Current Opinion in Biotechnology

Biomolecular plasmonics for quantitative biology and nanomedicine.

Publication Date: 2010 Aug 27 PMID: 20801636
Authors: Lee, S. E. - Lee, L. P.
Journal: Curr Opin Biotechnol

Free electrons in a noble metal nanoparticle can be resonantly excited, leading to their collective oscillation termed as a surface plasmon. These surface plasmons enable nanoparticles to absorb light, generate heat, transfer energy, and re-radiate incident photons. Creative designs of nanoplasmonic optical antennae (i.e. plasmon resonant nanoparticles) have become a new foundation of quantitative biology and nanomedicine. This review focuses on the recent developments in dual-functional nanoplasmonic optical antennae for label-free biosensors and nanoplasmonic gene switches. Nanoplasmonic optical antennae, functioning as biosensors to significantly enhance biochemical-specific spectral information via plasmon resonance energy transfer (PRET) and surface-enhanced Raman spectroscopy (SERS), are discussed. Nanoplasmonic optical antennae, functioning as nanoplasmonic gene switches to enable spatiotemporal regulation of genetic activity, are also reviewed. Nanoplasmonic molecular rulers and integrated photoacoustic-photothermal contrast agents are also described.

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Exploitation of peptide motif sequences and their use in nanobiotechnology.

Publication Date: 2010 Aug 19 PMID: 20728339
Authors: Shiba, K.
Journal: Curr Opin Biotechnol

Short amino acid sequences extracted from natural proteins or created using in vitro evolution systems are sometimes associated with particular biological functions. These peptides, called peptide motifs, can serve as functional units for the creation of various tools for nanobiotechnology. In particular, peptide motifs that have the ability to specifically recognize the surfaces of solid materials and to mineralize certain inorganic materials have been linking biological science to material science. Here, I review how these peptide motifs have been isolated from natural proteins or created using in vitro evolution systems, and how they have been used in the nanobiotechnology field.

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Systems biology at work.

Publication Date: 2010 Aug 18 PMID: 20727733
Authors: Dos Santos, V. A. - Damborsky, J.
Journal: Curr Opin Biotechnol

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Functional nucleic acid nanostructures and DNA machines.

Publication Date: 2010 Aug 18 PMID: 20727732
Authors: Teller, C. - Willner, I.
Journal: Curr Opin Biotechnol

The information encoded in the base sequence of DNA provides instructions for the structural and functional properties of this biopolymer. Structural information includes the formation of duplexes, supramolecular crossover tiles, G-quadruplexes, i-motifs, base-metal-ion complexes, and more. Functional information encoded in the DNA is reflected by specific binding (aptamers) or catalytic properties (DNAzymes). Recent advances in tailoring supramolecular DNA structures for DNA-based machinery and for amplified biosensing are reviewed. Different DNA machines that perform 'tweezer', 'walker' or 'metronome' functions are discussed, and the control of macroscopic surface properties or the motility of micro-objects by molecular DNA devices is introduced. Furthermore, the design of DNA machines for the ultrasensitive detection of DNA, low-molecular-weight substrates, and macromolecules is discussed. Supramolecular aptamer and DNAzyme structures are used as molecular tools for amplified sensing.

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Diseases as network perturbations.

Publication Date: 2010 Aug 13 PMID: 20709523
Authors: Del Sol, A. - Balling, R. - Hood, L. - Galas, D.
Journal: Curr Opin Biotechnol

The tremendous amount of the data obtained from the study of complex biological systems changes our view on the pathogenesis of human diseases. Instead of looking at individual components of biological processes, we focus our attention more on the interaction and dynamics of biological systems. A network representation and analysis of the physiology and pathophysiology of biological systems is an effective way to study their complex behavior. Specific perturbations can trigger cascades of failures, which lead to the malfunctioning of cellular networks and as a result to the development of specific diseases. In this review we discuss recent developments in the field of disease network analysis and highlight some of the topics and views that we think are important for understanding network-based disease mechanisms.

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Challenges in synthetically designing mammalian circadian clocks.

Publication Date: 2010 Aug 12 PMID: 20708919
Authors: Susaki, E. A. - Stelling, J. - Ueda, H. R.
Journal: Curr Opin Biotechnol

Synthetic biology, in which complex, dynamic biological systems are designed or reconstructed from basic biological components, can help elucidate the design principles of such systems. However, this engineering approach has only been applied to a few simple biological systems. The circadian clock is appropriate for this approach, since it is a dynamic system with complex transcriptional and post-transcriptional circuits that have been comprehensively described. Rational synthesis of the properties of the suprachiasmatic nucleus, the central clock tissue of the circadian system that controls many dynamic behaviors, will be important for understanding the neural-circuit systems that control physiological behaviors. These approaches will provide a deeper understanding of the biological clock, and of clinical problems associated with it, such as sleep disorders.

