Archive for December, 2009

It’s Not the Heat, It’s the Mutivity

Wednesday, December 23rd, 2009

If you don’t know what mutivity is, don’t worry.  I didn’t either. It’s a virus’s ability to adapt to survive; either to a new host, against drugs or anything like that.

It’s relevant because an interdisciplinary team here at the University of Idaho is beginning an investigation into whether or not viruses that have adapted to higher temperatures - like those of a new host or a future with where global warming has come true - can withstand mutations and jump species more easily.

If their idea is correct, it could mean we’ll be seeing a lot more viruses like the Avian Flu and H1N1 jump hosts from animals to humans.

To learn more, read the full press release.

Designing a Better Building

Tuesday, December 22nd, 2009

My final stop in Boise was the Integrated Design Lab, which is actually located several blocks northwest of the Water Center in a historic building just around the corner from an amazing French restaurant called Le Cafe De Paris. (French tuna sandwich and pumpkin soup… yums!)

The IDL is all about designing and building structures that are greener, more energy efficient, smarter and more comfortable to work in. They take into account design features ranging from the shape, size and orientation of windows to provide the optimum amount of natural light to creating naturally flowing air currents to keep the rooms cool and ventilated without necessarily having to turn on any air conditioning units.

Exterior view of the "cloudy sky" box, as I like to call it.To achieve this, they have two very cool modeling tools in their workshop. The first is a giant box completely filled with mirrors and a few lights that can be adjusted to different levels of lighting. The result is that the box creates the same conditions as a cloudy day, where it is lighter overhead but becomes darker as you go down to the horizon.

To test designs, a technician will build their concept model in the center of the box. Then, small cameras are pointed into the model and photos are taken at various light levels as well as for various window orientations and designs. The photos are then analyzed on a computer program to find the optimum design.

Similarly, sitting just a few feet from this “cloudy day” box is a platform that rotates on all three axis. A theater spotlight is bounced off of an overhead mirror to simulate a sunny day. The platform can then be rotated to simulate different times of year and different times of day; basically any angle of direct sunlight imaginable. Photos are again taken and analyzed as described for the box.The rotating platform that can mimmic any sun angle.

The result is a wide suite of options that can be presented to the customer. An example is pictured below, which was from a building being modeled for a project in conjunction with CTA Architects and Engineers of Boise, one of the many local collaborations and projects the IDL is involved in.

But Kevin Van Den Wymelenberg, director of the IDL, is taking customer service to a whole new level.

Kevin currently is working on a research project for an integrated automated lighting system.

An example of a photo taken inside a model and the resulting light data and graph.Imagine, if you will, an office where there are light sensors connected to the lighting system that adjust automatically - not just to the ambient conditions, but to the individual’s ideal working conditions. Blinds that open and close automatically depending on the outside conditions and the levels of glare produced from with windows.

These are just a few of the possibilities for creating an optimum work enviornment while saving as much energy as possible that Kevin is working on. Coming soon to an office near you…

Flume U

Monday, December 21st, 2009
The flume models the real environment of a riverbed.

The flume models the real environment of a riverbed.

My second stop during my visit to the University of Idaho’s main structure in Boise took me to what I would consider the facility’s pride and joy - the water flume.

The flume looks like a cross between a giant, mechanized bed of a dump truck and a slip-and-slide. The main feature is a ramp with walls extending nearly 70-feet long and measuring 6 -feet wide. One end of the flume can be lowered or raised up to the ceiling to give the flume a different degree of elevation; up to 11 degrees.

The purpose of the flume is to study how waters run in river beds. Scientists fill the device with pebbles and rocks measuring up to 2.5 inches in diameter, raise the flume’s degree of incline to match the conditions of the river bed and run a whole bunch of water over the simulated riverbed.

As this is happening, a motorized sensor sits on railings over the stream of water. It shoots up and down the entire length of the flume, all the while taking detailed measurements with lasers of up to six separate parameters. The result is a detailed look at how the water is flowing over the rocks, how the sediment is traveling with the water and the overall complex system of a riverbed.

The flume is one of the largest, most versatile, most impressive of its kind in the entire world.

