Archive for the ‘Bio-Engineering’ Category

Mystery solved: How bleach kills germs

Saturday, November 15th, 2008

Molecular, Cellular, and Developmental Biology Associate Professor Ursula Jakob Reuters – Molecular, Cellular, and Developmental Biology Associate Professor Ursula Jakob (L) and Jeannette Winter, …

CHICAGO (Reuters) – Bleach has been killing germs for more than 200 years but U.S. scientists have just figured out how the cleaner does its dirty work.

It seems that hypochlorous acid, the active ingredient in bleach, attacks proteins in bacteria, causing them to clump up much like an egg that has been boiled, a team at the University of Michigan reported in the journal Cell on Thursday.

The discovery, which may better explain how humans fight off infections, came quite by accident.

“As so often happens in science, we did not set out to address this question,” Ursula Jakob, who led the team, said in a statement.

The researchers had been studying a bacterial protein called heat shock protein 33, which is a kind of molecular chaperon that becomes active when cells are in distress, for example from the high temperature of a fever.

In this case, the source of the distress was hypochlorous acid or hypochlorite.

Jakob’s team figured out that bleach and high temperatures have very similar effects on proteins.

When they exposed the bacteria to bleach, the heat shock protein became active in an attempt to protect other proteins in the bacteria from losing their chemical structure, forming clumps that would eventually die off.

“Many of the proteins that hypochlorite attacks are essential for bacterial growth, so inactivating those proteins likely kills the bacteria,” Marianne Ilbert, a postdoctoral fellow in Jakob’s lab, said in a statement.

The researchers said the human immune system produces hypochlorous acid in response to infection but the substance does not kill only the bacterial invaders. It kills human cells too, which may explain how tissue is destroyed in chronic inflammation.

Hypochlorous acid is an important part of host defense,” Jakob said. “It’s not just something we use on our countertops.”

Fish Tale Has A DNA Hook - Students Find Bad Labels

Friday, August 22nd, 2008

From the New York Times - August 22, 2008

Many New York sushi restaurants and seafood markets are playing a game of bait and switch, say two high school students turned high-tech sleuths.

In a tale of teenagers, sushi and science, Kate Stoeckle and Louisa Strauss, who graduated this year from the Trinity School in Manhattan, took on a freelance science project in which they checked 60 samples of seafood using a simplified genetic fingerprinting technique to see whether the fish New Yorkers buy is what they think they are getting.

They found that one-fourth of the fish samples with identifiable DNA were mislabeled. A piece of sushi sold as the luxury treat white tuna turned out to be Mozambique tilapia, a much cheaper fish that is often raised by farming. Roe supposedly from flying fish was actually from smelt. Seven of nine samples that were called red snapper were mislabeled, and they turned out to be anything from Atlantic cod to Acadian redfish, an endangered species.

What may be most impressive about the experiment is the ease with which the students accomplished it. Although the testing technique is at the forefront of research, the fact that anyone can take advantage of it by sending samples off to a laboratory meant the kind of investigative tools once restricted to Ph.D.’s and crime labs can move into the hands of curious diners and amateur scientists everywhere.

The project began, appropriately, over dinner about a year ago. Ms. Stoeckle’s father, Mark, is a scientist and early proponent of the use of DNA bar coding, a technique that greatly simplifies the process of identifying species. Instead of sequencing the entire genome, bar coders — who have been developing their field only since 2003 — examine a single gene. Dr. Stoeckle’s specialty is birds, and he admits that he tends to talk shop at the dinner table.

One evening at a sushi restaurant, Ms. Stoeckle recalled asking her father, “Could you bar code sushi?”

Dr. Stoeckle replied, “Yeah, I think you could — and if you did that, I think you’d be the first ones.”

Ms. Stoeckle, who is now 19, was intrigued. She enlisted Ms. Strauss, who is now 18.

Their field technique was simple, Ms. Stoeckle said. “We ate a lot of sushi.”

Or, as Dr. Stoeckle put it, “It involved shopping and eating, in which they were already fluent.”

They hit 4 restaurants and 10 grocery stores in Manhattan. Once the samples were home, whether in doggie bags or shopping bags, they cut away a small piece and preserved it in alcohol. They sent those off to the University of Guelph in Ontario, where the Barcode of Life Database project began. A graduate student there, Eugene Wong, works on the Fish Barcode of Life (dubbed, inevitably, Fish-BOL) and agreed to do the genetic analysis. He compared the teenagers’ samples with the global library of 30,562 bar codes representing nearly 5,500 fish species. (Commercial labs will also perform the analysis for a fee.)

