Suspension arrays of microspheres analyzed using flow cytometry offer a new approach to multiplexed assays for large-scale screening applications. By optically encoding micron-sized polymer particles, suspension microarrays can be created to enable highly multiplexed analysis of complex samples. Each element in the array is comprised of a subpopulation of particles with distinct optical properties and each array element bears a different surface receptor. Nucleic acids, proteins, lipids or carbohydrates can serve as receptors to support the analysis of a wide range of biomolecular assemblies, and applications in genomic and proteomic research are being developed. Coupled with recent innovations for rapid serial analysis of samples, molecular analysis with microsphere arrays holds significant potential as a general analysis platform for both research and clinical applications.
Laboratory systems for microscopic computed tomography (micro-CT) have recently evolved from specialized prototype tools to become essential components of many research laboratories. The availability of commercial systems with almost microscopic resolution and the capability to image live animals has opened up entirely new applications for micro-CT in laboratory investigation. This review describes the technical aspects of micro-CT and highlights some current research applications. Micro-CT has the potential to replace serial histology as the reference standard in many in vitro studies, and provides a practical approach to obtain quantitative information during some longitudinal investigations in vivo.
The chemical industry is exploring the use of renewable feed stocks to improve sustainability, prompting the exploration of bioprocesses for the production of chemicals. Attractive features of biological systems include versatility, substrate selectivity, regioselectivity, chemoselectivity, enantioselectivity and catalysis at ambient temperatures and pressures. However, a challenge facing bioprocesses is cost competitiveness with chemical processes because capital assets associated with the existing commercial processes are high. The chemical industry will probably use biotechnology with existing feed stocks and processes to extract higher values from feed stocks, process by-products and waste streams. In this decade, bioprocesses that offer either a process or a product advantage over traditional chemical routes will become more widely used.
Since its introduction three decades ago, computed tomography (CT) has been regarded as an imaging technique that is good at providing structural information but poor at providing physiological (functional) data to help with diagnosis. For instance, although it can reveal an abnormal mass present in the lung or liver, it cannot always differentiate a benign mass from a malignant growth. The introduction of fast CT scanners in the past decade, together with the development of better analysis techniques, has helped to launch functional CT as a new method to investigate the physiological basis of function and disease in the human body.
Wood is almost as important to humanity as food, and the natural forests from which most of it is harvested from are of enormous environmental value. However, these slow-growing forests are unable to meet current demand, resulting in the loss and degradation of forest. Plantation forests have the potential to supply the bulk of humanity's wood needs on a long-term basis, and so reduce to acceptable limits the harvest pressures on natural forests. However, if they are to be successful, plantation forests must have a far higher yield of timber than their natural counterparts, on much shorter rotation times. To achieve this in reasonable time, biotechnology must be applied to the tree-improvement process, for which large increases in public and private capital investment are needed. However, additional obstacles exist in the form of opposition to plantations, some forest ecocertification schemes, and concerns about aspects of forest biotechnology, especially genetic engineering. It is the intention of this article to explain, in detail, why plantation forests are needed to sustainably meet the world's demand for wood, why they are not being developed fast enough, and why the application of biotechnology to tree improvement is essential to speeding up this process.
A series of exciting reports over the past two years has established the usefulness of protein chips and made important advances in preparing protein arrays. However, several technical challenges must still be addressed to make these tools available to the wider community of researchers. Here, we discusses these challenges and survey recent opportunities for creating quantitative assays, preparing and immobilizing large numbers of proteins, using detection methods to analyze the results of chip-based experiments, and using informatics tools to interpret these results.
Multidimensional peptide separation will play an increasingly important role in the drive to identify and quantitate the proteome. By increasing the peak and load capacity, multidimensional approaches increase the number and dynamic range of peptides that can be analyzed in a complex biological organism. Separation methods using different physical properties of peptides have been combined with varying degrees of success. The ultimate goal is a rapid separation strategy that can be coupled with analytical methods, such as mass spectrometry, to provide comprehensive monitoring of the changing concentration, interactions, and structures of proteins in the proteome.
A great deal of current biological and clinical research is directed at the interpretation of the information contained in the human genome sequence in terms of the structure, function and control of biological systems and processes. Proteomics, the systematic analysis of proteins, is becoming a critical component in this endeavor because proteomic measurements are carried out directly on proteins - the catalysts and effectors of essentially all biological functions. To detect changes in protein profiles that might provide important diagnostic or functional insights, proteomic analyses necessarily have to be quantitative. This article summarizes recent technological advances in quantitative proteomics.
Specific measurement of recombinant protein titer in a complex environment during industrial bioprocessing has traditionally relied on labor-intensive and time-consuming immunoassays. In recent years, however, developments in analytical technology have resulted in improved methods for protein product monitoring during bioprocessing. The choice of product-monitoring technology for a particular bioprocess will depend on a variety of assay factors and instrument-specific factors. In this article, we have compiled an overview of the advantages and disadvantages of the most commonly used technologies used: electrochemiluminescence, optical biosensors, rapid chromatography and nephelometry. The advantages of each technology for measuring both small and large recombinant therapeutic proteins are compared with a conventional enzyme-linked immunosorbent assay (ELISA) technique.
