http://nanosapiens.net/2011/12/careers/biotechnology-careers/killer-plants/ http://nanosapiens.net/2011/12/careers/biotechnology-careers/killer-plants/#comments Wed, 07 Dec 2011 18:24:08 +0000 Gabrielle DeMarco http://approach.rpi.edu/?p=2804

The human immune system is a marvelous machine. Bacteria enter the body (perhaps through those nasty, chalky mints at the local diner that you simply could not resist diving in to). Above is a gross image of the mints’ effects as you see salmonella bacteria attacking human tissue. To fight the invasion, our white blood cells immediately get to work to attack the bacteria. If you are lucky, the bacteria are neutralized by the immune system and you can peel yourself off the bathroom floor and move on with your life, hopefully avoiding future contact with publicly shared jars of candy.

Scientists are discovering that plants also have a type of immune system that attacks bacteria and fungi. Instead of white blood cells, plants produce an abundance of things called flavonoids. And some very ingenious scientists here at Rensselaer are starting to ask the question, “If it works for plants, might it also work for humans?”

Why bother checking if flavonoids stop the spread of bacteria in humans? The answer is simple: society is running out of ways to kill bacteria. New methods to stop bacteria are becoming essential as the old methods – antibiotics like Z-pak, penicillin, amoxicillin, and the like – become less and less effective.

Despite being very simple organisms, bacteria have developed some exceptionally smart survival systems. As they and their brethren have been bombarded by decades by pills and sticky medicines, they have slowly adapted to survive the barrage. One of these adaptations actually allows bacteria to pump toxic compounds like antibiotics out of their systems before the drugs can leave lasting damage. And so, the antibiotics go in and the bacteria spit them right back out. To combat this, doctors need entirely new molecules to throw at the bacteria. When faced with a new molecule, the bacteria simply will not have the systems in place to combat it and they will be killed.

Of course there are a lot of different chemicals and compounds out there besides antibiotics that will kill bacteria on contact. But, drinking pool chlorine or injecting battery acid is not something I look forward to. I am guessing you are with me on at least this point. So, new drugs to combat bacteria also need to be safe for the very sensitive human system.

Flavonoids have long been praised for their health benefits (eat your kale), but little is understood about their antimicrobial effects. Mattheos Koffas who works in the Center for Biotechnology and Interdisciplinary Studies and a team of researchers at the State University of Buffalo and in the pharmaceutical industry are looking at how effective flavonoids might be in combating bacteria in the human system. The scientists recently published a paper in the journal PLoS One that shared some very promising results on the future uses of flavonoids in medicine.

What they found was that naturally occurring flavonoids in plants had strong antibacterial and antifungal properties. They were also safe to human cells. Koffas and the team then took the research an important step forward by designing non-natural flavonoids in the lab. These new molecules took all the best aspects of the natural flavonoids and essentially turned up the volume.

What they found was that these chemically-synthesized non-natural flavonoids were even more potent against bacteria and fungi. They also appeared safe for human use.

The research provides an important path forward for a new class of antimicrobial agents – flavonoids. Koffas plans to continue to study the potential of these new molecules.

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Word recently reached the street that Rensselaer is making a contribution to Saratoga First Night 2012 in signature techie style with the “Hands-off Arcade,” a collection of retro games retooled for the Microsoft Kinect gaming hardware. Shawn Lawson, an associate professor of arts and faculty member in the Rensselaer Games and Simulation Arts and Sciences program, said all the games will obey the hands-free theme:

There’s no remote, no joystick, no nothing. It’s just the person the body, hands free interactive games experiences.

Lawson and collaborators Ben Chang (associate professor of arts and GSAS co-director) and Silvia Ruzanka, artist and RPI lecturer, debuted one of the games – Broken Breakout – during the Gamefest, the annual showcase of student-designed games hosted at Rensselaer. The game is a Kinect twist on the classic “Breakout.” That’s a video of Broken Breakout at the top of this post. Here’s how it’s explained by its creators:

While the interface for the original game consisted of a small knob, here one plays through the movement of the whole body. Cascading balls pour out of the bricks, as they are broken, filling up the screen and quickly overwhelming the original rules and purpose of the game. New interactions emerge as the player wades through the piles of rainbow-hued debris, scooping and pushing masses around.

