Category Archives: Science

Monoclonal Antibodies Found That Stop All Flu Types

A new kind of drug cocktail kills all types of flu bugs and could protect against pandemic or seasonal flu. “I certainly believe that a therapy for all kinds of influenza may be within our grasp,” study researcher Robert Liddington, DPhil, director of infectious diseases at the Burnham Institute in La Jolla, Calif., said at a news conference announcing the finding.

The treatment is based on new monoclonal antibodies that attack flu viruses in a shared Achilles heel. Of the many different subtypes of flu, there are only two basic patterns for this vulnerable, essential part of the flu virus.

And despite heroic efforts, researchers could not breed a flu strain resistant to the treatment — suggesting that there’s only a very small chance that mutated viruses could render the treatment obsolete. The breakthrough finding is a joint effort from labs at the Burnham Institute; Dana-Farber Cancer Institute in Boston; and the CDC in Atlanta.

Like many breakthroughs, the finding was partly accidental. The researchers were, at first, trying only to create a treatment to stop the H5N1 bird flu virus, the most likely candidate for igniting the next worldwide flu pandemic.
…
While monoclonal antibodies against flu are new, a wide range of drugs are based on this technology. That means the new, fully human anti-flu antibodies could become new human drugs relatively quickly…

“We hope these antibodies are in clinical trials during the 2011-2012 flu season — maybe earlier,” Marasco said. “This really is an important advance in the field of antiviral therapy. The possibility of having a universal therapy for flu is made more real and possible because of these discoveries.”

Study on Citation of Open Access Papers v. Closed Access Papers

Open Access to Scientific Papers May Not Guarantee Wide Dissemination

To test this theory, James A. Evans, an assistant professor of sociology at the University of Chicago, and Jacob Reimer, a student of neurobiology also at the University of Chicago, analyzed millions of articles available online, including those from open source publications and those that required payment to access.

The results were surprising. On average, when a given publication was made available online after being in print for a year, being published in an open source format increased the use of that article by about 8 percent. When articles are made available online in a commercial format a year after publication, however, usage increases by about 12 percent.

“Across the scientific community,” Evans said in an interview, “it turns out that open access does have a positive impact on the attention that’s given to the journal articles, but it’s a small impact.”

Yet Evans and Reimer’s research also points to one very positive impact of the open source movement that is sometimes overlooked in the debate about scholarly publications. Researchers in the developing world, where research funding and libraries are not as robust as they are in wealthier countries, were far more likely to read and cite open source articles.

The University of Chicago team concludes that outside the developed world, the open source movement “widens the global circle of those who can participate in science and benefit from it.”

So while some scientists and scholars may chose to pay for scientific publications even when free publications are available, their colleagues in other parts of the world may find that going with open source works is the only choice they have.

I remain a strong advocate for open science. The out of date model of publishing research in closed journals does not make sense. Especially not for any government funded research or any research supported by foundations, universities or others that aim to promote science.

The quote above and the interview webcast also provide unclear data on what the actual impact is (on how often a paper is cited in other papers). Maybe the article would be clearer but I can’t tell because it is closed access. This link has some worthwhile comments: Generalizing the OA impact advantage.

Magenta is a Color

Electromagnetic spectrum chart from the Wikimedia Commons

Yes, Virgina, there is a magenta by Chris Foresman

There is a nasty rumor making its way around the interconnected series of tubes we call the Internet.
…
As visible light enters the eye and strikes the cone cells, the cells send electrical signals along the optic nerve to the brain. This is how our body “senses” light. Our brain interprets those three separate sensations to produce the perception that we call “color.”
…
The truth is, no color actually exists outside of our brain’s perception of it. Everything we call a color—and there are a lot more than what comes in your box of Crayolas—only exists in our heads. We define color in terms of how our brains process the stimuli produced by a mix of wavelengths in the range of 400–700nm hitting specialized cells in our eyes—”one, or any mixture, of the constituents into which light can be separated in a spectrum or rainbow,” says the OED. Elliot’s article might be better titled, “Magenta is not a single wavelength of electromagnetic radiation in the ‘visible’ spectrum, but our brain perceives it anyway.”

This is a great article that uses science to explain interesting details about our brains and how we perceive the external world.

Science Seeks Stimulas Spending

Scientists Hope Stimulus Will Give Jolt To Research by Richard Harris

The stimulus package contains billions of dollars of funding for the National Institutes of Health — money that could create a quick financial jolt for young workers and university towns.

There are 3,000 institutions around the country that receive NIH grants to fund biomedical research. Raynard Kington, the NIH’s acting director, says those labs are also well-positioned to absorb a jolt of financial stimulus quickly.

“We have literally 14,000 applications that have been peer reviewed, that have been found to be scientifically meritorious and that have been approved for funding — but that we don’t have funds to support,” he says.

Give the NIH the money, he says, and in just a few weeks the money can flow out the door and into a thousand labs or more.

Promoting Bio-Literacy

Wisconsin State Herbarium tries to ‘counteract bio-illiteracy’

“In a past century people could go outside and name the flowers or trees,” said Ken Cameron, the herbarium’s director. “Now you take a kid outside and the most they can say is, ‘It’s a tree.’ If we can get students in and get them excited, then I think we’ve helped to counteract bio-illiteracy.”
…
Herbaria are becoming more of a rarity. And the UW-Madison has the third largest collection of any public university in the country, behind the universities of California and Michigan. At many universities, botany has been absorbed into large biology departments, and collections put into storage. That has not happened at UW-Madison.

“The combination of having a botany department and a big herbarium is getting pretty rare,” said David Baum, botany department chairman. “And more and more herbaria are closing or making the decision to move off campus into storage, which has a real negative effect on research.”

The University of Wisconsin-Madison Herbarium, founded in 1849 (the year the University was founded), is a museum collection of dried, labeled plants of state, national and international importance, which is used extensively for taxonomic and ecological research, as well as for teaching and public service. It contains the world’s largest collection of Wisconsin plants, about one-third of its 1,000,000 specimens having been collected within the state. Most of the world’s floras are well represented, and the holdings from certain areas, such as the Upper Midwest, eastern North America and western Mexico, are widely recognized as resources of global significance.

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.

Tardigrades

Tardigrades (commonly known as water bears) have eight legs and are their own phylum on the tree of life. Some can survive temperatures close to absolute zero, temperatures as high as 151 Â°C (303 Â°F), 1,000 times more radiation than any other animal, nearly a decade without water, and even the vacuum of space.

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
…
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.

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