Synthesis of 12-aminododecenoic acid by coupling transaminase to oxylipin pathway enzymes.

Biobased polymers derived from plant oils are sustainable alternatives to petro based polymers. In recent years, multienzyme cascades have been developed for the synthesis of biobased ω-aminocarboxylic acids, which serve as building blocks for polyamides. In this work, we have developed a novel enzyme cascade for the synthesis of 12-aminododeceneoic acid, a precursor for nylon-12, starting from linoleic acid. Seven bacterial ω-transaminases (ω-TAs) were cloned, expressed in Escherichia coli and successfully purified by affinity chromatography. Activity towards the oxylipin pathway intermediates hexanal and 12-oxododecenoic acid in their 9(Z) and 10(E) isoforms was demonstrated for all seven transaminases in a coupled photometric enzyme assay. The highest specific activities were obtained with ω-TA from Aquitalea denitrificans (TRAD), with 0.62 U mg-1 for 12-oxo-9(Z)-dodecenoic acid, 0.52 U mg-1 for 12-oxo-10(E)-dodecenoic acid and 1.17 U mg-1 for hexanal. A one-pot enzyme cascade was established with TRAD and papaya hydroperoxide lyase (HPLCP-N), reaching conversions of 59% according to LC-ELSD quantification. Starting from linoleic acid, up to 12% conversion to 12-aminododecenoic acid was achieved with a 3-enzyme cascade comprising soybean lipoxygenase (LOX-1), HPLCP-N and TRAD. Higher product concentrations were achieved by the consecutive addition of enzymes compared to simultaneous addition at the beginning. KEY POINTS: • Seven ω-transaminases converted 12-oxododecenoic acid into its corresponding amine. • A three-enzyme cascade with lipoxygenase, hydroperoxide lyase, and ω-transaminase was established for the first time. • A one-pot transformation of linoleic acid to 12-aminododecenoic acid, a precursor of nylon-12 was achieved.

Synthesis of Polymer Precursor 12-Oxododecenoic Acid Utilizing Recombinant Papaya Hydroperoxide Lyase in an Enzyme Cascade.

Hydroperoxide lyases (HPLs) catalyze the splitting of 13S-hydroperoxyoctadecadienoic acid (13S-HPODE) into the green note flavor hexanal and 12-oxo-9(Z)-dodecenoic acid, which is not yet used industrially. Here, HPL from Carica papaya (HPLCP) was cloned and functionally expressed in Escherichia coli to investigate synthesis of 12-oxo-9(Z)-dodecenoic acid in detail. To improve the low catalytic activity of full-length HPLCP, the hydrophobic, non-conserved N-terminal sequence was deleted. This enhanced enzyme activity from initial 10 to 40 U/l. With optimization of solubilization buffer, expression media enzyme activity was increased to 2700 U/l. The tetrameric enzyme was produced in a 1.5 l fermenter and enriched by affinity chromatography. The enzyme preparation possesses a slightly acidic pH optimum and a catalytic efficiency (kcat/KM) of 2.73 × 106 s-1·M-1 towards 13S-HPODE. Interestingly, HPLCP-N could be applied for the synthesis of 12-oxo-9(Z)-dodecenoic acid, and 1 mM of 13S-HPODE was transformed in just 10 s with a yield of 90%. At protein concentrations of 10 mg/ml, the slow formation of the 10(E)-isomer traumatin was observed, pointing to a non-enzymatic isomerization process. Bearing this in mind, a one-pot enzyme cascade starting from safflower oil was developed with consecutive addition of Pseudomonas fluorescens lipase, Glycine max lipoxygenase (LOX-1), and HPLCP-N. A yield of 43% was obtained upon fast extraction of the reaction mixtures after 1 min of HPLCP-N reaction. This work provides first insights into an enzyme cascade synthesis of 12-oxo-9(Z)-dodecenoic acid, which may serve as a bifunctional precursor for bio-based polymer synthesis.

Formation of cyclic structures in the cationic ring-opening polymerization of 1,3-dioxolane.