Curious about how you build a video game, I asked Lawson a little bit about went into the process. In the case of the Hands-off Arcade, Lawson said the process is part creation and part integration.

We come up with the idea – how the game will work, how it will look, how it will sound, how it will interact with Kinect – that’s all built from scratch. But a lot of the things that we use aren’t build from scratch – the graphics drawing engine, the physics engine, OpenNI and NITE (a natural user interfaces)- all of these components are open source drivers and libraries that we use as pieces in a game that we design.

In other words, the vision for the game is creation, but the mechanics integrates existing software drivers and libraries – packaged sections of computer code that are available for all the world to use in performing specific tasks.

For example, the games employ a “physics engine” which is a section of software that determines how virtual objects will interact (when a ball collides with an object, will it bounce away, or break the object into pieces?). Similarly a “graphics engine” allows the designers to input information about graphic elements.

Our graphics Engine – OpenGL – talks directly to the hardware of the graphics card. When you say, ‘I need to draw a polygon here,’ you say ‘here’s the information about a polygon, these are the locations for the vertices, this is the style, this is the texture, here’s where the camera is, focal length of the camera, go draw this for me and put it here on the screen.’

The team have one other game  – Missle Command – in the bag, and are working on a few others. One game they are building, at the request of the Saratoga Arts, is a spinoff of a website interface “B-Flat.” The original website interface allowed users to mix video snippets of performances in the key of b-flat major to create an entirely new composition. The new version “B-Flat 2.0,” will fit the hands-free theme.

Lawson said the team hope the games they are creating for Hands-off Arcade are ”as much art project as video game.”

They’re kind of subversive in that we’re not really adhering to cannonical game play and themes: there’s no high score list, there’s no saving the princess. We’re sort of using a gaming format to explore ideas, artistic themes, or finding out what you can do.

The end result may not appeal to hard-core gamers, but it does have the makings of a good time on a fun night.

Having watched a lot of people play these things, they kind of understand that this is just here to be an experience – there’s no anxiety of ‘I’m terrible at this game,’ because you can’t really win, you can’t really lose. … It’s just to play and have fun.

Incoming search terms:

• silvia ruzanka

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Wayne Bequette is a professor in the Department of Chemical and Biological Engineering. We ask Wayne about his work:

Q: Tell me a little bit about your work on creating an artificial pancreas to help people with juvenile diabetes.

A: Developing a fully closed-loop artificial pancreas requires a continuous glucose sensor, a continuous insulin infusion pump and a control algorithm to connect the sensor and pump. We have been tackling this problem one step at a time: first by developing a hypoglycemic alarm to warn of low blood glucose; next by constructing a simple pump shut-off algorithm to prevent hypoglycemia at night; then finally developing a fully closed-loop system. It is absolutely critical for engineers to have good medical collaborators to have a true impact, and I am fortunate to have excellent colleagues at Stanford University who perform the clinical studies.

You started your chemical engineering career working in the oil refinery industry. How did you end up in leading-edge biomedical engineering?

When I arrived at Rensselaer, I took the time to meet with just about every faculty member who was doing systems and control research. This led to me being asked to be on the dissertation committee of a graduate student in Biomedical Engineering, who was working on a drug infusion system to control a patient’s blood pressure and cardiac output. I introduced him to model predictive control (MPC), which was (and remains) the most commonly used advanced control technique in the oil refining industry. In no time he had coded up an algorithm and applied it to his drug infusion problem. About 10 years ago I decided to move into diabetes technology. One motivation was that a sister of mine has type 1 (also known as juvenile) diabetes; it turns out that many researchers in the area have a similar personal connection to the disease.

You seem to have a bit of a green streak, as your research also brushes up against fuel cells, biodiesel, and coal gasification. Is sustainability and efficiency important to you?

In addition to performing research in “green technologies,” I try to live a reasonably energy-efficient lifestyle. Most days (well, nine months out of the year), I bike to campus from my home in Albany. The 25-mile round trip by bike saves a 32-mile roundtrip by car, reducing fuel consumption and carbon dioxide production. The main challenge with my bike ride is that, in both directions, it ends with an uphill climb.

Tell me a little about the books you’ve authored. It has to take a ton of work to write a textbook. Was it challenging?

You certainly learn a lot by writing a textbook. My first textbook, focused on process dynamics and emphasized nonlinear behavior; I wrote it at a time in my career when I was learning about chaos and related topics. My second textbook, focused on control system design, was the first in chemical engineering to emphasize a model-based approach.

