Category Archives: Research

Genes Counter a Bacterial Attack

Gene against bacterial attack unravelled

Humans have an innate defence system against deadly bacteria. However, how the step from gene to anti-bacterial effect occurs in the body is not yet known. To date, B. Pseudomallei, a bacterium suitable for bioweapons, had managed to elude medics. It can remain hidden in the human body for many years without being detected by the immune system. The bacteria can suddenly become activated and spread throughout the body, resulting in the patient dying from blood poisoning. AMC physician Joost Wiersinga and the Laboratory for Experimental Internal Medicine discovered which gene-protein combination renders the lethal bacteria B. pseudomallei harmless.

Wiersinga focussed on the so-called Toll-like receptors. These are the proteins that initiate the fight against pathogens. There are currently ten known Toll-like receptors which are located on the outside of immune cells, our body’s defence system. The toll-like receptors jointly function as a 10-figure alarm code. Upon coming into contact with the immune cell each bacterium enters its own Toll code. For known pathogens this sets off an alarm in the immune system and the defence mechanism is activated. Yet B. pseudomallei fools the system by entering the code of a harmless bacterium. As a result the body’s defence system remains on standby.

Yet some people are resistant: they become infected but not ill. Wiersinga found a genetic cause for this resistance. He discovered which toll receptor can fend off B. pseudomallei. He did this by rearing mice DNA in which the gene for Toll2 production was switched on and off. ‘The group where the gene for Toll2 was switched off, survived the bacterial infection’, says Wiersinga. ‘The other receptor that we investigated, Toll4, had no effect – even though for the past ten years medics had regarded this as the most important receptor.’ The ultimate aim of this study is to develop a vaccine.

PLoS paper: MyD88 Dependent Signaling Contributes to Protective Host Defense against Burkholderia pseudomallei

Magnetic Portals Connect Sun and Earth

Magnetic Portals Connect Sun and Earth by Dr. Tony Phillips

During the time it takes you to read this article, something will happen high overhead that until recently many scientists didn’t believe in. A magnetic portal will open, linking Earth to the sun 93 million miles away. Tons of high-energy particles may flow through the opening before it closes again, around the time you reach the end of the page.

“It’s called a flux transfer event or ‘FTE,'” says space physicist David Sibeck of the Goddard Space Flight Center. “Ten years ago I was pretty sure they didn’t exist, but now the evidence is incontrovertible.”
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Researchers have long known that the Earth and sun must be connected. Earth’s magnetosphere (the magnetic bubble that surrounds our planet) is filled with particles from the sun that arrive via the solar wind and penetrate the planet’s magnetic defenses. They enter by following magnetic field lines that can be traced from terra firma all the way back to the sun’s atmosphere.

“We used to think the connection was permanent and that solar wind could trickle into the near-Earth environment anytime the wind was active,” says Sibeck. “We were wrong. The connections are not steady at all. They are often brief, bursty and very dynamic.”
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On the dayside of Earth (the side closest to the sun), Earth’s magnetic field presses against the sun’s magnetic field. Approximately every eight minutes, the two fields briefly merge or “reconnect,” forming a portal through which particles can flow. The portal takes the form of a magnetic cylinder about as wide as Earth.

See more posts on scientific inquiry and scientists advancing our understanding of how things work.

Toward a More Open Scientific Culture

Michael Nielsen wrote a great post, The Future of Science, which is also the topic of a book he is writing. He discusses how scientific advancement has often been delayed as those making discoveries did not share them openly. And how 300 years ago scientific journals and reward systems created ways for scientists to be rewarded for publication. And he continues with the need for the process to again change and promote more open sharing of scientific knowledge, which I agree with and have written about previously: Publishers Continue to Fight Open Access to Science, Science Journal Publishers Stay Stupid, The Future of Scholarly Publication, etc..

Why were Hooke, Newton, and their contemporaries so secretive? In fact, up until this time discoveries were routinely kept secret.
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This cultural transition was just beginning in the time of Hooke and Newton, but a little over a century later the great physicist Michael Faraday could advise a younger colleague to “Work. Finish. Publish.” The culture of science had changed so that a discovery not published in a scientific journal was not truly complete. Today, when a scientist applies for a job, the most important part of the application is their published scientific papers.

This has been a great advance. Now we need to continue that advance to use the internet to make that publication open and increase the advantage of shared knowledge to society.

The adoption of the journal system was achieved by subsidizing scientists who published their discoveries in journals. This same subsidy now inhibits the adoption of more effective technologies, because it continues to incentivize scientists to share their work in conventional journals, and not in more modern media.
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This means: making many more types of content available than just scientific papers; allowing creative reuse and modification of existing work through more open licensing and community norms; making all information not just human readable but also machine readable; providing open APIs to enable the building of additional services on top of the scientific literature, and possibly even multiple layers of increasingly powerful services. Such extreme openness is the ultimate expression of the idea that others may build upon and extend the work of individual scientists in ways they themselves would never have conceived.
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To create an open scientific culture that embraces new online tools, two challenging tasks must be achieved: (1) build superb online tools; and (2) cause the cultural changes necessary for those tools to be accepted.

