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.     

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.     

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.     

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.     

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.     

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.     

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.     

Engineering plant metabolism into microbes: from systems biology to synthetic biology

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Highlights► Microbial production of pharmaceutical and fuel molecules. ► Systems biology tools advanced our understanding about synthetic pathway design. ► Synthetic biology led us to cell factories tailor-made for chemical production. ► Combinatorial gene assembly for synthetic pathway diversification. ► Engineering static, dynamic and spatial control for better production phenotype.     

New opportunities by synthetic biology for biopharmaceutical production in Pichia pastoris

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Highlights► The application of Pichia pastoris for biopharmaceutical production is described. ► Synthetic biology approaches and perspectives to improve production are reviewed. ► Glycoengineering efforts to produce humanized, uniform glycoproteins are covered. ► The design and application of synthetic promoter variants are highlighted. ► The molecular toolbox available for synthetic biology in P. pastoris is discussed.     

Expanded genetic code for the engineering of ribosomally synthetized and post-translationally modified peptide natural products (RiPPs)

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Highlights► RiPPs have high capabilities of target interaction far beyond the field of anti-infectives. ► RiPPs are especially suitable for design and engineering with the genetic code expansion. ► First published studies yielded RiPPs with unnatural/synthetic amino acids. ► Achievement: expanded scope of the in vivo (mainly bacterial) RiPPs synthesis. ► Perspective: design of RiPPS with novel chemistries and unique sequence combinations.     

Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy

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Highlights► Individual DNA molecules hundreds of kbp long may be stretched and visualized by optical microscopy. ► An optical barcode is generated by fluorescent labeling of short sequence motifs along the stretched DNA. ► Optical maps complement DNA sequencing for gap closing, finishing, validation and de novo assembly of genomes. ► Genome structural variations not accessible to sequencing or DNA arrays may be directly visualized. ► Epigenetic marks such as DNA methylation and DNA binding proteins may also be mapped on single genomic fragments.     

Pathway and protein engineering approaches to produce novel and commodity small molecules

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Highlights► Production of novel pharmaceutical and commodity chemicals. ► Protein and pathway engineering pave the way for product diversifications. ► ‘Omics’ data have helped assembly of pathways from different species. ► Recombination of enzymatic domains and site-directed mutagenesis. ► Tunable control of pathways for better production.     

Metagenomics of microbial life in extreme temperature environments

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Highlights► Metagenomic microbial community characterization. ► Extreme environment microbiology. ► High and low temperature adaptation.     

The emerging field of transport engineering of plant specialized metabolites

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Highlights► Transport engineering has the potential to increase nutritional value of crops. ► Transport engineering can increase yield of synthetic biology approaches. ► Neo-functionalization of primary metabolite transporters to specialized metabolism. ► Elimination of glucosinolate seed accumulation is achieved via transport engineering. ► Glucosinolates in Arabidopsis: a model for transport of specialized metabolites.     

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.     

Advances in nanoreactor technology using polymeric nanostructures

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Highlights► Functional polymer nanostructures as efficient supports for confined catalysis. ► Polymer scaffold can provide protection of active catalyst for prolonged activity. ► Hydrophobic cavities allows for efficient organic reactions to take place in water. ► Stimuli-responsive polymers can provide control over nanoreactor catalytic activity. ► Folding of single polymer chains show potential for future enzyme mimic systems.     

Clawing back: broadening the notion of metal chelators in medicine

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Highlights► Not all chelators are the same: more than metal sequestration and elimination. ► Metal chelates can redistribute metals across biological membranes. ► Metal-chelating fragments provide leads for metalloenzyme inhibition. ► Metal chelation can enhance metal reactivity and thus cytotoxicity. ► Prochelators provide site-activated metal chelation and passivation.