Tag Archives: Research

2009 Nobel Prize in Chemistry: the Structure and Function of the Ribosome

graphic image of the components of a cell

Cross section of a cell by the Royal Swedish Academy of Sciences. A ribosome is about 25 nanometters (a millionth of a millimeter) in size. A cell contains tens of thousands of ribosomes.

The Nobel Prize in Chemistry for 2009 awards studies of one of life’s core processes: the ribosome’s translation of DNA information into life. Ribosomes produce proteins, which in turn control the chemistry in all living organisms. As ribosomes are crucial to life, they are also a major target for new antibiotics.

This year’s Nobel Prize in Chemistry awards Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for having showed what the ribosome looks like and how it functions at the atomic level. All three have used a method called X-ray crystallography to map the position for each and every one of the hundreds of thousands of atoms that make up the ribosome.

Inside every cell in all organisms, there are DNA molecules. They contain the blueprints for how a human being, a plant or a bacterium, looks and functions. But the DNA molecule is passive. If there was nothing else, there would be no life.

The blueprints become transformed into living matter through the work of ribosomes. Based upon the information in DNA, ribosomes make proteins: oxygen-transporting haemoglobin, antibodies of the immune system, hormones such as insulin, the collagen of the skin, or enzymes that break down sugar. There are tens of thousands of proteins in the body and they all have different forms and functions. They build and control life at the chemical level.

Details from the Nobel Prize site (which continues to do a great job providing scientific information to the public openly).
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Bacteria Use Nitric Oxide to Resist Antibiotics

Scientists Discover Mechanism to Make Existing Antibiotics More Effective at Lower Doses

Eliminating this NO[nitric oxide]-mediated bacterial defense renders existing antibiotics more potent at lower, less toxic, doses. With infectious diseases the major cause of death worldwide, the study paves the way for new ways of combating bacteria that have become antibiotic resistant.

NO is a small molecule composed of one atom of oxygen and one of nitrogen. It was known as a toxic gas and air pollutant until 1987, when it was first shown to play a physiological role in mammals, for which a Nobel Prize was later awarded. NO has since been found to take part in an extraordinary range of activities including learning and memory, blood pressure regulation, penile erection, digestion and the fighting of infection and cancer. A few years ago, the Nudler’s group from NYU demonstrated that bacteria mobilize NO to defend against the oxidative stress. The new study from the same group supports the radical idea that many antibiotics cause the oxidative stress in bacteria, often resulting in their death, whereas NO counters this effect. This work suggests scientists could use commercially available inhibitors of NO-synthase, an enzyme producing NO in bacteria and humans, to make antibiotic resistant bacteria like MRSA and ANTHRAX more sensitive to available drugs during acute infection.
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The study by Nudler and his colleagues was funded by a 2006 Pioneer Award from the National Institutes of Health in Bethesda, Maryland. The Pioneer Award, a $2.5 million grant over five years, is designed to support individual scientists of exceptional creativity who propose pioneering and possibly transforming approaches to major challenges in biomedical and behavioral research.

Engineer Tried to Save His Sister and Invented a Breakthrough Medical Device

Here is another remarkable example of the great benefit engineers provide society.

How a software engineer tried to save his sister and invented a breakthrough medical device

I wanted to help my sister as much as I could. I went to Medline, where there are hundreds of thousands of documents describing clinical studies, to see what I could find.

There are billions of dollars spent every year on clinical studies. I was surprised to discover that there were sometimes clinical studies of treatments for which there were no clinical applications. The trials would show successful results but no clinical applications.

I found a 1987 Italian funded set of clinical studies that showed successful treatment of tumors by the application of chemotherapy directly into the tumors. But I could find nothing since then.
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It took us two years to do the engineering. And it has taken the FDA seven years and two months to approve the product for sale. We were able to shorten the FDA process a little by saying that it was similar to other devices that had already been approved.

Great stuff.

Scientific Illiteracy Leaves Many at Risk in Making Health Care Judgements

Scientific literacy is important for many reasons and that importance has increased greatly over the last century. Medical research is often difficult to interpret. Often various studies seem to contradict each other. Often the conclusions that are drawn are far too broad (especially as the research conclusions are passed on and people hear of them overly simplified ways).

