Category Archives: Research

Nanotube-producing Bacteria Show Manufacturing Promise

Genus Shewanella

Nanotube-producing Bacteria Show Manufacturing Promise:

The photoactive arsenic-sulfide nanotubes produced by the bacteria behave as metals with electrical and photoconductive properties. The researchers report that these properties may also provide novel functionality for the next generation of semiconductors in nano- and opto-electronic devices.

In a process that is not yet fully understood, the Shewanella bacterium secretes polysacarides that seem to produce the template for the arsenic sulfide nanotubes, Myung explained. The practical significance of this technique would be much greater if a bacterial species were identified that could produce nanotubes of cadmium sulfide or other superior semiconductor materials, he added.

“This is just a first step that points the way to future investigation,” he said. “Each species of Shewanella might have individual implications for manufacturing properties.”

Related: Self-assembling Nanotechnology in Chip ManufacturingBacteria Engineered to Sprout Conducting NanowiresUsing Bacteria to Carry Nanoparticles Into CellsNanotechnology Breakthroughs for Computer ChipsNanotechnology Research

Study Shows Why the Flu Likes Winter

Study Shows Why the Flu Likes Winter:

The answer, they say, has to do with the virus itself. It is more stable and stays in the air longer when air is cold and dry, the exact conditions for much of the flu season.

“Influenza virus is more likely to be transmitted during winter on the way to the subway than in a warm room,” said Peter Palese, a flu researcher who is professor and chairman of the microbiology department at Mount Sinai School of Medicine in New York and the lead author of the flu study. Dr. Palese published details of his findings in the Oct. 19 issue of PLoS Pathogens.

Reading a paper published in 1919 in the Journal of the American Medical Association on the flu epidemic at Camp Cody in New Mexico, he came upon a key passage: “It is interesting to note that very soon after the epidemic of influenza reached this camp, our laboratory guinea pigs began to die.”

Dr. Palese bought some guinea pigs and exposed them to the flu virus. Just as the paper suggested, they got the flu and spread it among themselves. So Dr. Palese and his colleagues began their experiments. By varying air temperature and humidity in the guinea pigs’ quarters, they discovered that transmission was excellent at 41 degrees. It declined as the temperature rose until, by 86 degrees, the virus was not transmitted at all.

The virus was transmitted best at a low humidity, 20 percent, and not transmitted at all when the humidity reached 80 percent. The animals also released viruses nearly two days longer at 41 degrees than at a typical room temperature of 68 degrees.

Very interesting and you can read the actual paper since it is open access: Influenza Virus Transmission Is Dependent on Relative Humidity and Temperature.

Related: I Support the Public Library of ScienceNew and Old Ways to Make Flu VaccinesOpen Access and PLoSDrug-resistant Flu Virus

More on the Problems with Bisphenol-A

Milwaukee Journal-Sentinel: Bisphenol-A, that plasticizer, gets a media reaming

But few reports that The Tracker has seen match, in fury and conviction, the lambasting that a team of Milwaukee Journal Sentinel reporters, Susanne Rust, Meg Kissinger, and Cary Spivak, have given to these things, especially bisphenol-A, in the last two weeks. They say they reviewed 250 papers, interviewed more than 100 scientists, industry reps, and government regulators, read thousands of pages of additional documents. They give it a one-two punch, with that second one the roundhouse. They are going for a knockout.

The stories make The Tracker, a person with a tendency to say “on the other hand…”, a little nervous. There aren’t many maybes in here, not much calibration. The reporters appear fully convinced bisphenol-A is a menace. I’ve heard reports on the stuff too, and it does give one the jim jams. But one seldom sees, as here and without equivocation, declarations that a recent government review was flatly biased in its selection of which studies to give most weight, the gov’t used outdated methods, it looked mainly at chemical industry-funded studies, it ignored academic and presumably unbiased work.

The original articles: Are your products safe? You can’t tell. Labels often fail to list compounds that can disrupt biological development – WARNING: The chemical bisphenol A has been known to pose severe health risks to laboratory animals. AND THE CHEMICAL IS IN YOU.

In the first analysis of its kind by a newspaper, the Journal Sentinel reviewed 258 scientific studies of the chemical bisphenol A, a compound detected in the urine of 93% of Americans recently tested. An overwhelming majority of these studies show that the chemical is harmful – causing breast cancer, testicular cancer, diabetes, hyperactivity, obesity, low sperm counts, miscarriage and a host of other reproductive failures in laboratory animals.

Studies paid for by the chemical industry are much less likely to find damaging effects or disease. U.S. regulators so far have sided with industry by minimizing concern about the compound’s safety.

I believe in there are real risks that should be addressed. And I am not convinced the regulators are doing a good job, see my previous post in April, 2007 on Bisphenol A.

Related: Flushed Drugs Pollute WaterFDA May Make Decision That Will Speed Antibiotic Drug ResistanceThe A to Z Guide to Political Interference in ScienceResearcher Provides Undisclosed Data to FDAScientists Denounce Global Warming Report ‘Edits’

Fighting Tuberculosis

Signaling an End to TB by Kathleen M. Wong

Once routinely treated with cheap antibiotics, TB is poised to make a terrifying comeback. More and more, doctors in developing nations are finding patients infected with strains of TB invulnerable to all but a handful of extremely expensive, exotic drugs. Worldwide, TB already infects one in every three people and sickens one in ten. Without new methods to stop the spread of drug-resistant strains, the cost of treating this ancient human pathogen could bankrupt even the most prosperous economies.

