Category Archives: Research

Molecular Bioengineering and Dynamical Models of Cells

Study Maps Life in Extreme Environments, Creating Potential for Molecular Bioengineering and Dynamical Models of Cells

The researchers focused on a little studied organism that can survive high salt, radiation, and other stresses that would be deadly to most other organisms. By focusing on such an organism the researchers were able to show definitively that they could understand and model the circuit controlling the cell directly from experiments designed to measure all genes in the genome simultaneously. These are called systems-biology experiments. This scholarship is part of a new scientific field, systems biology, which examines how genes influence each other via extremely large networks of interaction and how these networks respond to stimuli, adapting over time to new environments and cell states.
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“This is also a good model to explain how, in general, cells make stable decisions as they move through time scales,” added Bonneau, who is part of an NYU research group that handled the analysis of this genome. “If you want to understand how cells respond to their environments, the model offers a clearer window than previously existed for this domain of life.” The collaboration between Baliga’s and Bonneau’s research groups represents a type of partnership becoming more essential to biological and biomedical research: biologists and computer scientists teaming up to design experiments and analysis that synergize to decipher living systems, resulting in ever more complex and accurate models of the cell.

Smart Squirrels Sneaky Snake Strategy

Squirrels Use “Snake Perfume” to Fool Predators

To mask their odor from rattlesnakes, California ground squirrels and rock squirrels chew on sloughed-off snake skin and smear it on their fur, according to a new study. The act most likely persuades the predators that another snake, not a squirrel, is in the area.

“To our knowledge this is the first case where [this idea] has been tested systematically and shown to have an anti-predator function—protecting the squirrel from rattlesnake predation,” said study lead author Barbara Clucas.Rattlers and other snakes usually prey on baby squirrels, because the adults have proteins in their blood that make them immune to snake venom.

Pups, on the other hand, aren’t big enough to resist the poison. Clucas and colleagues therefore think that adult female and juvenile squirrels spend more time applying snake scent to their bodies. “Adult females actively protect their pups … and share their burrows with juveniles,” Clucas said.

The State of Physics

The Problem with Physics by Peter Woit

Physics has become obsessed with strings, branes and multiple dimensions, yet the big questions remain fundamentally unanswered. Has the time come to admit these wild conjectures have failed, and move on?
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Fundamental physics now finds itself in a historically unprecedented situation. The multi-decade dominance of string theory, along with its extremely speculative research into the implications of exotic scenarios far removed from any hope of testability, has changed the subject in dramatic and fundamental ways.

What used to be considered part of the dubious fringes of science has now become institutionalised within the mainstream. In physicist Lee Smolin’s recent book, The Trouble With Physics, he characterises the current sociology of the field as dominated by ‘groupthink’, with too few physicists willing to admit how far off the tracks things have gone. The nearly infinite complexity of string theory, M-theory, branes, higher dimensions and the multiverse has led to a vast number of possible challenging calculations for people to do to keep themselves busy, all embedded in a mathematical structure far too poorly understood to ever lead to definitive, falsifiable predictions.

The problems of the Standard Model that faced my colleague and I a quarter of a century ago continue to inspire new generations of young theorists to devote their lives to work that might some day lead to real progress. But these problems remain extremely difficult ones, and we have little in the way of promising ideas, with far too much effort going into the evasion of difficulties and the pursuit of the chimera of unification through ever more complex higher dimensional constructions inspired by string theory.

Strategic Research Plan for Nanotechnology

Productive Nanosystems report for the United States Department of Energy:

This Roadmap is a call to action that provides a vision for atomically precise manufacturing technologies and productive nanosystems. The United States nanotechnology advancement goal should be to lead the world towards the development of these revolutionary technologies in order to improve the human condition by addressing grand challenges in energy, health care, and other fields. The United States can accomplish this goal through accelerated global collaborations focused on two strategies that will offer ongoing and increasing benefits as the
technology base advances:

1. Develop atomically precise technologies that provide clean energy supplies and a cost-effective energy infrastructure.
2. Develop atomically precise technologies that produce new nanomedicines and multifunctional in vivo and in vitro therapeutic and diagnostic devices to improve human health.
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Close cooperation among scientific and engineering disciplines will be necessary because of the nature of the engineering problems involved. This cross-disciplinary collaboration will bring broad benefits through the cross-fertilization of ideas, instruments, and techniques that will result from developing the required technology base.

