Category Archives: Research

Black Raspberries Alter Hundreds of Genes Slowing Cancer

Black Raspberries Slow Cancer by Alter Hundreds of Genes

Researchers at the Ohio State University Comprehensive Cancer Center examined the effect of freeze-dried black raspberries on genes altered by a chemical carcinogen in an animal model of esophageal cancer
…
“We have clearly shown that berries, which contain a variety of anticancer compounds, have a genome-wide effect on the expression of genes involved in cancer development,” says principal investigator Gary D. Stoner
…
Stoner notes that black raspberries have vitamins, minerals, phenols and phytosterols, many of which individually are known to prevent cancer in animals. “Freeze drying the berries concentrates these elements about ten times, giving us a power pack of chemoprevention agents that can influence the different signaling pathways that are deregulated in cancer,” he says.
…
Their analyses included measuring the activity, or expression levels, of 41,000 genes. In the carcinogen-treated animals, 2,261 of these genes showed changes in activity of 50 percent or higher.

Pretty cool stuff.

Patent Gridlock is Blocking Developing Lifesaving Drugs

How patent gridlock is blocking the development of lifesaving drugs by Michael Heller, Forbes

Since a 1980 Supreme Court decision allowing patents on living organisms, 40,000 dna-related patents have been granted. Now picture a drug developer walking into an auditorium filled with dozens of owners of the biotech patents needed to create a potential lifesaving cure. Unless the drugmaker can strike a deal with every person in the room, the new drug won’t be developed.
…
Nicholas Naclerio, who used to head the BioChip Division at Motorola , told Scientific American, “If we want to make a medical diagnostic with 40 genes on it, and 20 companies hold patents on those genes, we may have a big problem.”
…
And it’s not just drugs we’re losing. Today anything high tech–banking, semiconductors, software, telecom–demands the assembly of innumerable patents. Innovation has moved on, but we’re stuck with old-style ownership that’s easy to fragment and hard to put together. This debacle’s only upside is that assembling fragmented property is one of the great entrepreneurial and political opportunities of our era.

This is a critical problem I have written about before. The broken patent system is a serious problem that needs to be fixed.

Dolphin Kick Gives Swimmers Edge

photo of Michael Phelps diving

Dolphin Kick Gives Swimmers Edge

Rajat Mittal, a professor of mechanical and aerospace engineering at the George Washington University, was studying dolphins for the U.S. Navy five years ago. “We were asked to understand how fish swim so efficiently,” Mittal says, “and it seemed like a natural extension to apply this to human swimming.”
…
They decided to “essentially compare these swimmers to the dolphin, assuming that the dolphin is the ultimate swimmer,” Mittal says. “And the thing that we found is that Michael [Phelps] is able to use his body in a way that is very, very different from the other athletes, and also seems to be much closer to dolphins than we have seen for any other swimmer.”

The dolphin kick first hit Olympic swimming big-time 20 years ago, after Harvard backstroker David Berkoff figured out something fundamental. “It seemed pretty obvious to me that kicking underwater seemed to be a lot faster than swimming on the surface,” Berkoff says.

That’s because there’s turbulence and air on the surface of the water, and they create resistance. The “Berkoff Blastoff,” as it was called, was used at the start and after turns, with long stretches of that underwater undulating kick.

Follow the link for a video of Michael Phelps demonstrating the technique and more interesting details. Photo by A. Dawson shows Michael Phelps diving into the water at the 2008 U.S. Olympic Swimming Trials.

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.
Continue reading →

Pseudogap and Superconductivity

MIT physicists shed light on key superconductivity riddle

Hudson’s team is focusing on the state of matter that exists at temperatures just above the temperature at which materials start to superconduct. This state, known as the pseudogap, is poorly understood, but physicists have long believed that characterizing the pseudogap is important to understanding superconductivity.

In their latest work, published online on July 6 in Nature Physics, they suggest that the pseudogap is not a precursor to superconductivity, as has been theorized, but a competing state. If that is true, it could completely change the way physicists look at superconductivity, said Hudson.

“Now, if you want to explain high-temperature superconductivity and you believe the pseudogap is a precursor, you need to explain both. If it turns out that it is a competing state, you can instead focus more on superconductivity,” he said.

