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Precise control of gene expression is essential for flux redistribution in metabolic pathways. Although the CRISPR interference (CRISPRi) system can effectively repress gene expression at the transcriptional level, it has still been difficult to precisely control the level without loss of specificity or an increase in cell toxicity. In this study, we developed a tunable CRISPRi system that performs transcriptional regulation at various levels. We constructed a single-guide RNA (sgRNA) library targeting repeat, tetraloop, and anti-repeat regions to modulate the binding affinity against dCas9. Each screened sgRNA could regulate the gene expression at a certain level between fully-repressing and non-repressing states (>45-fold). These sgRNAs also enabled modular regulation with various target DNA sequences. We applied this system to redistribute the metabolic flux to produce violacein derivatives in a predictable ratio and optimize lycopene production. This system would help accelerate the flux optimization processes in metabolic engineering and synthetic biology.

Pseudotargeted analysis combines the advantages of untargeted and targeted lipidomics methods based on chromatography-mass spectrometry (MS). This study proposed a comprehensive pseudotargeted lipidomics method based on three-phase liquid extraction (3PLE) and segment data-dependent acquisition (SDDA). We used a 3PLE method to extract the lipids with extensive coverage from biological matrixes. 3PLE was composed of one aqueous and two organic phases. The upper and middle organic phases enriched neutral lipids and glycerophospholipids, respectively, combined and detected together. Besides, the SDDA strategy improved the detection of co-elution ions in the lipidomics analysis. A total of 554 potential lipids were detected by the developed approach in both positive and negative modes using ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). Compared with the conventional liquid-liquid extraction (LLE) approaches, including methyl tert-butyl ether (MTBE) and Bligh-Dyer (BD) methods, 3PLE combined with SDDA significantly increased the lipid coverage 87.2% and 89.7%, respectively. Also, the proposed pseudotargeted lipidomics approach exhibited higher sensitivity and better repeatability than the untargeted approach. Finally, we applied the established pseudotargeted method to the plasma lipid profiling from the depressed rats and screened 61 differential variables. The results demonstrated that the pseudotargeted method based on 3PLE and SDDA broadened lipid coverage and improved the detection of co-elution ions with excellent sensitivity and precision, indicating significant potential for the lipidomics analysis.

Coupled transcription and translation processes in bacteria cause indiscriminate translation of intact and truncated messenger RNAs, inevitably generating nonfunctional polypeptides. Here, we devised a synthetic protein quality control (ProQC) system that enables translation only when both ends of mRNAs are present and followed by circularization based on sequence-specific RNA-RNA hybridization. We demonstrate that the ProQC system dramatically improved the fraction of full-length proteins among all synthesized polypeptides by selectively translating intact mRNA and reducing abortive translation. As a result, full-length protein synthesis increased up to 2.5-fold without changing the transcription or translation efficiency. Furthermore, we applied the ProQC system for 3-hydroxypropionic acid, violacein and lycopene production by ensuring full-length expression of enzymes in biosynthetic pathways, resulting in 1.6- to 2.3-fold greater biochemical production. We believe that our ProQC system can be universally applied to improve not only the quality of recombinant protein production but also efficiencies of metabolic pathways.

BACKGROUND The development of the endoscopic technique has resulted in an increasing number of patients undergoing percutaneous endoscopic gastrostomy (PEG) insertion; however, the protocols for increasing the volume of feeding formula after PEG insertion have not been established. Therefore, we compared the clinical outcomes of patients receiving low- and high-volume increase in enteral feeding formula. METHODS A total of 215 patients who underwent PEG insertion between January 2016 and March 2019 were included. They were divided into 2 groups according to the increase in volume of feeding formula: the low-volume group (n = 135) received ≤150 mL/d, and the high-volume group (n = 80) received ≥300 mL/d. Patient characteristics, procedure, and feeding-related clinical outcomes were retrospectively reviewed using medical records. RESULTS The adverse events of the feeding protocol did not significantly differ between the 2 groups. The number of days needed to attain the calorie targets was significantly lower in the high-volume group than in the low-volume group (5.4 ± 3.0 vs 2.4 ± 1.5; P < .001). The duration of supplemental parenteral nutrition and the length of hospitalization were also significantly lower in the high-volume group (3.9 ± 3.3 vs 1.2 ± 2.2; P < .001 and 5.8 ± 2.7 vs 4.6 ± 2.6; P = .007, respectively). CONCLUSION To rapidly attain the calorie targets in appropriately selected patients with PEG insertion, a high-volume increase in daily feeding can safely be recommended given the favorable outcomes.