Three hundred dollars’ worth of meals later, the young researchers had their data back from Guelph: 2 of the 4 restaurants and 6 of the 10 grocery stores had sold mislabeled fish.

Dr. Stoeckle said he was excited to see a technology used in a new way. “The smaller and cheaper you make something,” he said, “the more uses it has.” He compared bar coding to another high-tech wonder turned everyday gadget, GPS.

Eventually, he predicted, the process will become more automatic, cheaper and smaller so that a handheld device could perform a quick analysis and connect to the database remotely. What his daughter did, he said, is like dropping film off at the supermarket for developing. The next generation could be more like a digital camera that displays the results on the spot.

The results of Ms. Strauss and Ms. Stoeckle’s research are being published in Pacific Fishing magazine, a publication for commercial fishermen. The sample size is too small to serve as an indictment of all New York fishmongers and restaurateurs, but the results are unlikely to be a mere statistical fluke.

The experiment does serve as a general caveat emptor for fish lovers, particularly because the students, their parents and their academic mentor all declined to give the names of the vendors, citing fear of lawsuits. Besides, they noted, mislabeling could occur at any stage of the process.

Dr. Stoeckle was willing to divulge the name of one fish market whose products were accurately labeled in the test: Leonards’ Seafood and Prime Meats on Third Avenue. John Leonard, the owner, said he was not surprised to find that his products passed the bar code test. “We go down and pick the fish out ourselves,” he said. “We know what we’re doing.” As for the technology, Mr. Leonard said, “it’s good for the public,” since “it would probably keep restaurateurs and owners of markets more on their toes.”

Ms. Stoeckle said the underlying message of the research was simple: “If you’re paying for white tuna and you’re eating tilapia, I think you’d want to know that.”

Although the students did not present the project for a grade at school, they made sure to mention it on their college applications. Both will enroll at Johns Hopkins University this fall.

Neither, however, expects to major in the sciences. “I’ve always been into art history,” Ms. Strauss said, “which is really different from this.” Ms. Stoeckle, who is the granddaughter of the entertainer and arts patron Kitty Carlisle Hart, is thinking about studying writing or psychology. But that, they said, is the point. “If we found it interesting — which we did — I think lots of people like us can do it, too,” Ms. Stoeckle said.

Peter B. Marko, a professor at Clemson University who used a more detailed genetic technique in a 2004 paper to show that red snapper was commonly mislabeled, called their project “quite remarkable,” though he added that genetic analysis had been simplified to the point that high school students could now perform the task without sending samples off.

Mr. Marko prefers to work with whole genomes — “more information is better,” he explained — which can be sequenced now with lightning speed. He plans to perform a broad genetic comparison of fishes that were separated millions of years ago by the rise of the Isthmus of Panama. “The technology is allowing us to ask questions that really would not have been possible in the past.”

The students worked under the tutelage of Jesse H. Ausubel of Rockefeller University, a champion of the DNA bar coding technique. As for Ms. Strauss and Ms. Stoeckle, Dr. Ausubel said they “have contributed to global science” by adding to the database, built on a model similar to that of Wikipedia, in which people around the world can contribute.

In a way, Dr. Ausubel said, their experiment is a return to an earlier era of scientific inquiry. “Three hundred years ago, science was less professionalized,” he said, and contributions were made by interested amateurs. “Perhaps the wheel is turning again where more people can participate

 

Shark-Inspired Boat Surface

Sunday, August 10th, 2008

Materials Engineers Turn to Ferocious Fish for Nonstick Ship Coating

May 1, 2005 — Researchers are using shark skin as a model for creating new coatings that prevent adhesion of algae and barnacles to boats. The new coating is modeled after sharks’ placoid scales, which have a rectangular base embedded in the skin with tiny spines or bristles that poke up from the surface that prevent things from attaching to the shark’s skin.

GAINESVILLE, Fla.–In the boating industry, a huge problem exists that can be summed up in three words — algae, barnacles and slime. Until now, the only way to prevent these organisms from growing was toxic paint. But researchers are studying a more natural approach that’s inspired by the ocean’s fiercest predator.

In movies, they’re the enemy, but in the world of science, sharks are allies.

Materials engineer Tony Brennan, of University of Florida in Gainesville, uses shark skin as a model for creating new surfaces. “The shark scales have a roughness that approximates the roughness that we had predicted would be a good roughness to stop adhesion,” he says.

Brennan designed the surfaces to prevent algae and barnacles from growing on boats. He says, “We started making surfaces that are mimicking the shark’s skin.”

A computer program helped researchers create the pattern and structure…

“Whatever we can draw, we can make into a surface,” says UF graduate student, Jim Schumacher.

