Top Ten Innovations 2010

Take a look at 2010’s Top 10 Innovations. Their clever designs speak volumes about the bright future of scientific experimentation.

JONATHAN ROTHBERG is best known for pioneering high-speed, massively parallel DNA sequencing, an idea that came to him after his infant son was rushed to intensive care and he realized how critical individual genome sequencing is to human health. He founded 454 Life Sciences, bringing to market the first new method for sequencing genomes since Sanger and Gilbert won the Nobel Prize in 1980. Rothberg’s invention ushered in the era of personal genomes with the first streamlined sequencing of an individual genome—that of James Watson, codiscoverer of DNA’s molecular structure.

AMY A. CAUDY is a Lewis-Sigler Fellow at Princeton University’s Lewis-Sigler Institute for Integrative Genomics. Prior to her appointment at Princeton, she coauthored the textbook Recombinant DNA: Genes and Genomes, and, as a graduate student in the Watson School of Biological Sciences at Cold Spring Harbor Laboratory, cloned several components of RNAi complexes. Her lab combines genomic and metabolomic methods to discover the biological roles of uncharacterized enzymes, with the goal of identifying key drivers of cancer growth.

NEIL L. KELLEHER is a researcher at Northwestern University where his group is recognized as a significant force in top-down proteomics, natural-products biosynthesis/discovery, and chromatin biology. Kelleher has been successful in driving both technology development and applications for high-performance mass spectrometry at the interface of chemistry and biology. He is especially interested in the biosynthesis and discovery of polyketides and nonribosomally produced peptides.

H. STEVEN WILEY is the lead biologist at the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory, where he utilizes cell imaging, computational biology, and high-throughput proteomics to study cell communication. His work combines the techniques of molecular and cellular biology with both biochemical and optical assays, and uses the results to construct computer models of cellular processes. He sits on the editorial board of The Scientist, and is a frequent contributor to the magazine.

Courtesy of Pacific Biosciences

The long awaited “third-generation” sequencer from Pacific Biosciences takes first place in this year’s Top 10 Innovations contest. The technology qualifies as belonging to a new era because it’s “the first single-molecule real-time sequencer,” says Stephen Turner, the machine’s coinventor and the company’s chief technology officer, speaking to a packed auditorium at this year’s American Society of Human Genetics meeting.

Like other single-molecule sequencing machines, the PacBio RS reads a burst of fluorescent color as a tagged nucleotide is incorporated into a single molecule of DNA. However, what differentiates this technology from others is that the anchored DNA polymerase processes nucleotide binding in real time. Most second-generation technologies wash each type of nucleotide over the polymerase one at a time, simplifying detection, but slowing the process. The PacBio RS eliminates the need for multiple washings by anchoring a single DNA polymerase at the bottom of a chamber. The labeled nucleotides diffuse freely into the well, where they are excited by a laser and their fluorescence is detected by optics on the transparent underside of the chamber. Because the laser light emits a wavelength of about 600nm, it can’t penetrate farther than the bottom part of the 70-nm-wide well, keeping labeled nucleotides outside of the well in the dark, and thus greatly reducing background signal.

The surprising advantage of real-time sequencing is that the machine can detect a natural stalling when, for example, the DNA polymerase encounters a methylated or otherwise modified base. The amount of time the polymerase stalls can be used to calculate different epigenetic modifications, adding a new layer of information to the sequencing data. The instrument costs $695,000; consumables and sequencing kits are sold separately.

Rothberg: PacBio RS is a true technical tour de force. Nothing but awe comes with the observations of single molecules of DNA read out to thousands of bases—truly a seductive technology.

Caudy: Ultrafast sample analysis and long read lengths make this an exciting new entrant to the DNA sequencing field. My early-adopting pals suggest there are some initial hiccups—hope they can deliver on the promises.