So what can a scientist do with such a flume? Besides studying what the affects of a flooding of the Boise River would be and designing a whitewater recreation park for the city, Elowyn Yager, assistant professor at the Center for Ecohydraulic Research (CER), which is the name of the center that runs the flume, studies fluvial geomorphology. Just in case you’re not sure, that is the science of rivers in the landscape. She studies how rivers transport sediment in order to predict how environmental changes such as fires, logging and landslides will affect mountain ecosystems.

However, there are a ton of people who want to use the flume. It never sits idle. The center has a research team from Great Britain coming over the summer. Additionally, students from Nepal, Costa Rica, Chile, Italy, Australia, Germany, Bangladesh and Austria have all utilized the facility.

And to take it a step further, the director of CER, Peter Goodwyn, wants to link the computers to a world wide computing system, so researchers from around the world can receive data and run experiments with the flume from anywhere in the world.

As you can tell, I was very impressed with the flume, and in the near future, I think the whole state - even the whole country - will be as well.

The University of Idaho in Boise

Friday, December 18th, 2009
The new, imposing University of Idaho building in Boise.

The new, imposing University of Idaho building in Boise.

The final research and extension center I visited on my trip to southern Idaho last week was the new, gorgeous facility located in downtown Boise. It’s going to take me several days to get through all of the interesting machines I saw and brilliant people I met, so stick with me.

The Boise Center is located just southeast of central downtown Boise. The building itself is imposing; consisting of lots of windows, soaring ceilings, smart paint designs and a ton of research equipment.

The first lab I visited was is managed by Judy Steciak, associate professor of mechanical engineering, whose Energy and Efficiency Research Group (EERG) gets to set off miniature explosions in the laboratory every single day.

Don’t worry, when I say miniature, I mean very, very tiny.

The research group takes new biofuels in very, very small quantities, and ignites it under a very specific set of conditions. By doing this, the group can learn the exact temperature at which new fuels become vaporized. This is important because if it is not hot enough, it will not ignite. However, get the fuel too hot, and it results in large losses and inefficiencies.

In short, the group is looking for the ideal conditions for the combustion of new biofuels. This will help maximize them should a manufacturing company decide to build an engine to use them, or if someone wants to tweak their biodiesel engine to run on something slight different.

Additionally, the research helps determine which of the many, many new fuels (did you know there are 10 types of biodiesel???) is best for moving into the future of greener, cleaner engines.

Hagerman Science

Thursday, December 17th, 2009
The main trout and salmon growing facility at Hagerman.

The main trout and salmon growing facility at Hagerman.

The University of Idaho’s Hagerman Research Center is a fish lover’s dream. There has to be thousands – if not tens of thousands – of beautiful, healthy, delicious salmon and trout swimming around. From tubs chock full of hundreds of the little devils to bigger tubs filled with about a dozen nearly mature specimens, this whole place is about salmon.

(By the way, did you know salmon and trout are basically the same thing? Rainbow Trout and Pacific varieties of Salmon are the same genus – the first of the italicized words in the Latin name of an animal – meaning they’re so similar genetically they can breed. The same goes with Brown Trout and Atlantic varieties of salmon. And Steelhead? Nothing more than a Rainbow Trout that goes out to sea like a salmon. Confused? I know I am!)

So what are they doing with all these fish?

Genetics, of course.

Hagerman's egg incubation facility.

Hagerman's egg incubation facility.

Through a process of selective breeding, scientists are creating species of salmon and trout that are more resistant to disease, grow faster, grow larger and grow just as well on a vegetarian diet as on a diet consisting of fishmeal and oil.

(If it seems like I just said the word “grow” a lot, it’s because I did. A lot of the research goes towards the salmon farming industry.)

And they’ve had success. After four generations, trout and salmon now reach the same weight thy used to reach in a year in six months. And for the first time, a family of salmon grew just as fast on an all-plant protein diet as on a conventional fishmeal diet.

Additionally, the lab looks at the amount of phosphorus the fish take up and how much of it is in their food; an important factor in the environmental concerns of such facilities.

Hagerman's facilities for newly hatched trout and salmon. There are thousands of those little guys in there!

Hagerman's facilities for newly hatched trout and salmon. There are thousands of those little guys in there!

