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January 2010 - September 2012
October 2003 - September 2005
Publications
Publications (442)
This anthology brings together a diversity of key texts in the emerging field of Existential Risk Studies. It serves to complement the previous volume The Era of Global Risk: An Introduction to Existential Risk Studies by providing open access to original research and insights in this rapidly evolving field. At its heart, this book highlights the o...
Advances in genome engineering and associated technologies have reinvigorated natural products research. Here we highlight the latest developments in the field across the discover–design–build–test–learn cycle of bioengineering, from recent progress in computational tools for AI-supported genome mining, enzyme and pathway engineering, and compound...
Eicosanoids are a family of bioactive lipids, including derivatives of the ubiquitous fatty acid arachidonic acid (AA). The intimate involvement of eicosanoids in inflammation motivates the development of predictive in...
Phenylpropenes are a class of natural products that are synthesised by a vast range of plant species and hold considerable promise in the flavour and fragrance industries. Many in vitro studies have been carried out to elucidate and characterise the enzymes responsible for the production of these volatile compounds. However, there is a scarcity of...
Objective
Hesperetin is an important O-methylated flavonoid produced by citrus fruits and of potential pharmaceutical relevance. The microbial biosynthesis of hesperetin could be a viable alternative to plant extraction, as plant extracts often yield complex mixtures of different flavonoids making it challenging to isolate pure compounds. In this s...
Background
(Hydroxy)cinnamyl alcohols and allylphenols, including coniferyl alcohol and eugenol, are naturally occurring aromatic compounds widely utilised in pharmaceuticals, flavours, and fragrances. Traditionally, the heterologous biosynthesis of (hydroxy)cinnamyl alcohols from (hydroxy)cinnamic acids involved CoA-dependent activation of the sub...
Selenzyme is a retrobiosynthesis tool that suggests candidate enzymes for user query reactions. Enzyme suggestions are based on identical reactions, as well as similar reactions, since enzymes are often capable of promiscuous substrate binding. Selenzyme is a user-friendly, widely used web-tool for ranking enzymes based on reaction similarity and a...
Flavones and flavonols are important classes of flavonoids with nutraceutical and pharmacological value, and their production by fermentation with recombinant microorganisms promises to be a scalable and economically favorable alternative to extraction from plant sources. Flavones and flavonols have been produced recombinantly in a number of microo...
Background
(Hydroxy)cinnamyl alcohols and allylphenols, including coniferyl alcohol and eugenol, are naturally occurring aromatic compounds widely utilised in pharmaceuticals, flavours, and fragrances. Traditionally, the heterologous biosynthesis of (hydroxy)cinnamyl alcohols from (hydroxy)cinnamic acids involved CoA-dependent activation of the sub...
The Integrated Probabilistic Annotation (IPA) is an automated annotation method for LC-MS-based untargeted metabolomics experiments, that provides statistically rigorous estimates of the probabilities associated with each annotation. Here we introduce ipaPy2, a substantially improved and completely refactored Python implementation of the IPA method...
Transcription factors responsive to small molecules are essential elements in synthetic biology designs. They are often used as genetically encoded biosensors with applications ranging from the detection of environmental contaminants and biomarkers to microbial strain engineering. Despite our efforts to expand the space of compounds that can be det...
Objective
Hesperetin is an important O-methylated flavonoid produced by citrus fruits and of potential pharmaceutical relevance. The microbial biosynthesis of hesperetin could be a viable alternative to plant extraction, as plant extracts often yield complex mixtures of different flavonoids making it challenging to isolate pure compounds. In this s...
Seventy-five years ago, Pierre Bonnet issued a petition to the Commission for Zoological Nomenclature, requesting that action be taken to ensure the availability of Carl Clerck’s widely used names for some of Europe’s most common spiders, despite their publication before the official starting point of zoological nomenclature. His efforts were succe...
The identity of Aranea subterranea Roemer, 1789, the type species of the genus Atypus Latreille, 1804, has recently come under some suspicion. Here, the evidence regarding the case is reviewed and a lectotype is designated for Aranea subterranea and several of its synonyms, based on an illustrated specimen, to stabilise the currently accepted inter...
The extant primitively segmented spiders of the family Liphistiidae s. lat. are a monophyletic, morphologically and ecologically conservative group of "living fossils" that have undergone a surprisingly recent radiation in their small contiguous range in Southeast Asia. Splitting the family into two separate families, Liphistiidae s. str. and Hepta...
