Spring 2001 -- Vol. 18, No. 1

Busy Microarray Facility Puts Penn State in Strong Position

 

John Szot, facility manager for the DNA Microarray Facility at Penn State, places a tray that holds DNA and gene "ink" on the microarray robot. Using pins that act like fountain pens, the robot prints individual samples onto slides, with as many as 1,600 small dot-like samples in a square inch.

Like many who work in science, John Szot knows what to expect at family gatherings during the holidays or at summer events and reunions with the in-laws.  When he begins to describe his work, family members get that glassy look in their eyes followed by some head nods and almost reflexive "uh huhs."  Following a few minutes of explanation, they still have almost no idea what he does.

After all, facility manager for the Penn State DNA Microarray Facility does not stir the imagination and prompt easy understanding the way fireman, policeman, or even Webmaster might.

In a sense, though, Szot does all those things--and more--as he directs the year-old, on-campus facility and assists University researchers as they continue to improve their understanding of its cutting-edge DNA technology.

"We've grown from scratch and learned a lot along the way through trial and error," Szot said.  "It was a long process, and it's something some other microarray facilities did not have to do because many of the things we did ourselves now can be purchased or installed commercially.  But, we probably have a better understanding of the process and technology because we've done almost everything from the ground up."

Just as DNA sequencing reshaped scientific research 25 years ago, DNA microarray technology ranks as the current breakthrough in this field, largely because of its effectiveness and efficiency.

Thanks in large part to the leadership of Nina Fedoroff, professor of biology, the Verne M. Willaman Chair in Life Sciences, director of the Life Sciences Consortium, and director of the Penn State Biotechnology Institute, Penn State was one of the first universities to create its own microarray facility.  With funding from the Life Sciences Consortium, the facility made its home next to her laboratory on the second floor of Wartik Laboratory.  It quickly garnered support from the University, and has become an important resource for many Penn State scientists studying gene expression.

"If you think of it as a library, it's the difference between trying to infer what's going on by watching a student or two as opposed to following everyone at the same time," said Fedoroff.  "If you see everyone, you can begin to assess the whole process of library use.  Instead of one gene at a time, we're getting all this information from many genes at once.  It allows us to assess things in a much more comprehensive manner than has ever been possible before.  It's a wonderfully powerful tool."

Along with the experience of establishing a center and nurturing it through its growing pains, Penn State benefits simply because the on-campus facility makes research affordable and convenient.

"There are communities of scientists that have tried to organize microarray technology on a service basis, and I don't think that is going to work because these experiments always prompt more questions than answers," Fedoroff said.  "So, if they take a sample from you, process it and get back to you that's all you've got.  You've got data, but you've got to get back in line for the next question."

For those who want to utilize the scientific method efficiently, such a service-oriented approach provides a huge hurdle.  Fedoroff's design for the center, however, features almost regular availability for researchers at Penn State.

"Think about my library analogy from a larger perspective," Fedoroff said.  "If you were looking from another planet and trying to figure out why all these people were zooming around on Earth you would have to have ways of interfering with systems to see what happens to the information flow in this society.  To be a truly successful experimental scientist, you have to have the ability to change parameters and test systems repeatedly.  A microarray facility here makes that possible."

In terms of hands-on activity, Szot makes things possible once researchers decide to use the facility.  The process begins with DNA molecules--be they plant, mouse, yeast, or even human--from a clone library.  Using those samples, microarray technology allows researchers to print as many as 6,400 individual dots of DNA, with each dot representing a specific gene, onto a normal microscope slide.

All 6,400 dots, and there may be fewer depending on the number of genes tested in an individual experiment, are placed in about a square-inch area on the slide by a robot.  At Penn State, the robot can repeat this process on as many as 210 individual slides for an experimental set.  For perspective, though, a set that large requires 42 consecutive hours of operation for the robot to precisely place all 6,400 spots on the 210 slides.

