Pictures of Synthetic Biology

This article is concerned with the representation of Synthetic Biology in the media and by biotechnology experts. An analysis was made of German-language media articles published between 2004 and 2008, and interviews with biotechnology-experts at the Synthetic Biology conference SB 3.0 in Zurich 2007. The results have been reflected in terms of the definition of Synthetic Biology, applications of Synthetic Biology and the perspectives of opportunities and risks. In the media, Synthetic Biology is represented as a new scientific field of biology with an engineering-like thinking, while the scientists interviewed mostly define Synthetic Biology as contrary to nature and the natural system. Media articles present Synthetic Biology broadly with positive potential and inform the publics less about the potential risks than about the benefits of Synthetic Biology. In contrast, the experts interviewed reflect more on the risks than the opportunities of Synthetic Biology. Both used metaphors to describe Synthetic Biology and its aspects.     

Question 7: Construction of a Semi-Synthetic Minimal Cell: A Model for Early Living Cells

Using a Synthetic Biology approach we are building a semi-synthetic minimal cell. This represents an exercise to shape a minimal-cell model system recalling the simplicity of early living cells in early evolution. We have recently introduced into liposome compartments a minimal set of enzymes named “Puresystem” (PS) synthesizing EGFP proteins. To establish reproduction of the shell compartment with a minimal set of genes we have cloned the genes for the Fatty Acid Synthase (FAS) type I enzymes. These FAS genes introduced into liposomes, translated into FAS enzymes by PS and in the presence of precursors produce fatty acids. The resulting release of fatty acid molecules within liposome vesicles should promote vesicle growth and reproduction. The core reproduction of a minimal cell corresponding to the replication of the minimal genome will require a few genes for the DNA replication and the PS, and a minimum set of genes for the synthesis of t-RNAs. In future the reconstruction of a minimal ribosome will bring the number of genes for ribosomal proteins from 54 of an existing minimal genome down to 30–20 genes. A Synthetic Biology approach could bring the number of essential genes for a minimal cell down to 100 or less. International School of Complexity–4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

SBOL Visual: A Graphical Language for Genetic Designs

Synthetic Biology Open Language (SBOL) Visual is a graphical standard for genetic engineering. It consists of symbols representing DNA subsequences, including regulatory elements and DNA assembly features. These symbols can be used to draw illustrations for communication and instruction, and as image assets for computer-aided design. SBOL Visual is a community standard, freely available for personal, academic, and commercial use (Creative Commons CC0 license). We provide prototypical symbol images that have been used in scientific publications and software tools. We encourage users to use and modify them freely, and to join the SBOL Visual community: http://www.sbolstandard.org/visual.     

A turning point for natural product discovery--ESF-EMBO research conference: synthetic biology of antibiotic production

Synthetic Biology is in a critical phase of its development: it has finally reached the point where it can move from proof-of-principle studies to real-world applications. Secondary metabolite biosynthesis, especially the discovery and production of antibiotics, is a particularly relevant target area for such applications of synthetic biology. The first international conference to explore this subject was held in Spain in October 2011. In four sessions on General Synthetic Biology, Filamentous Fungal Systems, Actinomyces Systems, and Tools and Host Structures, scientists presented the most recent technological and scientific advances, and a final-day Forward Look Plenary Discussion identified future trends in the field.     

Special focus: Synthetic biology

Special focus: Synthetic biology What is synthetic biology? SynBERC – The Synthetic Biology Engineering Research Center Ars Synthetica iGEM – The International Genetically Engineered Machine competition Some synthetic biology companies Paper watch: Synthetic biology Building blocks for novel functions Knowledge-making distinctions in synthetic biology Scaffold design and manufacturing: From concept to clinic Peptidomimetics – a versatile route to biologically active compounds Metabolic engineering of E. coli E. coli needs safety valves Systems-level metabolic engineering Mammalian synthetic biology Chemical aspects of synthetic biology Synthesis of DNA fragments in yeast Synthetic biology and patentable subject matter Patenting artificial life? Metabolic effects of synthetic rewiring Engineering for biofuels Regulatory elements for synthetic biology Book highlight Systems Biology and Synthetic Biology     

