Current Opinion in Biotechnology

Recent advances in single-molecule sequencing.

Publication Date: 2010 Mar 2 PMID: 20202812
Authors: Treffer, R. - Deckert, V.
Journal: Curr Opin Biotechnol

Recent advances in sequencing technologies exhibit a tendency towards single-molecule sequencing, which eventually will lead to the commercial implementation of such platforms. For this purpose dye labelling is currently the foundation of most approaches and an overview is provided on the latest developments. For label-free sequencing the detection of conductivity changes using nanopores or nano-edges will be discussed as well as another promising method that is based on Raman spectroscopy. Here the most recent advance aims to utilize the high lateral resolution of tip-enhanced Raman scattering. For this sequencing procedure Raman spectra must be collected along the DNA or RNA strand, while the difference spectra will provide a direct sequence reading without prior labelling.

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Valuable processes and products from marine intertidal microbial communities.

Publication Date: 2010 Mar 2 PMID: 20202811
Authors: Ortega-Morales, B. O. - Chan-Bacab, M. J. - De la Rosa-Garcia, S. D. - Camacho-Chab, J. C.
Journal: Curr Opin Biotechnol

Microbial communities are ubiquitous in marine intertidal environments. These communities, which grow preferentially as biofilms on natural and artificial surfaces, carry out key processes contributing to the functioning of coastal environments and providing valuable services to human society, including carbon cycling, primary productivity, trophic linkage, and transfer and removal of pollutants. In addition, their surface-associated life style greatly influences the integrity and performance of marine infrastructure and archaeological heritage materials. The fluctuating conditions of the intertidal zone make it an extreme environment to which intertidal biofilm organisms must adapt at varying levels. This requirement has probably favored the development and spread of specific microorganisms with particular physiological and metabolic processes. These organisms may have potential biotechnological utility, in that they may provide novel secondary metabolites, biopolymers, lipids, and enzymes and even processes for the production of energy in a sustainable manner.

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Mining the active proteome in plant science and biotechnology.

Publication Date: 2010 Feb 28 PMID: 20197235
Authors: Kolodziejek, I. - van der Hoorn, R. A.
Journal: Curr Opin Biotechnol

Protein activity is essential functional information, yet difficult to predict from transcript or protein data. Activity-based protein profiling (ABPP) displays active proteins in proteomes using small molecule probes that irreversibly label proteins in their active state. Here, we review proof-of-concept ABPP studies in plant science. These studies displayed activities of dozens of plant cysteine proteases, lipases, methylesterases and the proteasome. ABPP in plants revealed differential protein activities in development and immunity and uncovered striking selectivity of pathogen-derived inhibitors and unexpected targets of commercial inhibitors. The unique, high-content information of ABPP and the robustness and simplicity of the assays will make ABPP a powerful tool in future plant science and biotechnology.

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Approaches for novel enzyme discovery from marine environments.

Publication Date: 2010 Feb 26 PMID: 20189795
Authors: Lee, H. S. - Kwon, K. K. - Kang, S. G. - Cha, S. S. - Kim, S. J. - Lee, J. H.
Journal: Curr Opin Biotechnol

The enormous pool of biodiversity in marine ecosystems is an excellent natural reservoir for acquiring an inventory of enzymes with potential for biotechnological applications. Moreover, the opportunity for sustainable resource management has been greatly enhanced by recent advances in culturing methods for recalcitrant microbes. In this review, we will focus primarily on successful examples in culturing marine microbes and provide an overview of work examining the biotechnological potential of the marine reservoir, mainly through genomic strategies, such as activity-based functional screening of genomic and metagenomic libraries and homology-driven screening of enormous amounts of sequence data.

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Biotechnology of water and salinity stress tolerance.

Publication Date: 2010 Feb 26 PMID: 20189794
Authors: Pardo, J. M.
Journal: Curr Opin Biotechnol

Drought and salinity are among the environmental factors that constrain agricultural productivity most dramatically. Classical breeding programs aiming to improve stress tolerance have been hampered by the multigenic nature of the trait and the seemingly scarce natural genetic variability in crop plants. Novel genetic determinants governing the function of stomata and improving the performance of plants under water shortage have been identified and show promise of application in crops. Moreover, receptors of the stress hormone abscisic acid have been characterized and their interplay with key regulatory components is being understood. A critical factor of salinity tolerance in plants is the ability to exclude Na(+) from the shoot, and the modification of specific Na(+) transport processes has yielded enhanced salinity tolerance.

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Analytical biotechnology: from single molecule and single cell analyses to population dynamics of metabolites and cells.

Publication Date: 2010 Feb 25 PMID: 20189376
Authors: Schmid, A. - Neubauer, P.
Journal: Curr Opin Biotechnol

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Scale-down simulators for metabolic analysis of large-scale bioprocesses.

