Science and Technology News

laboratoryequipment:

Organisms Repair Abnormalities in Head and Face

Developmental biologists at Tufts Univ. have identified a “self-correcting” mechanism by which developing organisms recognize and repair head and facial abnormalities. This is the first time that such a mechanism has been reported for the face and the first time that this kind of flexible, corrective process has been rigorously analyzed through mathematical modeling.

The research, reported in the May 2012 issue of the journal Developmental Dynamics, used a tadpole model to show that developing organisms are not genetically “hard-wired” with a set of pre-determined cell movements that result in normal facial features. Instead, the process of development is more adaptive and robust. Cell groups are able to measure their shape and position relative to other organs and perform the movements and remodeling needed to compensate for significant patterning abnormalities, the study shows.

Read more: http://www.laboratoryequipment.com/news-Organisms-Repair-Abnormalities-in-Head-and-Face-042612.aspx

(via blamoscience)

laboratoryequipment:

Caffeine May Ease Dry Eye

Researchers at the Univ. of Tokyo’s School of Medicine have shown for the first time that caffeine intake can significantly increase the eye’s ability to produce tears, a finding that could improve treatment of dry eye syndrome. This common eye condition affects about four million people age 50 and older in the United States. For many, dry eye syndrome is simply uncomfortable and annoying, but for others it escalates into a vision-threatening disease. All of the 78 participants in the new study produced significantly more tears after consuming caffeine than after taking a placebo. The study is available in Ophthalmology, the journal of the American Academy of Ophthalmology.

Dry eye syndrome involves malfunction of the rate of tear production, the quality of tears, and/or the rate of evaporate from the surface of the eye. Anyone can experience dry eye, though it is more common among women. Symptoms can include gritty, scratchy or burning sensations, excessive tearing, and/or production of stringy mucus.

Read more: http://www.laboratoryequipment.com/news-Caffeine-May-Ease-Dry-Eye-041812.aspx

(via blamoscience)

quantumaniac:

New Process Improves Catalytic Rate of Enzymes by 3,000 Percent

Light of specific wavelengths can be used to boost an enzyme’s function by as much as 30 fold, potentially establishing a path to less expensive biofuels, detergents and a host of other products.

In a paper published in The Journal of Physical Chemistry Letters, a team led by Pratul Agarwal of the Department of Energy’s Oak Ridge National Laboratory described a process that aims to improve upon nature — and it happens in the blink of an eye.

“When light enters the eye and hits the pigment known as rhodopsin, it causes a complex chemical reaction to occur, including a conformational change,” Agarwal said. “This change is detected by the associated protein and through a rather involved chain of reactions is converted into an electrical signal for the brain.”

With this as a model, Agarwal’s team theorized that it should be possible to improve the catalytic efficiency of enzyme reactions by attaching chemical elements on the surface of an enzyme and manipulating them with the use of tuned light.

The researchers introduced a light-activated molecular switch across two regions of the enzyme Candida antarctica lipase B, or CALB — which breaks down fat molecules — identified through modeling performed on DOE’s Jaguar supercomputer.

“Using this approach, our preliminary work with CALB suggested that such a technique of introducing a compound that undergoes a light-inducible conformational change onto the surface of the protein could be used to manipulate enzyme reaction,” Agarwal said.

While the researchers obtained final laboratory results at industry partner AthenaES, computational modeling allowed Agarwal to test thousands of combinations of enzyme sites, modification chemistry, different wavelengths of light, different temperatures and photo-activated switches. Simulations performed on Jaguar also allowed researchers to better understand how the enzyme’s internal motions control the catalytic activity.

“This modeling was very important as it helped us identify regions of the enzyme that were modified by interactions with chemicals,” said Agarwal, a member of ORNL’s Computer Science and Mathematics Division. “Ultimately, the modeling helped us understand how the mechanical energy from the surface can eventually be transferred to the active site where it is used to conduct the chemical reaction.”

Agarwal noted that enzymes are present in every organism and are widely used in industry as catalysts in the production of biofuels and countless other every day products. Researchers believe this finding could have immense potential for improving enzyme efficiency, especially as it relates to biofuels.

deconversionmovement:

First Glimpse at the Viral Birth of DNA

EARLY life underwent a massive system upgrade around 4 billion years ago. DNA’s simple code can encrypt a huge amount of information and its trademark double helix makes it remarkably stable. But most biologists agree that life began with a soup of RNA, a less stable genetic molecule. So at some point the vast majority of life must have switched its code.

For the first time, biologists have had a glimpse at how this may have happened. The rare insight points to archaic viruses as the inventors of DNA. Better yet, the process that enabled the ancient upgrade occasionally still happens today.