Streptomyces is one of the most relevant genera in biotechnology, and its rich secondary metabolism is responsible for the biosynthesis of a plethora of bioactive compounds, including several clinically relevant drugs. The use of Streptomyces species for the manufacture of natural products has been established for more than half a century; however,...
Marusik (2021) presented a brief analysis of the etymology and usage of the words epigyne and epigynum, widely used technical terms for the female external genitalia in spiders. Here a number of corrections to his arguments are presented.
The European wolf spider name Lycosa accentuata Latreille, 1817, has had a long and convoluted nomenclatural history. The interpretation of the name has baffled arachnologists for more than two centuries. Here we describe the historical development of the evolving interpretations and show that the name is certainly not a senior synonym of Alopecosa...
Breast cancer is one of the most common cancers threatening women worldwide. A limited number of available treatment options, frequent recurrence and drug resistance exacerbate the prognosis of breast cancer patients. Thus, there is an urgent need for methods to investigate novel treatment options, while taking into account the vast molecular heter...
Spider Recording Scheme News No. 101 in Newsletter of the British Arachnological Society 152.
Covering: Focus on 2015 to 2020Plant and soil microbiomes consist of diverse communities of organisms from across kingdoms and can profoundly affect plant growth and health. Natural product-based intercellular signals govern important interactions between microbiome members that ultimately regulate their beneficial or harmful impacts on the plant....
The genus Theraphosa was established by Thorell (1870) as the type genus of the simultaneously published family Theraphosidae, the most diverse group of mygalomorph spiders. This authorship and publication date have long been accepted by the majority of authors. However, there has been a long-standing minority view that the genus name should be att...
The recent accumulation of increasingly densely sampled phylogenetic analyses of spiders has greatly advanced our understanding of evolutionary relationships within this group. Here, this diverse literature is reviewed and combined with earlier morphological analyses in an attempt to reconstruct the first fully resolved phylogeny for the spider fau...
The proverbial phrase “you can't get blood from a stone” is used to describe a task that is practically impossible regardless of how much force or effort is exerted. This phrase is well-suited to humanity’s first crewed mission to Mars, which will likely be the most difficult and technologically challenging human endeavour ever undertaken. The high...
Planobispora rosea is the natural producer of the potent thiopeptide antibiotic GE2270A. Here, we present the results of a metabolomics and transcriptomics analysis of P. rosea during production of GE2270A. The data generated provides useful insights into the biology of this genetically intractable bacterium. We characterize the details of the shut...
In this work, we explore the use of human serum albumin (HSA) – a common protein obtained from blood plasma – as a binder for simulated Lunar and Martian regolith to produce so-called extraterrestrial regolith biocomposites (ERBs). In essence, HSA produced by astronauts in vivo could be extracted on a semi-continuous basis and combined with Lunar o...
Their biochemical versatility and biotechnological importance make actinomycete bacteria attractive targets for ambitious genetic engineering using the toolkit of synthetic biology. But their complex biology also poses unique challenges. This mini review discusses some of the recent advances in synthetic biology approaches from an actinomycete pers...
The ability to engineer biological systems, whether to introduce novel functionality or improved performance, is a cornerstone of biotechnology and synthetic biology. Typically, this requires the generation of genetic diversity to explore variations in phenotype, a process that can be performed at many levels, from single molecule targets (i.e., in...
The recent accumulation of increasingly densely sampled phylogenetic analyses of spiders has greatly advanced our understanding of evolutionary relationships within this group. Here, this diverse literature is reviewed and combined with earlier morphological analyses in an attempt to reconstruct the first fully resolved phylogeny for the spider fau...
The previously reported Streptomyces coelicolor M1146 is commonly used as a host strain for engineering of secondary metabolite production. In this study, absolute quantification of intracellular and extracellular metabolites of M1146 was performed in mid-log phase and stationary phase to observe major metabolites and the changes that occurred duri...
Cyclic adenosine monophosphate (cAMP) has been known to play an important role in regulating morphological development and antibiotic production in Streptomyces coelicolor. However, the functional connection between cAMP levels and antibiotic production and the mechanism by which cAMP regulates antibiotic production remain unclear. In this study, m...