I agree we need to take advantage of the new possibilities to advance the practice of science. His full post is well worth reading.

Extra-Universal Matter

Unknown “Structures” Tugging at Universe, Study Says

The presence of the extra-universal matter suggests that our universe is part of something bigger – a multiverse – and that whatever is out there is very different from the universe we know, according to study leader Alexander Kashlinsky, an astrophysicist at NASA’s Goddard Space Flight Center in Maryland.

The theory could rewrite the laws of physics. Current models say the known, or visible, universe – which extends as far as light could have traveled since the big bang – is essentially the same as the rest of space-time (the three dimensions of space plus time).
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Not everyone is ready to rewrite physics just yet. Astrophysicist Hume Feldman of the University of Kansas has detected a similar, but weaker, flow. He said the Kashlinsky team’s study is “very interesting, very intriguing, [but] a lot more work needs to be done.

“It’s suggestive that something’s going on, but what exactly is going on? It basically tells us to investigate,” he said. David Spergel, an astrophysicist at Princeton University, echoed the sentiment. “Until these results are reanalyzed by another group, I have strong doubts about the validity of the conclusions of this paper,” he wrote in an email.

Very interesting stuff and another example of the scientific process of discovery.

Bacteria and Efficient Food Digestion

Gut Bacteria May Cause And Fight Disease, Obesity

“We’re all sterile until we’re born,” says Glenn Gibson, a microbiologist at the University of Reading in Britain. “We haven’t got anything in us right up until the time we come into this big, bad, dirty world.”

But as soon as we pass out of the birth canal, when we are fetched by a doctor’s hands, placed in a hospital crib, put on our mother’s breast, when we drag a thumb across a blanket and stick that thumb in our mouths, when we swallow our first soft food, we are invaded by all sorts of bacteria. Once inside, they multiply – until the bacteria inside us outnumber our human cells.
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University of Chicago immunologist Alexander Chervonsky, with collaborators from Yale University, recently reported that doses of the right stomach bacteria can stop the development of type 1 diabetes in lab mice. “By changing who is living in our guts, we can prevent type 1 diabetes,” he told The Wall Street Journal.

The bottom line: We now have two sets of genes to think about – the ones we got from our parents and the ones of organisms living inside us. Our parents’ genes we can’t change, but the other set? Now that is one of the newest and most exciting fields in cell biology.

Follow link with related podcast: Gut bacteria may cause and fight, disease, obesity. This whole area of the ecosystem within us and our health I find fascinating. And I fall for confirmation bias on things like becoming inefficient at converting food to energy as a way reduce obesity.

You could have two people sitting down to a bowl of cheerios, they could each eat the same number of cheerios but because of a difference in their gut bacteria one will get more calories than the other.

They then gave an example of the difference being 95 calories versus 99 calories. Hardly seems huge but it would add up. Still that is a less amazing difference than I was expecting.

Plants can Signal Microbial Friends for Help

When under attack, plants can signal microbial friends for help

Researchers at the University of Delaware have discovered that when the leaf of a plant is under attack by a pathogen, it can send out an S.O.S. to the roots for help, and the roots will respond by secreting an acid that brings beneficial bacteria to the rescue.
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In a series of laboratory experiments, the scientists infected the leaves of the small flowering plant Arabidopsis thaliana with a pathogenic bacterium, Pseudomonas syringae. Within a few days, the leaves of the infected plants began yellowing and showing other symptoms of disease.

However, the infected plants whose roots had been inoculated with the beneficial microbe Bacillus subtilis were perfectly healthy. Farmers often add B. subtilis to the soil to boost plant immunity. It forms a protective biofilm around plant roots and also has antimicrobial properties, according to Bais.

Using molecular biological tools, the scientists detected the transmission of a long-distance signal, a “call for help,” from the leaves to the roots in the plants that had Bacillus in the soil. The roots responded by secreting a carbon-rich chemical–malic acid.

All plants biosynthesize malic acid, Bais explains, but only under specific conditions and for a specific purpose–in this case, the chemical was actively secreted to attract Bacillus. Magnified images of the roots and leaves showed the ratcheted-up defense response provided by the beneficial microorganisms.
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“Plants can’t move from where they are, so the only way they can accrue good neighbors is through chemistry,” Bais notes.