The development of peptide and protein microarrays has created enormous opportunities in biomedical research. Current chip-based assays are well suited for identifying candidate protein or enzyme activities but still require conventional solution phase experiments to validate hits. Here, three surface-engineering strategies for microarray design are described and are illustrated in the development of a peptide chip for the quantitative analysis of kinase activity on solid support. These strategies promise to widen the application of microarrays by permitting the evaluation of hits in a chip-based format.
A new generation of spectroscopic dyes is gradually becoming available to biological researchers, from an unexpected source: materials chemists who study the synthesis and properties of nano-sized inorganic objects. Research into tailoring the optical properties, surface chemistry and biocompatibility of metallic and semiconductor nanoparticles, exemplified in part by a recent report by Mirkin, Schatz and coworkers, is fulfilling the promise of these nanostructures as customizable substitutes for organic molecular probes.
Flow cytometry is a rapid method for the quantitative measurement of light scattering and fluorescent properties of cells. Although this technique has been widely applied to biomedical and environmental studies, its potential as a tool in ecotoxicological studies has not yet been fully exploited. This article describes the application of flow cytometry to the development of bioassays with marine and freshwater algae for assessing the bioavailability of contaminants in waters and sediments.
We raise some issues in detecting the conservation (or absence thereof) of co-regulation using gene order; how we think the variations in the cellular network in various species can be studied; and how to determine and interpret the higher order structure in networks of functional relations.
Bessou and colleagues recently suggested C. elegans as an excellent model to study Duchenne muscular dystrophy . [...]recently, it was widely accepted in the field that the progressive deterioration of muscle function typical for this disease might be the consequence of a functional conservation between dystrophin and its close relative, utrophin. In addition to the ease of genetic manipulations, this tiny nematode has one major advantage that might develop it into a superb tool for the biotech industry - C. elegans can easily be grown in microtiter plates in both 96- and 384-well formats.
Mass spectrometry has become a primary tool for proteomics because of its capabilities for rapid and sensitive protein identification and quantitation. It is now possible to identify thousands of proteins from microgram sample quantities in a single day and to quantify relative protein abundances. However, the need for increased capabilities for proteome measurements is immense and is now driving both new strategies and instrument advances. These developments include those based on integration with multi-dimensional liquid separations and high accuracy mass measurements and promise more than order of magnitude improvements in sensitivity, dynamic range and throughput for proteomic analyses in the near future.
The mouse is the preferred animal model for studying mammalian developmental genetics and many human diseases. Ultrasound biomicroscopy (UBM) provides a unique real-time, in vivo micro-imaging approach for analyzing the phenotypes of mutant and transgenic mice from embryonic to adult stages. We review recent advances in the use of UBM and high-frequency ultrasound Doppler for analyzing the developing mouse cardiovascular system, and the application of in utero UBM image-guided injections for direct manipulation of mouse embryos. We describe currently available instrumentation, summarize the strengths and limitations of UBM and discuss the potential for future improvements to the technology.
Biotechnology demands powerful methods for the functional characterisation and monitoring of molecular alterations in tissues in response to various stimuli. Currently, cellular biosensors provide information about cell and tissue internal transduction pathways. In this article, recent biosensor systems are briefly described and the use of 3D tissue aggregates as recognition elements is discussed. An example of an innovative approach for drug testing using 3D heart muscle aggregates, as well as tumor models, positioned in capillary systems for electrical potential recording and impedance measurement is described. The effectiveness of drugs and therapies can be tested and monitored in a short time using such biohybrid sensors.
There are many aims associated with the optimization of fermentation processes. Optimization is expected to increase the yield of the final product but the process must be compliant with good manufacturing practices, the available equipment and the expected final scale of operation. Dealing with genetically modified microorganisms that overproduce recombinant protein has the advantage that the vast majority of the processes use only three different species, namely Escherichia coli, Saccharomyces cerevisiae and Pichia pastoris. Standard processes for each organism are described in textbooks and serve as a basis for the development of a tailored process. This article outlines the general philosophy that we have devised to ensure an efficient approach of scaling up fermentation processes for biopharmaceutical purposes, in a multidisciplinary environment.
Recent progress in the development of high-resolution imaging techniques and reporter probes is expected to revolutionize molecular imaging research in animal models of human disease and, ultimately, clinical practice. These developments provide inroads to continuous monitoring and quantitation of gene delivery and gene expression during experimental gene therapy. Furthermore, techniques using novel imaging transgenes and reporter probes enable imaging of the regulation of gene expression in living animals. This could significantly aid the development of therapeutics targeted at individual populations of cells or even specific molecules.
Protein-based methodologies are catching up with established DNA-based methods at an astonishing speed. Recent developments in mass spectrometry enable high-throughput automated identification of proteins as is already the case with DNA sequencing methods. Furthermore, methods for the quantitation of relative protein abundance at the protein level are getting more advanced, which should complement gene expression monitoring at the mRNA level.