In this descriptive study, we aimed to identify factors related to emergency room nurses’ disaster triage ability. A total of 166 nurses who worked for emergency departments of general hospitals completed a structured questionnaire consisting of the Disaster Triage Ability Scale (DTAS), the Strategic Thinking Scale (STS), the Problem-Solving Inventory (PSI), and the Original Grit Scale (Grit-O). The data were analyzed using SPSS/WIN 25.0 by means of descriptive statistics, t-test, one-way ANOVA, the Scheffé post hoc test, Pearson’s correlation coefficients, and stepwise multiple regression. Participants’ DTAS averaged 14.03 ± 4.28 (Range 0–20) and showed a statistically significant difference according to their experience of triage education (t = 2.26, p = 0.022) as a disaster triage-related attribute. There were significant correlations among DTAS and confidence in the PSI (r = 0.30, p < 0.001), the approach-avoidance style in the PSI (r = −0.28, p < 0.001), and futurism in the STS (r = 0.19, p = 0.019). The strongest predictor was confidence in the PSI; in addition, 14.1% of the DTAS was explained by confidence in the PSI, approach-avoidance in the PSI, and futurism in the STS. Emergency room nurses who received triage education showed a higher level of the DTAS and their DTAS could be explained by problem-solving skills and strategic thinking. Therefore, it is necessary to develop and implement triage education programs integrated with stress management to improve the approach-avoidance style to ensure better problem-solving skills and to utilize various training methods to enhance confidence to improve problem-solving skills and futurism as part of strategic thinking.

Although cellular secretion is important in industrial biotechnology, its assessment is difficult due to the lack of efficient analytical methods. This study describes a synthetic cellular communication-based microfluidic platform for screening strains with the improved secretion of 3-hydroxypropionic acid (3-HP), an industry-relevant platform chemical. 3-HP-secreting cells were compartmentalized in droplets, with receiving cells equipped with a genetic circuit that converts the 3-HP secretion level into an easily detectable signal. This platform was applied to identify Escherichia coli genes that enhance the secretion of 3-HP. As a result, two genes (setA, encoding a sugar exporter, and yjcO, encoding a Sel1 repeat-containing protein) found by this platform enhance the secretion of 3-HP and its production. Given the increasing design capability for chemical-detecting cells, this platform has considerable potential in identifying efflux pumps for not only 3-HP but also many important chemicals.

Proper carbon flux distribution between cell growth and production of a target compound is important for biochemical production because improper flux reallocation inhibits cell growth, thus adversely affecting production yield. Here, using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolve cells under the selective condition toward the acquisition of genotypes that optimally reallocate cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determine that mutations in the conserved regions of proteins involved in global transcriptional regulation alter the expression of several genes associated with central carbon metabolism. These changes rewire central carbon flux toward the 3-HP production pathway, increasing 3-HP yield and reducing acetate accumulation by alleviating overflow metabolism. Our study provides a perspective on adaptive laboratory evolution (ALE) using synthetic biosensors, thereby supporting future efforts in metabolic pathway optimization., This research was supported by the C1 Gas Refinery Program (NRF-2018M3D3A1A01055754 and NRF-2015M3D3A1A01064882), the Global Research Laboratory Program (NRF-2016K1A1A2912829), and the Bio & Medical Technology Development Program (NRF-2018M3A9H3020459) through the National Research Foundation of Korea (NRF of Korea), funded by the Ministry of Science and ICT (MSIT). S.W.S. is partially supported by the Creative-Pioneering Researchers Program through Seoul National University (SNU).