Once all the gene samples have been placed on the slides, the slides are treated in an ultraviolet oven to affix the samples permanently to the slide with a covalent bond.  They also are treated with a combination of messenger RNA and florescent dyes--a process that requires another 24 hours.

Later, with the combination of messenger RNA and dyes having had time to "label" the genes, researchers can clearly see, thanks to laser pictures and significant magnification, which genes were activated under specific conditions.  Because of base pairing, the RNA "sticks" to the individual genes it came from.  And, because the dyes are of distinct colors, researchers can determine which specific genes are activated.  According to Szot, red and green dyes were selected because their spectra do not overlap and that reduces the chance of false signals and innaccurate results.

"You could imagine it as a light bulb hanging off each of the genes," Fedoroff said.  "A gene that appears brightly in a certain color has lots and lots of light bulbs, in this case RNA, hanging off of it. Another gene, under a certain set of conditions, does not light up as brightly because it was not activated."

Even with all the "light bulbs" lit, the research has only just begun.  All the colorful dots do not mean a thing until researchers digest the data from the respective genes.

With as many as 6,400 gene samples, 210 slides, and a good experiment requiring as many as 10 to 12 repetitions for accuracy and statistical validity, the resulting data can seem overwhelming.

"We can help with any aspect from the set up to the analysis of the data. We want to be a resource for our reasearchers." John Szot, DNA microarray facility manager

"It's kind of like the old question about tacos," Szot said.  "Is there more fun in making them or eating them?  When it might seem like all the work has ended after you set up a microarray it's really only getting started."

In addition, quality microarray work requires an appreciation and willingness for interdisciplinary efforts.

For example, mathematical and statistical principles must be applied to derive meaningful answers for biological questions prompted by the DNA studies.  Already, Fedoroff has collaborated with people such as Jayanth Banavar, professor and head of the Department of Physics at Penn State, to address fundamental patterns in gene expression.  Their work, published earlier this year in the Proceedings of the National Academy of Science, created a "buzz," according to Szot, and determined that some simple regularities exist amid the overwhelming amount of data.

"Overwhelming" seems to define the factors involved in making the microarray facility a reality and coordinating its ongoing work.  Yet, none of the daunting chores and time-consuming start-up work prevented Fedoroff, Szot, and many others from making the facility a reality.

From the robot itself, which was built at Penn State with plans found on-line and which provides room for almost twice as many slides as any other such facility, to the computer program necessary to run the robot, meticulous planning and repeated trial-and-error adjustments have produced a unique and valuable tool.  In terms of the computer program--which specifies how the robot makes each and every one of its movements to place printing heads of DNA just microns apart thousands of times--a typical text file containing the program could take up as much as 6.6 megabytes of computer space.

In addition, because people at Penn State did much of their own work, and continue to do so in terms of seemingly simple things such as slide preparation, the facility provides an extremely affordable option for researchers at the University.

For example, Szot--who serves as the facility's director and one-man staff--can produce slides at a cost of about $20 to $25 each.  Should researchers order their slides through the mail, the cost could be as much as $2,000 each.  Plus, Szot and the Penn State facility offer flexibility.

"We can put together an array any way they need it to be done," Szot said.  "We can help with any aspect from the set-up to the analysis of the data.  We want to be a resource for our researchers."

-- By Steve Sampsell

Back to Science Journal Spring 2001 Index

Penn State Home Page | Eberly College of Science | Find a Person | Locate a Building | Search | Site Index

Students | Alumni | Visitors | Researchers | Faculty and Staff | Postdoctoral Fellows | Corporate Interests
Academic Programs | Research | Dean"s Office | Development and Alumni Relations | News and Events | Directory

This page was last updated on 12 March 2001

If you would like to communicate with the keepers of the Eberly College of Science Web server, send electronic mail to: science-web@thunder.science.psu.edu
Technology Webmaster: Joseph K. Carlson < jkc3@psu.edu >
Content Webmaster: Barbara Kennedy < science@psu.edu >