Innovation Can Save Us
Innovation can save us. If developing interesting new technologies and products really is the lifeblood of economic health, then the life sciences industry is innovation’s beating heart.
The Scientist received more than 60 entries to our third annual Top 10 Innovations competition, presenting our judges—Northwestern University molecular chemist Neil Kelleher, sequencing pioneer Jonathan Rothberg, Princeton University genomicist Amy Caudy, and Pacific Northwest National Laboratory biologist H. Steven Wiley—with the very challenging task of winnowing these products down to the 10 best.
This year’s winners include essential tools, such as sequencers, imagers, and cell counters, that have the potential to simplify and streamline work in biology labs; and cutting-edge advances, from tailor-made disease-model cell lines to heart cells derived from induced pluripotent stem cells.
Take a look at 2010’s Top Innovations. Their clever designs speak volumes about the bright future of scientific experimentation.
* Third-Gen Sequencing
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.
* Handheld Automated Cell Counter
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.
* The Diffinity RapidTip
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.
* Heart Cells on Demand
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
* Biologic Fluorescence Movies in Focus
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.
* Centering Cells with Sound
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.
* Picture-Perfect Gels
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.
Make a Full Screen and TURN YOUR SOUND ON!
Sit back, relax and turn the volume up! This video shows a large range of different cell types spanning many different areas of life science; from neurones to neutrophils, liver cells and islets, T cells and skin cells, whole maggots and drosophila embryos, they all dance to a favorite tune!
The cell images were all analyzed using Volocity 3D-4D cellular imaging and analysis software from Improvision, a PerkinElmer company. Many of the images you see were acquired using our UltraVIEW live-cell confocal imaging system. If you want more information on any of these products, please visit http://www.improvision.com/ —-by Simon Vipoir
This video belongs to:
SHAPE SHIFT The polymath in 1975. Photograph from I.B.M.
His Fractal Vision
He saw the same patterns in cauliflower florets and crop prices — and changed how we view the world.
The New York Times, December 23, 2010, By JAMES GLEICK
HERE IS A mathematician’s nightmare I heard in the 1980s when that irritating, unconforming, self-regarding provocateur Benoît Mandelbrot was suddenly famous — fractals, fractals everywhere. The mathematician dreamed that Mandelbrot died, and God spoke: “You know, there really was something to that Mandelbrot.”
Mandelbrot created nothing less than a new geometry, to stand side by side with Euclid’s — a geometry to mirror not the ideal forms of thought but the real complexity of nature. He was a mathematician who was never welcomed into the fraternity (“Fortress Mathematics,” he said, where “the highest ambition is to wall off the windows and preserve only one door”), and he pretended that was fine with him. When Yale first hired him to teach, it was in engineering and applied science; for most of his career he was supported at I.B.M.’s Westchester research lab. He called himself a “nomad by choice.” He considered himself an experienced refugee: born to a Jewish family in Warsaw in 1924, he immigrated to Paris ahead of the Nazis, then fled farther and farther into the French countryside.
‘The questions the field attacks are questions people ask
themselves. They are questions children ask. What shape is a mountain?
Why is a cloud the way it is?’
In various incarnations he taught physiology and economics. He was a nonphysicist who won the Wolf Prize in physics. The labels didn’t matter. He turns out to have belonged to the select handful of 20th-century scientists who upended, as if by flipping a switch, the way we see the world we live in.
He was the one who let us appreciate chaos in all its glory, the noisy, the wayward and the freakish, from the very small to the very large. He gave the new field of study he invented a fittingly recondite name: “fractal geometry.” But he wanted me to understand it as ordinary.
“The questions the field attacks are questions people ask themselves,” he told me. “They are questions children ask: What shape is a mountain? Why is a cloud the way it is?” Only his answers were not ordinary.
Clouds are not spheres — the most famous sentence he ever wrote — mountains are not cones, coastlines are not circles and bark is not smooth, nor does lightning travel in a straight line.
If you closely examine the florets of a cauliflower (or the bronchioles of a lung; or the fractures in oil-bearing shale), zooming in with your magnifying glass or microscope, you see the same fundamental patterns, repeating. It is no accident. They are all fractal. Clouds, mountains, coastlines, bark and lightning are all jagged and discontinuous, but self-similar when viewed at different scales, thus concealing order within their irregularity. They are shapes that branch or fold in upon themselves recursively.
I was following him from place to place, reporting a book on chaos, while he evangelized his newly popular ideas to scientists of all sorts. Wisps of white hair atop his outsize brow, he lectured at Woods Hole to a crowd of oceanographers, who had heard that fractals were relevant to cyclone tracks and eddy cascades. Mandelbrot told them he had seen the same channels, flows and back flows in dry statistics of rising and falling cotton prices. At Lamont-Doherty Geological Observatory, as it was then known, the geologists already spoke fractally about earthquakes. Mandelbrot laid out a mathematical framework for such phenomena: they exist in fractional dimensions, lying in between the familiar one-dimensional lines, two-dimensional planes and three-dimensional spaces. He revived some old and freakish ideas — “monsters,” as he said, “mathematical pathologies” that had been relegated to the fringes.
William P. O’Donnell/The New York Times
“I started looking in the trash cans of science for such phenomena,” he said, and he meant this literally: one scrap he grabbed from a Paris mathematician’s wastebasket inspired an important 1965 paper combining two more fields to which he did not belong, “Information Theory and Psycholinguistics.” Information theory connected to fractals when he focused on the problem of noise — static, errors — in phone lines. It was always there; on average it seemed manageable, but analysis revealed that normal bell-curve averages didn’t apply. There were too many surprises — outliers. Clusters and quirks always defied expectations.