Spider silk is renowned for its impressive mechanical properties. It is one of the strongest known biomaterials, possessing mechanical properties that outmatch both steel and Kevlar. However, the farming of spiders for their silk is unfeasible. Consequently, production of recombinant spider silk proteins (spidroins) in more amenable hosts is an exc...
Natural plant-based flavonoids have drawn significant attention as dietary supplements due to their potential health benefits, including anti-cancer, anti-oxidant, and anti-asthmatic activities. Naringenin, pinocembrin, eriodictyol and homoeriodictyol are classified as (2S)-flavanones, an important sub-group of naturally-occurring flavonoids, with...
Antibiotic production is coordinated in the Streptomyces coelicolor population through the use of diffusible signaling molecules of the γ-butyrolactone (GBL) family. The GBL regulatory system involves a small, and not completely defined two-gene network which governs a potentially bi-stable switch between the “on” and “off” states of antibiotic pro...
Protein-based adhesives could have several advantages over petroleum-derived alternatives, including substantially lower toxicity, smaller environmental footprint and renewable sourcing. Here, we report that non-covalently crosslinked bovine serum albumin (BSA) and recombinant spider silk proteins have high adhesive strength on glass (8.53 and 6.28...
Spider silk spidroins consist of long repetitive protein strands, flanked by globular terminal domains. The globular domains are often omitted in recombinant spidroins, but are thought to be essential for the spiders’ natural spinning process. Mimicking this spinning process could be an essential step towards producing strong synthetic spider silk....
Horizon scanning is intended to identify the opportunities and threats associated with technological, regulatory and social change. In 2017 some of the present authors conducted a horizon scan for bioengineering (Wintle et al., 2017). Here we report the results of a new horizon scan that is based on inputs from a larger and more international group...
Horizon scanning is intended to identify the opportunities and threats associated with technological, regulatory and social change. In 2017 some of the present authors conducted a horizon scan for bioengineering (Wintle et al., 2017). Here we report the results of a new horizon scan that is based on inputs from a larger and more international group...
Horizon scanning is intended to identify the opportunities and threats associated with technological, regulatory and social change. In 2017 some of the present authors conducted a horizon scan for bioengineering (Wintle et al., 2017). Here we report the results of a new horizon scan that is based on inputs from a larger and more international group...
Terpenes are the largest class of natural products with extensive structural diversity and are widely used as pharmaceuticals, herbicides, flavourings, fragrances, and biofuels. While they have mostly been isolated from plants and fungi, the availability and analysis of bacterial genome sequence data indicates that bacteria also possess many putati...
List of German names for the spiders of Germany (Araneae).
Common names play an important role in the efficient communication of scientific results in biology, for instance in the area of applied conservation science, in popular articles and in Citizen Science projects. Common names can increase the readability of texts aimed at the general public...
Bio-based production of industrial chemicals using synthetic biology can provide alternative green routes from renewable resources, allowing for cleaner production processes. To efficiently produce chemicals on-demand through microbial strain engineering, biomanufacturing foundries have developed automated pipelines that are largely compound agnost...
Eric Duffey's spider collection in the Manchester Museum, accumulated over more than 40 years, contains more than 300 samples from a diverse range of biotopes in most southern European countries. Most of this material was previously unsorted. It has now been sorted and identified to species level. It contains more than 2500 specimens of more than 5...
Spider silk is one of the strongest biomaterials available in nature. Its mechanical properties make it a good candidate for applications in various fields ranging from protective armour to bandages for wound dressing to coatings for medical implants. Spider silk is formed by an intricate arrangement of spidroins, which are extremely large proteins...
Spider silk spidroins consist of long repetitive protein strands, flanked by globular terminal domains. The globular domains are often omitted in recombinant spidroins, but are thought to be essential for the spiders natural spinning process. Mimicking this spinning process could be an essential step towards producing strong synthetic spider silk....
Synthetic biology utilises the Design-Build-Test-Learn pipeline for the engineering of biological systems. Typically, this requires the construction of specifically designed, large and complex DNA assemblies. The availability of cheap DNA synthesis and automation enables high-throughput assembly approaches, which generates a heavy demand for DNA se...
Nutritional supplementation with fish oil or ω‐3 (n‐3) polyunsaturated fatty acids (PUFAs) has potential benefits for skin inflammation. Although the differential metabolism of the main n‐3PUFA eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) could lead to distinct activities, there are no clinical studies comparing their relative efficac...
