Wednesday, January 11, 2012

Modifications to chromosomal proteins help ensure that brain-specific sugars are produced only in appropriate tissues

The ß1,6-branched O-mannosyl glycan appears only in the mammalian brain. Naoyuki Taniguchi’s team at the RIKEN Advanced Science Institute in Wako recently characterized the , N-acetylglucosaminyltransferase IX (GnT-IX, also called GnT-Vb) that produces this particular glycan variant1 (Fig. 1). “We knew that some glycan-synthesizing enzymes are expressed in restricted tissues, but did not know how they are expressed,” says Yasuhiko Kizuka, a researcher in Taniguchi’s laboratory. “This led us to investigate how GnT-IX is specifically expressed in the brain.” 

Many genes are regulated by so-called ‘epigenetic mechanisms’, in which gene expression is modulated via modification of the histone scaffold that supports chromosomal DNA, and the researchers began by examining this possibility. When histone proteins undergo a modification known as acetylation, nearby genes are typically activated; conversely, removal of this acetylation has an inhibitory effect. 

Taniguchi and colleagues determined that the gene encoding GnT-IX is typically maintained in an inactive, non-acetylated state in 3T3-L1, a cell line derived from the fibroblasts that form connective . However, when the researchers treated these cells with a drug that promotes histone acetylation, they strongly expressed GnT-IX. The brain tumor-derived Neuro2A cell line, however, naturally expresses high levels of GnT-IX. The researchers found that these cells normally maintain the chromatin near this gene in a state that stimulates activation.

In subsequent experiments, Kizuka and Taniguchi not only identified specific DNA sequences that directly regulate GnT-IX activity, but also two proteins that bind to these sites to drive expression. They found one of these factors, CTCF, in both 3T3-L1 and Neuro2A cells, but its recruitment to the GnT-IX gene was far stronger under the favorable histone modification conditions found in the latter cells. 

Intriguingly, a preliminary screen of four other glycosylation enzymes suggested that similar mechanisms govern their tissue-specificity. “Our work suggests that expression of many other glyco-genes could be regulated epigenetically,” says Kizuka.

In future studies, the researchers intend to explore how this regulatory mechanism plays into the bigger picture of glycan function. “Our group has been trying to elucidate the ‘glycan cycle’—how glycans are dynamically synthesized, play diverse roles and are degraded—using a systems biology approach,” says Kizuka. “This work tells us that epigenetic regulation is a part of this cycle.”

More information: Kizuka, Y., et al. Brain-specific expression of N-acetylglucosaminyltransferase IX (GnT-IX) is regulated by epigenetic histone modifications. The Journal of Biological Chemistry published online, 19 July 2011. doi: 10.1074/jbc/M111.251173

Provided by RIKEN (news : web)

Jumping droplets take a lot of heat, as long as it comes in a cool way

Microscopic water droplets jumping between surfaces that repel and attract moisture could hold the key to a wide array of more energy efficient products, ranging from large solar panels to compact laptop computers.

Duke University engineers have developed a new way of producing thermal diodes, devices which regulate heat to preferentially flow in a certain direction, effectively creating a thermal conductor in the forward direction and an insulator in the reverse direction. While thermal diodes can be made from solid materials, these solid-state diodes are not nearly as effective as "phase-change" thermal diodes that rely on vaporization and condensation to transport heat.

These phase-change diodes can transfer over a hundred times more heat in the forward direction compared to the reverse, but with major limitations -- they are dependent on gravity or restricted by a tubular configuration. These limitations severely constrain the application of phase-change thermal diodes, for example, in mobile electronics which require orientation independence or solar panels which require a large surface area.

The Duke engineers believe they have figured out a way to solve these limitations to existing thermal diodes by exploiting self-propelled water droplets, which can jump from a superhydrophobic (highly water-repellent) surface to a superhydrophilic (highly absorbent) surface, but not the other way around. The results of the Duke experiments were published online in the journal Applied Physical Letters.

Chuan-Hua Chen, assistant professor of mechanical engineering and materials science at Duke's Pratt School of Engineering, and his research group was the first to actually videotape the self-propelled jumping motion of water droplets on a superhydrophobic surface. They found that the droplets literally jumped straight up and off the surface. In their current experiments, a superhydrophilic plate was placed opposite to the superhydrophobic one, creating an asymmetry crucial for the directional transport of heat in their thermal diode.

"When the superhydrophobic surface is colder than the superhydrophilic surface, the heat transport is very effective with phase-change processes, much like sweat taking away body heat; when the superhydrophobic surface is hotter, the heat flow is blocked and the diode behaves like a double-paned window," said Chen. "Because the jumping droplets in our system are very small, gravity has negligible effect on them. Therefore, devices based on this approach can be oriented in any direction without the need to worry about gravity."