Publication Date: 2010 Feb 23 PMID: 20185293
Authors: Neubauer, P. - Junne, S.
Journal: Curr Opin Biotechnol

Analytical approaches for a comprehensive understanding of the metabolic networks in microbial cultures are mostly based on small-scale cultures which are in a steady state or undergo dynamic changes. For drawing conclusions to industrial-scale bioprocesses, however, it is important to understand that cells in large-scale bioreactors are exposed steadily to fast changes, because of an inhomogeneous environment. Analytical approaches that aim for large-scale bioprocess understanding need to apply specific laboratory simulators. Recent developments in cell cultivation techniques and computational tools provide improved possibilities to evaluate how a process will behave in the final scale. These simulators will pave the way for screening robust strains and process conditions.

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From fluxes and isotope labeling patterns towards in silico cells.

Publication Date: 2010 Feb 23 PMID: 20185292
Authors: Dauner, M.
Journal: Curr Opin Biotechnol

Fluxes and metabolites are the functional manifestations of a living cell. Metabolic flux analysis evolved as a powerful means for systems biology to quantitatively analyze intracellular flux distributions. With the integration of data from tracer experiments, the formerly descriptive methodology has turned into a versatile tool to validate assumptions on genome-derived flux networks. Powerful modeling frameworks balancing 'isotopomers', 'cumomers', or 'elementary modeling units' have reduced computational effort and introduced rigorous statistical quality measures. The advent of metabolomics, stimulus response experiments, and highly sensitive mass spectrometry techniques for mass isotopomer analysis has extended the reach of metabolic flux analysis from steady-state to highly dynamic conditions. With the integration of regulatory circuits and more 'omics' data into mechanistic flux models, the simulation-based prediction of cellular responses to environmental and network perturbations becomes possible-an in silico cell.

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Genetic and biotechnological approaches for biofuel crop improvement.

Publication Date: 2010 Feb 22 PMID: 20181473
Authors: Vega-Sanchez, M. E. - Ronald, P. C.
Journal: Curr Opin Biotechnol

Research and development efforts for biofuel production are targeted at converting plant biomass into renewable liquid fuels. Major obstacles for biofuel production include lack of biofuel crop domestication, low oil yields from crop plants as well as recalcitrance of lignocellulose to chemical and enzymatic breakdown. Researchers are expanding the genetic and genomic resources available for crop improvement, elucidating lipid metabolism to facilitate manipulation of fatty acid biosynthetic pathways and studying how plant cell walls are synthesized and assembled. This knowledge will be used to produce the next generation of biofuel crops by increasing fatty acid content and by optimizing the hydrolysis of plant cell walls to release fermentable sugars.

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Biotechnological concepts for improving plant innate immunity.

Publication Date: 2010 Feb 22 PMID: 20181472
Authors: Gust, A. A. - Brunner, F. - Nurnberger, T.
Journal: Curr Opin Biotechnol

Saving the world's food supply constitutes one of the major challenges of the future. As a complement to classical and molecular breeding technologies, novel strategies for biotechnological improvement of plant immunity aim at enhancing host recognition capacities for potential pathogens, at boosting the executive arsenal of plant immunity, and at interfering with virulence strategies employed by microbial pathogens. In addition, chemical and biological priming provides means for triggering plant defenses in a non-transgenic manner. Major advances in our understanding of the molecular basis of plant immunity and of microbial infection strategies have opened new ways for engineering durable disease resistance in crop plants that are highlighted in this review.

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Computational methods for metabolic reconstruction.

Publication Date: 2010 Feb 18 PMID: 20171871
Authors: Pitkanen, E. - Rousu, J. - Ukkonen, E.
Journal: Curr Opin Biotechnol

In the wake of numerous sequenced genomes becoming available, computational methods for the reconstruction of metabolic networks have received considerable attention. Here, we review recent methods and software tools useful along the reconstruction workflow, from sequence annotation and network assembly to model verification and testing against experimental data. Reconstruction methods can be divided into three categories, depending on the magnitude of network context which is taken into account in the process of assembling the metabolic model: First, each enzyme may be predicted independently by annotation transfer or machine learning methods. Second, the presence of a metabolic pathway may be detected from genome and experimental evidence, often utilizing a reference pathway database. Third, the method may attempt to directly reconstruct a consistent metabolic network without relying on predefined reference pathways. Regardless of the chosen context, all methods strive to reconstruct genome-scale metabolic reconstructions. Currently a gap exists between software platforms dedicated to genome annotation and computational tools for automatically repairing network inconsistencies and validating against measurement data. We argue that to accelerate the reconstruction efforts, computational tools need to be developed that bridge the phases of the reconstruction workflow. In particular, the goal of finding consistent metabolic models suitable for computational analysis should be taken into account already in the beginning phases of reconstruction.

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Application of Fourier-transform ion cyclotron resonance mass spectrometry to metabolic profiling and metabolite identification.