Many health care options are not obviously all good, or all bad, but instead a mix of benefits and risks, both of which include interactions with the individuals makeup. So we often see contradictory (and seemingly contradictory) advice. Without a level of scientific literacy it is very difficult for people to know how to react to medical advice.

We have numerous posts on the scientific inquiry process showing that acquiring scientific knowledge is complex and can be quite confusing in many instances. While understanding things are often less clear cut than they are presented it is still true that most often strategies for healthy living have far better practices that will provide far better results than alternatives.

The scientific illiteracy that has some think because their are risks no matter what is done that means there is no evidence some alternatives are far superior is very dangerous. As you can see in action now with those that risk their and others lives and health by doing things like not vaccinating their children, or driving when drunk, or driving when talking on a cell phone.

Without a scientifically literate society even completely obvious measures like not using antibiotics on viral infections are ignored.

Atomic Force Microscopy Image of a Molecule

The delicate inner structure of a pentacene molecule imaged with an atomic force microscope. For the first time, scientists achieved a resolution that revealed the chemical structure of a molecule. The hexagonal shapes of the five carbon rings in the pentacene molecule are clearly resolved. Even the positions of the hydrogen atoms around the carbon rings can be deduced from the image. (Pixels correspond to actual data points). Image courtesy of IBM Research – Zurich

IBM scientists have been able to image the “anatomy” — or chemical structure — inside a molecule with unprecedented resolution. “Though not an exact comparison, if you think about how a doctor uses an x-ray to image bones and organs inside the human body, we are using the atomic force microscope to image the atomic structures that are the backbones of individual molecules,” said IBM Researcher Gerhard Meyer. “Scanning probe techniques offer amazing potential for prototyping complex functional structures and for tailoring and studying their electronic and chemical properties on the atomic scale.”

The AFM uses a sharp metal tip to measure the tiny forces between the tip and the sample, such as a molecule, to create an image. In the present experiments, the molecule investigated was pentacene. Pentacene is an oblong organic molecule consisting of 22 carbon atoms and 14 hydrogen atoms measuring 1.4 nanometers in length. The spacing between neighboring carbon atoms is only 0.14 nanometers—roughly 1 million times smaller then the diameter of a grain of sand. In the experimental image, the hexagonal shapes of the five carbon rings as well as the carbon atoms in the molecule are clearly resolved. Even the positions of the hydrogen atoms of the molecule can be deduced from the image.

Read full press release: IBM Scientists First to Image the “Anatomy” of a Molecule
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Battery Breakthrough

New battery could change world

Inside Ceramatec’s wonder battery is a chunk of solid sodium metal mated to a sulphur compound by an extraordinary, paper-thin ceramic membrane. The membrane conducts ions — electrically charged particles — back and forth to generate a current. The company calculates that the battery will cram 20 to 40 kilowatt hours of energy into a package about the size of a refrigerator, and operate below 90 degrees C.

This may not startle you, but it should. It’s amazing. The most energy-dense batteries available today are huge bottles of super-hot molten sodium, swirling around at 600 degrees or so. At that temperature the material is highly conductive of electricity but it’s both toxic and corrosive. You wouldn’t want your kids around one of these.

The essence of Ceramatec‘s breakthrough is that high energy density (a lot of juice) can be achieved safely at normal temperatures and with solid components, not hot liquid.

Ceramatec says its new generation of battery would deliver a continuous flow of 5 kilowatts of electricity over four hours, with 3,650 daily discharge/recharge cycles over 10 years. With the batteries expected to sell in the neighborhood of $2,000, that translates to less than 3 cents per kilowatt hour over the battery’s life. Conventional power from the grid typically costs in the neighborhood of 8 cents per kilowatt hour.
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A small three-bedroom home in Provo might average, say, 18 kWh of electric consumption per day in the summer — that’s 1,000 watts for 18 hours. A much larger home, say five bedrooms in the Grandview area, might average 80 kWh, according to Provo Power.;Either way, a supplement of 20 to 40 kWh per day is substantial. If you could produce that much power in a day — for example through solar cells on the roof — your power bills would plummet.

Ceramatec’s battery breakthrough now makes that possible.