TB could, in theory, develop resistance to this new class of drugs, too. But Alber thinks he can skew the odds to favor humans. Identifying a drug capable of knocking out several TB enzymes at once could make it next to impossible for the bacterium to evolve resistance on multiple fronts.

Though TB is a daunting foe, Alber remains confident about the prospects of beating the disease. “As a bacterium, it should be easier to treat than HIV or malaria. Those kinds of diseases-caused by viruses and protozoans-we generally don’t know how to cure,” Alber says. “From a scientific perspective, TB is a simpler problem.”

Good luck, it may be easier but it still isn’t easy. Related: Tuberculosis Risk‘Virtually untreatable’ TBExtensively Drug-resistant Tuberculosis (XDR TB)TB Pandemic Threat

Evidence of Short DNA Segment Self Assembly

Tiny DNA Molecules Show Liquid Crystal Phases, Pointing Up New Scenario For First Life On Earth, University of Colorado:

CU-Boulder physics Professor Noel Clark said the team found that surprisingly short segments of DNA, life’s molecular carrier of genetic information, could assemble into several distinct liquid crystal phases that “self-orient” parallel to one another and stack into columns when placed in a water solution. Life is widely believed to have emerged as segments of DNA- or RNA-like molecules in a prebiotic “soup” solution of ancient organic molecules.

Such DNA polynucleotides had previously been shown to organize into liquid crystal phases in which the chains spontaneously oriented parallel to each other, he said. Researchers understand the liquid crystal organization to be a result of DNA’s elongated molecular shape, making parallel alignment easier, much like spaghetti thrown in a box and shaken would be prone to line up in parallel, Clark said.

The CU-Boulder and University of Milan team began a series of experiments to see how short the DNA segments could be and still show liquid crystal ordering, said Clark. The team found that even a DNA segment as short as six bases, when paired with a complementary segment that together measured just two nanometers long and two nanometers in diameter, could still assemble itself into the liquid crystal phases, in spite of having almost no elongation in shape.

Structural analysis of the liquid crystal phases showed that they appeared because such short DNA duplex pairs were able to stick together “end-to-end,” forming rod-shaped aggregates that could then behave like much longer segments of DNA. The sticking was a result of small, oily patches found on the ends of the short DNA segments that help them adhere to each other in a reversible way — much like magnetic buttons — as they expelled water in between them, Clark said.

“In essence, the liquid crystal phase condensation selects the appropriate molecular components, and with the right chemistry would evolve larger molecules tuned to stabilize the liquid crystal phase. If this is correct, the linear polymer shape of DNA itself is a vestige of formation by liquid crystal order.”

Related: One Species’ Genome Discovered Inside Another’sGalactic Dust with the Ability to Reproduce?DNA Repair ArmyOld Viruses Resurrected Through DNA

Who Should Profit from Yellowstone’s Microbes

The Gold in Yellowstone’s Microbes

Year by year, Yellowstone’s hot waters are yielding remarkable new microbial specimens with implications for medicine, agriculture and energy, as well as offering clues to the formation of earliest life on Earth and maybe even on Mars. The potential financial windfalls are enormous, as evidenced by one big jackpot.

Yellowstone microbes (and those from a few other hot spots on the planet) may also hold great promise for bioremediation — cleaning up chemical pollution, oil slicks and smokestack emissions — as well as the means to accelerate biomass fermentation and develop drought-resistant crops. And there is more to be discovered: Probably less than one percent of Yellowstone’s microscopic life forms have been discovered and studied.

the National Park Service signed a secretive research-sharing agreement with Diversa Corporation in 1998. Non-profit groups quickly cried “bio-piracy!” when they found out and sued the Service over the arrangement. While a federal court dismissed the case, it ordered the Park Service to address the issue… But the Park Service is still trying to come up with an acceptable, benefits-sharing agreement that might allow bio-prospecting of microbes and disclosure of findings, with a fair return to the Park from any commercial success.

Related: Patenting Life, a Bad IdeaLight-harvesting Bacterium Discovered in YellowstoneYellowstone National Park PhotosLife-patentsScientists Chart Record Rise in Yellowstone Caldera

Six Cool Ideas

Six Ideas That Will Change the World

The Pollution Magnet – Eighty-two thousand people die from cancer in Bangladesh every year, many due to arsenic poisoning. But building upon her discovery of a way to get rust nanoparticles to bind to arsenic, Vicki Colvin has invented a new, astonishingly easy way to clean the water supply: Sauté a teaspoon of rust in a mixture of oil and lye, which breaks down the rust into nano-sized pieces. Retrieve the rust particles with a household magnet. Then immerse the rust-covered magnet into a pot of contaminated water. Pull out the arsenic. The system is up to a hundred times more efficient than existing methods, and requires no electricity or manufacturing infrastructure, so even the poorest of villagers can use it.