Furthermore, Chen said, this approach can be easily scalable, which means technology based on this design can be used for thermal management of devices as small as computer chips and as large as building roofs. The jumping-drop approach uniquely combines large-area scalability, orientation independence, and effective thermal rectification into one device. This combination of properties is extremely useful for thermal diodes but has remained elusive until Chen's invention.

Typical phase-change thermal diodes rely on evaporating water to transfer heat from one surface to another, with gravity pulling the subsequent condensate down to restart the cycle again. For example, these so-called thermosyphons are in use in the Alaskan oil pipeline, in order to keep the heat from the pipes from melting the permafrost.

Chen believes that this new approach could make thermal diodes more practical and effective for a variety of applications. These applications range from energy-efficient solar panels to smart "skins" of thermally adaptive buildings. For example, in the summertime a diode panel on a building could let heat escape out but prevent heat from creeping in. In space vehicles, thermal diodes can be used to regulate diurnal thermal fluctuations in the outer space, or even to harvest solar energy for powering satellites.

Chen's research is supported by the Defense Advanced Research Projects Agency. Other Duke members of the team are and Yuejun Zhao.

Story Source:

The above story is reprinted from materials provided by Duke University. The original article was written by Richard Merritt.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Jonathan B. Boreyko, Yuejun Zhao, Chuan-Hua Chen. Planar jumping-drop thermal diodes. Applied Physics Letters, 2011; 99 (23): 234105 DOI: 10.1063/1.3666818

Note: If no author is given, the source is cited instead.

Swiss researchers create unscratchable gold

By combining a gold alloy with , an extremely hard ceramic that’s used in bulletproof vests, a team of EPFL researchers has succeeded in making the world’s toughest 18-karat gold (75% gold). With a Vickers hardness number of 1000, it’s harder than most tempered steels (600 Vickers) and thus almost impossible to scratch, except with a diamond. This discovery is the result of a three-year collaboration between the Mechanical Metallurgy Laboratory in EPFL’s Institute of Materials, under the leadership of Professor Andreas Mortensen, and the Swiss watchmaking company Hublot.

The process for developing this material is relatively complicated. Powdered boron carbide is heated to almost 2000°C, where it forms a rigid, porous structure by a process called sintering. A liquid molten alloy of gold is infiltrated under very high pressure into the pores of this structure, and then solidified, yielding a pore-free composite material. The final material is thus made up of two kinds of crystals that are intimately interconnected in space, like two three-dimensional labyrinths. Because the molten gold used is a previously-made alloy based on 24-karat gold and aluminum (3%) for strength, the final gold is thus 3% aluminum, 75% gold and 22% boron carbide
By definition, gold is very soft. Managing to harden it to this degree while still maintaining 18-karat purity was a real challenge for the EPFL scientists. They overcame the obstacle by taking the ceramic-metal composite approach. Composite materials are created by artificially combining several materials that conserve their individual characteristics even after they’re assembled. In this they are different from alloys, in which atoms mix together to form a new, homogeneous, material.

The EPFL researchers aren’t the first to play around with different materials in an effort to make more resistant gold. They are, however, the first to have attained this degree of hardness in 18-karat gold. The first watches made using this new will be presented in 2012 at BaselWorld, the world watch and jewelry show.

Provided by Ecole Polytechnique Federale de Lausanne

Why certain flavor combinations melt in your mouth

British chef Heston Blumenthal is credited with originating the "food pairing hypothesis" which posits that foods that form pleasing combinations -- from strawberries and chocolate to the more unexpected caviar and -- do so because they share numerous responsible for flavor.

A study published in Scientific Reports examines this hypothesis, concluding that for some cuisines it holds true, including North American and Western European food, but that for others, including East Asian food, it is false. The researchers examined the relationships between individual ingredients with the techniques of , which is often used to investigate the organization of .

"It's really natural to think in terms of networks because the food pairing hypothesis is really about making connections between different ingredients," said Yong-Yeol Ahn, a statistical physicist at the University of Indiana in Bloomington and a member of the research team.

Flavor is a crucial element of food pairing. But what is it? Flavor is different than taste. The tongue recognizes tastes -- the familiar sensations of salty, sour, bitter and sweet, as well as savoriness, called umami. Flavor encompasses much more of the sensory experience of eating.

"Eighty percent of our eating experience is determined by the nose," said Bernard Lahousse, the science director of Sense For Taste, a research company that supplies information to chefs, and .

Rounding out the eating experience are texture, sound, and more. Although scientists understand some of the basics, much mystery remains.

