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Synthetic biology provides a significant platform in creating novel pathways/organisms for producing useful compounds, while it remains a challenge to enhance the production efficiency. Recently we constructed a recombinant Escherichia coli for glutarate production using a synthetic α-ketoacid reduction pathway, in which α-ketoglutarate is reduced to 2-hydroxyglutarate then converted to glutarate. However, the production titer was low, which may be due to 1) oxygen-sensitive nature of 2-hydroxyglutaryl-CoA dehydratase (HgdABC) and 2) limited cell growth in anaerobic cultivation. Therefore, we developed an aerobic-anaerobic two-stage strategy by growing more cells aerobically, then shifting to anaerobic cultivation to ensure the functional HgdABC for glutarate biosynthesis. The two-stage cultivation resulted in higher production of glutarate and other two C5 dicarboxylic acids – glutaconate and 2-hydroxylglutarate than the original anaerobic process. Furthermore, we used an anaerobically-inducible nar promoter to improve the hgdABC expression responding to aerobic-anaerobic shift. Finally, the glutarate, glutaconate and 2-hydroxyglutarate titer was increased about 2, 5 and 3 times, reaching 11.6, 108.8 and 399.5 mg/L, respectively. The work demonstrated an effective strategy for ameliorating α-ketoacid reduction pathway to produce C5 dicarboxylic acids, as well as the potential of integration of bioprocess and metabolic engineering for enhancing chemicals production by an engineered microorganism. [ABSTRACT FROM AUTHOR]

Metaphors are not just decorative rhetorical devices that make speech pretty. They are fundamental tools for thinking about the world and acting on the world. The language we use to make a better world matters; words matter; metaphors matter. Words have consequences - ethical, social and legal ones, as well as political and economic ones. They need to be used 'responsibly'. They also need to be studied carefully - this is what we want to do through this editorial and the related thematic collection. In the context of synthetic biology, natural and social scientists have become increasingly interested in metaphors, a wave of interest that we want to exploit and amplify. We want to build on emerging articles and books on synthetic biology, metaphors of life and the ethical and moral implications of such metaphors. This editorial provides a brief introduction to synthetic biology and responsible innovation, as well as a comprehensive review of literature on the social, cultural and ethical impacts of metaphor use in genomics and synthetic biology. Our aim is to stimulate an interdisciplinary and international discussion on the impact that metaphors can have on science, policy and publics in the context of synthetic biology. [ABSTRACT FROM AUTHOR]

Synthetic biology is revolutionising the biotech industry and is increasingly applied in previously unthought-of markets. Here, we discuss the importance of this industry to the bioeconomy and two of its key factors: the synthetic biology approach to research and development (R&D), and the unique nature of the carefully designed, stakeholder-inclusive, community-directed evolution of the field. [ABSTRACT FROM AUTHOR]

Benthic organisms are among the most diverse and abundant in the marine realm, and some species are a key factor in studies related to bioengineering. However, their importance has not been well noted in biogeographic studies. Macrofaunal assemblages associated with subtidal beds of the ribbed mussel ( Aulacomya atra) along South America were studied to assess the relationship between their diversity patterns and the proposed biogeographic provinces in the Southeastern Pacific and Southwestern Atlantic Oceans. Samples from ribbed mussel beds were obtained from 10 sites distributed from the Peruvian coast (17°S) to the Argentinean coast (41°S). The sampling included eight beds in the Pacific and two in the Atlantic and the collections were carried out using five 0.04 m2 quadrants per site. Faunal assemblages were assessed through classification analyses using binary and log-transformed abundance data. Variation in the size and density of mussels, and in the species richness, abundance and structure of their faunal assemblages were tested using a permutational multivariate analysis of variance. Faunal assemblages showed a north-south latitudinal gradient along both the Pacific and Atlantic coasts. Binary and abundance data showed a difference in the resulting clustering arrangement of Pacific sites between 40°S and 44°S, indicating a pattern of continuity in the species distribution associated with biological substrates. At a regional scale, the distribution of species along the South American coast matched the general provincial pattern shown by prior studies, which show two biogeographic units on the Pacific coast separated by an intermediate (probably transitional) zone and a single province on the Atlantic coast extending up to Northern Argentina. Biological substrates such as ribbed mussel beds play an important ecological role by making a similar habitat type available on a large scale for a variety of invertebrate species. Despite such habitat homogeneity, however, the associated fauna exhibit marked distribution breaks, suggesting strong constraints on dispersal. This therefore suggests that macrofaunal assemblages could possibly be used as biogeographic indicators. [ABSTRACT FROM AUTHOR]

The article focuses on the aspects of the biological computing and the application of microprocessors in the field of microbiology. Topics discussed include the development of computer software which could control molecular scale such as viruses which infect the human body, the invention of techniques which has the capacity to reprogram biological computers or synthetic biology, and the concerns on the potential of synthetic biology in overtaking the potential of electronics.

