Stable isotope probing of carbon flow in the plant holobiont.


:Microbial communities associated with a plant host, constituting a holobiont, affect the physiology and growth of the plant via metabolites that are mainly derived from their photosynthates. The structure and function of active microbial communities that assimilate root exudates can be tracked by using stable isotope probing (SIP) approaches. This article reviews results from ongoing SIP research in plant-microbe interactions, with a specific focus on investigating the fate of fresh and recalcitrant carbon in the rhizosphere with 13C enriched-root exudates, in addition to identifying key players in carbon cycling. Finally, we discuss new SIP applications that have the potential to identify novel enzymes implicated in rhizoremediation or plant genes dedicated to root exudation by combining SIP approaches and genome wide associations studies.


Curr Opin Biotechnol


Haichar FEZ,Heulin T,Guyonnet JP,Achouak W




Has Abstract


2016-10-01 00:00:00












  • Flux analysis in plant metabolic networks: increasing throughput and coverage.

    abstract::Quantitative information about metabolic networks has been mainly obtained at the level of metabolite contents, transcript abundance, and enzyme activities. However, the active process of metabolism is represented by the flow of matter through the pathways. These metabolic fluxes can be predicted by Flux Balance Analy...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Junker BH

    更新日期:2014-04-01 00:00:00

  • Advances and current limitations in transcript-level control of gene expression.

    abstract::Gene expression control is critical to increase production of recombinant proteins, fine-tune metabolic pathways and reliably express synthetic pathways. The importance of transcriptional control seems to be most important in eukaryotic systems. In this review, we highlight recent developments in the field of transcri...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Leavitt JM,Alper HS

    更新日期:2015-08-01 00:00:00

  • Tracing metabolic flux through time and space with isotope labeling experiments.

    abstract::Metabolism is dynamic and must function in context-specific ways to adjust to changes in the surrounding cellular and ecological environment. When isotopic tracers are used, metabolite flow (i.e. metabolic flux) can be quantified through biochemical networks to assess metabolic pathway operation. The cellular activiti...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Allen DK,Young JD

    更新日期:2020-08-01 00:00:00

  • Stem cell niche engineering through droplet microfluidics.

    abstract::Stem cells reside in complex niches in which their behaviour is tightly regulated by various biochemical and biophysical signals. In order to unveil some of the crucial stem cell-niche interactions and expedite the implementation of stem cells in clinical and pharmaceutical applications, in vitro methodologies are bei...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Allazetta S,Lutolf MP

    更新日期:2015-12-01 00:00:00

  • Strategies for the aerobic co-metabolism of chlorinated solvents.

    abstract::Recent field and laboratory studies have evaluated the potential for aerobic co-metabolism of chlorinated solvents. Different co-metabolic substrates and different methods of application have been tried, including growing indigenous microbes in situ, and injecting into the soil subsurface strains grown in subsurface r...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Semprini L

    更新日期:1997-06-01 00:00:00

  • Emerging protein delivery methods.

    abstract::The efficient and safe delivery of therapeutic proteins is the key to commercial success and, in some cases, the demonstration of efficacy in current and future biotechnology products. Numerous delivery technologies and companies have evolved over the past year. To critically evaluate the available options, each metho...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Cleland JL,Daugherty A,Mrsny R

    更新日期:2001-04-01 00:00:00

  • Plant protection and growth stimulation by microorganisms: biotechnological applications of Bacilli in agriculture.

    abstract::The increasing demand for a steady, healthy food supply requires an efficient control of the major pests and plant diseases. Current management practices are based largely on the application of synthetic pesticides. The excessive use of agrochemicals has caused serious environmental and health problems. Therefore, the...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Pérez-García A,Romero D,de Vicente A

    更新日期:2011-04-01 00:00:00

  • Isothermal titration calorimetry for characterization of recombinant proteins.

    abstract::Isothermal titration calorimetry is widely used to measure the affinities and enthalpies of interaction between proteins and/or small molecules. The quantitative nature of the technique is especially useful in the characterization of recombinant proteins while determining the fraction of protein capable of binding a s...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Baranauskiene L,Kuo TC,Chen WY,Matulis D

    更新日期:2019-02-01 00:00:00

  • RNA as a drug target: chemical, modelling, and evolutionary tools.

