Improving microarray analysis

According to some industry sources, scientific breakthroughs are as common as London buses.

You wait for a while, and then three come along at once.

This rarely happens.

Breakthroughs are dramatic and important discoveries or developments that often involve a culmination of hard work and hours of toil that, until that point, have been generally overlooked and/or disregarded. The breakthrough comes when a satisfactory conclusion is made and the world finally sits up and takes notice.

In the world of science, real progress is slow and painful, so breakthroughs don't come along in flocks, herds or schools, but rather as rare, but very welcomed and isolated events.

Few scientific developments warrant this description.

The birth of the jet engine stemming from the heroic efforts of Frank Whittle is certainly one, while the endeavours of Scottish inventor John Logie Baird in his quest to achieve the world's first transmission of television images is certainly another. Biopharmaceutical breakthroughs rely on the analysis of literally millions of material samples to unearth critical pieces of information that will facilitate the progression of a study. Technology plays an important role in this process, especially as the spectre of commerce now hangs ominously over most research facilities.

Time is money after all, and the latest testing equipment is designed with this mercantile mantra very much in mind.

This truism extends from laboratory desks and extraction units to syringes and petrie dishes.

Technological innovation has speeded up analytical progress in order to cater for the growing demands of big business.

Cell analysis One of the foundations of biopharmaceutical research has been cell analysis.

It is estimated that there are about 6x10e13 cells in a human body and about 320 different types.

Cell sizes vary depending on the cell type and circumstances.

For example, a human red blood cell is about 5um in diameter, while the diameter of an animal or plant cell can range between 10 and 100um.

All organisms consist of cells.

Analysis of these building blocks of life is achieved using specialist optical equipment, such as conventional microscopes and 3''x1'' slides, otherwise known as microarrays.

According to the European Bioinformatics Institute, microarrays are constructed from glass (or some other material) - on to which DNA molecules are attached at fixed locations (spots).

There may be tens of thousands of spots on an array, each containing a huge number of identical DNA molecules (or fragments of identical molecules).

The spots are either printed on the microarrays by a robot, or synthesized by photo-lithography (similarly as in computer chip productions) or by ink-jet printing.

This description forms part of a wider study looking at the fundamental elements of biology.

It appears on the organisation's website and goes on to point out that microarrays are used to analyse different cell types at particular times, under particular conditions.

For instance, microarrays can be used to compare gene expression between normal and diseased, ie cancerous, cells.

The narrative continues: "The raw data - produced from microarray experiments are hybridised microarray images.

"To obtain information about gene expression levels, these images should be analysed, each spot on the array identified, its intensity measured and compared to the background".

This is called image quantitation. "To obtain the final gene expression matrix from spot quantiations, all the quantities related to some gene - have to be combined and the entire matrix has to be scaled to make different arrays comparable." Not an easy process, but one that often produces data crucial to the development of some of the most important biopharmaceutical theories.

To make the process more cost efficient and, more importantly, accurate, technological innovation has once again played an important part in defining modern microarray analysis.

Microarray preparation. The traditional way to prepare, or spot, microarrays is to use split pins that are dipped into the well plates in order to pick up sample liquids.

The pins are subsequently touched down onto the microarray slides thereby depositing a spot.

Unfortunately, the pins need to be washed and dried after spotting before another set of liquids can be handled.

This method can be slow, laborious and unreliable, and can produce large and variable spots.

It also uses a considerable quantity of liquid, much of which is wasted.

With numerous microarrays required to complete a testing procedure, the process of spotting can be time consuming and expensive.

It is unsurprising that over the years this basic principal has been refined and improved upon.

By incorporating the latest innovations in pin and plate design, greater levels of efficiencies and performance have been achieved.

These, however, pale into insignificance against the technological strives made by an Edinburgh-based company founded by a Cambridge physicist, Dr Howard Manning, and University of Edinburgh molecular biologists, Prof Peter Ghazal and Dr Douglas Roy.

Prototype solution.