And just like shark skin, spores can’t fit in the ridges and don’t want to balance on top of the surface Brennan and his team designed in the lab. “That’s a tremendous benefit to energy consumption, dollars and maintenance,” Brennan says.

Getting rid of those barnacles and other organisms would mean less cleaning and not having to drag around the extra weight would lower fuel costs.

“If it’s effective, it would tremendously affect the industry,” Emerson says.

When the surface hits the market in the next year, it could impact private boaters and Navy vessels, too. Researchers are also studying the shark-coated surface for medical applications.

Exploring Energy Conservation Through Shark Research

Sunday, August 10th, 2008

Web address:
     http://www.sciencedaily.com/releases/2007/11/
     071130155548.htm 

Dr. Amy Lang and a graduate student work in UA’s water tunnel lab researching skin friction over solid surfaces. (Credit: University of Alabama Photography)ScienceDaily (Dec. 1, 2007) — The stars of the “Jaws” films–sharks–have recently become the subject of a University of Alabama engineering research project. Conducted by Dr. Amy Lang, assistant professor of aerospace engineering and mechanics, the project explores energy conservation and boundary layer control in regard to a shark’s surface.

The project findings will allow researchers to explore natural solutions for the reduction of skin friction over solid surfaces, which could result in new innovations and applications concerning energy conservation. This research will not only provide a greater understanding of the evolutionary development of sharks, but it will also investigate methods of flow control and drag reduction that can be easily applied to mobile vehicles.

Research has shown the issue of reducing drag over solid surfaces can save thousands of dollars. For example, it is estimated that even a 1 percent reduction in drag can save an airline company up to $200,000 and at least 25,000 gallons of fuel per year per aircraft. The resulting reduction in emissions into the air is equally impressive.

Funded through a National Science Foundation Small Grant, the project is investigating the boundary layer flow over a surface that mimics the skin of a fast-swimming shark. The boundary layer is the area closest to the surface where viscous conditions cause drag–in this instance a shark’s skin.

Lang hopes to explain why fast sharks that swim upwards of 60 mph have smaller denticles, or scales, than slower shark species. Evidence suggests that sharks with smaller denticles have the ability to stick out their scales when they swim, allowing them to swim faster and creating a unique surface pattern on the skin that results in various mechanisms of boundary layer control.

“We hope to explain how a shark’s skin controls the boundary layer to decrease drag and swim faster,” said Lang. “If we can successfully show there is a significant effect, future applications to reduce drag of aircraft and underwater vehicles could be possible.”

Lang’s research is being conducted using a water tunnel facility in Hardaway Hall. The water tunnel lab can increase the shark skin geometry by 100 times with a corresponding decrease in flow over the model. This makes the flow over the skin observable, and it allows for the visualization and measurement of flow using modern experimental techniques.

In addition to the National Science Foundation Small Grant, Lang recently received a Lindbergh Grant for this research project. Lindbergh Grants are made in amounts up to $10,580, a symbolic amount representing the cost of building Charles Lindbergh’s plane, the Spirit of St. Louis.
University of Alabama (2007, December 1). Exploring Energy Conservation Through Shark Research. ScienceDaily. Retrieved August 10, 2008, from http://www.sciencedaily.com­ /releases/2007/11/071130155548.htm

“Dinosaur eel” points to body armour of the future

Monday, July 28th, 2008

So say Pentagon-backed scientists who have pored over the scales of Polypterus senegalus, also called the Senegal bichir or the dinosaur eel.

Long and skinny and of ancient heritage, the 40-centimetre (16-inch) predator has multiple layers of scales that first dissipate the energy of a strike, then protect against any penetration to the soft tissues below and finally limit any damage to the shield to the immediate area surrounding the assault.

Experts at the Massachusetts Institute of Technology (MIT) used nano-scale measurements to look at several scales that were harmlessly removed from a living fish.

They found the scales — about 500 millionths of a metre thick — have four layers. The tiny shield was then put to the test, in a simulation of a biting attack.

The team believe the scales’ protection is remarkably effective because of the different composite materials, the geometry and thickness of each of these layers.

The overlapping junctions between the layers themselves also play an important role.

The design is “fascinating, complex and multiscale,” say the scientists.

“Such fundamental knowledge holds great potential for the development of improved biologically-inspired structural materials,” said Christine Ortiz, an MIT associate professor in materials science and engineering.

“Many of the design principles we describe — durable interfaces and energy-dissipating mechanisms, for instance — may be translatable to human armour systems.”

The study appears on Sunday in a specialist journal, Nature Materials.