Publication Date: 2010 Feb 18 PMID: 20171870
Authors: Ohta, D. - Kanaya, S. - Suzuki, H.
Journal: Curr Opin Biotechnol

Metabolomics, as an essential part of genomics studies, intends holistic understanding of metabolic networks through simultaneous analysis of a myriad of both known and unknown metabolites occurring in living organisms. The initial stage of metabolomics was designed for the reproducible analyses of known metabolites based on their comparison to available authentic compounds. Such metabolomics platforms were mostly based on mass spectrometry (MS) technologies enabled by a combination of different ionization methods together with a variety of separation steps including LC, GC, and CE. Among these, Fourier-transform ion cyclotron resonance MS (FT-ICR/MS) is distinguished from other MS technologies by its ultrahigh resolution power in mass to charge ratio (m/z). The potential of FT-ICR/MS as a distinctive metabolomics tool has been demonstrated in nontargeted metabolic profiling and functional characterization of novel genes. Here, we discuss both the advantages and difficulties encountered in the FT-ICR/MS metabolomics studies.

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Imaging approach for monitoring cellular metabolites and ions using genetically encoded biosensors.

Publication Date: 2010 Feb 16 PMID: 20167470
Authors: Okumoto, S.
Journal: Curr Opin Biotechnol

The spatiotemporal patterns of ion and metabolite levels in living cells are important in understanding signal transduction and metabolite flux. Imaging approaches using genetically encoded sensors are ideal for detecting such molecule dynamics, which are hard to capture otherwise. Recent years have seen iterative improvements and evaluations of sensors, which in turn are starting to make applications in more challenging experimental settings possible. In this review, we will introduce recent progress made in the variety and properties of biosensors, and how biosensors are used for the measurement of metabolite and ion in live cells. The emerging field of applications, such as parallel imaging of two separate molecules, high-resolution transport studies and high-throughput screening using biosensors, will be discussed.

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Chemical and biological single cell analysis.

Publication Date: 2010 Feb 16 PMID: 20167469
Authors: Schmid, A. - Kortmann, H. - Dittrich, P. S. - Blank, L. M.
Journal: Curr Opin Biotechnol

Single cells represent the minimal functional unit of life. A major goal of biology is to understand the mechanisms operating in this minimal unit. Nowadays, analysis of the single cell can be performed at unprecedented resolution using new lab-on-a-chip devices and advanced analytical methods. While cell handling and cultivation devices can be classified into finite volume reactors and flow systems, the analytical approaches differ in respect to invasive (i.e. chemical) and noninvasive (i.e. biological/living cell) analysis. Using these new and exciting technologies cell-to-cell differences, originating from regulatory circuits and distinct microenvironments, can now be explored. For example, it could be shown that the rates of transcription and translation are stochastic. Chemical and biological single cell analyses provide an unprecedented access to the understanding of cell-to-cell differences and basic biological concepts.

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Metabolic flux analysis in eukaryotes.

Publication Date: 2010 Feb 15 PMID: 20163950
Authors: Niklas, J. - Schneider, K. - Heinzle, E.
Journal: Curr Opin Biotechnol

Metabolic flux analysis (MFA) represents a powerful tool for systems biology research on eukaryotic cells. This review describes recent advances, the challenges as well as applications of metabolic flux analysis comprising fungi, mammalian cells and plants. While MFA is widely established and applied in microorganisms, it remains still a challenge to adapt these methods to eukaryotic cell systems having a higher complexity particularly concerning compartmentation or media composition. In fungi MFA was used in the past few years to analyze a variety of conditions and factors and their effects on cellular metabolism. In mammalian cells MFA was applied mainly in cell culture technology and in medical and toxicological research. (13)C metabolic studies on native whole plants are additionally challenging by the fact that CO(2) is usually the only carbon source.

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In situ passive solid-phase adsorption of micro-algal biotoxins as a monitoring tool.

Publication Date: 2010 Feb 11 PMID: 20153627
Authors: Mackenzie, L. A.
Journal: Curr Opin Biotechnol

Laboratory and field studies of the passive solid-phase adsorption toxin tracking (SPATT) method have been carried out around the world. A wide range of marine micro-algal toxins have been detected and the potential of the method to provide reliable, sensitive, time-integrated sampling to monitor the occurrence of toxic algal bloom events has been demonstrated. The method has several important advantages over current phytoplankton and shellfish monitoring methods. Trials of various adsorption substrates have been carried out and the best candidates have been selected for the lipophilic marine biotoxin groups; however, research continues to locate suitable substrates for the more polar water-soluble compounds such as domoic acid and the saxitoxins. The technique has also been successfully applied to the detection of a range of freshwater cyanobacterial toxins.

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Fast sampling for quantitative microbial metabolomics.

Publication Date: 2010 Feb 9 PMID: 20149631
Authors: van Gulik, W. M.
Journal: Curr Opin Biotechnol

Targeted metabolomics, aimed at the study of metabolic reaction networks and their regulation in vivo, is a rapidly emerging field in systems biology. Obtaining proper quantitative snapshots of the microbial metabolome requires fast sampling, immediate quenching of enzymatic activity, separation of exometabolome and endometabolome, complete metabolite extraction from the cells, and reliable high-throughput analysis methods. This review addresses the current state of the art of rapid sampling and quenching for microbial metabolomics. Several robust and reliable rapid sampling devices have been developed. Various quenching and separation procedures have been proposed and applied, but with respect to the reliability of the different methods the literature is contradictory. To date a reliable universal method applicable to different microbial species is still lacking.

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