As the main structural components of cellular and sub-cellular membranes, lipids are a major source of energy and play an important role in various biological processes such as cellular signaling. Lipid profiling has attracted increasing attention in recent years, and chromatography-mass spectrometry techniques for lipid profiling occupy a dominant position in this regard. Sample preparation, which aims at enriching trace substances and reducing matrix interferences, is a crucial step in the analysis of lipids for the intricacy of sample matrices. Here, we review recent developments in sample preparation techniques based on chromatography-mass spectrometry and their application to lipid profiling. Various sample preparation techniques are described and summarized. The extraction methods based on liquid phase included liquid-liquid extraction and single organic solvent extraction. The extraction methods based on solid phase involved solid-phase extraction and solid-phase microextraction. The field-assisted extraction methods cover supercritical fluid extraction, pressurized liquid extraction, microwave-assisted extraction, and ultrasound-assisted extraction. Moreover, online coupling sample preparation methods and sample preparation methods for

Pediococcus acidilactici is a probiotic bacterium that is industrially utilized in the food industry and antibiotics development. Here, we determine the complete nucleotide sequence of the genome of Pediococcus acidilactici ATCC 8042. The genome was sequenced by the PacBio RSII to generate a single contig consisting of circular chromosome sequence. Illumina MiniSeq sequencing platform and Sanger sequencing method were additionally utilized to correct errors resulting from the long-read sequencing platform. The sequence consists of 2,009,598 bp with a G + C content of 42.1% and contains 1,865 protein-coding sequences. Based on the sequence information, we could confirm and predict the presence of four peptidoglycan hydrolases by HyPe software. This work, therefore, provides the complete genomic information of P. acidilactici ATCC 8042 with a profitable potential of genome-scale comprehension of anti-pathogenic activity, which can be applied in nutraceutical and pharmaceutical biotechnology field.

Supercritical fluid chromatography (SFC) meets with great favor due to its high efficiency, low organic solvent consumption, and the specialty for the identification of the isomeric species. This review describes the advances of SFC in targeted and untargeted lipid profiling. The advancement of the SFC instruments and the stationary phases are summarized. Typical applications of SFC to the targeted and untargeted lipid profiling are discussed in detail. Moreover, the perspectives of SFC in the lipid profiling are also proposed. As a useful and promising tool for investigating lipids in vitro and in vivo, SFC will predictably obtain further development. Keywords: Supercritical fluid chromatography, Online SFC technique, Untargeted lipid profiling, Targeted lipid profiling, Lipidomics

An enhanced pseudotargeted method using a segment data-dependent acquisition mode based on ultra-high performance liquid chromatography-tandem mass spectrometry was developed. This segment data dependent acquisition-based pseudotargeted method could improve the detection of co-eluted ions and extend the coverage of analytes. A set of 502 multiple reaction monitoring channels were obtained by this segment strategy, which was twice the number created by the traditional data-dependent acquisition mode. Compared with the untargeted method, the pseudotargeted profiling demonstrated higher sensitivity and higher precision. More than 90% of the metabolites detected by the enhanced pseudotargeted method had relative standard deviations less than 15%. The segment data dependent acquisition-based pseudotargeted method was successfully applied to the metabolomics study of the depressed rats with the treatment of liquiritin. Forty-seven differential metabolites were screened and five metabolic pathways were found to be related to depression including retinol metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis, phenylalanine metabolism, terpenoid backbone biosynthesis, and lysine degradation. The segment data dependent acquisition-based pseudotargeted method widened the coverage of metabolites with good sensitivity and precision, which exhibited great potential in the discovery of differential metabolites in metabolomics studies.