The cationic ring-opening polymerization of acetals is prone to cyclization of the polymer chains. This is also the case for the polymerization of 1,3-dioxolane. Literature states that this cyclization can be reduced by applying the Active Monomer mechanism, at least if no competition with the Active Chain End mechanism occurs. In this work, a detailed characterization of the different distributions resulting from the cationic ring-opening polymerization of 1,3-dioxolane via the Active Monomer mechanism is made by a combination of gel permeation chromatography, 1H NMR, and for the first time by matrix assisted laser desorption/ionization time of flight mass spectrometry. The influence of monomer addition speed, catalyst to initiator ratio and solvent were studied on both kinetics and composition of the product. Furthermore, it was found that increasing the conversion and monomer to initiator ratios leads to an increased amount of cyclic structures and to broader distributions, in correspondence with the Jacobson-Stockmayer theory. Furthermore, ion trapping experiments using 31P NMR provide insights into the actual reaction mechanism. Finally, purification of the products after the reactions led to a reduction of the cyclic fraction.

Testing one or multiple: How beliefs about sparsity affect causal experimentation.

What is the best way of discovering the underlying structure of a causal system composed of multiple variables? One prominent idea is that learners should manipulate each candidate variable in isolation to avoid confounds (sometimes known as the control of variables [CV] strategy). We demonstrate that CV is not always the most efficient method for learning. Using an optimal actor model, which aims to minimize the average number of tests, we show that when a causal system is sparse (i.e., when the outcome of interest has few or even just one actual cause among the candidate variables), it is more efficient to test multiple variables at once. Across a series of behavioral experiments, we then show that people are sensitive to causal sparsity and adapt their strategies accordingly. When interacting with a dense causal system (high proportion of actual causes among candidate variables), they use a CV strategy, changing one variable at a time. When interacting with a sparse causal system, they are more likely to test multiple variables at once. However, we also find that people sometimes use a CV strategy even when a system is sparse. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Identification of LcpRBA3(2), a novel regulator of lcp expression in Streptomyces coelicolor A3(2).

Streptomyces coelicolor A3(2) is a rubber-degrading actinomycete that harbors one gene coding for a latex clearing protein (lcpA3(2)). Within the genome of S. coelicolor A3(2), we identified a gene coding for a novel protein of the TetR family (LcpRBA3(2)) downstream of lcpA3(2) and demonstrated its binding upstream of lcpA3(2). This indicates a role of LcpRBA3(2) in the regulation of lcp expression. LcpRBA3(2) shows no homology to LcpRVH2, a putative regulator of lcp expression in Gordonia polyisoprenivorans VH2. Additionally, LcpRVH2 homologs did not occur in the genome of S. coelicolor A3(2). Reverse transcriptase (RT) experiments showed that the expression of lcpA3(2) and lcpRBA3(2) is induced with poly(cis-1,4-isoprene) as sole carbon source. For further experiments, we heterologously expressed lcpRBA3(2) in Escherichia coli, purified the protein, and subsequently verified a binding of LcpRBA3(2) upstream of lcpA3(2). The operator site was examined by a DNase I footprinting assay: it comprises 31 bp and exhibits an inverted repeat of nine bases for the putative binding region. Interestingly, two N-terminal DNA-binding HTH domains of the TetR-type (PF00440) were identified within the sequence of LcpRBA3(2). The native molecular weight of LcpRBA3(2) was determined as 44 kDa by size exclusion chromatography which correlates to the molecular weight of a monomer. Normally, proteins of the TetR family occur as dimers so that the monomeric state is a novelty. Furthermore, LcpRBA3(2) homologs were identified in silico in several Lcp-containing actinomycetes, suspecting a conserved regulation mechanism. Apparently, the expression of lcps is regulated either by an LcpRB or by an LcpR.

LcpRVH2 - regulating the expression of latex-clearing proteins in Gordonia polyisoprenivorans VH2.

Gordonia polyisoprenivorans VH2 harbours two latex clearing proteins, which are responsible for the cleavage of poly(cis-1,4-isoprene) into oligoisoprenes, thereby allowing growth in presence of, e.g. natural rubber. A gene coding for a putative regulator of the TetR-family (lcpRVH2) is located 131 bp upstream of lcp1VH2. We heterologously expressed lcpRVH2 in Escherichia coli, and purified and characterized the protein with respect to its ability to bind to the operator region of lcp1VH2. LcpRVH2 forms a dimer in its native state. The size of the dimer was determined to be 52.7 kDa by size exclusion chromatography, whereas the calculated size of a monomer was 24.1 kDa. Electrophoretic mobility shift assays (EMSAs) with the purified protein revealed a shift upon binding to the intergenic region between lcpRVH2 and lcp1VH2. Within this region, an inverted repeat was identified in silico, probably being the binding site of LcpRVH2. This binding sequence was confirmed by a DNase I footprinting assay. A shift also occurred in EMSAs with this 44 bp sequence only. Interestingly, no regulator was detected upstream of the second lcp (lcp2VH2). Therefore, we performed EMSA studies with LcpRVH2 and the putative operator region upstream of lcp2VH2, and discovered by DNase I footprinting another binding sequence upstream of lcp2VH2. Hence, we concluded that LcpRVH2 binds the operator region of both lcps and, most likely, regulates their expression in G. polyisoprenivorans VH2.