It’s the same with brainwaves, fluid turbulence, seismic tremors and — oh, yes — finance.
From his first paper studying fluctuations in the rise and fall of cotton prices in 1962 until the end of his life, he maintained a simple and constant message about extraordinary economic events. The professionals plan for “mild randomness” and misunderstand “wild randomness.” They learn from the averages and overlook the outliers. Thus they consistently, predictably, underestimate catastrophic risk. “The financiers and investors of the world are, at the moment, like mariners who heed no weather warnings,” he wrote near the peak of the bubble, in 2004, in “The (Mis)behavior of Markets,” his last book.
Fractals have made their way into the economics mainstream, as into so many fields, though Mandelbrot was not really an economist; nor a physiologist, physicist, engineer. . . .
“Very often when I listen to the list of my previous jobs, I wonder if I exist,” he said once. “The intersection of such sets is surely empty.”
Clostridium perfringens Source:: Wikimedia commons, CDC
Another example of commensal microbes that affect host immunity may hold implications for the treatment of autoimmune diseases and other ailments
[Published 23rd December 2010 07:00 PM GMT]
The-Scientist.com, December 23, 2010, by Jeff Akst — An abundant type of bacteria that resides in the intestines is critical for keeping the immune system of the colon in check, according to a study published online today (December 23) in ScienceExpress. The results add to the growing body of literature that commensal microbes in the gut are key regulators of host immunity, and may provide potential therapeutic avenues for inflammatory bowel disease (IBD), allergies, and autoimmune diseases.
“This is a big step forward in understanding how the commensal microbiota shapes the host immune system,” immunologist Paul Forsythe of McMaster University in Ontario, who was not involved in the study, told The Scientist in an email. “These results suggest that not only are there specific immune responses to distinct bacterial species, but that these responses are region-specific within the intestine.”
The new study provides “tantalizing data that fits with the story,” he said. “That some bugs are important for one type of immunity and other bugs are important for another type of immunity, and it’s really the balance of these bugs that gives the perfect immune system.”
Over the past several years, evidence has been accumulating that the gut microbiome affects the balanced host immune system. Segmented filamentous bacteria (SFB), for example, appear to induce the production of intestinal Th17 cells, helper T cells that are critical to fighting pathogens.
Too many Th17 cells, however, can promote autoimmunity without the proper balance of regulatory T cells (Tregs) to suppress the immune response against one’s own cells. To see whether certain commensal bacterial species might regulate the production of Tregs in the intestines, immunologist Kenya Honda of the University of Tokyo and his colleagues compared normal mice to germ-free mice that harbored no bacteria. They found no major differences in the the small intestine, but significantly fewer Tregs in the colon, suggesting that the missing bacteria may be inducing Treg production.
Antibiotic and chloroform-based tests revealed that the responsible microbes were likely spore-forming, Gram-positive bacteria. As Clostridia are one of the most abundant gut bacteria that fit this description, Honda and his colleagues colonized germ-free mice with a cocktail of 46 different strains of Clostridia. The results confirmed their suspicion — the bacterial treatment resulted in the accumulation of Tregs in the colon. Treg levels in the small intestine did not change, however, suggesting that Clostridia only affect the production of Tregs in the lower part of the digestive tract.
“This is one of the first studies that identifies a specific example of a commensal microbe affecting regulatory T cells,” said coauthor Ivaylo Ivanov, an immunologist at the Columbia University Medical Center in New York. There was a study published earlier this year, he noted, that suggested another bacteria, Bacteroides fragilis, could also induce Treg production in the gut, but those researchers “saw a very marginal induction of regulatory T cells,” said Ivanov, who collaborated on the research while at New York University School of Medicine. “This study identifies Clostridia as a really strong inducer.”
To read more, please click on this hot link…….. New gut bacteria regulate immunity – The Scientist – Magazine of the Life Sciences
K. Atarashi, et al., “Induction of colonic regulatory T cells by indigenous Clostridium species,” ScienceExpress, 10.1126/science. 1198469, 2010.
Published Online 23 December 2010
< Science Express Index
Science DOI: 10.1126/science.1198469
Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species
+ Author Affiliations1. 1Department of Immunology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan. 2. 2Yakult Central Institute for Microbiological Research, Tokyo 186-8650, Japan. 3. 3Department of Molecular Bacteriology, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima 770-8503, Japan. 4. 4Department of Veterinary Public Health, The University of Tokyo, Tokyo 113-8657, Japan. 5. 5Laboratory of Immune Regulation, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan. 6. 6Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095–1781, USA. 7. 7Laboratory for Cell Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan. 8. 8Research Unit for Immune Homeostasis, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan. 9. 9Laboratory of Pathophysiology and Signal Transduction, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan. 10. 10Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA. 11. 11Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Saitama 332-0012, Japan.
1. †To whom correspondence should be addressed. E-mail: firstname.lastname@example.org
1. ↵* These authors contributed equally to this work.
CD4+ T regulatory cells (Tregs), expressing the Foxp3 transcription factor, play a critical role in the maintenance of immune homeostasis. Here, we show that in mice, Tregs were most abundant in the colonic mucosa. The spore-forming component of indigenous intestinal microbiota—particularly clusters IV and XIVa of the genus Clostridium—promoted Treg cell accumulation. Colonization of mice by a defined mix of Clostridium strains provided an environment rich in transforming growth factor–β (TGF-β) and affected Foxp3+ Treg number and function in the colon. Oral inoculation of Clostridium during the early life of conventionally reared mice resulted in resistance to colitis and systemic IgE responses in adult mice, suggesting a new therapeutic approach to autoimmunity and allergy.