Although plasmid-based expression systems have advantages in multi-copy expression of genes, heterogeneity of plasmid copy number (PCN) in individual cells is inevitable even with the addition of antibiotics. Here, we developed a synthetic auxotrophic system for stable and tunable maintenance of the PCN in Escherichia coli without addition of antibiotics. This auxotroph expresses infA, one of the essential genes encoding a translation initiation factor, on a plasmid instead of on the chromosome. With this system, the gene expression was stably maintained for 40 generations with minimized cell-to-cell variation under antibiotic-free conditions. Moreover, varying the expression level of infA enabled us to rationally tune the PCN by more than 5.6-fold. This antibiotic-free PCN control system significantly improved the production of itaconic acid and lycopene compared to the conventional system based on antibiotics (2-fold). Collectively, the developed strategy could be a platform for the production of value-added products in antibiotic-free cultivation.

3-Hydroxypropionic acid (3-HP) is an important platform chemical, and biological production of 3-HP from glycerol as a carbon source using glycerol dehydratase (GDHt) and aldehyde dehydrogenase (ALDH) has been revealed to be effective because it involves a relatively simple metabolic pathway and exhibits higher yield and productivity than other biosynthetic pathways. Despite the successful attempts of 3-HP production from glycerol, the biological process suffers from problems arising from low activity and inactivation of the two enzymes. To apply the directed evolutionary approach to engineer the 3-HP production system, we constructed a synthetic selection device using a 3-HP-responsive transcription factor and developed a selection approach for screening 3-HP-producing microorganisms. The method was applied to an ALDH library, specifically aldehyde-binding site library of alpha-ketoglutaric semialdehyde dehydrogenase (KGSADH). Only two serial cultures resulted in enrichment of strains showing increased 3-HP production, and an isolated KGSADH variant enzyme exhibited a 2.79-fold higher catalytic efficiency toward its aldehyde substrate than the wild-type one. This approach will provide the simple and efficient tool to engineer the pathway enzymes in metabolic engineering.

With the increased attention on bio-based industry, demands for techniques that enable fast and effective strain improvement have been dramatically increased. Evolutionary engineering, which is less dependent on biological information, has been applied to strain improvement. Currently, synthetic biology has made great innovations in evolutionary engineering, particularly in the development of synthetic tools for phenotypic perturbation. Furthermore, discovering biological parts with regulatory roles and devising novel genetic circuits have promoted high-throughput screening and selection. In this review, we first briefly explain basics of synthetic biology tools for mutagenesis and screening of improved variants, and then describe how these strategies have been improved and applied to phenotypic engineering. Evolutionary engineering using advanced synthetic biology tools will enable further innovation in phenotypic engineering through the development of novel genetic parts and assembly into well-designed logic circuits that perform complex tasks.

Bio-based chemical production has enormous potential as an alternative to petroleum-based chemical production. To establish the economic feasibility of bio-based production, the metabolism of microbial cell factories should be engineered to maximize yield, titer, and productivity. Methods for regulating gene expression are critical for metabolic engineering because enzymes, the final products of gene expression, catalyze most of the reactions required to synthesize chemical products. Recent advances in the development of synthetic regulatory tools have enabled more complex but precise control of gene expression in either static or dynamic mode. These molecular tools have been successfully applied in the metabolic engineering of microorganisms to produce diverse chemicals. Here, we review the synthetic regulatory tools along with the design strategies and applications in the context of metabolic engineering.

