Recent trends in nanopores for biotechnology

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Highlights► Nanopores are single-molecule detectors with exceptional sensitivity and versatility. ► Over the past few years, progress has been made in making and using nanopores in biotechnology. ► Nanopore-based DNA sequencing can revolutionize healthcare by reducing both sequencing costs and time.     

Perspectives on the contribution of lactic acid bacteria to cheese flavor development

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Highlights► This review covers current know-how on cheese flavor development. ► Proteolysis, autolysis and amino acid catabolism by lactic acid bacteria are discussed. ► Systems biology approaches will drive future technology improvements. ► Next-generation sequencing holds promise for fast increase in exploitable knowledge. ► Culture heterogeneity may be significant for industrial flavor production by LAB.     

From measurement to implementation of metabolic fluxes

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Highlights► In vivo flux distributions can be determined with increasing accuracy and breadth. ► Enzyme activity can partly be identified from codon usage and other DNA features. ► Stoichiometric constraints of metabolism set a frame that can be exploited to design efficient metabolic networks. ► Insights into DNA-sequence–function relationships lead to first examples of rational DNA writing. ► Increasing DNA synthesis speed moves metabolic engineering from tinkering to green field design.     

Comparative genomics: a revolutionary tool for wine yeast strain development

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Highlights► Phylogeny of Saccharomyces cerevisiae reveals industry-relevant groupings. ► Comparative genomics reveals genomic variation across industrial yeast strains. ► Next-gen sequencing in next-gen wine yeast strain development. ► Precise mapping of QTLs for marker-assisted breeding of industrial yeast. ► Discovery of putative mobile gene cluster that uses novel type of transposition.     

DNA nanotechnology with one-dimensional self-assembled nanostructures

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Highlights► Hybridization chain reactions for amplified DNA detection and DNA assembly. ► Rolling circle amplification-synthesized DNAzyme chains for amplified DNA detection. ► Bi-enzyme cascades and biocatalytic synthesis of metallic nanowires on DNA templates. ► Self-assembled one-dimensional DNA nanostructures for biocatalytic cascades. ► Programmed assembly of metal nanoparticles on one-dimensional DNA nanostructures.     

Pangenomics – an avenue to improved industrial starter cultures and probiotics

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Highlights► Genome sequencing is an efficient, cost-effective way of characterizing microbes. ► Pangenome analysis gives new insight into texture formation in yoghurt. ► Pangenome analysis of probiotic strains has identified new effect or molecules. ► Pangenome analysis gives insight into probiotic–host specificity. ► Future perspectives include improved strains for food fermentations and probiotics.     

The enabled state of DNA nanotechnology

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Highlights► The expansion of shape space and growth of interest in structural DNA nanotechnology. ► Recent advances that support the design and practical fabrication of in particular DNA origami objects. ► DNA-based devices that support scientific discovery in different fields of science.     

Advances in monitoring environmental microbes

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Highlights► Environmental DNA and RNA provide unique insights into microbial communities. ► The techniques and methods may bias conclusions, since the biases are multiplicative. ► Multiple lines of ecogenomic evidence are thus needed for all study conclusions.     

Magnetic nanoparticles-based diagnostics and theranostics

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Highlights► Magnetic nanoparticles (MNPs) can be in engineered and functionalized. ► MNPs can be used as magnetic resonance imaging contrast agents and targeted MNPs can be used in theranostic applications. ► MNPs are useful for in vivo drug and gene delivery. ► MNPs are useful for photodynamic, phototherapy and hyperthermia. ► MNPs can be used for controlled released and manipulation of cell in vivo.     

Building robust functionality in synthetic circuits using engineered feedback regulation

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Highlights► Engineered feedback loops implement elaborate functionality in synthetic circuits. ► The homeostatic potential of feedback loops is under-utilized in synthetic biology. ► Feedback control of engineered or natural cellular functions can be achieved using biological components or in silico regulation. ► Optogenetics and microfluidic technologies are important for implementing in silico control.     

Application of stable isotope ratio analysis for biodegradation monitoring in groundwater

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Highlights► Stable isotopes provide insights about in situ biodegradation mechanisms and rates. ► Isotopic approaches can be confounded by abiotic processes and heterogeneity effects. ► Isotopic applications are improving with new methods of analysis and modeling. ► Isotopic data are most useful when combined with other approaches for fate assessment.     

In situ microbial metabolism of aromatic-hydrocarbon environmental pollutants

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Highlights► Microorganisms play a crucial role in detoxifying environmental pollutants. ► Proving that biodegradation processes occur in the real world (in situ) is important. ► Genetics, biochemistry, and physiology advance the science of microbial metabolism. ► Such advances provide new molecular-biomarker tools for documenting biodegradation. ► Applying new tools to contaminated sites reveals new microbial processes and diversity.     

The interplay between microevolution and community structure in microbial populations

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Highlights► The action of industrial processes depends on microbial community structure. ► Microbes evolve very rapidly. ► Microbial evolution is affected by community structure. ► Community structure is affected by microbial evolution. ► This feedback may be crucial when considering microbial communities in industry.     

Metabolomic investigations of anaerobic hydrocarbon-impacted environments

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Highlights► This review describes metabolomic studies of anaerobic hydrocarbon-impacted sites. ► The discovery of new pathways has provided new metabolic and molecular biomarkers. ► Assessment of in situ biodegradation is enhanced via integrative approaches.     

In situ treatment of PCBs by anaerobic microbial dechlorination in aquatic sediment: are we there yet?

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Highlights► Microbial catalysts with different PCB dechlorinating activities are cultured. ► Biostimulation and bioaugmentation has been successful in the laboratory. ► Molecular tools for monitoring dechlorinating bacteria in situ are available. ► Methods to deploy these catalysts in the field are currently under development.     

Can genetic engineering of lignin deposition be accomplished without an unacceptable yield penalty?

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Highlights► Manipulation of the phenylpropanoid polymer lignin can improve bioenergy crops but often leads to dwarfing. ► Decreasing lignin leads to vascular collapse, but it is unclear that this is the cause of dwarfing. ► Non-lignin phenylpropanoids may be essential for normal plant growth and development. ► Accumulation of lignin biosynthetic intermediates or byproducts may have toxic effects. ► Dwarfism may be mediated by an active cell wall integrity monitoring pathway.     

Bioremediation of uranium-contaminated groundwater: a systems approach to subsurface biogeochemistry

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Highlights► Microbial reduction of U(VI) can remove uranium from contaminated groundwater. ► Concerns about the stability of precipitated uranium need further study. ► Environmental omics is useful for diagnosing in situ physiological state of microbes. ► Genome-scale modeling of in situ activity of bioremediation organisms is possible.