But the center does, of course, also address environmental issues and natural conservation. Every year they use genetics to monitor the returning salmon from endangered populations and to archive their DNA as well.

The facilities here include a 5,000-square-foot fish research lab, an outdoor facility of holding tanks, an egg incubation system, a warm water fish lab, ornamental fish breeding tanks, and giant pools filled with sturgeon.

Believe it or not, the people that run the place want to get into breeding and growing ornamental fish. And why not?

Rare species, fully grown and healthy, con often fetch thousands of dollars each. And the sturgeon? Be on the lookout for Vandal caviar, someday coming to a store near you!

Hagerman's tanks for experimental ornamental fish breeding.

Hagerman's tanks for experimental ornamental fish breeding.

A Thousand Rivers Run Through It

Wednesday, December 16th, 2009
The Hagerman Research Center as seen from a helicopter.

The Hagerman Research Center as seen from a helicopter.

Nearly 100 miles southeast of Boise and 35 miles northwest of Twin Falls sits a geographic improbability. A giant aquifer residing in thousands of square miles of porous volcanic rock gushes out of canyon walls in steady streams of pristine water. The area is called the Thousand Springs and is a major reason the region is dubbed the Magic Valley.

So what would all of this pristine water be good for?

If you answered parks, recreation and resorts, you’re right. If you answered one of the largest, most advanced fish hatcheries and genetic research stations in the country, you’d also be right.

And I take pity on you.

The water streams are the ideal source for the Hagerman Fish Culture Experiment Station. Simple pipes are all that are needed for gravity to bring water down into the facility for the station to conduct its research in sustainable aquaculture and salmonid species at risk.

The research site was given to the University of Idaho in 1998 by a congressional bill signed by Bill.

Clinton, that is.

Eight years later, a new building was constructed to house a growing team of researchers and lab technicians. Today, the staff consists of 25 and funding has risen to $4 million per year, 90 percent of which comes from grants and contracts.

The new facility is absolutely gorgeous.

The Hagerman admin building before expansion.

The Hagerman admin building before expansion.

It consists of 14,000 square feet of spacious hallways, large meeting rooms equipped with advanced video conferencing abilities, and more genetic extraction and analysis equipment than most – if not all - labs in Moscow.

The machine I found the coolest allows scientists to put their samples into large test tubes, which are then automatically piped into tiny test plates required for DNA analysis. It saves time and cuts down on human errors. That second part is especially important since some of the test plates cost several hundreds of dollars each.

The labs have the ability to do DNA characterization for large populations, quantitative DNA/RNA analysis and gene expression research.

The Hagerman admin building after expansion.

The Hagerman admin building after expansion.

One cool aspect was the finding of salmon tissue samples in the Smithsonian dating back to more than 100 years ago. The find is allowing scientists to extract DNA and compare the genetics of salmon before human development to today’s varieties.

But the equipment isn’t all Idaho’s.

The costs are often shared with the Columbia River Inter-Tribal fisheries Commission (CRITFIC) and the United States Department of Agriculture (USDA), which has a facility about 200 yards away. Through these strong collaborations, space at the facility is shared by by three USDA researchers and four CRITFC scientists and six technicians.

Because of this collaboration, they get space, and everyone gets to enjoy some of the best genetic research equipment on the market today.

But enough about today.

Tomorrow I’ll tell you about what they’re doing with the equipment.

The machine that pipes samples into tiny dimples on DNA dishes.

The machine that pipes samples into tiny dimples on DNA dishes.

Lighting the Way to Hydrogen Fuel Cells

Tuesday, December 15th, 2009
The Advanced Proton Source at Argonne National Laboratory will provide research facilities to explore materials for hydrogen fuel cells.

The Advanced Photon Source at Argonne National Laboratory will provide research facilities to explore materials for hydrogen fuel cells.

Everyone knows that one of President Obama’s big mandates is for more research into green, renewable energy sources. This means a lot more research grants are being given out to people working in these areas. Luckily, the University of Idaho has plenty.

One area Idaho excels in is the development of new battery technology. Besides working on lead acid batteries for hybrid electric vehicles (such as the Humvee they used to test them on, featured in the video below) the university is also looking into hydrogen fuel cells.