"Odor is fascinating," said Jeff Potter, the author of "Cooking for Geeks". Whereas taste is simple to describe … We have a hypothesis for a model of how we think our nose smells things."

The Experiment

To find out what foods people actually enjoy in combination, Ahn and his team went online. With the 56,000 recipes they gathered from three databases, two in English and one in Korean, they began building their analysis of the food pairing hypothesis.

The researchers compared the combinations found in the recipes to a flavor network they created based on the presence of flavor compounds in different ingredients. The comparison revealed the relative popularity of different food combinations and enabled them to compare the tendencies employed by different cuisines .

Why certain flavor combinations melt in your mouth This "Food Pairing Tree" displays several of the foods whose flavors most closely align with the flavors of lobster. Credit: ?, 2011 All rights reserved

They found that the most common ingredients in North American and Western European foods were milk, butter, eggs, wheat, and vanilla. The recipes contained pairs of ingredients with many common flavors at a rate much higher than random chance. They also reported in their study that for East Asian foods, "the more flavor compounds two ingredients share, the less likely they are to be used together."

Ahn noted that his research in this area was in its early stages and that his team is working to improve the quality of their data and analysis. Other researchers dispute their approach.

Flavor's Nuance

Lahousse criticized Ahn's model because it does not filter out what he considers the unimportant flavors that comprehensive chemical analysis identifies.

"Each flavor molecule has its own flavor threshold," said Lahousse. "You really have to look at what are relevant flavors, how can they react with the flavors of other products."

Lahousse, a bioengineer by training, and his company have also researched the relationships between ingredients and their use in recipes. He said that their own analysis of a different dataset of 180,000 recipes showed different results than Ahn's, especially for Japanese food, which he called "the biggest success story we have with food pairing."

Some of their flavor-pairing insights are available online in a tool (see below) endorsed by many highly-regarded chefs. The application highlights foods that share common tastes and is designed to help identify unexpectedly tasty combinations. However, much of their work has not been made available to scientists for scrutiny. Ahn said he was unable to compare his approach to that of Sense for Taste because the methods the company uses are not fully disclosed. Lahousse said he understands this criticism, but that the company balances the amount of information made public against its efforts to run as a business.

Beyond Flavor

Lahousse also admitted that there many unanswered questions about how food is experienced.

"You cannot explain everything by looking at food pairing because a recipe is more than flavor alone," he said. "It's much more complex."

Sometimes, despite mixing ingredients that should form agreeable flavor combinations, a dish does not work. Often, a chef may need to add ingredients that introduce additional elements for reasons of balance. For example, a dish may be calling for an additional taste of sweetness, or perhaps a bit of lemon to add a sour note to round out the dish. But the chef is not necessarily making those adjustments because of the flavors that element brings.

Ahn believes that even if an ingredient is applied this way, solely for the benefit of taste to the tongue, its contribution to overall flavor should still be analyzed. Lahousse believes that this is where careful analysis of a food's most important flavors pays off. For example, he said, garlic and onions add flavor, but also sweetness. They also influence the browning of meat as it is cooked.

Eggs are another popular ingredient, especially in baking. Lahousse said they are not added for their flavor profile, but for their contribution to texture.

Ahn said it is important to consider eggs' flavor contribution, because even though they influence a food's structural properties, that recipes evolve, and if the flavors were not pleasing to those who ate it, the recipe would change over time to reflect flavor preferences as well as those of texture.

Finding Harmony

Even if the flavor notes of two foods line up, a deft hand may still be required to make a combination sing.

The visualization of lobster's most closely-related foods hosted on Lahousse's website, clearly highlights the crustacean's affinity to strawberry. But, he said, many factors influence how those items are best combined and balanced, including the culture of those eating the dish and even the qualities of the individual lobster and strawberries.

"If you start to add strawberry to lobster you have to be a very good chef," said Lahousse. "The chance is very high that you will add too much sweetness to this dish. You have to be able to make a really good balance."

Potter likened the combination of flavors to notes or chords on a piano. Some will join together in a more pleasing way than others. Two wildly differing sets of odor molecules might not mesh if they didn't have any accompaniment. He pointed again to lobster, and to chocolate as its pairing.

"That's not to say that a really talented chef couldn't make lobster and chocolate work," said Potter. "I'm sure there's a combination with an appropriate set of ingredients where those dissonant chords do actually produce a pleasing sound."

For home cooks facing a nearly empty refrigerator and a lack of inspiration, Potter recommends taking inventory and Googling a list of your seemingly mismatched ingredients to identify opportunities to create your own culinary innovations.

"I'm a huge fan of experimentation; there's no single better way to learn how to cook than to go into the kitchen and try doing something," said Potter.

Provided by Inside Science News Service (news : web)