Synthetic Biology

Cover illustration: Synthetic Biology. This special issue, edited by Alfonso Jaramillo and Jean-Loup Foulon, highlights articles from the International conference on Synthetic Biology (December 2010) organized by the Genopole and iSSB. The cover image depicts a tentative synthetic leaf in half revealing its genetic circuitry. A zoom box details the leaf's interior circuits, which are made up of three multiplexed light sensors regulating gene expression controlled by red, green and blue light. The image (provided by Daniel Camsund) illustrates the application of light sensors reported in this issue (http://dx.doi.org/10.1002/biot.201100091 ).     

Communicating Synthetic Biology: from the lab via the media to the broader public

We present insights from a study on communicating Synthetic Biology conducted in 2008. Scientists were invited to write press releases on their work; the resulting texts were passed on to four journalists from major Austrian newspapers and magazines. The journalists in turn wrote articles that were used as stimulus material for eight group discussions with select members of the Austrian public. The results show that, from the lab via the media to the general public, communication is characterized by two important tendencies: first, communication becomes increasingly focused on concrete applications of Synthetic Biology; and second, biotechnology represents an important benchmark against which Synthetic Biology is being evaluated.     

Synthetic ACTH-Like Peptide GKVLKKRR,Corresponding to the Fragment 81–88 of Human Pro-Interleukin-1α, Acts as an Antagonist of ACTH Receptor

Synthetic adrenocorticotropic hormone (ACTH)-like octapeptide leukocorticotropin (GKVLKKRR), corresponding to the amino acid sequence 81–88 of pro-interleukin-1α, was labeled with tritium (specific activity of 22 Ci/mmol) and was found to bind to rat adrenal cortex membranes with high affinity and specificity (K _d = 2.2 ± 0.1 nM). Synthetic ¹²⁵I-labeled ACTH fragment 11–24 was also obtained (specific activity of 98 Ci/mmol) and shown to bind to ACTH receptor on rat adrenal cortex with high affinity (K _d = 1.8 ± 0.1 nM). Unlabeled leukocorticotropin was found to actively replace ¹²⁵I-labeled ACTH (11–24) in the receptor-ligand complex (K _i = 2.0 ± 0.1 nM). Leukocorticotropin at concentration range of 1–1000 nМ did not affect the adenylate cyclase activity in adrenocortical membranes. Thus, leukocorticotropin is an antagonist of ACTH receptor. ACTH-like peptide GKVLKKRR is an antagonist of ACTH This work financeed by the Russian Foundation for Basic Research (grant No. 05-04-48060), by the programs Leading Scientific Schools (grant No. 312.2003.4), Molecular and Cellular Biology (chairman V.M. Lipkin), and Naukogrady (grant No. 04-04-97200), and by the International Science and Technology Center (project No. 2615). V.V. Yurovsky is supported by the American Heart Association (grant No. 0555415U).     

Publisher's Expression of Concern

The American Society for Microbiology (ASM) and Molecular and Cellular Biology (MCB) are issuing this Expression of Concern to alert readers to doubts about the integrity of the data in papers coauthored by Dr. Shigeaki Kato.In 2012, ASM was notified that the University of Tokyo Institute of Molecular and Cellular Biosciences is conducting an investigation of possible scientific misconduct by Dr. Kato. Among the publications under investigation for possible data manipulation are these five MCB articles. The Expression of Concern is only for papers coauthored by Dr. Kato that have been published since 2007, in accordance with the DHHS/ORI six-year limitation on research misconduct (http://ori.dhhs.gov/sites/default/files/42_cfr_parts_50_and_93_2005.pdf).MCB has contacted the Research Promotion Department of the University of Tokyo and asked to be informed of the findings of their ongoing investigation. Once ASM has been notified of the outcome of the investigation by the University of Tokyo, MCB will take appropriate action regarding these publications.     

