Graphene for multi-functional synthetic biology: The last ‘zeitgeist’ in nanomedicine

The high versatility of graphene has attracted significant attention in many areas of scientific research from electronics to physics and mechanics. One of the most intriguing utilisation of graphene remains however in nanomedicine and synthetic biology. In particular, the last decade has witnessed an exponential growth in the generation of novel candidate therapeutics of multiple biological activities based on graphene constructs with small molecules, such as anti-cancer drugs. In this Digest, we summarise the different synthetic strategies and routes available to fabricate these promising graphene conjugates and the opportunities for the design of multi-functional tools for synthetic biology that they offer.     

Cartoons on bacterial balloons: scientists’ opinion on the popularization of synthetic biology

How do scientists perceive the media coverage of synthetic biology (SB)? In this paper, we approach this question by studying a set of cartoons devoted to SB. Based on a categorization of the cartoons into five large thematic groups an international survey was carried out to assess the opinion of SB research groups on science communication with regard to the public image of their discipline. The 101 responses obtained indicate that in general, their perception of the communication is not negative, although many respondents raised concerns on the media’s inclination to sensationalism and over-simplification. However, the results also suggest that (in the light of the unfortunate experiences with GMO communication) scientists should think twice before proposing metaphorical interpretations of their research.     

Technological biology? Things and kinds in synthetic biology

Social scientific and humanistic research on synthetic biology has focused quite narrowly on questions of epistemology and ELSI. I suggest that to understand this discipline in its full scope, researchers must turn to the objects of the field—synthetic biological artifacts—and study them as the objects in the making of a science yet to be made. I consider one fundamentally important question: how should we understand the material products of synthetic biology? Practitioners in the field, employing a consistent technological optic in the study and construction of biological systems, routinely employ the mantra ‘biology is technology’. I explore this categorization. By employing an established definition of technological artifects drawn from the philosophy of technology, I explore the appropriateness of attributing to synthetic biological artifacts the four criteria of materiality, intentional design, functionality, and normativity. I then explore a variety of accounts of natural kinds. I demonstrate that synthetic biological artifacts fit each kind imperfectly, and display a concomitant ontological ‘messiness’. I argue that this classificatory ambivalence is a product of the field’s own nascence, and posit that further work on kinds might help synthetic biology evaluate its existing commitments and practices.     

Are we doing synthetic biology?

Synthetic Biology is a singular, revolutionary scenario with a vast range of practical applications but, is SB research really based on engineering principles? Is it contributing to the artificial synthesis of life or using approaches “sophisticated” enough to fall outside the scope of biotechnology or metabolic engineering? We have reviewed the state of the art on synthetic biology and we conclude that most research projects actually describe an extension of metabolic engineering. We draw this conclusion because the complexity of living organisms, their tight dependence on evolution and our limited knowledge of the interactions between the molecules they are made of, actually make life difficult to engineer. We therefore propose the term synthetic biology should be used more sparingly.     

From ‘ecologist’ to ‘conceptual ecologist’: the utility of the conceptual ecology analogy for teachers of biology

This paper advocates the application of established teaching models to the professional development of biology teachers. This is achieved by using the analogy of conceptual ecologies, made explicit through concept mapping. The approach is designed to support teachers' developing understanding of pupils' conceptual change by using familiar terminology and biological analogies. Monitoring of students' understanding at an ecosystemic level may also help distinguish between instances of conceptual change and contextual switching (described here with reference to photosynthesis).     

Biomimetic oxidation of glutathione by synthetic analogues of the active centres of ‘blue’ copper proteins

The model process of oxidation of reduced glutathione through chelate copper complexes has been studied, the former being structural analogues of the active centers of ‘blue’ copper proteins. Glutathione forms the relatively stable intermediate CuLSG⁺ with copper complexes in acetonitrile. The intramolecular electron transfer S(glutathione)→Cu(II) is the rate-determining step of the substrate oxidation. On the basis of rate constant (k_obs) values as well as activation energy (E³) values, we have concluded that there is a possibility of functional modelling of active centers of type 1 Cu by copper complexes with thioaza ligands.     

Importance of the 5′ regulatory region to bacterial synthetic biology applications

The field of synthetic biology is evolving at a fast pace. It is advancing beyond single-gene alterations in single hosts to the logical design of complex circuits and the development of integrated synthetic genomes. Recent breakthroughs in deep learning, which is increasingly used in de novo assembly of DNA components with predictable effects, are also aiding the discipline. Despite advances in computing, the field is still reliant on the availability of pre-characterized DNA parts, whether natural or synthetic, to regulate gene expression in bacteria and make valuable compounds. In this review, we discuss the different bacterial synthetic biology methodologies employed in the creation of 5′ regulatory regions – promoters, untranslated regions and 5′-end of coding sequences. We summarize methodologies and discuss their significance for each of the functional DNA components, and highlight the key advances made in bacterial engineering by concentrating on their flaws and strengths. We end the review by outlining the issues that the discipline may face in the near future.     

