Current trends in natural products research from the CBNP10 Symposium at Warwick

Natural products are compounds that are produced by living organisms. They have numerous applications in our everyday life, from antibiotics to herbicides. They possess great chemical and structural diversity, which gives them a leading position as a source of new drugs. Many institutions worldwide are focusing more and more on natural product research, with microorganisms and plants being the most common source for discovery of new compounds. On the 30th June and 1st July 2016, early-career scientists working in the field of natural products gathered at the University of Warwick for the 10th edition of the Chemistry and Biology of Natural Products Symposium (CBNP10). This critical reflection reviews, in the context of the current research in the field, the major considerations that arose from this meeting

Editing streptomycete genomes in the CRISPR/Cas9 age

This article aims to highlight advantages, drawbacks and issues that users should consider when implementing the use of CRISPR/Cas9-tools for genome editing in streptomycetes, the most prolific source of antimicrobial natural products to date. Here, we examine four toolkits that have so far been made available for streptomycete in vivo-engineering and one for in vitro-editing, and review how they have been applied over the last three years. Our critical evaluation of these toolkits intends to support potential users in determining what they could achieve, what they should consider and what system they should select/optimise for their application

Design of a New Medium-temperature Stirling Engine for Distributed Cogeneration Applications☆

Abstract This paper presents and discusses the design and first prototype realization for a brand new generation of Stirling engines. This unit is realized within the DiGeSPo Project, in which it is coupled with a small-size parabolic trough concentration solar field. The engine is conceived for working with low-temperature heat sources (200-300 C), in order to match the typical temperatures for the solar field itself. The first part presents the thermodynamic design, which is realized by using models and simulations, and give the specifications for each component, including pistons dimensions; the number, length, diameter for the heat exchangers tubes; regenerators porosity, length and diameter. Four independent and equally working spaces were chosen, as a compromise between the compactness of the overall system, limits imposed by the maximum charging pressure, and the target electrical power (3 kW). The parameters of the overall system were optimized during this phase with an iterative procedure, taking into account different concurrent constraints, such as the heat exchange requirements, mechanical friction power losses, and small dead spaces. The engine has been subsequently arranged in a double-acting mechanical configuration, in which the cylinders are opposed as in a boxer engine. This configuration gives the advantages of reducing leaking losses and can work with four pistons. The heat exchangers, which are the most crucial and complex components, have been realized by the Selective Laser Melting (SLM) manufacturing technique. The specific scientific and technical details related to a low-temperature Stirling engine, and the solutions adopted, are discussed and presented trough the paper, and finals recommendations are provided

Natural products from filamentous fungi and production by heterologous expression

Filamentous fungi represent an incredibly rich and rather overlooked reservoir of natural products, which often show potent bioactivity and find applications in different fields. Increasing the naturally low yields of bioactive metabolites within their host producers can be problematic, and yield improvement is further hampered by such fungi often being genetic intractable or having demanding culturing conditions. Additionally, total synthesis does not always represent a cost-effective approach for producing bioactive fungal-inspired metabolites, especially when pursuing assembly of compounds with complex chemistry. This review aims at providing insights into heterologous production of secondary metabolites from filamentous fungi, which has been established as a potent system for the biosynthesis of bioactive compounds. Numerous advantages are associated with this technique, such as the availability of tools that allow enhanced production yields and directing biosynthesis towards analogues of the naturally occurring metabolite. Furthermore, a choice of hosts is available for heterologous expression, going from model unicellular organisms to well-characterised filamentous fungi, which has also been shown to allow the study of biosynthesis of complex secondary metabolites. Looking to the future, fungi are likely to continue to play a substantial role as sources of new pharmaceuticals and agrochemicals—either as producers of novel natural products or indeed as platforms to generate new compounds through synthetic biology

Novel system for distributed energy generation from a small scale concentrated solar power