The increasing ease of producing nucleic acids and proteins to specification offers potential for design and fabrication of artificial synthetic "organisms" with a myriad of possible capabilities. The prospects for these synthetic organisms are significant, with potential applications in diverse fields including synthesis of pharmaceuticals, sources of renewable fuel and environmental cleanup. Until now, artificial cell technology has been largely restricted to the modification and metabolic engineering of living unicellular organisms. This review discusses emerging possibilities for developing synthetic protocell "machines" assembled entirely from individual biological components. We describe a host of recent technological advances that could potentially be harnessed in design and construction of synthetic protocells, some of which have already been utilized toward these ends. More elaborate designs include options for building self-assembling machines by incorporating cellular transport and assembly machinery. We also discuss production in miniature, using microfluidic production lines. While there are still many unknowns in the design, engineering and optimization of protocells, current technologies are now tantalizingly close to the capabilities required to build the first prototype protocells with potential real-world applications. [ABSTRACT FROM AUTHOR]

The article presents a study which investigates the mechanisms of the formation and morphogenetic types of fluid additions in crystals of artificial minerals. The study explains that the investigation of artificial inclusions in the artificial minerals received at the beginning and assured conditions might be given an answer to the most essential query regarding the indicator role of inclusions. It mentions that the result of the study of artificial fluid additions, enables the researchers to solve general problems of the mechanism of their formation in natural minerals along with the arguments and the potentials of diagnostic approaches and in gemology.

BrisSynBio is the Bristol-based Biotechnology and Biological Sciences Research Council (BBSRC)/Engineering and Physical Sciences Research Council (EPSRC)-funded Synthetic Biology Research Centre. It is one of six such Centres in the U.K. BrisSynBio's emphasis is on rational and predictive bimolecular modelling, design and engineering in the context of synthetic biology. It trains the next generation of synthetic biologists in these approaches, to facilitate translation of fundamental synthetic biology research to industry and the clinic, and to do this within an innovative and responsible research framework. [ABSTRACT FROM AUTHOR]

The article discusses the foray of multiple artists and exhibitions into science, with the aim of applying the tools of synthetic biology to their creations. It highlights the 2012 exhibit of artist Howard Boland entitled "Stress-o-stat," wherein he illustrated biological processes for viewers. It offers information on the Synthetic Aesthetics project, which aims to examine the relationship between art, design, and synthetic biology.

The methionine biosynthetic pathway found in bacteria is controlled at the first step, acylation of the γ-hydroxyl of homoserine. This reaction is catalyzed by one of two unique enzymes, homoserine transacetylase or homoserine transsuccinylase, which have no amino acid sequence similarity. We cloned, expressed, and purified homoserine transsuccinylase from the thermophilic bacterium Thermotoga maritima. Substrate specificity experiments demonstrated that acetyl-coenzyme A (CoA) is the preferred acyl donor and is used at least 30-fold more efficiently than succinyl-CoA. Steady-state kinetic experiments confirm that the enzyme utilizes a ping-pong kinetic mechanism in which the acetate group of acetyl-CoA is initially transferred to an enzyme nucleophile before subsequent transfer to homoserine. The maximal velocity, V/ K acetyl-CoA and V/ K homoserine, all exhibited bell-shaped pH curves with apparent p Ks of 6.0–6.9 and 8.2–8.8. The enzyme was inactivated by iodoacetamide in a pH-dependent manner, with an apparent p K of 6.3, suggesting the presence of an active-site cysteine residue which forms an acetyl-enzyme thioester intermediate during catalytic turnover, similar to observations with other transsuccinylases. In addition, the enzyme is highly stable at elevated temperatures, maintaining full activity at 70°C. Taken together, these data suggest that the T. maritima enzyme functions biochemically as a transacetylase, despite having the sequence of a transsuccinylase. [ABSTRACT FROM AUTHOR]

Cys2His2 zinc-fingers (C2H2 ZFs) mediate a wide variety of protein–DNA and protein–protein interactions. DNA-binding C2H2 ZFs can be shuffled to yield artificial proteins with different DNA-binding specificities. Here we demonstrate that shuffling of C2H2 ZFs from transcription factor dimerization zinc-finger (DZF) domains can also yield two-finger DZFs with novel protein–protein interaction specificities. We show that these synthetic protein–protein interaction domains can be used to mediate activation of a single-copy reporter gene in bacterial cells and of an endogenous gene in human cells. In addition, the synthetic two-finger domains we constructed can also be linked together to create more extended, four-finger interfaces. Our results demonstrate that shuffling of C2H2 ZFs can yield artificial protein-interaction components that should be useful for applications in synthetic biology. [ABSTRACT FROM AUTHOR]

Presents research which prepared a cuboctahedron from 20 tridentate and bidentate subunits in one step. Commonness of self-assembled polyhedral structures in biology; Preparation of synthetic polyhedral molecular assemblies; Self-assembly of molecular units driven by coordination to transition-metal ions; Features of the cuboctahedron; Diameter of the polyhedral capsules.

Discusses research which is attempting to fabricate artificial liver tissue. How the liver works; Research by Mehmet Toner, Harvard Medical School; Idea of artificial liver; Synthetic liver tissue; Methods for production of tissue; Preparation of an arbitrary ratio of cell types on substrate.