    abstract::Dramatic technical progress in RNA synthesis and structure determination has allowed several difficulties inherent to the preparation, handling and structural analysis of RNA to be overcome, and this has led to a wealth of information about RNA structure and its relationship with biological function. It is now fully r...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Hermann T,Westhof E

    更新日期:1998-02-01 00:00:00

  • Advances in monitoring environmental microbes.

    abstract::Culture-independent approaches, such as next-generation sequencing and microarray-based tools, provide insight into the identity and functional diversity of microbial communities. Although these approaches are potentially powerful tools in understanding microbial structure and function, there are a number of limitatio...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Hazen TC,Rocha AM,Techtmann SM

    更新日期:2013-06-01 00:00:00

  • Fungal enzymes for environmental management.

    abstract::Fungal ligninolytic enzymes have broad biotechnological applications. Particularly laccases and certain fungal class II peroxidases from white-rot basidiomycetes are considered in degradation of persistent organic pollutants. Promising processes with reusable immobilized laccases in special reactors have been develope...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Kües U

    更新日期:2015-06-01 00:00:00

  • Transgene integration in plants: poking or patching holes in promiscuous genomes?

    abstract::Transgene integration in plants transformed by either Agrobacterium or direct DNA delivery methods occurs through illegitimate recombination (IR). The precise mechanism(s) for IR-mediated transgene integration and the role of host double-strand break repair enzymes remain unknown. A recent wealth of sequenced transgen...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Somers DA,Makarevitch I

    更新日期:2004-04-01 00:00:00

  • Logic of gene regulatory networks.

    abstract::Regulatory networks of transcription factors and signaling molecules lie at the heart of development. Their architecture implements logic functions whose execution propels cells from one regulatory state to the next, thus driving development forward. As an example of a subcircuit that translates transcriptional input ...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Materna SC,Davidson EH

    更新日期:2007-08-01 00:00:00

  • Transgenic animal models of cardiovascular disease.

    abstract::Transgenic experimentation has become a crucial part of hypertension and atherosclerosis research, and is growing more important in several other areas of cardiovascular disease. It has recently made a particular contribution to understanding the role of the renin-angiotensin system in controlling hypertension. The st...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Barrett G,Mullins JJ

    更新日期:1992-12-01 00:00:00

  • Cardiomyocyte generation from somatic sources - current status and future directions.

    abstract::Transdifferentiation of one cell type to another has garnered significant research efforts in recent years. As cardiomyocyte loss following myocardial infarction becomes debilitating for cardiac patients, the option of an autologous source of cardiomyocytes not derived from multi/pluripotent stem cell sources is an at...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Monaghan MG,Holeiter M,Layland SL,Schenke-Layland K

    更新日期:2016-08-01 00:00:00

  • Acquisition and use of calorimetric data for prediction of the thermodynamics of ligand-binding and folding reactions of proteins.

    abstract::The commercialization of high-precision microcalorimeters has led to a sharp increase in the acquisition and utilization of calorimetric data on the binding and folding reactions of proteins. This thermodynamic database, together with high-resolution structures of proteins and their complexes with ligands, has facilit...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Connelly PR

    更新日期:1994-08-01 00:00:00

  • Engineering carbon fixation with artificial protein organelles.

    abstract::Based on projections for global population growth, current techniques for improving agricultural yields will not be able to address future demands for major food crops. Improving photosynthetic efficiency by engineering carbon fixation has been identified as one of the most important approaches for increasing agricult...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Giessen TW,Silver PA

    更新日期:2017-08-01 00:00:00

  • Bioactivity: phenylpropanoids' best kept secret.

    abstract::Plant growth and development are tightly regulated by compounds produced in trace amounts in the plant. Besides the classical phytohormones, many plant metabolites have been described to affect plant development. Among these are several phenylpropanoids, although conclusive evidence for their bioactivity at physiologi...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Vanholme B,El Houari I,Boerjan W

    更新日期:2019-04-01 00:00:00

  • Mismatch repair and cancer susceptibility.

    abstract::Mismatch-repair systems have been identified in organisms ranging from Escherichia coli to humans. They can repair almost all DNA base pair mismatches as well as small insertion/deletion mismatches. Molecular and biochemical analyses have shown that the core components of eukaryotic mismatch-repair systems are highly ...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Kolodner RD,Alani E

    更新日期:1994-12-01 00:00:00

  • The application of DNA repair vectors to gene therapy.