Courtesy of Sigma-Aldrich

Sigma-Aldrich cracked the upper reaches of our inaugural Top 10 Innovations list in 2008, snagging third place with its CompoZr custom zinc-finger nuclease service. Ever since then, the platform has borne serious fruit. Last year, Sigma-Aldrich’s knockout rat, made using CompoZr, took fifth place. This year, the company scores silver with the next step in realizing the potential of zinc-finger technology: custom-made cell lines. “This year it’s all about cells and cell biology,” says Dave Smoller, president of Sigma’s research biotech business unit.

Sigma first offered the design-your-own-cell-line service to biopharmaceutical companies in February, according to Supriya Shivakumar, the company’s global commercial marketing manager. “It’s very interesting what customers are bringing to us and having us make for them, because it’s beyond even what we had thought of,” Shivakumar says, adding that companies have requested more-efficient engineered cells capable of pumping out specific therapeutic proteins and custom cells that mimic a particular human disease. “We’ve made everything from simple to large deletions; we’ve inserted big chunks of fluorescent protein genes, and even made single-nucleotide changes.”

Though Smoller won’t say how many custom orders have been filled, he notes that the price varies from “north of $40,000 to $50,000 all the way up to $100,000” for a custom-made cell line, depending on the genetic manipulations requested.

In November, Sigma began shipping off-the-shelf cell lines—starting with human osteosarcoma cells containing fluorescently-tagged organelle marker proteins—created using CompoZr, and selling for approximately $6,000 a pop, according to Smoller.

Sigma is betting that the ease, convenience, and precision of their service will attract more business as it expands. “There’s a lot of demand for having something that’s guaranteed, everything is done for you, and everything you wanted is delivered to your door,” Shivakumar says.

Caudy: Designer cell lines without the work of mouse engineering are an exciting development that brings the power of zinc finger technology to the masses.

Kelleher: Making precise molecular surgery in mammalian systems is hard and tedious work. Many such systems have endogenous backgrounds that make teasing out of the mechanisms and effects of pharmacophores in cell biology difficult.

Courtesy of EMD Millipore

Forget the days of squinting at slides with a clicker in hand, or operating bulky benchtop machines to determine the number of cells in your sample. Cell counting is now portable, using the new Scepter Handheld Automated Cell Counter from EMD Millipore.

“It takes the tedium away,” says Grace Johnston, product manager for Scepter. Introduced in March 2010, the EMD Millipore Scepter—currently the only handheld automated cell counter available—sold over 1,000 units in its first six months on the market.

The Scepter handles like a pipette and is equipped with a screen that displays instructions to guide the user through the process. “A lot of scientists get nervous about adapting to an automated instrument, but it’s really straightforward and easy to use,” says Johnston.

Instead of relying on object recognition software like some automated benchtop counters, the Scepter draws samples into a disposable sensor where they pass through an opening charged with a current. As cells disrupt the current, the Scepter records each change in voltage. Within seconds—14, on average—the screen displays cell concentration, average cell diameter, and average cell volume, as well as histograms of each distribution.

“You can have accurate and reliable cell counts from one sample to the next, and all of that can be done right at the culture hood within 30 seconds,” says Johnston. At a list price of $2,995, it’s also the most inexpensive automated cell counter on the market, she adds.

Wiley: Cell counting is normally a very tedious process and usually only provides minimal information on the cell population. This instrument, which is only slightly larger than an automatic pipette, allows you to count cells in your tissue-culture hood, simplifies the procedure, and provides much useful data, such as the fraction of intact cells.

Caudy: At last, an alternative to lining up for the Coulter counter, and far easier than sweating over fragile hemocytometers.

Courtesy of Diffinity

The Diffinity RapidTip is a one-step pipette tip for use in DNA purification. Following a polymerase chain reaction (PCR), samples contain more than just the DNA of interest. They also contain nucleotides, primers, and other impurities that must be removed. Traditional techniques for purifying the DNA involve several steps of washing, buffering, and rinsing that can take up to 30 minutes or longer. With the Diffinity RapidTip, all those steps are combined into a single, normal-looking pipette tip.

