"Build-a-Genome is an intensive laboratory course at Johns Hopkins University that introduces undergraduates to the burgeoning field of synthetic biology. In addition to lectures that provide a comprehensive overview of the field, the course contains a unique laboratory component in which the students contribute to an actual, ongoing project to construct the first synthetic eukaryotic cell, a yeast cell composed of man-made parts. In doing so, the students acquire basic molecular biology skills and gain a truly "graduate student-like experience" in which they take ownership of their projects, troubleshoot their own experiments, present at frequent laboratory meetings, and are given 24-h access to the laboratory, albeit with all the guidance they will need to complete their projects during the semester. In this chapter, we describe the organization of the course and provide advice for anyone interested in starting a similar course at their own institution."
SynBioFromLeukipposInstitute
130.0K views |
+1 today
 Your new post is loading...
Your new post is loading...
Scoop.it!
"Tuur van Balen gives a provocative how-to presentation at the Next Nature Power Show, showing how to use the Synthetic Biology Parts Registry to engineer yogurt ..." 
Scoop.it!
"Studies in the structural biology of the multicomponent protein complex, metabolic engineering, and synthetic biology frequently rely on the efficient over-expression of these subunits or enzymes in the same cell. As a first step, constructing the multiple expression cassettes will be a complicated and time-consuming job if the classic and conventional digestion and ligation based cloning method is used. Some more efficient methods have been developed, including (1) the employment of a multiple compatible plasmid expression system, (2) the rare-cutter-based design of vectors, (3) in vitro recombination (sequence and ligation independent cloning, the isothermally enzymatic assembly of DNA molecules in a single reaction), and (4) in vivo recombination using recombination-efficient yeast (in vivo assembly of overlapping fragments, reiterative recombination for the chromosome integration of foreign expression cassettes). In this review, we systematically introduce these available methods."
Scoop.it!
(2012). Synthetic Biology: Life as App Store. Capitalism Nature Socialism: Vol. 23, No. 1, pp. 6-18. "Since the early 19 th century, scientists have proposed a variety of naturalistic explanations
Scoop.it!
Science profile "Untangling the biology of diseases such as cancer and diabetes requires finding patterns in enormous amounts of data, such as the torrent of information now pouring out of big genomics projects. Identifying the needles in such haystacks-culprit proteins or genes causing disease-demands a new kind of science. Three years ago, Stephen Friend co-launched a nonprofit called Sage Bionetworks with the goal of persuading drug companies, academics, clinicians, and patients to share genomic and other biomedical information freely in a huge database that researchers could use to map out the intracellular pathways that contribute to human diseases and build computational models of those conditions that would be better than the animal models now used in preclinical drug development. Friend wants to bring to biomedical science the same open-source ethos embraced by the computer programmers who wrote the Linux operating system and by the people who contribute information to Wikipedia."
Scoop.it!
"Singularity University is partnering with Triple Ring Technologies to mentor and develop select synthetic biology teams between May and August 2012. We are looking for promising biotechnology entrepreneurs who we can help to incorporate and develop products and services that can be made and tested in a short amount of time (three months), and with little capital (on average less than $50k)..."
Scoop.it!
"George Church is a professor at Harvard University and founder of the personal genome project. He has patents in the fields of genome reading and writing, automation and instrumentation, and advocates open source and transparency; for example, by developing the open access next generation sequencing platform (Polonator.org) and the open access human genome plus trait dataset (PersonalGenomes.org)."
Scoop.it!
"The native stem cell niche is a dynamic and complex microenvironment. Recapitulating this niche is a critical focus within the fields of stem cell biology, tissue engineering, and regenerative medicine and requires the development of well-defined, tunable materials. Recent biomaterial design strategies seek to create engineered matrices that interact with cells at the molecular scale and allow on-demand, cell-triggered matrix modifications. Peptide and protein engineering can accomplish these goals through the molecular-level design of bioinductive and bioresponsive materials. This brief review focuses on engineered peptide and protein materials suitable for use as in vitro neural stem cell niche mimics and in vivo central nervous system repair. A key hallmark of these materials is the immense design freedom to specify the exact amino acid sequence leading to multi-functional bulk materials with tunable properties. These advanced materials are engineered using rational design strategies to recapitulate key aspects of the native neural stem cell niche. The resulting materials often combine the advantages of biological matrices with the engineering control of synthetic polymers. Future design strategies are expected to endow these materials with multiple layers of bi-directional feedback between the cell and the matrix, which will lead to more advanced mimics of the highly dynamic neural stem cell niche."
Scoop.it!
"I’ve been meaning to out some of this stuff together for a while but got distracted. During our post Architecture in the Information Age meeting the topic of Biological Architecture came up. One of the things that interests me about an architects education is that we have elements almost all major disciplines from Physics through to Philosophy and History and Psychology but we dont really look at Chemistry and Biology. Biology, in particular has provided much inspiration in Architecture (its worth looking at Steadman’s The Evolution of Designs for an overview) and there is, I believe, some relationship between Buckminster Fuller’s geometric explorations and the way we represent and understand molecular structures in Chemistry. More recently, however, the analogy between architecture and has been questioned by the fast emerging technologies from biotechnology. There is an underlying thread of research and experimentation on approaches to architecture which use evolutionary theory, bottom up approaches to design and, perhaps most progressively, the use of biological materials in construction. The interest for me was triggered an article related to this project undertaken by students at Newcastle University on the creation of a bacterial that would fill in cracks in concrete. I wrote to the project supervisors but got no response unfortunately. After that though I started looking into examples where biological materials were being developed in architectural contexts. WHat I found is mostly experimental and speculative and there is no coherent ‘Synthetic Biology of Architecture’ research but there are some examples..."