In a typical untargeted metabolomics experiment, the huge amount of complex data generated by mass spectrometry necessitates automated tools for the extraction of useful biological information. Each metabolite generates numerous mass spectrometry features. The association of these experimental features to the underlying metabolites still represents...
The paper comments the usefulness of barcode data for genus-level taxonomy.
The paper gives a counterpoint to the recent critique of the “pragmatic classification” of jumping spiders (Arthropoda: Arachnida: Araneae: Salticidae).
Synthetic biology has a huge potential to produce the next generation of advanced materials by accessing previously unreachable (bio)chemical space. In this prospective review, we take a snapshot of current activity in this rapidly developing area, focusing on prominent examples for high-performance applications such as those required for protectiv...
DNA barcode sequencing has rapidly become one of the most powerful tools for biodiversity assessments. Beyond its original uses for the identification of animal species, including the discovery of cryptic diversity in difficult taxonomic groups, the growing public sequence datasets also offer opportunities for more wide-ranging applications. This c...
Neighbour-joining trees and multidimensional scaling results for each family
Maximum likelihood trees for selected species groups
The phylogenetic relationships and taxonomy of the crab spider genus Xysticus and its closest relatives (i.e., the tribe Coriarachnini, also including, e.g., Ozyptila, Coriarachne and Bassaniana) have long been controversial, with several alternative classifications being proposed, none of which has gained universal acceptance. As Coriarachnini is...
Previous classifications of Coriarachnini and selected barcode-based phylogenetic reconstructions.
The rapid prototyping and optimizing of plasmid-based recombinant gene expression is one of the key steps in the development of bioengineered bacterial systems. Often, multiple genes or gene modules need to be co-expressed, and for this purpose compatible, inducible plasmid systems have been developed. However, inducible expression systems are not...
The biosynthetic machinery responsible for the production of bacterial specialised metabolites is encoded by physically clustered group of genes called biosynthetic gene clusters (BGCs). The experimental characterization of numerous BGCs has led to the elucidation of sub-clusters of genes within BGCs, jointly responsible for the same biosynthetic f...
The Noble False Widow, Steatoda nobilis (Thorell, 1875) (Araneae, Theridiidae), is, due to its relatively large size and potential medical importance, one of the most notable invasive spider species worldwide. Probably originating from the Canary Islands and Madeira, the species is well established in Western Europe and large parts of the Mediterra...
Engineering biology is a key enabling technology at the forefront of the new industrial bioeconomy. Rapid prototyping for bio-based production of chemicals and materials in the new biofoundries faces the challenge of dealing with increasingly complex libraries of genetic circuits consisting of multiple gene variants from different sources and with...
The field of synthetic biology aims to make the design of biological systems predictable, shrinking the huge design space to practical numbers for testing. When designing microbial cell factories, most optimisation efforts have focussed on enzyme and strain selection/engineering, pathway regulation and process development. In silico tools for the p...
Antimicrobial resistance is a rapidly growing problem worldwide, with bacteria showing resistance to last‐resort antibiotic treatments such as carbapenems and colistin becoming more abundant. Synthetic biology may be able to contribute to solving this growing antimicrobial resistance crisis by facilitating the engineering of diversified collections...
Ensemble modeling in molecular systems biology requires the reproducible translation of kinetic parameter data into informative probability distributions (priors), as well as approaches that sample parameters from these distributions without violating the thermodynamic consistency of the overall model. Although a number of pioneering frameworks for...
Background: Streptomyces species produce a vast diversity of secondary metabolites of clinical and biotechnological importance, in particular antibiotics. Recent developments in metabolic engineering, synthetic and systems biology have opened new opportunities to exploit Streptomyces secondary metabolism, but achieving industry-level production wit...
The microbial production of fine chemicals provides a promising biosustainable manufacturing solution that has led to the successful production of a growing catalog of natural products and high-value chemicals. However, development at industrial levels has been hindered by the large resource investments required. Here we present an integrated Desig...
Metabolomics plays an increasingly central role within the Design-Build-Test cycle of synthetic biology, in particular in applications targeting the discovery, diversification and optimised production of a wide range of natural products. For example, improved methods for the online monitoring of chemical reactions accelerate data generation to be c...
Chemically inducible transcription factors are widely used to control gene expression of synthetic devices. The bacterial quorum sensing system is a popular tool to achieve such control. However, different quorum sensing systems have been found to cross-talk, both between themselves and with the hosts of these devices, and they are leaky by nature....
