Tag Archives: cool

Microbes Beneath the Sea Floor

This stuff is cool. Here is the full press release from Penn State, Microbes beneath sea floor genetically distinct

Tiny microbes beneath the sea floor, distinct from life on the Earth’s surface, may account for one-tenth of the Earth’s living biomass, according to an interdisciplinary team of researchers, but many of these minute creatures are living on a geologic timescale.

“Our first study, back in 2006, made some estimates that the cells could double every 100 to 2,000 years,” says Jennifer F. Biddle, PhD. recipient in biochemistry and former postdoctoral fellow in geosciences, Penn State. Biddle is now a postdoctoral associate at the University of North Carolina, Chapel Hill.

The researchers looked at sediment samples from a variety of depths taken off the coast of Peru at Ocean Drilling Site 1229. They report their findings in today’s (July 22) online issue of the Proceedings of the National Academy of Sciences.

“The Peruvian Margin is one of the most active surface waters in the world and lots of organic matter is continuously being deposited there,” says Christopher H. House, associate professor of geoscience. “We are interested in how the microbial world differs in the subsea floor from that in the surface waters.”

The researchers used a metagenomic approach to determine the types of microbes residing in the sediment 3 feet, 53 feet, 105 feet and 164 feet beneath the ocean floor. The use of the metagenomics, where bulk samples of sediment are sequences without separation, allows recognition of unknown organism and determination of the composition of the ecosystem.

“The results show that this subsurface environment is the most unique environment yet studied metagenomic approach known today,” says House. “The world does look very different below the sediment surface.” He notes that a small number of buried genetic fragments exist from the water above, but that a large portion of the microbes found are distinct and adapted to their dark and quiet world.

The researchers, who included Biddle; House; Stephan C. Schuster, associate professor; and Jean E. Brenchley, professor, biochemistry and molecular biology, Penn State; and Sorel Fitz-Gibbon, assistant research molecular biologist at the Center for Astrobiology, UCLA, found that a large percentage of the microbes were Archaea, single-celled organisms that look like Bacteria but are different on the metabolic and genetic levels. The percentage of Archaea increases with depth so that at 164 feet below the sea floor, perhaps 90 percent of the microbes are Archaea. The total number of organisms decreases with depth, but there are lots of cells, perhaps as many as 1,600 million cells in each cubic inch.
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Magnetic Movie

Magnetic Movie from Semiconductor on Vimeo

Magnetic Movie was shot in NASA’s Space Sciences Laboratories at UC Berkeley for Chanel 4 in association with the Arts Council of England.

In Magnetic Movie, Semiconductor have taken the magnificent scientific visualisations of the sun and solar winds conducted at the Space Sciences Laboratory and Semiconducted them. Ruth Jarman and Joe Gerhardt of Semiconductor were artists-in-residence at SSL. Combining their in-house lab culture experience with formidable artistic instincts in sound, animation and programming, they have created a magnetic magnum opus in nuce, a tour de force of a massive invisible force brought down to human scale, and a “very most beautiful thing.”

Magnetic Movie is the aquavit, something not precisely scientific but grants us an uncanny experience of geophysical and cosmological forces.

Cool video: I must admit I am confused at how extensive the artistic license taken with the animation is.

Measuring Protein Bond Strength with Optical Tweezers

Using a light touch to measure protein bonds

MIT researchers have developed a novel technique to measure the strength of the bonds between two protein molecules important in cell machinery: Gently tugging them apart with light beams. “It’s really giving us a molecular-level picture of what’s going on,” said Matthew Lang, an assistant professor of biological and mechanical engineering
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The researchers studied the interactions between the proteins by pinning one actin filament to a surface and controlling the motion of the second one with a beam of light. As the researchers tug on a bead attached to the second filament, the bond mediated by the actin-binding protein eventually breaks.

With this technique, the researchers can get a precise measurement of the force holding the proteins together, which is on the order of piconewtons (10^-12 newtons).

Cell Signals Webcast

Very cool animation, by Cold Spring Harbor Laboratory and Interactive Knowledge, of the working of the inner workings of our bodies as they react to a cut. If you want to get right to the science, skip the first minute. Providing these types of educational animations is a great way for educational institutions to take advantage of technology to achieve their mission in ways not possible before.

It is annoying how many of those “educational” institutions don’t provide such educational material online (and even take material offline that was online). Have they become more focused on thinking and operating the way they did in 1970 than promoting science education? It is a shame some “educational” institutions have instead become focused on looking backward. I will try to promote those organizations that are providing online science education.

Transferring Train Passengers Without Stopping

The webcast shows a train transferring passengers without stopping. Essentially passenger modules are picked up and dropped off at each station. Looks pretty cool and would seem to require somewhat complex engineering – which can be a problem as complexity allows for more things to go wrong. Still it looks pretty cool. The sound is not in English but you can see what the idea is.

Inventor rolls out efficient non-stop train system

Taking the Kaohsiung MRT system as an example, Peng says that its maximum speed is 85 kph. Because it must stop at every station, it achieves an average speed over its route of just 35 kph. If the non-stop system were in place, the top velocity of 85 kph could be maintained throughout the system, saving time and energy.

via: trains that pick you up without stopping

Fold.it – the Protein Folding Game

Foldit is a revolutionary new computer game enabling you to contribute to important scientific research. This is another awesome combination of technology, distributed problem solving, science education…

Essentially the game works by allowing the person to make some decisions then the computer runs through some processes to determine the result of those decisions. It seems the human insight of what might work provides an advantage to computers trying to calculate solutions on their own. Then the results are compared to the other individuals working on the same protein folding problem and the efforts are ranked.

