a local maximum and consequently being unable to find the real maximum. By including some individuals who are not performing as well, we decrease our likelihood of getting stuck.

Correlation is Not Causation: “Fat is Catching” Theory Exposed

“Fat is catching” theory exposed

Their study was reported to have shown that you can “catch” obesity from having fat friends and that obesity is so contagious, it can be spread long-distance by email and instant messaging. Even healthcare professionals, who didn’t understand the etiology of true obesity or how statistics can be misused, failed to detect the implausibility of “second-hand obesity.” In fact, some doctors became so enamored with the new “science of networking” they believed it should be a new medical specialty: network medicine.
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Jason M. Fletcher, Ph.D., assistant professor at the Yale School of Public Health in New Haven, Connecticut, along with Boston economist, Ethan Cohen-Cole, Ph.D., designed an ingenious study. They selected conditions that no one would seriously believe were spread by social networking and online friendships: height, headaches and acne. They then applied the same standard statistical methods used in Christakis and Fowler’s social networking research to “find” that acne, height and headaches have the same “social network effect.”
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As they explained, patterns of association among people can lead to correlations in health conditions between friends that are not caused by direct social network effects at all.
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There is a need for caution when attributing causality to correlations in health outcomes between friends using non-experimental data. Confounding is only one of many empirical challenges to estimating social network effects.

Excellent reminder of the risks of analyzing data for correlations. We continue to, far to often, fail to interpret data properly. Both authors of the study, received PhD’s from the University of Wisconsin-Madison which strengthens my belief that it is teaching students well (just kidding).

Also another example of the scientific inquiry process where scientists challenge the conclusions drawn by other scientists. It is a wonderful system, even if confusing and not the clean idea so many have of how science works.