The product is extremely easy to use, says the company’s CEO and president Jeff Helfer. “Put [the tip] on the pipettor, aspirate, and dispense. It’s that simple.” The process requires 10–12 repetitions of pulling up and releasing the solution, and takes about one minute, making it about 50 times faster than traditional post-PCR purification techniques, Helfer says. The company plans to release a newer version of the RapidTip in January, one that would require only two or three repetition cycles, making it even more efficient.

“You start and end the [purification] process with the very same disposable pipette tip,” Helfer says. “It’s green, much less expensive, and at the end of the day, we improve lab work flow and productivity.”

The tips contain a proprietary substance that removes the impurities from a PCR reaction while simultaneously repelling the amplified double-stranded DNA of interest. Using similar differential-affinity technology, Diffinity is developing several other tips for use in a variety of applications, including automated applications, restriction-digest experiments, DNA extraction from electrophoresis gels, and next-generation sequencing library preparation. The list price is $1.50/tip, available in boxes of 48 or 96. Discounts and free samples are available.

Wiley: A great technology that saves time and effort in the lab while improving sample handling and experimental reproducibility. This would be great when using robotics.

Caudy: Finally, the convenience I’ve enjoyed for years in peptide sample cleanup, applied to DNA.

Courtesy of Cellular Dynamics International

iCell Cardiomyocytes are essentially human heart cells in a test tube. Researchers at Cellular Dynamics International (CDI) induce human fibroblasts to become pluripotent stem cells (iPSC). The iPSCs are then reprogrammed to become a mixture of cells that are representative of the human heart and exhibit the typical electrophysiological characteristics of a living heart.

“The main purpose of [the] iCell Cardiomyocytes product is for drug discovery,” says Joleen Rau, senior director of marketing and communications at CDI. “Cardiotoxicity is a serious problem in drug development and is the second biggest reason for drug withdrawal from the market. We saw a market need based on a serious human health issue and realized there was an opportunity to save pharma money, make drug development safer, and perhaps save lives.”

The cardiomyocytes express monomeric red fluorescent protein, which allows for their easy identification under appropriate conditions, and a blasticidin-resistance gene, which allows CDI to achieve cardiomyocyte cultures that are at least 95 percent pure.

CDI can also create iCell Cardiomyocytes from peripheral blood samples, meaning that doctors and researchers can send in blood drawn from any human donor and have CDI generate the iPSCs needed to make personalized cardiomyocyte cultures.

“This capability to generate cells from diverse groups will help our customers to better understand how drug effects vary across different populations,” Rau says, as well as to “generate cardiomyocytes from patients afflicted with diseases such as hypertrophy and long QT syndrome (a potentially fatal condition), which will also aid in drug discovery.”

A vial that contains a minimum of 1.5 million plateable cells lists for $1,500, and is guaranteed to cover a single 96-well plate.

Kelleher: A symbol of just how fast a basic-science breakthrough can lead to new products.

Wiley: This is the first of what we expect to be many commercially available cell lines from differentiated human stem cells. This will start to move experimental biology from using the most convenient types of cell to those most relevant to a particular study.

Cytometry A. 2006 Aug 1;69(8):748-58. Multispectral imaging in biology and medicine: slices of life. Levenson RM, Mansfield JR. This material is reproduced with permission of John Wiley & Sons, Inc.,

Watching drugs or biologics pulse through a patient in real time usually takes expensive equipment such as a PET and/or CT scanner. For in vivo mouse studies on tight budgets researchers commonly bind a fluorescent marker to the compound of interest, and take a fluorescence snapshot. The natural background fluorescence of the entire mouse—which makes it hard to distinguish the target from normal tissue—is then subtracted away to sharpen the image. But subtracting background fluorescence in a live movie proved challenging. So the scientists and engineers at Cambridge Research & Instrumentation Inc. (CRI) took a page from PET scan technology: using the compound’s pharmacokinetics—the rate at which the drug is absorbed, circulated, and excreted—they improved the resolution by compensating for the background at every time point.

The kinetic imaging movie is of a bolus of indocyanine green travelling through the vasculature of a mouse over about 2 minutes following a tail vein injection. The dye mixes into the general blood pool, then accumulates in the liver.

