13C metabolic flux analysis: optimal design of isotopic labeling experiments

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Highlights► Design of isotopic labeling experiments determines the precision of flux estimates. ► New approaches were developed to select optimal isotopic tracers and measurements. ► Tandem mass spectrometry provides more informative data for ¹³C flux analysis. ► Parallel labeling experiments can improve the quality of flux estimates. ► New methods are needed for optimal design of parallel labeling experiments.     

Lipid metabolism in microalgae distinguishes itself

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Highlights► Triacylglycerol assembly in microalgae might occur at plastid envelopes. ► Starch-less mutants provide clues for the engineering of carbon partitioning in algae. ► New algal species emerge as models for lipid and biofuel research.     

Biological conversion of carbon dioxide and hydrogen into liquid fuels and industrial chemicals

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Highlights► Electrofuels are non-photosynthetic, energy-dense fuels made from carbon dioxide. ► Herein, we review electrofuel production in hydrogen-utilizing organisms. ► We review both current and emerging electrofuel platforms and organisms. ► New advancements in genetic tools for electrofuel host organisms are examined.     

Vaccine design: emerging concepts and renewed optimism

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Highlights► Highly variable and complex pathogens remain challenging vaccine targets. ► Systems biology and reverse vaccinology continue to foster success. ► New ways of presenting conserved, functionally critical epitopes hold promise. ► Adjuvant systems allow for enduring, native antigen presentation. ► An ideal vaccine provides synergy between innate, cellular, and humoral immunity.     

Profiling and inhibiting reversible palmitoylation

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Highlights► New methods allow direct enrichment of palmitoylated proteins for LC–MS annotation. ► SILAC proteomics methods enhance the annotation of low abundance palmitoyl proteins. ► Alkynyl fatty acids facilitate pulse-chase labeling for measuring palmitoylation dynamics. ► Thioesterase inhibitors are promising new tools to dissect palmitoylation dynamics.     

Aerobic degradation of aromatic compounds

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Highlights► Metabolic and regulatory networks are finely tuned for biodegradation of aromatics. ► New pathways and widespread bacterial biodegradation capabilities revealed by omics. ► Full characterization of hybrid pathways expands the scope of aromatic biodegradation. ► The metabolism of aromatics plays a pivotal role in cell to cell communication. ► Computational and synthetic biology approaches design novel biodegradation pathways.     

Proteomics approaches for the analysis of enriched microbial subpopulations and visualization of complex functional information

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Highlights► Access to proteomics is now possible after flow cytometry-based cell sorting. ► New visualization tools like Voronoi treemaps or streamgraphs now allows interpretation of complex omics data. ► Useful instrumentation to study microbial subpopulation from, for example, host–pathogen interaction assays.     

Tandem mass spectrometry for measuring stable-isotope labeling

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Highlights► Tandem MS combines efficient separation, high sensitivity and selectivity. ► Tandem MS is used for measuring stable-isotopic labeling for ¹³C-flux analysis. ► Complete positional isotopomer distribution of aspartate was measured by tandem MS. ► Measurement accuracy is improved by 2-fold to10-fold compared to GC–MS and LC–MS. ► Validated libraries of parent–daughter fragments are needed for accurate ¹³C-analysis.     

Nanotechnology meets electrophysiology

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Highlights► We focus on the latest developments in nanotechnology-based electrophysiology. ► Methods for extracellular recording via nanoFET-based devices are described. ► Metal nanoelectrodes for the recording of electrogenic cells are reviewed. ► The latest developments of intracellular FET-based probes are shortly covered. ► Pioneering electrical scaffold devices for the interfacing with tissues are described.     

Enzyme and metabolic engineering for the production of novel biopolymers: crossover of biological and chemical processes

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Highlights► Poly(ω-hydroxy fatty acids) are polyethylene-like biobased polyester. ► Medium-chain-length polyhydroxyalkanoate homopolymers are processed to stretchy film. ► Microbial lactate-based polyesters exhibit transparent and flexible properties. ► Enzyme and metabolic engineering facilitates the expanding of bio-based polymers.     

Bioreporters and biosensors for arsenic detection. Biotechnological solutions for a world-wide pollution problem

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Highlights► A wide variety of bioreporter and biosensor assays for arsenic detection exists. ► Assay detection limits are mostly in the range of 10–50 μg As per L and below. ► New focus is on reporter integration into microdevices for more optimal detection. ► A number of case studies show realistic field applicability of bioreporter assays.     

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.     

Human milk and related oligosaccharides as prebiotics

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Highlights► The intestinal microbiome is recognized as an important determinant of health. ► Galacto-oligosaccharides are non-digestible carbohydrates. ► Galacto-oligosaccharides stimulate growth and activity of gut bacteria. ► Subtle differences in structure can result in significant differences in activity. ► Less abundant oligosaccharides from bovine milk are similar to those from human milk.     

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.     

Biodegradation of gasoline ether oxygenates

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Highlights► The different types of MTBE and TBA-degrading microorganisms are summarized. ► The pathways involved in aerobic and anaerobic MTBE biodegradation are described. ► The roles of key and novel enzymes in these processes are highlighted. ► The impacts of biochemical studies on stable isotope-based analyses are discussed.     

Metabolomics platforms for genome wide association studies—linking the genome to the metabolome

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Highlights► Genome-wide association studies with metabolomics constitute mGWAS. ► mGWAS provide insights into genetic and environmental impact on metabolic processes. ► We review essential strategies for mGWAS. ► Examples of mGWAS in large cohort studies are discussed.     

The role of membrane transport in metabolic engineering of plant primary metabolism

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Highlights► The plastidial pyruvate transporter in plants is driven by sodium symport. ► The mitochondrial pyruvate transporter MPC has been identified. ► All transporters needed for a synthetic PEP-CK/C₄ photosynthetic cycle are now known. ► The SWEET proteins define a new class of sugar efflux carriers in plants.     

Metal-based methods for protein inactivation

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Highlights► The irreversible inactivation of protein targets by metal complexes is described. ► The article summaries catalysts that hydrolyze or oxidize proteins. ► Cyclen-based catalysts that selectively hydrolyze peptides and proteins are described. ► Catalysts that generate reactive oxygen species are important for protein inactivation. ► Metal-based oxidants are potent and selective agents for protein inactivation.     

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.     

Recent progress in the metabolic engineering of alkaloids in plant systems

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Highlights► Recent metabolic engineering efforts for plant alkaloids. ► Characterizing, reconfiguring and fine-tuning metabolic ‘parts’ improves titers. ► Additional strategies are necessary to produce ‘unnatural’ natural products.