Clyde Shepherd of Alpine is floored by the prospect. He recently installed the second of two windmills on his property that are each rated at 2.4 kilowatts continuous output. He’s searching for a battery system that can capture and store some of that for later use when it’s calm outside, but he hasn’t found a good solution.

“This changes the whole scope of things and would have a major impact on what we’re trying to do,” Shepherd said. “Something that would provide 20 kilowatts would put us near 100 percent of what we would need to be completely independent. It would save literally thousands of dollars a year.”

Very interesting stuff. If they can take it from the lab to production this could be a great thing, I would like one.

HHMI Science Internships

Undergraduate Scholars Live the Scientific Life at Janelia Farm

With Janelia Farm lab heads as their mentors, the students have delved into projects that include identifying the neurons that control feeding behavior in fruit flies, designing better labeling molecules for use with sophisticated microscopy techniques, increasing the longevity of dragonflies, and developing computer programs for automated image analysis. The Janelia environment, they said, provides a unique opportunity to focus intently on research.
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The summer program offers students more than just hands-on experience in the lab – it aims to expose them to a more complete picture of what it is to work and think as a scientist does. An important component of the program is a weekly seminar in which students present their work to one another and field questions. Likewise, scholars are encouraged to attend the campus’s frequent seminars, conferences, and journal clubs, for exposure to research other their own.

For Gloria Wu, who is majoring in biochemistry at the University of California, Berkeley, the interdisciplinary nature of research at Janelia Farm and the diversity of backgrounds among her fellow scholars were important assets. “A lot of students are coming from math or computer science backgrounds, and that really stimulates a lot of discussion between us, so we can see other approaches to solving biological questions. That is something really wonderful about this program,” she said.

Crows Can Recognize People

Crows can recognize people and remember them for years. Listen to this interesting report from NPR. Researchers alienated a crow, and then were razzed and harassed by its family and neighbors wherever they go.

The Calorie Delusion

The calorie delusion: Why food labels are wrong

Nutritionists are well aware that our bodies don’t incinerate food, they digest it. And digestion – from chewing food to moving it through the gut and chemically breaking it down along the way – takes a different amount of energy for different foods. According to Geoffrey Livesey, an independent nutritionist based in Norfolk, UK, this can lower the number of calories your body extracts from a meal by anywhere between 5 and 25 per cent depending on the food eaten.
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Dietary fibre is one example. As well as being more resistant to mechanical and chemical digestion than other forms of carbohydrate, dietary fibre provides energy for gut microbes, and they take their cut before we get our share. Livesey has calculated that all these factors reduce the energy derived from dietary fibre by 25 per cent
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“Cooking gives food energy,” says Wrangham. It alters the structure of the food at the molecular level, making it easier for our body to break it up and extract the nutrients.

In plants, for example, much of the energy from starch is stored as amylopectin, which is semi-crystalline, does not dissolve in water, and cannot be easily digested. Heat starchy foods with water, though, and the crystalline forms begin to melt. The starch granules absorb water, swell, and eventually burst. The amylopectin is shattered into short starch molecules called amylose, which are easily digested by the enzyme amylase.

It seems pretty obvious, just looking around, as you walk around in any city that people are much fatter, on average, than we were 20 years ago. And the data shows people were much larger (taller, but also fatter) 20 years ago than they were 100 years ago. And we know obesity causes many human health issues. The failure to address the obesity problem in the USA is another example of the failed “health care” system. Instead of a working health care system we just manage diseases that result for unhealthy living. We should be do better at providing information to people on healthy eating (including more accurate calorie counts as it concerns food we eat) and healthy lifestyle choices.

Pigeon Solves Box and Banana Problem

Laboratory footage showing a pigeon solving Wolfgang Kohler’s famous box-and-banana problem, which he studied with chimpanzees in the early 1900s. Depending on their previous experience, pigeons could solve this problem in a human-like fashion in as little as a minute. This pigeon has learned to push boxes and to climb, and it has been rewarded with grain for pecking at a small toy banana.

In this situation, the banana is out of reach and the box is not beneath it. At first the pigeon looks confused, then it begins pushing the box – sighting the toy banana as it pushes – and then stops pushing when the box is beneath the banana, then climbs and pecks. This and related studies were summarized in Dr. Epstein‘s 1996 book, Cognition, Creativity, & Behavior.

This is another example of interesting thoughtful bird behavior.