According to the prevailing dogma, the earliest life forms arose from a loose mix of proteins and nucleic acids that used RNA as their genetic material. At some point, most of life began storing genetic information in DNA; all the cellular life we know today, and most modern viruses as well, are DNA-based. The switch created a problem familiar to anyone who has upgraded their laptop to a new operating system: how do you port over your old software to the new platform? The genes of RNA life contained solutions to many of the challenges of existence, but because RNA cannot combine with DNA there was no obvious way for the new DNA life to use this information.

The discovery of an unusual hybrid virus living in one of the harshest environments on the planet suggests a solution. Ken Stedman, of Portland State University in Oregon, stumbled on it by accident while studying the microbes that live in a hot, acidic lake in California’s Lassen Volcanic National Park. He filtered all the virus-sized particles from 40 litres of lake water, and randomly sequenced some 400,000 pieces of viral DNA to see what was there.

He found something odd: a gene, made of DNA, that looked like the gene for a protein coat from an RNA virus. Some viruses, called retroviruses, have a reverse transcriptase enzyme to translate RNA into DNA, but this gene did not come from a retrovirus. So how had the gene leapt from RNA to DNA?

Intrigued, Stedman’s student, Geoff Diemer, produced a full sequence of the strange virus’s genome. He found that alongside the RNA-derived gene it contained a gene for DNA replication typical of a DNA virus.

Finding these two genes in one organism was a bit like finding a sunflower gene in a chimpanzee, except that plants and animals probably share a much more recent common ancestor than DNA and RNA viruses, which are thought to have diverged billions of years ago. “Our first thought was that we messed up somehow,” says Stedman.

They re-sequenced the entire viral genome but the two genes were still there, Diemer reported this week at NASA’s Astrobiology Science conference in Atlanta, Georgia. The work will appear in Biology Direct.

To see whether this motley virus was just a one-off, Stedman and Diemer scanned databases of viral DNA sequences. They found that something very similar had turned up in samples of ocean water sequenced by a team led by Craig Venter, of the J Craig Venter Institute. “These hybrid viruses are present not just in this acidic hot lake, but in at least a couple of oceanic samples, and probably other places as well,” says Stedman.

The find proves that modern viruses can combine information coded in the two normally separate genetic molecules. And it lends support to the idea that it was viruses that performed the upgrade from RNA and effectively gave rise to DNA.

Stedman and Diemer’s hybrid virus is not a living fossil - a left-over that has stuck around since the dawn of life. Its genes are similar to their parent genes in RNA and DNA viruses, and the team estimates that it hybridised within the last 10 million years.

Stedman suggests that it may have formed when an RNA virus, DNA virus and retrovirus all infected a cell at the same time. This perfect viral storm could have triggered a three-way genetic mash-up (see diagram). The retrovirus used its reverse transcriptase enzymes to mistakenly make a DNA copy of an RNA virus gene, which combined with the DNA virus’s genome to yield the unlikely hybrid. A few earlier studies had hinted that such viral super-hybrids could exist, but Stedman’s study is the first to show it directly.

“These are two lineages that we never think of as overlapping,” says virologist Luis Villarreal of the University of California at Irvine. The lack of respect for species boundaries echoes what many biologists suspect the original virus world must have been like around the birth of DNA 4 billion years ago, he says.

The parallel with the ancient virus world is not perfect, since the modern viruses’ life cycles are very different from those of their ancestors. The primordial virus world was a non-cellular stage in the evolution of life, the details of which are very obscure, says Eugene Koonin, an evolutionary genomicist at the National Center for Biotechnology Information in Bethesda, Maryland. “Nowadays, viruses replicate exclusively within cells.”

Still, the finding proves that a community of viruses can move information from RNA into DNA - and that modern DNA viruses do have access to genes evolved by those in the very separate world of RNA viruses. This bolsters the argument that a similar transfer happened during early life’s RNA-to-DNA transition.

It also tells us that our modern world retains at least a trace of the uninhibited genetic free-for-all that must have preceded our current staid, cellular existence. Or as Koonin puts it: “The virus world, in its diversity and unpredictability, is still with us.”

Image Info:  Hybrid viruses in this acid lake contained both RNA-derived genes and genes for DNA replication

Image Credit: Wendy White/Alamy

(via alohahn)

expose-the-light:

New cosmic survey might mean serious trouble for dark matter

Dark matter makes up approximately 83% of the matter in the universe. We need it to explain why galaxy clusters hold together. All available evidence suggests it’s very real. So why is there almost none of it around the Sun?