DNA Passed to Descendants Changed by Your Life

How your behaviour can change your children’s DNA

Until recently that would also have been the opinion of most scientists. Genes, it was thought, were highly resilient. Even if people did wreck their own DNA through bad diet, smoking and getting fat, that damage was unlikely to be passed to future generations.

Now, however, those assumptions are being re-examined. At the heart of this revolution is a simple but controversial idea: that DNA can be modified or imprinted with the experiences of your parents and grandparents.

According to this new science, known as epigenetics, your ancestors’ diet, smoking habits, exposure to pollutants and levels of obesity could be affecting you today. In turn, your lifestyle could affect your children and grandchildren.
…
If we drink heavily, take drugs, get fat or wait too long to reproduce, then epigenetics might start tying up some of the wrong genes and loosening the bonds on others. Sometimes those changes will affect sperm and egg cells.

It seems to me this area is still far from having conclusive proof. But it is another great example of scientists seeking to improve our knowledge of how things work.

Finding the Host Genes Viruses Require

Flu-infected fly cells reveal dependencies of the virus

The new study is important because it demonstrates a rapid-fire technique for identifying host factors such as proteins and carbohydrates that a virus commandeers to successfully infect a cell. By exposing the virus’s dependencies, the Wisconsin team has uncovered a target-rich environment for influenza drug developers.
…
By working in fly cells, the Wisconsin team was able to deploy a technique to rapidly and selectively silence thousands of genes to see which were used by the flu virus. Screening a library of some 13,000 genes, the group identified more than 100 whose suppression in fly cells hindered the virus’s ability to successfully take over the cell and make new viruses.

A Whale of a Turbine

A whale of a turbine

a flipperlike prototype is generating energy on Canada’s Prince Edward Island, with twin, bumpy-edged blades knifing through the air. And this summer, an industrial fan company plans to roll out its own whale-inspired model – moving the same amount of air with half the usual number of blades and thus a smaller, energy-saving motor.

Some scientists were sceptical at first, but the concept now has gotten support from independent researchers, most recently some Harvard engineers who wrote up their findings in the respected journal Physical Review Letters.
…
when models of the bumpy flippers were tested in a wind tunnel, Fish and his colleagues found something interesting. The flippers could be tilted at a higher angle before stall occurred.

The scientific literature had scant reference to the flipper bumps, called tubercles. Fish reasoned that because the whale’s flippers remained effective at a high angle, the mammal was therefore able to manoeuvre in tight circles. In fact, this is how it traps its prey, surrounding smaller fish in a “net” of bubbles that they are unwilling to cross.

In 2004, along with engineers from the US Naval Academy and Duke University, Fish published hard data: Whereas a smooth-edged flipper stalled at less than 12 degrees, the bumpy, “scalloped” version did not stall until it was tilted more than 16 degrees – an increase of nearly 40 percent.

Fish then partnered with Canadian entrepreneur Stephen Dewar to start WhalePower, a Toronto-based company that licenses the technology to manufacturers.
…
It has all been a bit of a culture shock for Fish, who is more at home in the open world of academia than the more secretive realm of inventions and patents. Two decades ago, his only motivation was to figure out what the bumps were for.

“I sort of found something that’s in plain sight,” he says. “You can look at something again and again, and then you’re seeing it differently.”

The Brain Hides Information From Us To Prevent Mistakes

“The main finding of the study is that it has enabled us to confirm that tactile sensations are initially located unconsciously in anatomical coordinates, but they reach our awareness only when the brain has formed an image of their origin in the spatial coordinates, external to the body,” explained Salvador Soto-Faraco. The coexistence of different spatial reference frames in the brain has been known for some time. So has the fact that confusions between them may result in some cases, such as when we invert the usual anatomical position of some body parts (e.g. when crossing our arms over the body midline). “The brain sorts out problems of this kind rapidly, in a matter of tenths of a second. To do so, however, it has to integrate information arriving in formats that are quite disparate”, Sotoa-Faraco added. “Our research has helped us understand how this process works and how the brain manages spatial realignment when faced with conflict”, he concluded.

Interesting. I think my brain might be hiding more from me lately (like right now where the key to my shed is) 🙂

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.