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Cell biologists study the physiological properties, behavior, interactions, and environment of cells, at the microscopic and molecular levels. That broad job description covers a wide variety of individual activities. “For basic researchers, the key areas are the very fundamental processes that cells undergo. They study adhesion, differentiation, apoptosis, migration, and many specialized functions of specific cell types,” says Laurel Donahue, manager of technical development at Sigma-Aldrich. “Industrial cell biologists have narrower focus. They look at the underlying mechanisms that improve the longevity of cells in culture, as well as other processes that will improve protein production. They look at processes that will produce consistent cultures of cells at large scale, and they focus a lot on cell based assays for identifying targets and screening compounds for pharmacological activity.”

Whether they work in research or development, most modern cell biologists have one key goal in mind. “The main theme is gaining a better understanding of diseases, through good statistical correlation of molecular interactions with phenotypes,” says Ulrich Simon, head of the microscopy business group at Carl Zeiss. “We try to shine more light into understanding the root causes of diseases.”

That effort divides naturally into specific project areas. For example, the diversity of signal transduction pathways has recently emerged as a critical focus for researchers. “When cells interact with the extracellular milieu, they have to be able to activate the pathways,” says Erik Schaefer, vice president for R&D in the signal transduction area at BioSource International, a company recently acquired by Invitrogen. “Understanding that is the area of functional genomics and proteomics.”

Stem Cells and Beyond
Jörg Pochert, director of the pharma and biotech group at Hamilton Life Science Robotics, highlights another area of frantic activity: stem cells. “Scientists face issues of how to do stem cell culturing right,” he says. “Also related to stem cells are the questions of what kinds of differentiation protocols are available and how good and stable they are, to ensure that scientists can start a stem cell line and differentiate it into the kind of tissue they need.”

To achieve their goals, cell biologists use a mixture of traditional and new tools and technologies, from cell cultures to microscopes to protein microarrays. “Recent techniques include higher resolution mass spectrometry and developments involving very good antibodies,” says Mike Schutkowski, vice president of R&D and operations for JPT Peptide Technologies. Donahue points out other approaches that have emerged in cell biology labs. “Short interfering RNA continues to be a very important tool,” she says. “In addition, information from genomic and proteomic profiling is leading to more hypotheses that can be tested. Industrially, in silico modeling from such companies as Genomatica allows for predictive biology. And on the horizon is nanotechnology.”

Laboratory automation has also found a critical role in the cell biology lab. “Every major pharma and all the major biotechnology companies have a great deal of automation in both their discovery and manufacturing sites,” explains Doug Gurevitch, a senior development engineer at the University of California, San Diego who is program chair for the Association for Laboratory Automation.

Whatever tools they use, cell biologists face a critical problem common to many other life scientists. “The key factor we see over and over again is trying to bring together the data from all the tools out there,” explains Brendan Yee, strategic product manager at Beckman Coulter. “Cell biologists, especially in drug development, are running into a roadblock created by the amount of data they collect.”

The effort to overcome that and other problems in pursuing cell biology involves R&D scientists in academe and industry. “I’m involved in the Cell Migration Consortium,” Schaefer says. “This has multimillion dollar projects aimed at bringing together large groups of scientists and making discoveries commercially available. We’re working with the consortium to commercialize tools.”

Medieval Methodologies
The study of any living cell starts with the use of cell culture media and reagents. “Cell culture media, sera, and related reagents are critically important – more than even investigators who have done cell culture for a long time think,” Donahue says. “Culture systems are downright medieval at times.” To bring cell cultures into the 21st century and keep cells alive and well during in vitro experiments, researchers and manufacturers have developed a range of growth media, some of which contain only well-defined or synthetic components. Scientists can supplement these “defined” or “serum-free” media with growth factors to study the living cells’ responses to changing environments.

Companies such as ATCC, Cambrex, Invitrogen, and Sigma-Aldrich offer cell culture media, sera, and reagents to grow cells ranging from HeLa to embryonic stem cells. “We look at systems that are being utilized by researchers and try to create products and culture systems that are, for example, serum-free or better defined,” Donahue says. “For our industrial customers, who have regulatory constraints, we focus on the development of animal derived component–free media.” Recent products from Sigma-Aldrich include EX–CELL Vero, a medium for cells used in research on or production of viral vaccines and two kits that permit industrial researchers to optimize the media for their protein expressing CHO cell lines.

All About Automation A special supplement in the 13 January 2006 issue of Science will focus on laboratory automation. The supplement will examine selected tools for lab automation and will outline how these devices improve the efficiency of life science research and drug development efforts.

Automation can play a particularly effective role in cell cultures. “Bulk cell culture has been automated for years,” Gurevitch explains. “We’ve been pushing newer work with microcultures for quick, tailored cell development for research, development, and eventually tissue engineering.”

Hamilton recently created what it calls its MICROLAB STAR-based CellHost System. Developed in conjunction with Oliver Bruestle of Germany’s University of Bonn, this automates several aspects of stem cell culture, including media exchange, cell harvesting after trypsinization, plating cells, and the addition of growth factor or other substances to the cell cultures. “The system offers full weekend walk-away times for lab personnel,” Pochert says. “It ensures that all the cells are treated homogeneously and that the biological bandwidth of cells you are culturing is narrower than if you use manual methods. We have used it for mouse stem cells, on which we have published two papers.”

