Category Archives: Science

Another Bacteria DNA Trick

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.

Turning Trash into Gas

Frank Pringle has found a way to squeeze oil and gas from just about anything

Everything that goes into Frank Pringle’s recycling machine—a piece of tire, a rock, a plastic cup—turns to oil and natural gas seconds later.
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The machine is a microwave emitter that extracts the petroleum and gas hidden inside everyday objects—or at least anything made with hydrocarbons, which, it turns out, is most of what’s around you. Every hour, the first commercial version will turn 10 tons of auto waste—tires, plastic, vinyl—into enough natural gas to produce 17 million BTUs of energy (it will use 956,000 of those BTUs to keep itself running).
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Or rather, he had extracted it. Petroleum is composed of strings of hydrocarbon molecules. When microwaves hit the tire, they crack the molecular chains and break it into its component parts: carbon black (an ash-like raw material) and hydrocarbon gases, which can be burned or condensed into liquid fuel. Pringle figured that some gases from his microwaved tire had lingered, and the cold air in the shop had condensed them into diesel. If the process worked on tires, he thought, it should work on anything with hydrocarbons. The trick was in finding the optimum microwave frequency for each material—out of 10 million possibilities.

Genomics Course For College Freshman Supported by HHMI at 12 Universities

HHMI Selects 12 Institutions to Launch Nationwide Science Education Experiment

The Howard Hughes Medical Institute (HHMI) has selected 12 colleges and universities to participate in a nationwide genomics course that will involve first-year college students in authentic research. The new course is the first major initiative from HHMI’s Science Education Alliance, which seeks to enhance the teaching of science and inspire new generations of scientists.

In Fall 2008, first-year students at the six undergraduate institutions and six research-intensive institutions will take part in a year-long research course — the Phage Genomics Research Initiative – which is being developed by the Science Education Alliance (SEA). The SEA, headquartered at HHMI’s Janelia Farm Research Campus in Northern Virginia, will foster the development of a national network of scientists and educators who work collaboratively to develop and distribute new materials and methods to the education community.
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HHMI is committing a total of $4 million over the first four years of the program.
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Approximately 20 students at each institution will participate in the two-semester phage genomics research course, in which they will be taught to use sophisticated research techniques. Students will isolate bacterial viruses (phages) from their local soil, prepare the viral DNA for sequencing, and annotate and compare the sequenced genome. The goal is to immerse students in the process of doing science, and equip them with the critical thinking and communication skills necessary for successful research careers.

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.

Time’s Top 10 Scientific Discoveries of 2007

Time’s Top 10 Scientific Discoveries of 2007 – I don’t really agree with these but a couple are interesting:

#1. Stem Cell Breakthroughs
In November, Shinya Yamanaka of Kyoto University and molecular biologist James Thomson of the University of Wisconsin reported that they had reprogrammed regular skin cells to behave just like embryonic stem cells. The breakthrough may someday allow scientists to create stem cells without destroying embryos
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#4. Hundreds of New Species
…700 new species of organisms — including carnivorous sponges and giant sea spiders — some 2,300 ft. to 19,700 ft. (700 m to 6,000 m) down in the Weddell Sea off Antarctica. Scientists also reported the identification of 24 new species in an isolated area of Suriname, where the exploration for bauxite, which is used to make aluminum, led to the discovery of 12 dung beetles, an ant species, six species of fish and five new frogs, including one with fluorescent purple markings. Other fauna finds include a legless amphibian near Goa, India; 11 new species of plants and animals in central Vietnam’s tropical “green” corridor; a new monkey in Uganda; a sucker-footed bat in Madagascar; a clouded leopard in Sumatra and Borneo, and a sea cucumber off the coast of Taiwan, nicknamed “Little Strawberry.”

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.