That’s the troublesome result from a new survey conducted by the European Southern Observatory. The astronomers meticulously measured the motions of some 400 stars in a 13,000 light-year vicinity of our solar systems. They used those motion measurements to calculate the amount of mass around each star, and then they compared that to all the materials we could observe. The two measurements matched up almost perfectly. And, as team leader Christian Moni Bidin explains, that’s exactly the problem:

“The amount of mass that we derive matches very well with what we see — stars, dust and gas — in the region around the Sun. But this leaves no room for the extra material — dark matter — that we were expecting. Our calculations show that it should have shown up very clearly in our measurements. But it was just not there!”

Now, for those hoping this might somehow mean an end to dark matter, I should stress that that isn’t what these results mean. Dark matter is still crucial for explain the gravitational interactions of galaxy clusters, as all available evidence suggests there isn’t enough mass at that scale for them to remain intact in the way we observe them. (For more specifics, check out Dr. Dave Goldberg’s excellent primer.)

But it does mean that dark matter seems weirdly absent at a local level, and that’s a deeply puzzling result. Our current best guess is that the Milky Way is surrounded by some sort of halo of dark matter, and we should have seen evidence of it during this survey. It’s possible the halo has a highly unusual shape - like, say, it’s extremely elongated - that would cause it to evade detection. But we have no reason to think that apart from these results.

What’s more, this could mean bad news for the hunt for the dark matter particle. If dark matter really is as rare in our neck of the galactic woods as it appears to be, then our changes of detecting the particle just dropped drastically. Whatever is going on, the hunt is far from over, as Bidin himself concludes:

“Despite the new results, the Milky Way certainly rotates much faster than the visible matter alone can account for. So, if dark matter is not present where we expected it, a new solution for the missing mass problem must be found. Our results contradict the currently accepted models. The mystery of dark matter has just become even more mysterious. Future surveys, such as the ESA Gaia mission, will be crucial to move beyond this point.”

Via ESO. Artist’s impression by ESO/L. Calçada.

(via expose-the-light)

fuckyeahmolecularbiology:

It’s Breast Cancer…Right?

A landmark study has revealed that what we currently think of as breast cancer should be thought of as 10 completely separate diseases.

The new categorisation of breast cancer could improve treatment options enormously by tailoring drugs for a patient’s exact type of breast cancer. In some cases, it could also help predict survival and life expectancy more accurately.

“Breast cancer is not one disease, but 10 different diseases,” said the lead researcher on the study, Professor Carlos Caldas. “Our results will pave the way for doctors in the future to diagnose the type of breast cancer a woman has, the types of drugs that will work and those that won’t, in a much more precise way than is currently possible.”

In order to explain their research, the team took to analogy, comparing breast cancer to a map of the world. They said that current hospital tests were quite broad - dividing breast cancer up into the equivalent of “continents” - but their latest findings could allow you to give the map more detail and complexity, down to the level of “countries.”

Dr. Harpal Kumar, the director of Cancer Research UK - the organisation that funded the study - believes the study marks a new era in cancer research. “This will change the way we look at breast cancer, it will have an enormous impact in the years to come in diagnosing and treating breast cancer…[Cancer Research UK] thinks this is a landmark study.”

The full study, published in Nature, can be found here.

The BBC News - Health reported on the study here.

Image: A breast cancer cell undergoing cell division. Cancer cells will divide rapidly and randomly.

(via alohahn)

blamoscience:

Egg-laying may very well have been the downfall of the dinosaurs, a new study shows. Since there are limits to how large an egg can be, due to the fact that they require a great number of the mother’s resources to produce, the newly hatched offspring of dinosaurs was astonishingly small in comparison to their parents. Not so for mammals, who’s offspring could be born much larger. While most species occupy one ecological niche, the widely varying sizes of dinosaurs had to pass through several niches before reaching adult hood, putting them at a competitive disadvantage. 

Full story here. 

laboratoryequipment:

Nanotubes Can Replace Platinum in Solar Cells

Forests of carbon nanotubes are an efficient alternative for platinum electrodes in dye-sensitized solar cells (DSC), according to new research by collaborators at Rice Univ. and Tsinghua Univ.

The single-wall nanotube arrays, grown in a process invented at Rice, are both much more electroactive and potentially cheaper than platinum, a common catalyst in DSCs, says Jun Lou, a materials scientist at Rice. In combination with newly developed sulfide electrolytes synthesized at Tsinghua, they could lead to more efficient and robust solar cells at a fraction of the current cost for traditional silicon-based solar cells.

Read more: http://www.laboratoryequipment.com/news-Nanotubes-Can-Replace-Platinum-in-Solar-Cells-041712.aspx

(via darylelockhart)