Silk E.coli Sensors

“Edible Optics” Could Make Food Safer

Scientists at Tufts University’s School of Engineering have demonstrated for the first time that it is possible to design such “living” optical elements that could enable an entirely new class of sensors. These sensors would combine sophisticated nanoscale optics with biological readout functions, be biocompatible and biodegradable, and be manufactured and stored at room temperatures without use of toxic chemicals. The Tufts team used fibers from silkworms to develop the platform devices.
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The possibility of integrating optical readout and biological function in a single biocompatible device unconstrained by these limitations is tantalizing. Silk optics has captured the interest of the Defense Department, which has funded and been instrumental in enabling rapid progress on the topic. The Defense Advanced Research Projects Agency (DARPA) awarded Tufts a research contract in 2007 and is funding Tufts and others on groundbreaking projects that could someday result in biodegradable optical sensing communications technology.
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To form the devices, Tufts scientists boiled cocoons of the Bombyx mori silkworm in a water solution and extracted the glue-like sericin proteins. The purified silk protein solution was ultimately poured onto negative molds of ruled and holographic diffraction gratings with spacing as fine as 3600 grooves/mm.
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The Tufts team embedded three very different biological agents in the silk solution: a protein (hemoglobin), an enzyme (horseradish peroxidase) and an organic pH indicator (phenol red). In the hardened silk optical element, all three agents maintained their activity for long periods when simply stored on a shelf. “We have optical devices embedded with enzymes that are still active after almost a year of storage at room temperature.

Stanford Gets $75 Million for Stem Cell Center

Stanford gets $75 million for stem cell center

With today’s announcement, Lokey more than doubles his commitment. School officials say he is the lead contributor for a $200 million stem cell research building that will break ground Oct. 27 and be finished in the summer of 2010. In a statement released by the medical school, Lokey said stem cells would be “as significant as the silicon chip that created Silicon Valley,” producing treatments for disease and saving lives.

He said he was driven to fund research after President Bush, in August 2001, forbid the use of federal funds for stem cell research that involved the destruction of human embryos. “It’s very narrow-minded,” Lokey said of the position. “This is about lives being saved.”
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Some 350 scientists will work in the 200,000-square-foot Lorry I. Lokey Stem Cell Research Building, the school said. The center is also getting a $43.6 million grant from the California Institute for Regenerative Medicine. The institute, the state’s $3 billion stem cell funding unit, was created by a 2004 state initiative from research advocates opposed to Bush’s restrictions.

Holographic Television on the Way

Ok, there really isn’t much new since I posted that holographic TV is getting closer. But won’t it be cool when I can have one in my house? And you might need to plan for it in your new house addition 🙂 Also, with the economic news lately a good distraction might be useful – Holographic television to become reality

The reason for renewed optimism in three-dimensional technology is a breakthrough in rewritable and erasable holographic systems made earlier this year by researchers at the University of Arizona.

Dr Nasser Peyghambarian, chair of photonics and lasers at the university’s Optical Sciences department, told CNN that scientists have broken a barrier by making the first updatable three-dimensional displays with memory.

“This is a prerequisite for any type of moving holographic technology. The way it works presently is not suitable for 3-D images,” he said. The researchers produced displays that can be erased and rewritten in a matter of minutes.
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According to Peyghambarian, they could be constructed as a screen on the wall (like flat panel displays) that shows 3-D images, with all the image writing lasers behind the wall; or it could be like a horizontal panel on a table with holographic writing apparatus underneath.
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Peyghambarian is also optimistic that the technology could reach the market within five to ten years. He said progress towards a final product should be made much more quickly now that a rewriting method had been found.

However, it is fair to say not everyone is as positive about this prospect as Peyghambarian. Justin Lawrence, a lecturer in Electronic Engineering at Bangor University in Wales, told CNN that small steps are being made on technology like 3-D holograms, but, he can’t see it being ready for the market in the next ten years.

I would have to say I am with those that think this might take a bit longer to be in place. But I would be glad to be wrong.

MicroRNAs Emerged Early in Evolution

New Research Shows MicroRNAs Emerged Early in Evolution

“MicroRNAs have been available to regulate and shape gene expression as far back as we can go in animal evolution—they might even predate animals,” says Bartel, a leader in the discovery and functional study of microRNAs. “They might have helped to usher in the era of multi-cellular animal life.”

First discovered in 1993, microRNAs are strands of RNA that are 21-24 nucleotides in length. They dampen gene expression by intercepting messenger RNA before it can turn the cellular crank that translates a gene into a protein. Earlier, Bartel’s research team showed that each microRNA can regulate the expression of hundreds of genes.

The ability of microRNAs to silence gene expression likely evolved from a more ancient defense against viruses, bacteria, and other mobile genetic elements that can mutate host DNA.
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The scientists determined that the starlet sea anemone has both microRNAs and piRNAs. In addition, the anemone makes proteins resembling those that interact with these small RNAs in humans. Both types of small RNA were also found in the sponge. The third target of their search, Trichoplax, did not contain any microRNAs, though Bartel suspects they may have existed in ancestral forms and later disappeared.