USA Teens 29th in Science

The 2006 Programme for International Student Assessment (PISA) report has been released. The report examines the science of 15 year olds from 57 countries in math, science and reading. Once you get passed the poor design of the PISA web site you can find a great deal of data (which gives a great deal more depth to the results than just a simple listing of the top countries by mean score). But that list is interesting too.

*Rant* I find it amazing that sites can be so poorly run that they fail to even display without Javascript enabled. That is how badly run the PISA web site is, though. Here is the home page they direct you too: www.pisa.oecd.org/pages/0,2987,en_32252351_32235731_1_1_1_1_1,00.html – they need to have some people read about web usability (they should hire someone that knows how to apply the ideas of Jakob Neilsen, Jared Spool or 37 Signals).

Results for the Science portion (rank – country – mean score)(I am not listing all countries):

1 – Finland – 563
2 – Hong Kong – 542
3 – Canada – 534
4 – Taiwan – 532
6 – Japan – 531
7 – New Zealand – 530
8 – Australia – 527
9 – Netherlands – 525
11 – Korea – 522
13 – Germany – 516
14 – United Kingdom – 515
25 – France – 495
29 – USA – 489
49 – Mexico – 410

Girls Sweep Top Honors at Siemens Competition in Math, Science and Technology

Girls Make History by Sweeping Top Honors at a Science Contest

Janelle Schlossberger and Amanda Marinoff, both 17 and seniors at Plainview-Old Bethpage John F. Kennedy High School on Long Island, split the first prize – a $100,000 scholarship – in the team category for creating a molecule that helps block the reproduction of drug-resistant tuberculosis bacteria.

Isha Himani Jain, 16, a senior at Freedom High School in Bethlehem, Pa., placed first in the individual category for her studies of bone growth in zebra fish, whose tail fins grow in spurts, similar to the way children’s bones do. She will get a $100,000 scholarship.
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Three-quarters of the finalists have a parent who is a scientist. The parents of Alicia Darnell, who won second place, are medical researchers at Rockefeller University, and her maternal grandparents were scientists, too. Isha Himani Jain, who took home the top individual prize, published her first research paper with her father, a professor at Lehigh University, when she was 10 or 11; her mother is a doctor.

Read about projects by the finalists.

Dinosaur Remains Found with Intact Skin and Tissue

Hadrosaur Dinasaur

“Dinosaur Mummy” Found; Has Intact Skin, Tissue by John Roach, National Geographic News:

Scientists today announced the discovery of an extraordinarily preserved “dinosaur mummy” with much of its tissues and bones still encased in an uncollapsed envelope of skin. Preliminary studies of the 67-million-year-old hadrosaur, named Dakota, are already altering theories of what the ancient creatures’ skin looked like and how quickly they moved, project researchers say
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The hadrosaur, or duck-billed dinosaur, was discovered in 1999 by then-teenage paleontologist Tyler Lyson on his family’s North Dakota property.
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Plant-eating hadrosaurs are often called the “cows of the Cretaceous”—the geologic period that spanned 145 million to 65 million years ago—Manning said. They had horny, toothless beaks but hundreds of teeth in their cheeks and a long, stiff tail that was likely used for balance. Preliminary studies are revealing a surprising side to these reptiles, suggesting that Dakota—even though roughly 35 feet (12 meters) long and weighing some 35 tons—was no slowpoke.
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The preliminary calculations suggest Dakota could run 28 miles (45 kilometers) an hour. Tyrannosaurus rex tops out at about 20 miles (32 kilometers) an hour, according to the model

The dig and subsequent scanning are the subjects of Dino Autopsy, a National Geographic Channel special airing on December 9th.

Amazing find of dinosaur ‘mummy’, BBC:

this hadrosaur came complete with fossilised skin, ligaments, tendons and possibly some internal organs, according to researchers. “It’s unbelievable when you look at it for the first time,” said palaeontologist Phillip Manning from the University of Manchester, UK. “There is depth and structure to the skin. The level of detail expressed in the skin is just breathtaking.”

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