合成生物学与国际遗传工程机器大赛对培养大学生双创思维与能力的影响

合成生物学是21世纪前沿交叉学科,是现代生物学最具发展空间的领域之一.随着合成生物学的迅速发展,国际基因工程机器大赛(International Genetically Engineered Machine,iGEM)应运而生.iGEM竞赛项目基于合成生物学学科基础,应用现代生物学技术手段,立足解决社区和身边的实际生物...     

合成生物学应用产品开发现状与趋势

目的：从产品开发角度分析全球合成生物学发展现状和趋势。方法：在伍德罗·威尔逊国际学者中心的合成生物学产品和应用清单（synthetic biology products and applications inventory）的数据基础上,对全球合成生物学产品的开发状态、市场应用和发展前景等进行补充检索和分析。结果：至2015年,全球至少已有81家企业（或研究机构）的116种合成生物学产品得到了市场应用开发,主要开发者为美国企业（或研究机构）,产品主要集中于化学和医药领域。结论：合成生物学实现了从生物学分析向生物学合成的范式转移,其产品开发将给一系列的行业带来深刻的变革。     

Chromosomal location of a gene for resistance to septoria tritici blotch (Mycosphaerella graminicola)in the hexaploid wheat ’Synthetic 6x’

Septoria tritici blotch, caused by the fungus Mycosphaerella graminicola,is currently the major foliar disease of wheat world-wide, and new sources of resistance and knowledge about the genetics of resistance are needed to improve breeding for resistance to this disease. Sears’s ’Synthetic 6x’ hexaploid wheat, derived from a hybrid of Triticum dicoccoides and Triticum tauschii, was resistant to 12 of 13 isolates of M. graminicola tested. Chromosome 7D of ’Synthetic 6x’ was identified as carrying resistance to all 12 isolates in tests of seedlings of inter-varietal chromosome substitution lines of ’Synthetic 6x’ into ’Chinese Spring’ and to two isolates in tests of adult plants. A septoria tritici blotch resistance gene, named Stb5, was identified using the M. graminicola isolate IPO94269 and mapped on the short arm of chromosome 7D, near the centromere, in a population of single homozygous chromosome-recombinant lines for the 7D chromosome. Received: 1 February 2001 / Accepted: 17 April 2001     

Root Border Cell Development is a Temperature-Insensitive and Al-Sensitive Process in Barley

The above article appeared in Plant and Cell Physiology 45(6):751–760 (2004). Fig. 5 in the printed and pdf versionsof     

Book review

Making up the toolkit for marine conservation science Elliott A. Norse & Larry B. Crowder, Editors (2005), Marine Conservation Biology. The Science of Maintaining the Sea's Biodiversity. Island Press, Washington, 2005, 470 pp. ISBN 1559636610 (hardback) $89.95, and 1559636629 (paperback) $49.95, http: //www.islandpress.org/     

An integrated approach for automating validation of extracted ion chromatographic peaks

SUMMARY: Accurate determination of extracted ion chromatographic peak areas in isotope-labeled quantitative proteomics is difficult to automate. Manual validation of identified peaks is typically required. We have integrated a peak confidence scoring algorithm into existing tools which are compatible with analysis pipelines based on the standards from the Institute for Systems Biology. This algorithm automatically excludes incorrectly identified peaks, improving the accuracy of the final protein expression ratio calculation. SOURCE AND SUPPLEMENTARY INFORMATION: http://www.chem.uky.edu/research/lynn/Nelson.pdf.     