With international cooperation, the benefits of productive nanosystems will be delivered to the world faster. Coordinating a full international
effort is extremely desirable in order to minimize duplication of effort in smaller national programs conducted independently.

Another Bacteria DNA Trick

A DNA shift never before seen in nature

For several decades, researchers have known that it is possible to modify synthetic oligonucleotides (short strands of DNA) by adding sulfur to the sugar-phosphate DNA backbone as a phosphorothioate. Researchers often use such modifications in the laboratory to make DNA resistant to nucleases (enzymes that snip DNA in certain locations) as a step toward gene and antisense therapies of human diseases.

Dedon said he and his co-workers were surprised to discover that a group of bacterial genes, known as the dnd gene cluster, gives bacteria the ability to employ the same modification on their own. “It turns out that nature has been using phosphorothioate modifications of DNA all along, and we just didn’t know about it,” he said.
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He theorizes that the modification system might serve as either protection against foreign (unmodified) DNA, or as a “bookmark” to assist with transcription or replication of DNA.

Bacteria really are amazing. I am starting to read more about bacteria and virus so maybe I will post more on these topics over the next few months.

Long-Eared Jerboa

photo of a long eared jerboa

Mysterious mammal caught on film, the link has videos too:

The long-eared jerboa, a tiny nocturnal mammal that is dwarfed by its enormous ears, can be found in deserts in Mongolia and China.
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Until now, the creatures had proven extremely difficult to study, thanks to their minuscule size, nocturnal nature and the harsh desert environment that they inhabit.
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“These creatures hop just like a kangaroo; it is amazing to watch. Little hairs on their feet, almost like snow shoes, allow them to jump along the sand,” he explained.
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The expedition formed part of ZSL’s Edge programme, which focuses its efforts on conservation plans for animals that are both endangered and evolutionary distinctive. The long-eared jerboa is one of 10 species that the programme is looking at this year.

The Zoological Society of London Evolutionarily Distinct and Globally Endangered (EDGE) web site is a great source of all sorts of information. Including more on the Long-Earned Jerboa in the Gobi Desert. Great stuff, they have done a very nice job with their web site – even if they do force people to download the flash player for some material.

Capture Wind Energy with a Tethered Turbine

magenn floating wind power (photo)

The technology looks interesting. The ability to deploy the turbine high in the air without expensive towers seems like a huge advantage (of course it will have to work in the practice which I imagine will be the most challenging part). The wind is much more consistent and stronger further off the ground. Many attempts at new energy solutions will help find the best solutions. for emergency use, fast deployment seems like another winning feature.

While this seems a bit unconventional I think some of the ideas that seem crazy are going to be important sources of energy in the future. It will be interesting to see if it can catch on. Some interesting details from Mangenn’s web site:

Magenn Power is currently in the prototype phase of our Magenn Air Rotor System (MARS). Magenn Power plans to ship our first official product, a 10 kW version in 2008. A 4 kW version may also be available in 2008.
Magenn assumes a depreciable life span of at least 15 years before major refits are required.
The Magenn Air Rotor System is a closed inflatable structural design with inherent integrity, stability, and low cost. Furthermore, MARS is a buoyant system that only requires a low cost tensioning cable to secure it and transfer energy to the ground.
MARS units will be deployed for disaster relief, to third world communities with limited or no infrastructure, for various military applications, to remote locations, and in harsh climates.
The MARS 10 kW unit will be approximately 25′ x 65′ when inflated, it will come standard with a 400 foot tether; this configuration will have a shipping weight under 500 lbs.
Magenn Air Rotors can be raised to higher altitudes, thus capitalizing on higher winds aloft. Altitudes from 400-ft to 1,000-ft above ground level are possible, without having to build an expensive tower, or use a crane to perform maintenance.
Final pricing is yet to be determined on the 10kW MARS unit: target list price will be between $3 dollars to $5 dollars per watt. (Please Note: This price is subject to change).
MARS will be deployed up to 1,000-ft altitude at this time. The benefits of higher altitudes are being investigated. Future MARS units may be deployed at altitudes far beyond 1,000-ft.