    abstract::The nature of DNA, the sequence of the human genome and our increased understanding of the genetic basis of many inherited and acquired disorders have made the possibility of curing diseases a reality. The modulation of a host's genome is now the ultimate goal in the treatment of genetic diseases. Historically, gene t...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Kren BT,Steer CJ

    更新日期:2002-10-01 00:00:00

  • Biological function made crystal clear - annotation of hypothetical proteins via structural genomics.

    abstract::Many of the gene products of completely sequenced organisms are 'hypothetical' - they cannot be related to any previously characterized proteins - and so are of completely unknown function. Structural studies provide one means of obtaining functional information in these cases. A 'structural genomics' project has been...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Eisenstein E,Gilliland GL,Herzberg O,Moult J,Orban J,Poljak RJ,Banerjei L,Richardson D,Howard AJ

    更新日期:2000-02-01 00:00:00

  • Engineering of silk proteins for materials applications.

    abstract::Silk combines biological properties, such as non-toxicity and biodegradability, with physico-chemical ones, for example, mechanical strength. Base on molecular engineering, nowadays also new non-silk functions can be implemented in silk materials. Driven by rational design and ingenuity, innovative recombinant silk pr...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Saric M,Scheibel T

    更新日期:2019-12-01 00:00:00

  • Crosslinking of enzymes for improved stability and performance.

    abstract::Stabilization of enzymes without diminishing and diluting their activity is crucial for their use as industrial catalysts. One practically proven approach involves crystallization of the enzyme (size 1-200 microm) followed by subsequent crosslinking. In many cases, the resulting crosslinked enzyme crystals exhibit inc...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Govardhan CP

    更新日期:1999-08-01 00:00:00

  • Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production.

    abstract::The biosynthesis of the solvents 1-butanol and acetone is restricted to species of the genus Clostridium, a diverse group of Gram-positive, endospore forming anaerobes comprising toxin-producing strains as well as terrestrial non-pathogenic species of biotechnological impact. Among solventogenic clostridia, Clostridiu...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Lütke-Eversloh T,Bahl H

    更新日期:2011-10-01 00:00:00

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

    abstract::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 imp...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章


    authors: Okumoto S

    更新日期:2010-02-01 00:00:00

  • Local sequence-structure correlations in proteins.

    abstract::Considerable progress has been made in understanding the relationship between local amino acid sequence and local protein structure. Recent highlights include numerous studies of the structures adopted by short peptides, new approaches to correlating sequence patterns with structure patterns, and folding simulations u...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Bystroff C,Simons KT,Han KF,Baker D

    更新日期:1996-08-01 00:00:00

  • Cranberry components for the therapy of infectious disease.

    abstract::Summary of the in vitro data support a beneficial effect of cranberry or its proanthocyanin constituents by blocking adhesion to and biofilm formation on target tissues of pathogens. In vivo data partially support these beneficial effects. Consumption of various cranberry products benefited young and elderly females i...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Shmuely H,Ofek I,Weiss EI,Rones Z,Houri-Haddad Y

    更新日期:2012-04-01 00:00:00

  • RNA-based dynamic genetic controllers: development strategies and applications.

    abstract::Dynamic regulation of gene expression in response to various molecules is crucial for both basic science and practical applications. RNA is considered an attractive material for creating dynamic genetic controllers because of its specific binding to ligands, structural flexibility, programmability, and small size. Her...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Jang S,Jang S,Yang J,Seo SW,Jung GY

    更新日期:2018-10-01 00:00:00

  • Making bio-sense of toxicity: new developments in whole-cell biosensors.

    abstract::Bacterial whole-cell biosensors are very useful for toxicity measurements of various samples. Semi-specific biosensors, containing fusions of stress-regulated promoters and reporter genes, have several advantages over the traditional, general biosensors that are based on constitutively expressed reporter genes. Furthe...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Sørensen SJ,Burmølle M,Hansen LH

    更新日期:2006-02-01 00:00:00

  • Techniques for the experimental investigation of the protein corona.

    abstract::Due to its enormous relevance the corona formation of adsorbed proteins around nanoparticles is widely investigated. A comparison of different experimental techniques is given. Direct measurements of proteins, such as typically performed with mass spectrometry, will be compared with indirect analysis, in which instead...

    journal_title:Current opinion in biotechnology

    pub_type: 杂志文章,评审


    authors: Carrillo-Carrion C,Carril M,Parak WJ

    更新日期:2017-08-01 00:00:00