Tom Bitterwolf, professor of chemistry, recently got a grant to explore the possibilities of using ruthenium and rhodium for hydrogen fuel cells. The grant will fund the use of the most powerful x-rays in the western hemisphere at Argonne National Laboratory to take an amazingly detailed look at real-time chemical reactions of the two metals.

For more information, check out the recent press release.

Not Just Potatoes…

Tuesday, December 15th, 2009

The Kimberly Research and Extension Center isn’t all just potatoes.

Rows of beans growing in Kimberly's greenhouse have become very resistant to white mold.

Rows of beans growing in Kimberly's greenhouse have become very resistant to white mold.

It’s beans, too.

But don’t bring up soy beans or you may just insult some of the proud Idaho growers. There are no soy beans grown in Idaho, the industry is completely reliant on dry beans such as pinto and great northern.

The dry bean program in Kimberly – like the potato program – is very much into the genetic side of agriculture. Scientists are constantly analyzing the genomes of varieties of pinto beans, searching for markers that indicate a resistance to numerous diseases. The team is currently trying to breed a plant resistant to white mold.

White mold has caused serious losses in bean production programs across the country. The fungus – which affects more than 360 species of plants – causes the plant’s tissues to become pale colored, water-soaked lesions, which enlarge to become covered with a white, cottony fungal growth.

Obviously, nobody wants to eat a bean with cottony white mold on it.

To test for resistance, researchers cut off a branch stem and directly attach a piece of infected stem, covering it with a plastic tip. They then wait and see if the disease spreads to the rest of the plant.

White mold growing on a plant.When the testing first began, bean plants would become infected and die within a couple of weeks. The plants in the greenhouse today are in their second month of testing. And when the staff members tried to find a plant infected with white mold to show me what it looks like, they couldn’t find one.

Research in Kimberly

Monday, December 14th, 2009

Greetings again everyone. My apologies for the brief hiatus last week, but I was traveling across the southern portion of the gigantic state I call home. While traveling, I had the opportunity to visit three of the University of Idaho’s research centers: Kimberly, Hagerman and the Boise Water Center. I saw a ton of great facilities and work being done, and am eager to share it all with you. So without further ado, let’s start with Kimberly.

When I say the words, “Key to the future of potatoes in Idaho and the rest of the world,” chances are an image of Sanjay Gupta does not immediately pop into your head.

Sanjay Gupta - the man behind the next great potato variety.

Sanjay Gupta - the man behind the next great potato variety.

Born and educated in India, Gupta has been working with potatoes in the United States for over a decade. Most recently, Gupta was researching spuds in Minnesota. That is, before the University of Idaho enticed him to join the team at the Kimberly Research and Extension Center located just outside of Twin Falls, Idaho.

Standing about 5’ 9”, sporting glasses, a quick smile and a thick accent, Gupta will be the first to tell you that he is in spud heaven. Everything he needs to conduct his cutting-edge research is within a hundred yards of his all-too-eager hands.

His official title is Potato Post-Harvest Physiologist. Just in case that is not clear, here’s a brief rundown of what that entails.

Gupta specializes in the biochemistry of potatoes after they have been removed from the ground. He takes tiny square samples and places them in test tubes, which are in turn submerged in liquid nitrogen. Once frozen solid, the spud is shaken in the test tube along with a metal rod, pulverizing the spud into a fine powder. This allows Gupta to analyze the exact chemical makeup of the potato.

Farmers are always looking for the next great potato. Currently, the Russet Burbank is the standard. It is grown in about 80 percent of the country’s fields. But that doesn’t stop growers from trying to create varieties that can be stored longer, taste better, fry more golden, resist diseases better and grow more abundantly.

But believe it or not, it can take 15 years for a potato to be completely tested.

First, a grower creates a new variety. Then, the farm spends years growing enough potatoes to put through testing.

The storage tests take three years in themselves, which doesn’t even include subsequent tests for growing seasons, regions, taste and many other important factors.

One of the nine potato storage test centers at the Kimberly Research Center.

One of the nine potato storage test centers at the Kimberly Research Center.

Gupta is trying to cut down on this time.