This level of interaction is very cool. SETI@home, Rosetta@home and the like are useful tools to tap the computing resources of millions on the internet. But the use of human expertise really makes fold.it special. And you can’t help but learn by playing. In addition, if you are successful you can gain some scientific credit for your participation in new discoveries.

The site includes some excellent educational material on proteins and related material. What is a protein:

Proteins are the workhorses in every cell of every living thing. Your body is made up of trillions of cells, of all different kinds: muscle cells, brain cells, blood cells, and more. Inside those cells, proteins are allowing your body to do what it does: break down food to power your muscles, send signals through your brain that control the body, and transport nutrients through your blood. Proteins come in thousands of different varieties, but they all have a lot in common. For instance, they’re made of the same stuff: every protein consists of a long chain of joined-together amino acids.
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structure specifies the function of the protein. For example, a protein that breaks down glucose so the cell can use the energy stored in the sugar will have a shape that recognizes the glucose and binds to it (like a lock and key) and chemically reactive amino acids that will react with the glucose and break it down to release the energy.
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Proteins are involved in almost all of the processes going on inside your body: they break down food to power your muscles, send signals through your brain that control the body, and transport nutrients through your blood. Many proteins act as enzymes, meaning they catalyze (speed up) chemical reactions that wouldn’t take place otherwise. But other proteins power muscle contractions, or act as chemical messages inside the body, or hundreds of other things.

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Video Cat Cam

I first wrote about the Cool Cat Cam about a year ago. Next, I interviewed the cat cam engineer. And
a few months ago I posted some photos by Fritz the Cat. Now enjoy some video catcat webcasts: Fritz in Aktion mit Catcam mit Musik – Catcam Smaka takes photos/Video! – Cat wears spy camera, makes film – Mr. Lee CatCam im MDR Aussenseiter-Spitzenreiter And then order your cat cam.

Bacteria Evolutionary Shift Seen in the Lab

Bacteria make major evolutionary shift in the lab

A major evolutionary innovation has unfurled right in front of researchers’ eyes. It’s the first time evolution has been caught in the act of making such a rare and complex new trait. And because the species in question is a bacterium, scientists have been able to replay history to show how this evolutionary novelty grew from the accumulation of unpredictable, chance events.
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sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use. Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species.
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The replays showed that even when he looked at trillions of cells, only the original population re-evolved Cit+ – and only when he started the replay from generation 20,000 or greater. Something, he concluded, must have happened around generation 20,000 that laid the groundwork for Cit+ to later evolve.

Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.

Printing Buildings

Projections indicate costs will be around one fifth as much as conventional construction. Using this process, a single house or a colony of houses, each with possibly a different design, may be automatically constructed in a single run, embedded in each house all the conduits for electrical, plumbing and air-conditioning.
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The machine will cost between $500K to $700K for average size (2000 sq ft — 200 m2) detached houses. This is not much given that a concrete pump truck is now $300k-$400K. Note that with one machine numerous homes can be built. The first commercial machines to be available this year, 2008. The machine will be collapsible to form into an easy truck load. The unloading and setup will take between 1-2 hours.

Behrokh Khoshnevis is the visionary who has been driving this concept. He is the Director of the Center for Rapid Automated Fabrication Technologies (CRAFT) and Director of Manufacturing Engineering Graduate Program at USC.

Very cool stuff. Related: Open Source 3-D Printing – A plane You Can Print – $35 million to the USC School of Engineering – Contractor Warned NYC About Crane – Sandwich Brick, Reusing Waste Material

Life Far Beneath the Ocean

Huge hidden biomass lives deep beneath the oceans

Recently, he and his colleagues examined samples of a mud core extracted from between 860 metres and 1626 metres beneath the sea floor off the coast of Newfoundland. They found simple organisms known as prokaryotes in every sample. Prokaryotes are organisms that often have just one cell. Their peculiarity is that, unlike any other form of life, their DNA is not neatly packed into a nucleus.
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Where cells living so far beneath the sea floor could have come from remains a mystery. They may have been gradually buried in sediment as millions of years passed by, and adapted to the increasing temperatures and pressure, he says.

Another possibility is that they were sucked deep into the mud from the sea water above. Hydrothermal vents pulse hot water out of the seabed and into the ocean. This creates a vacuum in the sediment, which draws fresh sea water into the marine aquifer.

It is important to understand the way the cells got down there, because that has implications for their age. The cells are not very active and according to Parkes they have very few predators. “We find very few viruses, for example, down there,” he says. “At the surface, if you don’t divide you get eaten. But if there are no predators, the pressure to reproduce decreases and you can spend more energy on repairing your damaged molecules.”
Ancient life

This means it is conceivable – but unproven – that some of the cells are as old as the sediment. At 1.6 km beneath the sea, that’s 111 million years old. But in an underworld where cells divide excruciatingly slowly, if at all, age tends to lose its relevance, says Parkes.

More very cool stuff, this stuff is fun.