The pseudotargeted lipidomics method integrates the advantages of untargeted andtargeted lipidomics methods as a novel emerging approach. In this study, a green andefficient pseudotargeted lipidomics method based on ultra-high performancesupercritical fluid chromatography-tandem mass spectrometry (UHPSFC-MS/MS) wasdeveloped. The tandem mass spectra of the analytes were obtained by using UHPSFCwith quadrupole-time of flight MS (Q-TOF MS) in MS E mode and the multiplereaction monitoring (MRM) transitions of the lipidome were defined. Then, thecandidate MRM transitions were verified by UHPSFC with triple quadrupole massspectrometry (QqQ MS) in the scheduled MRM mode. In total, 758 potential lipidscorresponding to 509 and 249 MRM transitions were detected within 8 min in positiveand negative modes, respectively. The established pseudotargeted lipidomics methodwas validated to have excellent analytical characteristics. Compared with thepseudotargeted method based on ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), the UHPSFC-MS/MS-basedpseudotargeted method not only reduced the analytical time by half but also improvedthe sensitivity and resolution for most analytes, especially had better separation forlipid isomers. Besides, the UHPSFC-MS/MS-based pseudotargeted method showedhigher sensitivity and better repeatability for most analytes than the UHPSFC-MS/MS-based untargeted method. The established method was finally applied to investigatingthe lipid profiles of the plasma from the depressed rats and 33 differential variableswere screened, which related to three metabolic pathways. The results indicated thatthe UHPSFC-MS/MS-based pseudotargeted method is reliable and efficient and couldbe used in the lipidomics studies.

It has been observed that colloidal particles are anomalously repelled from the interface of nanoporous materials and water by up to hundreds of micrometers even if there is no additional external field present. Recently, the physical origin of this anomalous repulsion has turned out to be diffusiophoretic migration triggered by an ion exchange process through the interface. Since the repulsive force is induced by a salt gradient only, the phenomenon can be applied to a microscale water purification platform without the need for any external power sources. In this work, we suggest a micro/nanofluidic device for continuous water purification utilizing long-range diffusiophoretic migration around ion exchangeable surfaces. An ion concentration boundary layer was characterized by the Sherwood number (Sh) which is a key dimensionless number to describe the purification process. Depending on Sh, we have theoretically and experimentally demonstrated that long-range diffusiophoretic exclusion can be used for continuous water purification. Finally, our platform can be used as a highly energy-efficient and portable water treatment option for operations such as purification, disinfection, water softening, etc.

Graphical abstract, Highlights • Unique properties of RNA lead to the development of RNA-based dynamic genetic controllers. • Natural riboswitches are re-engineered to detect new molecules. • RNA-based regulatory mechanisms are exploited to construct novel dynamic RNA controllers. • Computational methods and in vitro–in vivo selection enable de novo design of dynamic RNA controllers. • Dynamic RNA controllers are utilized for metabolic engineering and synthetic biology., 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. Here, we review recent advances in strategies for developing RNA-based dynamic controllers and applications. First, we describe studies that re-engineered natural riboswitches to generate new dynamic controllers. Next, we summarize RNA-based regulatory mechanisms that have been exploited to build novel artificial dynamic controllers. We also discuss computational methods and high-throughput selection approaches for de novo design of dynamic RNA controllers. Finally, we explain applications of dynamic RNA controllers for metabolic engineering and synthetic biology.

A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the osmotic stress response in bacteria. Here, we reveal a genome-scale OmpR regulon in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 37 genes in 24 transcription units (TUs) belong to OmpR regulon. Among them, 26 genes show more than two-fold changes in expression level in an OmpR knock-out strain. Specifically, we find that: 1) OmpR regulates mostly membrane-located gene products involved in diverse fundamental biological processes, such as narU (encoding nitrate/nitrite transporter), ompX (encoding outer membrane protein X), and nuoN (encoding NADH:ubiquinone oxidoreductase); 2) by investigating co-regulation of entire sets of genes regulated by other stress-response TFs, stresses are surprisingly independently regulated among each other; and, 3) a detailed investigation of the physiological roles of the newly discovered OmpR regulon genes reveals that activation of narU represents a novel strategy to significantly improve osmotic stress tolerance of E. coli. Thus, the genome-scale approach to elucidating regulons comprehensively identifies regulated genes and leads to fundamental discoveries related to stress responses.

Additional file 1. Supplementary tables.