Physiological effects of 5-hydroxymethylfurfural on Saccharomyces cerevisiae

 The physiological effects of 5-hydroxymethylfurfural (HMF) on Saccharomyces cerevisiae CBS 8066 in the presence and absence of furfural were studied. Experiments were carried out by pulse addition of HMF (2–4 g/l) as well as HMF (2 g/l) together with furfural (2 g/l) to batch cultivations of S. cerevisiae. Synthetic medium with glucose (50 g/l) as carbon and energy source was used. Addition of 4 g/l of HMF caused a decrease (approx. 32%) in the carbon dioxide evolution rate. Furthermore, the HMF was found to be taken up and converted by the yeast with a specific uptake rate of 0.14 (±0.03) g/g · h during both aerobic and anaerobic conditions, and the main conversion product was found to be 5-hydroxymethylfurfuryl alcohol. A previously unreported compound was found and characterized by mass spectrometry. It is suggested that the compound is formed from pyruvate and HMF in a reaction possibly catalysed by pyruvate decarboxylase. When HMF was added together with furfural, very little conversion of HMF took place until all of the furfural had been converted. Furthermore, the conversion rates of both furfural and HMF were lower than when added separately and growth was completely inhibited as long as both furfural and HMF were present in the medium. Received: 16 December 1998 / Received revision: 30 November 1999 / Accepted: 19 December 1999     

Using Inquiry and Tree-Thinking to “March Through the Animal Phyla”: Teaching Introductory Comparative Biology in an Evolutionary Context

Biodiversity was originally taught in our Introductory Organismal Biology course at Michigan State University (LB144; freshman/sophomore majors) by rote memorization of isolated facts about organisms. When we moved to an inquiry-based laboratory framework to improve pedagogy, an unfortunate and unforeseen result was the loss of much of our study of biodiversity. In this paper, we describe the restructuring of LB144 to restore the study of biodiversity and organismal groups while retaining the benefits of an inquiry-based approach. The curricular intervention was accomplished through the creation and implementation of a four-week Comparative Biology laboratory stream. During this stream, student research teams recorded and organized observations that they made on a range of organisms and analyzed their data in a phylogenetic framework. During the stream, our students worked through a set of exercises designed to help them learn how to read, interpret, and manipulate phylogenetic trees. We placed particular emphasis on the concept that phylogenetic trees are hypotheses of relationship that can be tested with scientific data. This incorporation of phylogenies and phylogenetic analysis, or “tree-thinking,” into our students’ work provided an explicit synthetic evolutionary framework for their comparative biodiversity studies. End-of-stream products included a team phylogenetic analysis exercise and an individual comparative biology oral presentation.     

基于通识教育理念的合成生物学课程设计与实践

合成生物学作为生物学中新的分支学科,发展迅速,理论研究和应用潜力巨大,在带来了很多新的研究理念和研究方法的同时,给高校教学也带来了新的挑战.目前就合成生物学课程而言,国内可供参考的教学经验不多.文中以浙江大学"博雅技艺"类通识课程—"合成生物学"为例,从课程背景、课程设计、课程实施情况、课程成果与存在问题等方面,全方位...     

Engineering a novel self-powering electrochemical biosensor

This paper records the efforts of a multi-disciplinary team of undergraduate students from Glasgow University to collectively design and carry out a 10 week project in Synthetic Biology as part of the international Genetic Engineered Machine competition (iGEM). The aim of the project was to design and build a self-powering electrochemical biosensor called ‘ElectrEcoBlu’. The novelty of this engineered machine lies in coupling a biosensor with a microbial fuel cell to transduce a pollution input into an easily measurable electrical output signal. The device consists of two components; the sensor element which is modular, allowing for customisation to detect a range of input signals as required, and the universal reporter element which is responsible for generating an electrical signal as an output. The genetic components produce pyocyanin, a competitive electron mediator for microbial fuel cells, thus enabling the generation of an electrical current in the presence of target chemical pollutants. The pollutants tested in our implementation were toluene and salicylate. ElectrEcoBlu is expected to drive forward the development of a new generation of biosensors. Our approach exploited a range of state-of-the-art modelling techniques in a unified framework of qualitative, stochastic and continuous approaches to support the design and guide the construction of this novel biological machine. This work shows that integrating engineering techniques with scientific methodologies can provide new insights into genetic regulation and can be considered as a reference framework for the development of biochemical systems in synthetic biology.