Through his decade of experience, Gupta has discovered several key biochemical indicators that signal a potato’s potential to survive storage. Because of his 80 percent success rate, growers and the Potato Association of America are now sending all of their new potential varieties to Kimberly, Idaho for preliminary tests. If they pass the pulverizing powder biochemical exam, they go through storage testing at the facility.

Kimberly is outfitted with nine state-of-the-art simulated storage silos. These chambers exactly simulate the conditions potato farmers and the Snack Food Association store their potatoes in. They precisely control the temperature, humidity and general storage conditions in order to determine a spud’s perfect storage conditions.

So the next time you enjoy a golden brown and delicious chip or French fry, remember that the man behind ensuring the quality of your product from the ground up earned his Ph.D. in biochemistry from Chhatrapati Shahu Ji Maharaj University located in Kanpur, India.

Exploring the Unknown - Part 3 - What AB Bubbles Are

Monday, December 7th, 2009
The AB bubbles are shown "collaring" to a spherical mineral.

The AB bubbles are shown "collaring" to a spherical mineral.

In previous posts (parts 1 and 2), I described the work experience of Frank Andres and his discovery of a mysterious substance that produces AB bubbles, which purified a copper nugget and turned copper clear. After years of research in his basement, Andres has observed these mysterious bubbles removing trace amounts of precious metals – particularly gold – from organic materials and forming long, colorful tendrils with them.

As I said before, Frank Andres, Franklin Bailey and other colleagues at the University of Idaho have observed these AB bubbles forming colorful tendrils from precious metals removed from organic materials. But the question remains, what exactly are these AB bubbles?

Franklin Bailey isn’t exactly sure what they are, but he’s quite sure about what they are not. Some scientists dismiss the bubbles as hydrogen bubbles – or other natural forming gas – escaping from the minerals when hydrochloric acid is applied.

However, the bubbles have a membrane that protects the inside. When the solution is removed, the bubbles dry out, but they do not go away – they remain intact. Then, when a liquid is reapplied, the bubbles bounce back to life.

That’s not to say that they are alive, though. Neither Frank nor Franklin believes that to be the case. But they could be a byproduct of other living creatures. Specifically, Franklin Bailey thinks they may be the result of the interaction between a bacteria and fungus. The white substance originally found on the gold nugget, and ever since used in these experiments, does appear to be a fungus, though scientists still are not sure.

As for the bacteria… well… they haven’t exactly found it yet. Again, Franklin Bailey believe that the bacteria that is interacting with the fungus could be located inside the mycelia of the fungus.

It is such a confusing – but promising – subject that Franklin Bailey has brought several other scientists into the fold. Susan Childers, assistant professor of geomicrobiology, is also weighing in on the research. Actually, she was the first to suggest the substance producing the bubbles may be a fungus/bacteria interaction. Larry Forney, professor of biological sciences and director of the Initiative for Bioinformatics and Evolutionary Studies (IBEST), was so impressed by the potential that he urged the group to patent their discoveries to date.

But the real whopper of a theory comes from Frank Andres himself. When asked, he will tell you that he believes the AB bubbles are the key to discovering the origins of life on Earth. He theorizes that they were the cell membranes of the very first protocells to appear on the planet back when the formation of a protein was impressive.

The reason for this believe is the bubbles ability to “collar,” as seen in the photo above. This is how the bubbles attach themselves to the substance they remove the precious metals from. This is also an ability demonstrated by protocells, which Frank believes obtained the ability from interaction with the AB bubbles during the beginning stages of life.

This is certainly a very distant theory. But then again, so was the belief that the Earth was flat at one point.

No matter what they are, it is clear that they can find trace amounts of precious metals – particularly gold – and this fact alone has commercial value. That is why it is crucial for these scientists to discover what exactly is going on here.

And if you ask Frank, he doesn’t want any fame or fortune from whatever may come from the research. Here’s what he has to say on the issue:

“I want the University of Idaho to benefit in what’s going to be found from all of this. There are articles that come out every day about things like this that will bring students that are interested in researching it to the University of Idaho. That’s what I want. I want the university to benefit from an excieting, new find. That’s my whole game in this thing.”