The present work describes the realization of a modular 1-3 kWe, 3-9 kWth micro Combined Heat and Power (m-CHP) system based on innovative Concentrated Solar Power (CSP) and Stirling engine technology. The cogeneration of energy at distributed level is one of leading argument in large part of energy policies related to renewable energy resources and systems. This CSP m-CHP will provide electrical power, heating and cooling for single and multiple domestic dwellings and other small buildings. The developed system integrates small-scale concentrator optics with moving and tracking components, solar absorbers in the form of evacuated tube collectors, a heat transfer fluid, a Stirling engine with generator, and heating and/or cooling systems; it incorporates them into buildings in an architecturally acceptable manner, with low visual impact. Some good results have already been achieved, while developments on several technology subcomponents will be finalized through first part of 2013. Two Cer.Met. have been modelled, realized and tested. The up scaled receiver, in form of Cer.Met. coating based on TiO2 - Nb, has been confirmed an absorptance of 0.94 and emittance of 0.1 (@350°C). A second Cer.Met. coating based on SiO2 - W has demonstrated an absorptance of 0.93 and emittance of 0.09 (@350°C). A full-evacuated solar tube has been designed and realized, with absorber of 12 mm in diameter and length in 2 meters. The system is provided of a concentration ratio 12:1, and a single module is 200 cm long, 40 cm wide and 20-25 cm high. Two or more modules can be combined. The evacuated solar tube, located on the focus, has the selective absorber on a tube of 12 mm in diameter. A very thin glass mirror has been developed (< 1 mm). The overall mirror reflectivity has been measured, the verified value is 0,954. Research has proposed a high energy density, double acting Stirling engine, provided of innovative heat exchangers realized through Selective Laser Melting process. The engine is a low speed (250 RPM), high pressure (130 Bars) and compact solution able to be run at 300°C and generate 3,5 kW nominal power. The solar technology has actually entered the proof-of-concept stage. A solar plant has been installed in Malta, by Arrow Pharm company, supplying the industrial process of generated steam at 180°C and 3.5 absolute pressure. The solar collector's efficiency is close to 47% in presence of 900 W/m2 of direct solar radiation. During 2013, solar evacuated tubes with innovative Cer.Met. coating, together with new thin glass mirrors will upgrade the demonstration site, together with a new and innovative low temperature difference and high energy density Stirling. By end-2013, the system will be demonstrated, with the overall objective to achieve a minimum of 65% in solar collectors' efficiency at 300°C, and 12 - 15% of overall electrical efficiency by the Stirling cycle.peer-reviewe

Development of a pellet boiler with Stirling engine for m-CHP domestic application

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Probabilistic inductive constraint logic

AbstractProbabilistic logical models deal effectively with uncertain relations and entities typical of many real world domains. In the field of probabilistic logic programming usually the aim is to learn these kinds of models to predict specific atoms or predicates of the domain, called target atoms/predicates. However, it might also be useful to learn classifiers for interpretations as a whole: to this end, we consider the models produced by the inductive constraint logic system, represented by sets of integrity constraints, and we propose a probabilistic version of them. Each integrity constraint is annotated with a probability, and the resulting probabilistic logical constraint model assigns a probability of being positive to interpretations. To learn both the structure and the parameters of such probabilistic models we propose the system PASCAL for "probabilistic inductive constraint logic". Parameter learning can be performed using gradient descent or L-BFGS. PASCAL has been tested on 11 datasets and compared with a few statistical relational systems and a system that builds relational decision trees (TILDE): we demonstrate that this system achieves better or comparable results in terms of area under the precision–recall and receiver operating characteristic curves, in a comparable execution time

Recent developments of tools for genome and metabolome studies in basidiomycete fungi and their application to natural product research

Basidiomycota are a large and diverse phylum of fungi. They can make bioactive metabolites that are used or have inspired the synthesis of antibiotics and agrochemicals. Terpenoids are the most abundant class of natural products encountered in this taxon. Other natural product classes have been described, including polyketides, peptides, and indole alkaloids. The discovery and study of natural products made by basidiomycete fungi has so far been hampered by several factors, which include their slow growth and complex genome architecture. Recent developments of tools for genome and metabolome studies are allowing researchers to more easily tackle the secondary metabolome of basidiomycete fungi. Inexpensive long-read whole-genome sequencing enables the assembly of high-quality genomes, improving the scaffold upon which natural product gene clusters can be predicted. CRISPR/Cas9-based engineering of basidiomycete fungi has been described and will have an important role in linking natural products to their genetic determinants. Platforms for the heterologous expression of basidiomycete genes and gene clusters have been developed, enabling natural product biosynthesis studies. Molecular network analyses and publicly available natural product databases facilitate data dereplication and natural product characterisation. These technological advances combined are prompting a revived interest in natural product discovery from basidiomycete fungi

Triggering the expression of a silent gene cluster from genetically intractable bacteria results in scleric acid discovery

In this study, we report the rapid characterisation of a novel microbial natural product resulting from the rational derepression of a silent gene cluster. A conserved set of five regulatory genes was used as a query to search genomic databases and identify atypical biosynthetic gene clusters (BGCs). A 20-kb BGC from the genetically intractable Streptomyces sclerotialus bacterial strain was captured using yeast-based homologous recombination and introduced into validated heterologous hosts. CRISPR/Cas9-mediated genome editing was then employed to rationally inactivate the key transcriptional repressor and trigger production of an unprecedented class of hybrid natural products exemplified by (2-(benzoyloxy)acetyl)-L-proline, named scleric acid. Subsequent rounds of CRISPR/Cas9-mediated gene deletions afforded a selection of biosynthetic gene mutant strains which led to a plausible biosynthetic pathway for scleric acid assembly. Synthetic standards of scleric acid and a key biosynthetic intermediate were also prepared to confirm the chemical structures we proposed. The assembly of scleric acid involves two unique condensation reactions catalysed by a single NRPS module and an ATP-grasp enzyme that link a proline and a benzoyl residue to each end of a rare hydroxyethyl-ACP intermediate respectively. Scleric acid was shown to exhibit moderate inhibition activity against Mycobacterium tuberculosis, as well as inhibition of the cancer-associated metabolic enzyme Nicotinamide N-methyltransferase (NNMT)