When did you know or decide that you wanted to be a engineer?

In seventh grade I told a friend that I liked math and science and he convinced me that I should be an engineer.

What would you say to young students and high schoolers who are thinking about studying engineering or becoming an engineer?

I would say that some of the math that you learn in high school may seem abstract at the time, but the more math that you learn, the better prepared you will be for an engineering career.

Outside of the lab and the classroom, what do you like to do for fun?

Three years ago, motivated by the 2008 Olympics, I began strength training and pole vaulting again. At the age of 54, I am actually a better vaulter than I was in high school, which probably says more about how bad I was in the early 1970′s than how good I am now. In addition to hiking and biking much of the year, I ski in the winter—although not aggressively enough to keep up with my two kids (ages 12 and 15).

To read more about Bequette and his research, see a Rensselaer story here, an Approach post here, and a great Channel 13 story here.

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Earth may not be the only planet in the solar system to have supported life. Analyses of Mars reveal that during its history the Red Planet has had many of the right conditions in place to sustain microbial life and perhaps even more sophisticated organisms. But, it is a hard theory to prove when a trip to the Martian surface is a more-than eight-month journey through space and time.

On November 26, NASA made headlines around the globe as it launched the next big mission to Mars – an ultra-sophisticated rover called Curiosity. Curiosity is tasked with scouring Martian rocks and dusts for signs of water, organic materials, and other indicators of habitability. It will journey farther on the planet than any previous rover.  With 10 different scientific instruments on board for analysis and imaging, the rover is expected to provide exciting new information about our distant neighbor.

Our new Dean of Science, Laurie Leshin, is a member of the science team for Curiosity and was there for the heart-pounding launch. Dr. Leshin was kind enough to share some of her experiences from the launch here at The Approach. She will keep us updated periodically as the rovers makes the journey across our solar system.

I’m thrilled to be writing this from Cape Canaveral where I was privileged to watch the launch of the next Mars rover. Curiosity blasted off on the Saturday after Thanksgiving to begin its eight-and-a-half month journey to the Red Planet.

I have been working on MSL (NASA’s official mission name is the “Mars Science Laboratory” or MSL) for about 10 years dating back to the original “Science Definition Team.”  I am on the science team for two of Curiosity’s 10 instruments. Both are chemical analysis instruments that will allow us to understand the rock types and the volatile content of these rocks. We are especially excited about measuring water and carbon-bearing compounds – perhaps we will definitively detect organics for the first time on the surface of Mars!

Seeing a launch is an emotional experience – first you see the fire, and then a few seconds later (we watch from a safe distance of several miles away) the roar of the engines shakes you to your core.  It took over a million pounds of fuel to propel Curiosity out of Earth’s gravity well and set it on its trip to Mars.

Probably the best part of the launch was that I got to share it with my family.  Jon Morse, the Rensselaer Associate Vice President for Research for Physical Sciences and Engineering (and my husband) was there, as were my two stepsons, ages 8 and 12 – it was their first launch.  Overall, a great Thanksgiving for us!

Stay tuned for more updates on Curiosity. You can also follow updates on my Twitter feed (@RPISciDean) and get ready for landing on August 6 at 1 a.m. Rensselaer time!

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Earlier this year, the Center for Architecture, Science, and Ecology (CASE) received a 2011 R&D Award from the American Institute of Architects for one of their newest research projects – the Solar Enclosure for Water Reuse. Here are a few thoughts from the award announcement:

According to the World Health Organization and UNICEF, approximately one in eight people lack access to safe drinking water. In the United States, the building industry alone consumes 12 percent of all water withdrawals, and another 49 percent of water is used to create energy to power the built environment, according to the U.S. Geological Survey. In the face of such overwhelming evidence, the Center for Architecture Science and Ecology—a partnership between Skidmore, Owings & Merrill and Rensselaer Polytechnic Institute—developed a prototype that conserves energy and uses solar energy to passively filter graywater. And the system isn’t stashed in the basement or hidden from view. Instead it takes the unexpected form of a glass façade.

Sounds about right. The CASE invents materials that incorporate systems – like generating electricity, gathering water, treating sewage, or filtering air – directly into building materials for roofs, walls, windows and interior partitions. Their signature is an elegant solution that, as the award announcement recognizes, puts sustainability front and center in design.