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The Importance of Imaging
Whenever possible, cell biologists want their experiments to show rather than tell. Tools developed in recent years have facilitated that. One area of novel technology overcomes the inherent limitation that cells are colorless and translucent, and hence almost invisible under the lens of a standard light microscope. Biological stains and dyes enable microscopists to look at different cell types and the structures within these cells. “We want to use dyes to indicate how cells interact,” Carl Zeiss’s Simon explains. Companies such as Fisher Scientific, USB Corporation, and Wako Chemicals offer several stains and dyes, many of them highly purified and use-tested to ensure consistent performance in the laboratory.

Other methods for improving the visibility of cells complement microscopy methods. “Spectral deconvolution techniques introduced in confocal and microscopy techniques put the color issue under control,” Simon says. “It has added value to live imaging.” Zeiss has recently introduced LSM5 Live, a laser scanning microscope developed in collaboration with Scott Fraser of the California Institute of Technology. “This speeds up visualization by a factor of 20 to 30,” Simon says. “That opens up new dimensions on research; you can understand color and you’re capable of really understanding how proteins interact.” In addition to Zeiss, major producers of microscopes include Leica, Nikon Instruments, and Olympus. Beyond refining microscopes, those vendors have developed digital camera systems and software for data analysis.

Apogee/Biodimensions, meanwhile, has developed two noninvasive technologies for in vivo functional imaging at the molecular level. One monitors epithelial inflammation and the other recognizes concentrations of analytes that indicate disease or treatment status. The technology relies on the company’s Single System Image (SSI) high performance computing cluster. It permits scientists to compare results from image processing algorithms and photon simulation codes, and thereby evaluate the performances of the approaches during development and testing.

Assays and Antibodies
Imaging doesn’t work in isolation. Cell scientists also rely on biochemical assays to determine cellular function. Well-studied subjects of assaying include apoptosis, the cell’s cytoskeleton and extracellular matrix, protein phosphorylation, signal transduction pathways, ion channels, nitric oxide, and cell stress. Early entrants into assaying for cell biology include Alexis Biochemicals, BioSource, and Tocris Cookson. Apoptosis, or programmed cell death, has particular traction. Those companies and others such as EMD Biosciences, Roche Applied Science, and Trevigen offer assays for studying it.

Antibodies represent major research tools for cell biology and signal transduction. For example, a key development in the study of kinases – molecules that control many cellular functions – was the production of specific targeted antibodies that identify the active form of protein kinases. Those tools improved researchers’ understanding of the role of kinases in various signal transduction pathways. Companies such as BioSource, BD Biosciences Pharmingen, Chemicon, and Upstate offer antibodies to study the role of kinases in signal transduction.

BioSource has another focus. “One of the things we’ve done with our antibodies is put them into platforms to understand the kinetics and overall stoichiometry of phosphorylation events,” Schaefer explains. “We have patent-pending technology to detect phosphorylation for certain protein events and to work out how much is phosphorylated. We also have a phosphoarray chip platform. And we offer beads that allow you to get up to 100 combinations and dye signatures to capture proteins of interest, and identify them with a detection antibody.”

In September, Beckman Coulter introduced a custom kit to measure ZAP-70 protein expression in whole blood specimens using flow cytometry. ZAP-70 (Zeta-associated protein, 70 kiloDaltons) is an intracellular protein associated with signal transduction networks in lymphocyte populations whose expression has been associated with disease progression in a group of patients with chronic lymphocytic leukemia, the most common leukemia in the United States and Europe. “There’s interest in whether ZAP-70 protein expression marks a group of patients in whom the disease will progress rapidly,” explains Vincent Shankey, a senior staff development scientist at Beckman Coulter’s Advanced Technology Center. “Our kit contains an optimized antibody to ZAP-70, a unique fixation and permeabilization technique to monitor intracellular signal transduction protein epitopes, a gating and analysis technique to measure ZAP-70 protein expression in key cell populations within the sample, and a rigorous protocol for researchers to follow to set up a flow cytometer to measure the protein.”

Microarraying Methods
The introduction of DNA microarrays quickly sparked the idea of using this miniaturized platform with other biomolecules, such as proteins and peptides. Biacore and Ciphergen have developed proprietary array systems for analyzing proteins. And JPT Peptide Technologies has developed its own approach. “We were first on the market with peptide arrays in 2000,” Schutkowski says. “We have technology that synthesizes thousands of peptides per week.”

The firm’s unique peptide microarrays accelerate crucial steps in drug discovery programs by focusing on enzyme families such as kinases and proteases. The company’s pepSTAR platform identifies substrates in less than one week and profiles kinases and proteases. JPT also customizes peptide chips to target specific classes of enzymes. And it provides an all-in-one service that includes screening microarrays, evaluating data, and synthesizing, characterizing, and optimizing selected substrates. “The logical extension of these products,” Schutkowski explains, “is to use the microarrays with samples from human patients – looking for antibodies against HIV, for example.”

Advances in cell biology hold great promise for basic scientific understanding and the treatment of disease. The tools and techniques in application and under development offer the promise of discoveries that will add to scientists’ understanding of how cells function and the effective application of that knowledge.

Peter Gwynne (pgwynne767{at}aol.com) is a freelance science writer based on Cape Cod, Massachusetts, U.S.A. Gary Heebner (gheebner{at}cell-associates.com) is a marketing consultant with Cell Associates in St. Louis, Missouri, U.S.A.