The engineering of biological systems to achieve specific purposes requires design tools that function in a predictable and quantitative manner. Recent advances in the field of synthetic biology, particularly in the programmable control of gene expression at multiple levels of regulation, have increased our ability to efficiently design and optimize biological systems to perform designed tasks. Furthermore, implementation of these designs in biological systems highlights the potential of using these tools to build microbial cell factories for the production of chemicals and fuels. In this paper, we review current developments in the design of tools for controlling gene expression at transcriptional, post-transcriptional and post-translational levels, and consider potential applications of these tools.

Cerebral ischemia remains a major cause of mortality and a long-term disability with limited therapies. Isosteviol sodium (STV-Na) was proved to exert significant protective effects on cerebral ischemia, but the protective mechanism was not understood. In this study, the protective effects of STV-Na on cerebral ischemia were investigated by the metabolomics approach based on ultra-high performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry technique. The models of ischemic rats were established and the brain tissues were employed for metabolomics analyses. The principal component analysis showed that the model group was clearly separated from the sham group, while both STV-Na and edaravone groups were located between the sham and the model groups, which indicated that STV-Na as well as edaravone had protective effects on cerebral ischemia. Eighteen differential metabolites which had significant differences between the sham and the model groups were screened and identified. After the administration of STV-Na, all 18 differential metabolites were regulated to the levels between the sham and the model groups, and 12 of them presented significant differences between the model and STV-Na groups. The pathway analysis indicated that the protective effects of STV-Na on cerebral ischemia might be associated with the regulation of several metabolic pathways, i.e. glycerophospholipid metabolism, arachidonic acid metabolism and linoleic acid metabolism.

Translational efficiency in Escherichia coli is known to be strongly influenced by the secondary structure around the ribosome-binding site and the initiation codon in the translational-initiation region of the mRNA. Several quantitative studies have reported that translational efficiency is attributable to effects on ribosome accessibility predominantly caused by the secondary structure surrounding the ribosome-binding site. However, the influence of mRNA secondary structure around regions downstream of the initiation codon on translational efficiency after ribosome-binding step has not been quantitatively studied. Here, we quantitatively analyzed the relationship between secondary structure of mRNA surrounding the region downstream of the initiation codon, referred to as the downstream region (DR), and protein expression levels. Modified hairpin structures containing the initiation codon were constructed by site-directed mutagenesis, and their effects on expression were analyzed in vivo. The minimal folding free energy (DeltaG) of a local hairpin structure was found to be linearly correlated with the relative expression level over a range of fourfold change. These results demonstrate that expression level can be quantitatively controlled by changing the stability of the secondary structure surrounding the DR.

Many successful metabolic engineering projects have utilized evolutionary approaches, which consist of generating phenotypic diversity and screening for desired phenotype. Since conventional screening methods suffer from low throughput and limited target metabolites, a universal high-throughput screening platform for selection of improved strains should be developed to facilitate evolution of metabolite high producer. Recently, riboswitches have received attention as attractive sensor-actuator hybrids that can control gene expression in response to intracellular metabolite concentration. Our group developed a riboswitch-based selection device called "Riboselector" which can give a growth advantage to metabolite-overproducing strains by modulating expression of a selectable marker gene. We applied the device to expedite evolution of lysine producing Escherichia coli, and the selected strain showed a dramatic improvement of lysine production compared to its parental strain. Moreover, a tryptophan-responsive Riboselector was also developed using synthetic tryptophan aptamer. In this chapter, we provide a step-by-step overview of developing synthetic RNA devices comprising a riboswitch and a selection module that specifically sense inconspicuous metabolites and enrich high producer strains out of library.