I recently had a chance to visit the lower-Manhatten offices of the CASE in its lower-Manhattan offices (co-hosted by Rensselaer School of Architecture and architecture firm Skidmore, Owings & Merrill in the SOM offices on Wall Street). Their space is sort of half-office/half-lab and it was peppered with interesting prototypes and projects in progress. It was fun to see so many of their inventions in one space doing their thing.

For example, the picture at the top of this post shows one of the prototypes - an ”Integrated Concentrating Dynamic Solar Facade” -undergoing tests in an office window. The solar facade - which can be used for windows or facades - contains solar concentrators that track the sun and simultaneously generate electricity, gather heat from water circulating through the system, and diffuse light coming into a building.

In the top picture,  you can see two working solar energy collectors on the right - a photovoltaic cell is fixed at the apex of the glass and flexible tubing channels water through the system, and on the left is a sensor measuring the amount of light entering the system.

This closeup shot (above) shows the frontside of a collector with the lens and flexible water tubing surrounding the photovoltaic cell. As they refine their design, CASE researchers are gathering data on how much heat and eletricity the system gathers, as well as how much heat is lost as it travels through the system.

CASE Director Anna Dyson said CASE researchers are “expert integrators.”

We solve problems. We do something different because what’s out there isn’t good enough. We look at what’s out there that we incorporate in the solution, and we integrate it with building materials.

CASE not only develops building materials, it also trains an up-and-coming generation of architects to look across disciplines to solve problems. Center director Anna Dyson said that while CASE students (a mix of undergraduates, master’s and PhD candidates in architecture) are specialists within their field, “their specialization is in integration.”

Our students are expert integrators, expert organizers, they have taken science, they’ve taken math, social sciences, art, and architecture. We see very few people in the field who have the ability to integrate that our students are developing.

For example, when CASE built the first generation solar facade unit (several successive generations have since been built), they pulled together an existing mirror tracking system, a furnace lens, and the perfect solar cell for the job, but at the time, the solar cell was only available for satellites. Since they couldn’t buy it, a professor on Rensselaer’s campus actually had to build their first solar cell by hand. The CASE researchers had to consider: Would that cell eventually be available for commercial use? Would it be affordable at that point? Were better options coming down the pike?

Dyson and CASE Assistant Director Jason Vollen will also tell you that the lack of such “blue fingers” abilities in the building field is an impediment to greater integration of sustainability in building materials. As Vollen put it:

If you don’t have policies, and you don’t have the codes, then you can’t have the progress.

Dyson and Vollen have a lot to say on the subject, and they hope their insight and experience will play into a longhaul revolution in the philosophy of the building professions.

But please, let me not neglect my guests - there’s more to see.

CASE is working on a “phytoremediation system,” a modular wall unit that supports common house plants capable of filtering “off-gas,” the toxins emitted by modern furniture, office equipment and finishing materials in office environments (that’s Vollen in front of a prototype unit). In another example of integration, CASE researchers came up with the idea for the system, and then combed existing research to determine which plants best filter formaldehyde (English ivy, as it happens).

The plants create oxygen, while bacteria growing on their exposed roots break down volatile organic compounds (VOCs) and other pollutants. CASE estimates that the system is capable of lowering VOC levels found in typical offices by more than 80 percent, reducing the load on mechanical ventilation systems, and cutting HVAC energy consumption by up to 60 percent.

Another idea in the works combines knowledge of ceramics, and thermochromatic coatings with the particular sun position and climate in a given location to produce the “high performance masonry system.”

You can see some of the sample bricks (mounted on a conference room wall) on the left. An architect designing a building can choose from a palette of bricks to tune the absorption or diffusion of heat on a particular building based on the climate, orientation and even height of an exterior wall. As with the integrated solar facade materials, water can be piped past the underside of the bricks to heat or cool it as part of the domestic heat/hot water system of the building.

CASE regularly earns accolades and awards for their work – the phytoremediation system won a 2009 AIA R&D Award to mention one – and, while they’re not interested in commercialization, they do hope to see each of their inventions installed in an actual building - which is called a “test bed.” One of the advantages of the partnership with SOM is that they are regularly approached by architects working on a project that holds potential as a test bed for the CASE designs. It is a long road from drawing board to prototype to installation in a real live building, but, from what I hear, the destination is in sight.

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