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Engineering in complex systems.

Publication Date: 2010 Aug 11 PMID: 20708402
Authors: Bujara, M. - Panke, S.
Journal: Curr Opin Biotechnol

The implementation of the engineering design cycle of measure, model, manipulate would drastically enhance the success rate of biotechnological designs. Recent progress for the three elements suggests that the scope of the traditional engineering paradigm in biotechnology is expanding. Substantial advances were made in dynamic in vivo analysis of metabolism, which is essential for the accurate prediction of metabolic pathway behavior. Novel methods that require variable degrees of system knowledge facilitate metabolic system manipulation. The combinatorial testing of pre-characterized parts is particularly promising, because it can profit from automation and limits the search space. Finally, conceptual advances in orthogonalizing cells should enhance the reliability of engineering designs in the future. Coupled to improved in silico models of metabolism, these advances should allow a more rational design of metabolic systems.

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Programming cells: towards an automated 'Genetic Compiler'

Publication Date: 2010 Aug 9 PMID: 20702081
Authors: Clancy, K. - Voigt, C. A.
Journal: Curr Opin Biotechnol

One of the visions of synthetic biology is to be able to program cells using a language that is similar to that used to program computers or robotics. For large genetic programs, keeping track of the DNA on the level of nucleotides becomes tedious and error prone, requiring a new generation of computer-aided design (CAD) software. To push the size of projects, it is important to abstract the designer from the process of part selection and optimization. The vision is to specify genetic programs in a higher-level language, which a genetic compiler could automatically convert into a DNA sequence. Steps towards this goal include: defining the semantics of the higher-level language, algorithms to select and assemble parts, and biophysical methods to link DNA sequence to function. These will be coupled to graphic design interfaces and simulation packages to aid in the prediction of program dynamics, optimize genes, and scan projects for errors.

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Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks.

Publication Date: 2010 Aug 6 PMID: 20692823
Authors: Ruppin, E. - Papin, J. A. - de Figueiredo, L. F. - Schuster, S.
Journal: Curr Opin Biotechnol

With the advent of modern omics technologies, it has become feasible to reconstruct (quasi-) whole-cell metabolic networks and characterize them in more and more detail. Computer simulations of the dynamic behavior of such networks are difficult due to a lack of kinetic data and to computational limitations. In contrast, network analysis based on appropriate constraints such as the steady-state condition (constraint-based analysis) is feasible and allows one to derive conclusions about the system's metabolic capabilities. Here, we review methods for the reconstruction of metabolic networks, modeling techniques such as flux balance analysis and elementary flux modes and current progress in their development and applications. Game-theoretical methods for studying metabolic networks are discussed as well.

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Synthetic gene networks in mammalian cells.

Publication Date: 2010 Aug 4 PMID: 20691580
Authors: Weber, W. - Fussenegger, M.
Journal: Curr Opin Biotechnol

The design and construction of synthetic gene circuits with complex spatiotemporal dynamics was pioneered in bacteria, but it took almost a decade until synthetic biologists were able to construct genetic circuits with complex spatiotemporal dynamics in mammalian cells. This review highlights the most recent advances in mammalian synthetic biology, and it describes metabolite, hormone, and light-triggered genetic switches as well as the design and construction of synthetic networks that feature tunable oscillations. We conclude by discussing not only the current limitations but also possible ways to transform the construction of synthetic mammalian systems from an art into a predictive engineering discipline.

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Virus hybrids as nanomaterials for biotechnology.

Publication Date: 2010 Aug 3 PMID: 20688511
Authors: Soto, C. M. - Ratna, B. R.
Journal: Curr Opin Biotechnol

The current review describes advances in the field of bionanotechnology in which viruses are used to fabricate nanomaterials. Viruses are introduced as protein cages, scaffolds, and templates for the production of biohybrid nanostructured materials where organic and inorganic molecules are incorporated in a precise and a controlled fashion. Genetic engineering enables the insertion or replacement of selected amino acids on virus capsids for uses from bioconjugation to crystal growth. The variety of nanomaterials generated in rod-like and spherical viruses is highlighted for tobacco mosaic virus (TMV), M13 bacteriophage, cowpea chlorotic mottle virus (CCMV), and cowpea mosaic virus (CPMV). Functional biohybrid nanomaterials find applications in biosensing, memory devices, nanocircuits, light-harvesting systems, and nanobatteries.

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