The technology, called the Maestro Dynamic, could be especially useful for tracking how long cancer drugs remain at their target before being metabolized and/or excreted. Normally, to obtain data about drug accumulation in organs or tumors, one would sacrifice a cohort of mice every hour or two over the course of a day. By continually collecting data in real time, says James Mansfield, director of the company’s multispectral imaging systems, the number of mice needed could be reduced from around 100–200 to about 10.

Fluorescent labels can only yield information to a depth of a few centimeters, which just about covers the depth of the average mouse from all sides. For use in humans, however, CRI researchers have designed a mount for their fluorescence-detection camera “that you can swing over top of a surgical suite,” says Mansfield, giving doctors the ability to image the surface of the organs they’re working on in real time, to check, for example, that they’ve removed all of a tumor. The list price in the United States is $230,000.

Wiley: A kinetic in vivo imaging system that generates time-based kinetic images of fluorescent reagents and labeled antibodies. The kinetic data is used to greatly enhance the information that can be extracted from in vivo imaging, thus extending the usability of this technology to a far greater number of applications.

Caudy: The Maestro Dynamic takes whole-animal imaging from static to dynamic, operating over a range well into the tissue-permeating near-infrared spectrum.

Courtesy of Reinnervate Limited

Most three-dimensional cell-culturing technology is not what it should be, says Ashley Cooper, CEO of Reinnervate Limited. Many nanoscale scaffolds currently on the market are so large that cells grown in the material don’t even touch. “You get cells growing in two dimensions in a three-dimensional architecture,” he says.

This year, after eight years of development, Reinnervate introduces Alvetex, a thin, highly porous and uniform scaffold for 3-D cell culturing that better mimics the growth and formation of tissues in the body. “We’re defining once and for all what is proper three-dimensional cell culture,” says Cooper.

The inert, stable polystyrene scaffold is made of the same material as most of the clear plastic multiwell dishes used by cell biologists today. “It was a conscious design feature,” says Cooper, geared for easy assimilation of the new technology into the lab. The scaffold comes precut into thin 200μ discs, and the material can hold an average of 20 cell layers per disk. This allows every cell to be within easy reach of nutrients and air—never more than 100μ from the edge, the same as the average distance between cells in the body and blood vessels. “This is absolutely important for an avascular in vitro cell-culture system,” says Cooper. The scaffold requires no additional lab equipment and is compatible with a broad range of lab techniques, including immunofluorescence microscopy, he says.

Alvetex debuted at the Cell-Based Assays conference in London at the end of November, and is currently available in a 12-well plate format that costs $109. Additional formats, including 24-, 48- and 96-well plates and various well inserts, will become available over the next 12 months.

Wiley: This should enable the routine and reproducible creation of 3-D cell cultures in the laboratory. Extends the concept of 3-D culture beyond simple, reconstituted extracellular matrices to complex extracellular structures.

Kelleher: Another example of innovation to move us closer to better models for mimicking in vivo behavior of cells with the control of in vitro conditions.

Courtesy of Applied Biosystems

Invented by Applied Biosystems in California, the Attune Acoustic Focusing Cytometer is the first instrument that uses ultrasound waves to position cells flowing through a cytometer into a single line before they reach a laser-based detection device. The focusing technology allows for better efficiency without sacrificing resolution and sensitivity when quantifying and/or observing cells in real time. “The sample rates are greater than 10 times faster than traditional cytometers,” says Mike Olszowy, head of flow cytometry at Life Technologies, Applied Biosystems’ mother company.

Prior to the advent of the Attune cytometer, researchers controlling the sample stream had to choose between speed of sampling and resolution quality. Now, with the help of sound waves that line up cells in the center of the sample stream, researchers can maximize speed and resolution simultaneously and adjust the flow to perform cell-by-cell analyses at the detection point. The new machine can thus allow researchers to more efficiently identify cell surface proteins expressed by cells (immunophenotyping), detect rare cell populations, quantify DNA binding to cell surfaces, or simply count cells. Currently selling for around $100,000, the device was put on the market in June 2010, and Applied Biosystems has sold more than 25 of the benchtop counters worldwide.