‘Radicle' biochemistry: the biology of root-specific metabolism

The roots of higher plants are a fascinating and largely unexplored biological frontier. One of their features is the ability to synthesize a remarkable diversity of secondary metabolites, and to adjust their metabolic activities in response to biotic and abiotic stress. This includes the ability to exude a complex array of micro- and macromolecules into the rhizosphere, with the potential to affect the inter-relationships between plants and beneficial or deleterious soil-borne organisms. In the past, research on root biology has been hampered by the underground growth habit of roots and by the lack of a suitable experimental system. However, recent progess in growing roots in isolation has greatly facilitated the study of root-specific metabolism and contributed to our understanding of this remarkable plant organ.     

Easing the global burden of diarrhoeal disease: can synthetic biology help?

The Millennium Declaration committed the 193 member states of the United Nations to end poverty by 2015. Despite the efforts of the UN and World Health Organisation, and the G8 commitment to spend a fixed proportion of gross national income on overseas aid, more than 2.6 billion people still lack access to proper sanitation. The absence of effective public health strategies in developing countries results in significant health burdens following gastrointestinal infections. Diarrhoea associated with infections resulting from oral-faecal contamination is the second leading cause of death in children under 5 years of age, primarily in Africa and South Asia. Currently there are no appropriate vaccines that could be easily administered on a global scale to prevent these infections. Synthetic biology has the potential to contribute to development of such vaccines. Our work is directed at developing a range of multivalent oral vaccines against the most common diarrhoea-causing bacteria, e.g., Escherichia coli, Shigella and Salmonella. If synthetic biology is to avoid the suspicion and possible revulsion of the public, scientists need to demonstrate that this new field has something real to offer.     

Ensuring the security of synthetic biology—towards a 5P governance strategy

Over recent years the label “synthetic biology” has been attached to a number of diverse research and commercial activities, ranging from the search for a minimal cell to the quick delivery of customized genes by DNA synthesis companies. Based on the analysis of biosecurity issues surrounding synthetic biology during the SYNBIOSAFE project, this paper will first provide a rationale for taking security, in addition to safety aspects of this new field, seriously. It will then take stock of the initiatives and measures that have already been taken in this area and will lastly try to map out future areas of activities in order to minimise the security risks emanating from this promising new field of scientific inquiry and technological progress.     

‘Heparin’ – from anticoagulant drug into the new biology

This overview attempts to cover, from a personal viewpoint, the development of the heparin field during the last four decades. In particular, it emphasizes the metamorphosis of heparan sulfate (HS), from a disturbing contaminant in heparin production to the present-day key player in cell and developmental biology. Our understanding of the structural properties of the polysaccharides has been greatly promoted by studies of their biosynthesis. We now have a fairly detailed view of the various enzymatic reactions, that convert the initial [4GlcA1-4GlcNAc1-]_n polymer into sulfated products with highly variable proportions of GlcA/IdoA and of N-acetyl, N-sulfate and O-sulfate substituents. It is also recognized that the variously substituted domains of the polysaccharide serve to interact, in more or less specific fashion, with a multitude of proteins, and that these interactions are essential to the biological functions of the proteins. Molecular genetics has unravelled the gene structures for almost all of the enzymes required to synthesize a heparin or HS chain, and has shown that several of these proteins exhibit genetic polymorphism. While differences in substrate specificity between enzyme isoforms may help to explain the structural variability of, in particular, HS chains, we still only partly understand the key features of heparin/HS biosynthesis and its regulation.     

‘Ins’ and ‘outs’ of triple therapy

Chronic oral anticoagulant treatment is obligatory in patients (class I) with mechanical heart valves and in patients with atrial fibrillation with CHADS2 score >1. When these patients undergo percutaneous coronary intervention with placement of a stent, there is also an indication for treatment with aspirin and clopidogrel. Unfortunately, triple therapy is known to increase the bleeding risk. For this group of patients, the bottom line is to find the ideal therapy in patients with indications for both chronic anticoagulation therapy and percutaneous intervention to prevent thromboembolic complications such as stent thrombosis without increasing the risk of bleeding. (Neth Heart J 2010;18:444-50.)     

Observations on the biology of Leuciscus ‘svallize’ in the Kremasta reservoir (Greece)

The age, growth, feeding habits and reproductive biology of Leuciscus svallize in artificial lake Kremasta (Greece), are described. There is a considerable similarity in the feeding and reproductive characteristics between L. svallize and L. cephalus and also a similarity in the life span, growth patterns and age of maturation between L. svallize and some southern L. cephalus populations, which may suggest similar responses of closely related taxa to similar conditions.     

‘Generation Nemo’: motivations,satisfaction and career goals of marine biology students*

Marine biology is an increasingly preferred study major and career among youth. This is particularly the case of countries with extensive coastlines, such as Italy. In order to understand what exactly is fuelling this trend, and whether it culminates in the successful absorption of marine biologists as valued workforce by society, this study investigated the motivations, satisfaction and career goals of marine biology undergraduate students in Italy. Although it was expected that scientific literacy in formal education plays an important role in motivating marine biology students, the results showed that intrinsic motivations and informal education play a more crucial role. The students consider realistic career options, although these imply having to leave the country. The results of this study were used to make recommendations on the importance of marine and ocean literacy in the formal educational system in Italy, and the general improvement of scientific literacy in formal school education. Recommendations were also made on the potential improvements that can be made by higher education institutions, to better equip marine biologists with the skills required by emerging sectors in society. Finally, considerations were made regarding the dimensioning of supply, offer and marketing of employment opportunities for marine biologists in Italy.