Robot Water Striders

Scientists crack how insect bounces on water:

Walking on water may seem like a miracle to humans. But it is a humdrum achievement for the little water strider, which is able to bounce up and down on water too. Scientists have already solved the mystery of how their six slender, stilt-like legs evenly distribute their scant body weight over a relatively large area so that the “skin” formed by the surface tension of the water supports them, so four millimetre across dimples form under each foot as they skim about.

But scientists remained puzzled by how they could jump up and down upon the surface of water. Now a team in South Korea is about to report that it has at last explained the water strider’s baffling ability to leap onto water without sinking, in a forthcoming issue of the journal Langmuir, an achievement that could help further develop robots that can move about on lakes and reservoirs to monitor water quality, spy or explore.

Scientists Cure Mice Of Sickle Cell Using Stem Cell Technique

Using a recently developed technique for turning skin cells into stem cells, scientists have cured mice of sickle cell anemia — the first direct proof that the easily obtained cells can reverse an inherited, potentially fatal disease.
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researchers also cautioned that aspects of the new approach will have to be changed before it can be tried in human patients. Most important, the technique depends on the use of gene-altered viruses that have the potential to trigger tumor growth. “The big issue is how to replace these viruses,” said Rudolf Jaenisch of the Whitehead Institute for Biomedical Research in Cambridge, Mass., who led the new work with co-worker Jacob Hanna and Tim M. Townes of the University of Alabama Schools of Medicine and Dentistry in Birmingham.
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The researchers converted those skin cells into iPS cells by infecting them with viruses engineered to change the cells’ gene activity so they would resemble embryonic cells. Using DNA splicing techniques in those cells, the researchers then snipped out the small mutated stretches of DNA that cause sickle cell disease and filled those gaps with bits of DNA bearing the proper genetic code.

Next, the researchers treated the corrected iPS cells with another kind of virus — this time one designed to induce a genetic change that encouraged the cells to mature into bone marrow cells.

Finally, each mouse that gave up a few skin cells at the beginning of the experiment was given an infusion with the corrected marrow cells created from its own skin cells. Those cells set up permanent residence in the animals’ bones and began producing blood cells — the major function of marrow cells — and releasing them by the millions into the circulatory system.

But now the blood cells being produced were free of the sickle cell mutation.

Antibacterial Chemical Disrupts Hormone Activities

Antibacterial Chemical Disrupts Hormone Activities:

A new UC Davis study shows that a common antibacterial chemical added to bath soaps can alter hormonal activity in rats and in human cells in the laboratory — and does so by a previously unreported mechanism.

The findings come as an increasing number of studies — of both lab animals and humans — are revealing that some synthetic chemicals in household products can cause health problems by interfering with normal hormone action. Called endocrine disruptors, or endocrine disrupting substances (EDS), such chemicals have been linked in animal studies to a variety of problems, including cancer, reproductive failure and developmental anomalies.

The researchers found two key effects: In human cells in the laboratory, triclocarban increased gene expression that is normally regulated by testosterone. And when male rats were fed triclocarban, testosterone-dependent organs such as the prostate gland grew abnormally large. Also, the authors said their discovery that triclocarban increased hormone effects was new. All previous studies of endocrine disruptors had found that they generally act by blocking or decreasing hormone effects.

In their disclosure statement, the authors report that six of them have taken steps to patent their findings through the University of California.

Research paper Triclocarban enhances testosterone action: A new type of endocrine disruptor?.