Many successful metabolic engineering projects have utilized evolutionary approaches, which consist of generating phenotypic diversity and screening for desired phenotype. Since conventional screening methods suffer from low throughput and limited target metabolites, a universal high-throughput screening platform for selection of improved strains should be developed to facilitate evolution of metabolite high producer. Recently, riboswitches have received attention as attractive sensor–actuator hybrids that can control gene expression in response to intracellular metabolite concentration. Our group developed a riboswitch-based selection device called “Riboselector” which can give a growth advantage to metabolite-overproducing strains by modulating expression of a selectable marker gene. We applied the device to expedite evolution of lysine producing Escherichia coli , and the selected strain showed a dramatic improvement of lysine production compared to its parental strain. Moreover, a tryptophan-responsive Riboselector was also developed using synthetic tryptophan aptamer. In this chapter, we provide a step-by-step overview of developing synthetic RNA devices comprising a riboswitch and a selection module that specifically sense inconspicuous metabolites and enrich high producer strains out of library.

Balancing the amounts of enzymes is one of the important factors to achieve optimum performance of a designed metabolic pathway. However, the random mutagenesis approach is impractical since it requires searching an unnecessarily large number of variants and often results in searching a narrow range of expression levels which are out of optimal level. Here, we developed a predictive combinatorial design method, called UTR Library Designer, which systematically searches a large combinatorial space of expression levels. It accomplishes this by designing synthetic translation initiation region of mRNAs in a predictive way based on a thermodynamic model and genetic algorithm. Using this approach, we successfully enhanced lysine and hydrogen production in Escherichia coli. Our method significantly reduced the number of variants to be explored for covering large combinatorial space and efficiently enhanced pathway efficiency, thereby facilitating future efforts in metabolic engineering and synthetic biology.

An extension of directed evolution strategies to genome-wide variations increases the chance of obtaining metabolite-overproducing microbes. However, a general high-throughput screening platform for selecting improved strains remains out of reach. Here, to expedite the evolution of metabolite-producing microbes, we utilize synthetic RNA devices comprising a riboswitch and a selection module that specifically sense inconspicuous metabolites. Using L-lysine-producing Escherichia coli as a model system, we demonstrated that this RNA device could enrich pathway-optimized strains to up to 75% of the total population after four rounds of enrichment cycles. Furthermore, the potential applicability of this device was examined by successfully extending its application to the case of L-tryptophan. When used in conjunction with combinatorial mutagenesis for metabolite overproduction, our synthetic RNA device should facilitate strain improvement.

Precise prediction of prokaryotic translation efficiency can provide valuable information for optimizing bacterial host for the production of biochemical compounds or recombinant proteins. However, dynamic changes in mRNA folding throughout translation make it difficult to assess translation efficiency. Here, we systematically determined the universal folding regions that significantly affect the efficiency of translation in Escherichia coli. By assessing the specific regions for mRNA folding, we could construct a predictive design method, UTR Designer, and demonstrate that proper codon optimization around the 5'-proximal coding sequence is necessary to achieve a broad range of expression levels. Finally, we applied our method to control the threshold value of input signals switching on a genetic circuit. This should increase our understanding of the processes underlying gene expression and provide an efficient design principle for optimizing various biological systems, thereby facilitating future efforts in metabolic engineering and synthetic biology.

A pre-column derivatization method was developed to analyze polyamidoamine (PAMAM) dendrimers. The fluorescein isothiocyanate (FITC) derivation method improved the retention of PAMAM dendrimers on the reversed-phase column of high performance liquid chromatography (RP-HPLC). The derivation benefited the UV-Vis detection of PAMAM, although the fluorescence of FITC was quenched by PAMAM dendrimers. The primary amine-terminated PAMAM dendrimers, generation 3 (PAMAM-NH2 (G3)), were quantitatively determined by UV-Vis spectroscopy over the concentration range of 10–80 μg mL−1, with the calibration curve expressed as A = 131.6C (μg mL−1) − 295.6 (R2 = 0.9901) and the detection limit of 2.7 μg mL−1. The binding ratio of FITC to PAMAM-NH2 (G3) was determined as 8:1 by liquid chromatography-electrospray ionization-ion trap mass spectrometry (LC-ESI-IT-MS).