Depending upon government regulations, Colvin’s extraction system should go global in as few as five years. Yet ultimately, Colvin, a professor of chemistry and chemical and biomolecular engineering at Rice University, has bigger plans. She sees her method as just the first step toward developing an easy point-of-use water-purification system that would cover virtually every pollutant. The filter would have a dipstick to tell you what’s in the water and a reader to tell you what you need to add to pull it out — perhaps silver nanoparticles to kill bacteria or a protein to capture pesticides.

Related: 100 Innovations for 2006Strawjet: Invention of the YearTrash + Plasma = ElectricityLifestrawModern Marvels Invent Now Challenge10 Things That Will Change The Way We Live

Cool Crow Research

photo of crow vending machine

Very cool project – A Vending Machine for Crows

The goal of this project is to create a device that will autonomously train crows. Initially we’re training them to deposit dropped coins they find on the ground in exchange for peanuts, but eventually we hope to be able to train them to search and rescue, or to collect garbage, or who knows!

This is the highest-risk segment of the machine’s operation. At this point coins alone are made available whenever the bird lands on the perch. However, should a bird peck or sweep coins off the tray and cause a coin to fall down the funnel, the device then produces some peanuts. This stage is designed to cement in the crows’ mind the relationship between coins going down the funnel and peanuts being made available.

Finally we shift the device into its intended, and long-term state of only providing peanuts when coins go down the funnel. Nothing is otherwise provided aside from coins scattered around the device at the beginning of the project.

Joshua Klein Thesis presentation definitely watch this! (the webcast takes like 30 seconds before the talk starts – it is worth the wait). Watch a video from the University of Ithaca site (with Dr. Kevin McGowan).

Other sites that also are mentioned as possible sites: Dr. Anne Clark, University of Binghamton (with a captive population of crows); Dr. Natalie Jeremijenko (seed podcast), Dr. Carolee Caffrey, Harvard and Dr. James Ha, University of Washington. Read the Paper by Joshua Klein about the plans for the experiment.

Related: The Engineer That Made Your Cat a PhotographerBackyard Wildlife: FoxAnts on Stilts for Science

Disrupting Bacteria Communication

Princeton scientists break cholera’s lines of communication

A team of Princeton scientists has discovered a key mechanism in how bacteria communicate with each other, a pivotal breakthrough that could lead to treatments for cholera and other bacterial diseases.

The mechanism is a chemical that cholera bacteria use for transmitting messages to each other, known as CAI-1, and has been isolated in the lab of molecular biologist Bonnie Bassler. Her team has shown that the chemical also can be used to disrupt the communication that exists among the bacteria, potentially halting the disease’s progress. The discovery could lead to an entirely new class of antibiotics.

Higgins isolated the CAI-1 chemical, which occurs naturally in cholera. Then, Megan Pomianek, a graduate student in the laboratory of Martin Semmelhack, a professor of chemistry at Princeton, determined how to make the molecule in the laboratory. Higgins used this chemical essentially to control cholera’s behavior in lab tests.

The team found that when CAI-1 is absent, cholera bacteria act as pathogens. But when the bacteria detect enough of this chemical, they stop making biofilms and releasing toxins, perceiving that it is time to leave the body instead. “Our findings demonstrate that if you supply CAI-1 to cholera, you can flip their switches to stop the attack,” Higgins said.

Chemist Helen Blackwell of the University of Wisconsin-Madison praised the study, calling it a breakthrough for quorum sensing research, and possibly for medical science.

Related: Entirely New Antibiotic Developed to Fight MRSAHow do antibiotics kill bacteria?Antibiotic Discovery StagnatesHacking Your Body’s Bacteria

Smart Young Minds – Summer Jobs

At Janelia Farm (located in Northern Virginia and part of the Howard Hughes Medical Institute) each undergraduate research scholar will spend his or her summer conducting research under the guidance and direction of a Janelia Farm lab head. The undergraduate research scholars program will run from June 9-August 15, 2008. On-campus housing will be provided to undergraduate research scholars. Each scholar will also receive a $4,500 stipend and reimbursement for travel to and from Janelia Farm. Apply. Article on the first year of the program – 2007.

Jeanelia Farm also offers research campus fellows – We invite applications for fellows from biologists, chemists, computer scientists, engineers, mathematicians, neurobiologists and physicists who are passionate in their pursuit of important problems in basic scientific and technical research. JFRC Fellows are independent scientists, with labs of up to two additional members. Appointments are for a term of five years. We welcome applications from individuals at all career stages, as well as coordinated applications from groups of individuals.

We invite applications for group leader positions from biologists, chemists, computer scientists, engineers, mathematicians, neurobiologists and physicists who are passionate in their pursuit of important problems in basic scientific and technical research. JFRC group leaders will be independent scientists, similar to the HHMI investigators based at universities and independent research institutes, with labs of up to six additional members and an initial appointment of six years. We welcome applications from individuals at all career stages, as well as coordinated applications from groups of individuals.

Related: science internshipsengineering internshipsScience and Engineering Fellowship Applications Open Nowscience and engineering fellowship directory