Asking the right questions about the psychology of human inquiry: Nine open challenges.

The ability to act on the world with the goal of gaining information is core to human adaptability and intelligence. Perhaps the most successful and influential account of such abilities is the Optimal Experiment Design (OED) hypothesis, which argues that humans intuitively perform experiments on the world similar to the way an effective scientist plans an experiment. The widespread application of this theory within many areas of psychology calls for a critical evaluation of the theory's core claims. Despite many successes, we argue that the OED hypothesis remains lacking as a theory of human inquiry and that research in the area often fails to confront some of the most interesting and important questions. In this critical review, we raise and discuss nine open questions about the psychology of human inquiry.

Elastic materials for tissue engineering applications: Natural, synthetic, and hybrid polymers.

Elastin and collagen are the two main components of elastic tissues and provide the tissue with elasticity and mechanical strength, respectively. Whereas collagen is adequately produced in vitro, production of elastin in tissue-engineered constructs is often inadequate when engineering elastic tissues. Therefore, elasticity has to be artificially introduced into tissue-engineered scaffolds. The elasticity of scaffold materials can be attributed to either natural sources, when native elastin or recombinant techniques are used to provide natural polymers, or synthetic sources, when polymers are synthesized. While synthetic elastomers often lack the biocompatibility needed for tissue engineering applications, the production of natural materials in adequate amounts or with proper mechanical strength remains a challenge. However, combining natural and synthetic materials to create hybrid components could overcome these issues. This review explains the synthesis, mechanical properties, and structure of native elastin as well as the theories on how this extracellular matrix component provides elasticity in vivo. Furthermore, current methods, ranging from proteins and synthetic polymers to hybrid structures that are being investigated for providing elasticity to tissue engineering constructs, are comprehensively discussed. STATEMENT OF SIGNIFICANCE: Tissue engineered scaffolds are being developed as treatment options for malfunctioning tissues throughout the body. It is essential that the scaffold is a close mimic of the native tissue with regards to both mechanical and biological functionalities. Therefore, the production of elastic scaffolds is of key importance to fabricate tissue engineered scaffolds of the elastic tissues such as heart valves and blood vessels. Combining naturally derived and synthetic materials to reach this goal proves to be an interesting area where a highly tunable material that unites mechanical and biological functionalities can be obtained.

psiTurk: An open-source framework for conducting replicable behavioral experiments online.

Online data collection has begun to revolutionize the behavioral sciences. However, conducting carefully controlled behavioral experiments online introduces a number of new of technical and scientific challenges. The project described in this paper, psiTurk, is an open-source platform which helps researchers develop experiment designs which can be conducted over the Internet. The tool primarily interfaces with Amazon's Mechanical Turk, a popular crowd-sourcing labor market. This paper describes the basic architecture of the system and introduces new users to the overall goals. psiTurk aims to reduce the technical hurdles for researchers developing online experiments while improving the transparency and collaborative nature of the behavioral sciences.

Strategies to intervene on causal systems are adaptively selected.

How do people choose interventions to learn about causal systems? Here, we considered two possibilities. First, we test an information sampling model, information gain, which values interventions that can discriminate between a learner's hypotheses (i.e. possible causal structures). We compare this discriminatory model to a positive testing strategy that instead aims to confirm individual hypotheses. Experiment 1 shows that individual behavior is described best by a mixture of these two alternatives. In Experiment 2 we find that people are able to adaptively alter their behavior and adopt the discriminatory model more often after experiencing that the confirmatory strategy leads to a subjective performance decrement. In Experiment 3, time pressure leads to the opposite effect of inducing a change towards the simpler positive testing strategy. These findings suggest that there is no single strategy that describes how intervention decisions are made. Instead, people select strategies in an adaptive fashion that trades off their expected performance and cognitive effort.