Incorporated as a limited company in August 2000 and achieving two-stage funding from the Scotland-based investor group Archangels and a Smart award within a year, Arrayjet had ambition based on innovation.

The company's goal was to manufacture an effective prototype pick-and-place liquid-handling system for use with microarrays.

By the end of 2001, the fundamental technology behind Arrayjet had been demonstrated and the system went into production and testing.

The automated machine picks-up liquid samples from well plates and deposits them on microarray slides using standard ink-jet printheads.

The resulting 100-pico litre sample spots are much smaller than conventional sample sizes and, as a result, use less biological fluid.

More importantly, the machine is extremely accurate. Cameron Kennedy, senior mechanical engineer at Arrayjet, says the system's accuracy is critical both in terms of sample placement and subsequent information recovery.

"We were looking for an accuracy of +/-5um, or better," he explains. "This would enable us to place around 30,000 dots on each slide and, more importantly, it would help us determine accurately where each sample was located".

Creating a truly innovative machine that could potentially redefine biological research is a considerable undertaking.

For the Edinburgh-based company, it took nearly three years.

Central to this development process was the highly accurate linear motion components supplied by THK, a manufacturer of motion and guidance systems for machine tools, robots, semiconductor applications and computer-controlled systems.

For Arrayjet and its biotech robot, THK's linear motion systems were pivotal.

"They're utterly critical," says Cameron, "everything is based around them".

Linear motion guides.

Linear motion guides are machine components that move or position machinery and/or other component parts to perform specified tasks.

Extremely adaptable, linear motion guides can be installed on level surfaces, vertical planes, inverted positions, slopes or walls - in fact, any location that requires equipment to be moved from one place to another.

They are typically constructed using rails, or raceways, and guide blocks, or platforms, on which materials or components are transported along specified routes.

Various techniques are used to support this mechanism, although most systems employ steel ball bearings housed within the block that run along a groove in the rail.

This design creates a highly efficient unit delivering precise movement and pinpoint control.

The latest generation of linear motion products are extremely reliable, to the point that they are often regarded as fit-and-forget components.

A number of innovations have facilitated this reputation, none more so than the development of a system that holds the guide's ball bearings at an equal distance from each other by incorporating specially designed retainers.

The system, know as the caged ball design, enables smoother movements, less friction and fewer maintenance requirements.

More importantly for Cameron at Arrayjet, it enables a far greater degree of long-term accuracy.

"We wanted linear motion components that wouldn't need servicing during the life time of the machine," Cameron notes.

"We considered a roller mechanism, but we couldn't tolerate the inaccuracies a system like that would throw up.

"We needed a solution that would give us guaranteed and consistent levels of accuracy"Q.

Arrayjet incorporated eight linear motion guides into their machine with a number of THK's ballscrews and linear bearing units.

Their role was to manoeuvre the printhead over the well plates for sample loading and then reposition it over the microarray slides to deposit the liquids.

In each case, the linear motion relied on the precise, smooth movements and long-term, maintenance-free operation of the Caged Ball technology.

"We got exactly what we were looking for," Cameron says, "and that was precision.

"There's a lot of innovation in our machine, and I simply don't have the time to worry about the linear motion side of things. "So I opted for the best available solution".

Improved testing Arrayjet successfully developed an innovative technology that applies standard ink-jet printheads to the manufacture of microarrays.

It significantly improves the efficiencies of parallel testing, especially when producing large quantities of biological and chemical samples.

By enabling the accurate transfer of high-value samples in small quantities, Arrayjet has facilitated the production of superior slides at much higher speeds than existing robots and without the prospect of cross-contamination.

Faster, more efficient and extremely reliable, Arrayjet's liquid-handling unit represents the very latest development in microarray analysis.

Underpinning this technology is the latest linear motion technology that manoeuvres the system's printhead to within +/-5æ, or better.

By achieving highly accurate movements at exceptional speeds, modern linear motion guides make crucial testing procedures more reliable and less wasteful.

They also greatly enhance the prospect of more biopharm breakthroughs being completed within budget and on time.