Wiley: Designed to use sound waves to precisely control the movement of cells and increase instrument simplicity, sensitivity and throughput. Looks like it will be particularly useful for analyzing dilute cell samples. The simplicity and relatively low cost of the instrument should also increase the number of scientists who use flow cytometry.

Caudy: With a footprint small enough to fit in a laminar-flow hood and a completely new approach to fluidics, the Attune cytometer promises less clogging than other flow cytometers, even while speeding through huge populations of cells.

Courtesy of Bio-Rad Laboratories

Gel electrophoresis and blotting techniques are by far the most commonly employed methods for the identification and quantification of specific DNA, RNA, and proteins in a sample. But very often, capturing quality images of the separated bands and readying them for publication using photo-editing software can be laborious and time-consuming. With Gel Doc EZ, the newest gel imaging system from Bio-Rad Laboratories, researchers can load a gel and get print-quality images of up to 1200 dpi in seconds with just “a single push of a button,” says Ryan Short, marketing manager for Bio-Rad imaging.

The most user-friendly and versatile of the gel documentation systems on the market, according to Short, the Gel Doc EZ system offers four specialized gel trays for the imaging of fluorescent, colorimetric, and SYBR Green stains, as well as a novel stain-free option for imaging protein gels that circumvents the multiple washing and staining steps required. “The stain-free application can save scientists hours, if they’re doing traditional protein staining,” Short says.

With a high-quality camera and lens packed into a housing that’s just 44 x 26 x 38 cm, the system is also markedly compact and can easily fit on a benchtop with room to spare. The Gel Doc EZ costs $8,350 and includes software for image acquisition and analysis. Trays are sold separately and are priced at $1,150 each, with the exception of the stain-free tray, which costs $3,350. Stain-free precast gels are sold for $15 and $16.

Rothberg: Sometimes the best innovations are products that make the things you do simpler, faster, and cheaper. The Gel Doc EZ imager is one of those products.

Wiley: Combines a number of innovations to make a tedious lab chore easy. This is clearly a case where the whole is much greater than the sum of its parts.

Courtesy of Redd & Whyte

Redd & Whyte, a small UK-based life-science company, breaks into the top 10 this year thanks to the versatility of their new microplate dispenser—the Preddator. This bench top robot addresses the vexing limitations of existing fluid dispensers, which typically can’t handle cell-containing sample volumes smaller than 3 microliters. According to Redd & Whyte’s managing director, Roger Poole, the Preddator can dispense as little as 20 nanoliters of a variety of solutions, including normal aqueous solutions, cell-containing solutions, saline solutions, beads, mineral oils, and surfactants.

“This product gives [biologists] the platform to try things that they never would have dreamed that they could have done,” Poole says.

The Preddator, which has a price tag of about £26,000, was adapted from a robotic instrument that came to Redd & Whyte from the glue industry, where precision spots of adhesive are applied to manufacture an army of plastic goods. A suite of enhancements later, the microplate dispenser can drop virtually any fluid volume into 96-well to 3456-well plates in a variety of patterns that the user can program.

Poole says that the Preddator, which was officially released in October, was developed with Swiss pharmaceutical company Novartis, which fully endorses the product and uses the instrument to test targets and drugs in primary and secondary screenings. “This helps them significantly speed up the process and takes out a lot of the guesswork,” he says.

But high-throughput screening for drug discovery is only one of the applications to which the Preddator is suited. Poole adds that PCR work and protein crystallography could also benefit from the robot’s ability to handle exceedingly small quantities of a variety of sample types.

Wiley: Accurately dispensing beads and cells into high-density microtiter plates has been very challenging. This remarkably flexible and high-speed dispensing system appears to solve the problem, opening up new applications for high-throughput robotics.

Kelleher: The efficiency of high-throughput assays relies on flexible, low-volume liquid handling. Working with high precision at low volumes is often limited by reagent delivery. The Preddator system works right in a critical volume regime where pilot assays need to deliver smaller volumes to “go big” in terms of success.