Scoop.it!
"The new biology (Delgado, Funtowicz & Dankel 2012) and the emerging techno-sciences have the potential to change fundamentally our received definitions of humankind, culture and nature. Their promotion and support is advertised precisely in what makes them controversial, the blurring of the distinction between humans-nature and machines. The process of transformation from modern science and technology to “innovation” occurs in parallel to the growing crisis of credibility and legitimacy of a knowledge system grounded on the Cartesian ideal of prediction and control. During 2011, the Fukushima nuclear disaster was added to the on-going financial and economic problems, illustrating the vulnerability to corruption of complex technological systems and the hubris of quantitative-based experts who ignored what they chose to ignore. The modern state has co-evolved with modern science and the development of democratic societies. Karl Popper and Robert K. Merton among others, after World War II, identified science with liberal democracy, and Vannevar Bush provided the political vision establishing science-based technology as the cornerstone of progress and economic growth. Already in 1961, during his Farewell Address to the country, US President Eisenhower hinted the pathologies of such development and warned about the profound implications for science and democracy of the intimate relation between the knowledge system (including Academia), the industrial establishment and power. Fifty years later, we have to cope with the consequences of this trajectory, which is still given little recognition by the established authorities of science. The intellectual and practical challenge today is what to do to with a system of governance of science and society that resembles more and more an Ancien Regime, and also how to act in a growing societal culture of effrontery that knows neither guilt nor shame. The process of change has to include a new commitment to knowledge creation and transmission and its role in a plural and hybrid society (Funtowicz & Strand 2011, Benessia & Funtowicz 2012) The slogan “Occupy Science” may be difficult to understand, but that could be a sign of its relevance today. Literature: Delgado, A., Funtowicz, S., Dankel, D. (2012). Super-computers, evolution and the fabrication of life: How can Science and Technology Studies (STS) contribute to more reflexive developments in systems and synthetic biology? International Journal of Social Ecology and Sustainable Development (forthcoming). Funtowicz, S. and Strand, R. (2011). Change and commitment: beyond risk and responsibility. Journal of Risk Research Vol. 14, No. 8, September 2011, 995–1003. Benessia, A., Funtowicz, S., Bradshaw, G., Ferri, F., Ra´ez-Luna, EF., Medina, C.P. (2012). Hybridizing sustainability: towards a new praxis for the present human predicament. Sustainability science (forthcoming). Vannevar Bush, Science The Endless Frontier, July 1945. http://www.nsf.gov/about/history/vbush1945.htm Eisenhower's Farewell Address to the Nation, January 17, 1961. http://www.informationclearinghouse.info/article5407.htm "
Scoop.it!
Synthetic Biology and Metabolic Engineering Track
Scoop.it!
"Diversity-generating retroelements (DGRs) are in vivo sequence diversification machines that are widely distributed in bacterial, phage, and plasmid genomes. They function to introduce vast amounts of targeted diversity into protein-encoding DNA sequences via mutagenic homing. Adenine residues are converted to random nucleotides in a retrotransposition process from a donor template repeat (TR) to a recipient variable repeat (VR). Using the Bordetella bacteriophage BPP-1 element as a prototype, we have characterized requirements for DGR target site function. Although sequences upstream of VR are dispensable, a 24 bp sequence immediately downstream of VR, which contains short inverted repeats, is required for efficient retrohoming. The inverted repeats form a hairpin or cruciform structure and mutational analysis demonstrated that, while the structure of the stem is important, its sequence can vary. In contrast, the loop has a sequence-dependent function. Structure-specific nuclease digestion confirmed the existence of a DNA hairpin/cruciform, and marker coconversion assays demonstrated that it influences the efficiency, but not the site of cDNA integration. Comparisons with other phage DGRs suggested that similar structures are a conserved feature of target sequences. Using a kanamycin resistance determinant as a reporter, we found that transplantation of the IMH and hairpin/cruciform-forming region was sufficient to target the DGR diversification machinery to a heterologous gene. In addition to furthering our understanding of DGR retrohoming, our results suggest that DGRs may provide unique tools for directed protein evolution via in vivo DNA diversification."
Scoop.it!
"Scientists at The Scripps Research Institute in California and the Technion–Israel Institute of Technology have developed a “biological computer” made entirely from biomolecules that is capable of deciphering images encrypted on DNA chips. Although DNA has been used for encryption in the past, this is the first experimental demonstration of a molecular cryptosystem of images based on DNA computing..." - I am sometime wondering why we have the competition concept in science. Is this a residual from the industrial age with the human resource model. Is collaboration the adequate form adapted to the digital age? Why do we have several groups, who obvious have the goal to build a cellular computer competing each other instead to follow tis goal in collaboration. I recently read this exiting book: Michael Nielsen, Reinventing Discovery, The New Era of Networked Science, Princeton University Press 2012. “Michael Nielsen argues that we are living at the dawn of the most dramatic change in science in more than 300 years. This is being driven by powerful new cognitive tools, enabled by the internet, which are greatly accelerating scientific discovery....this is the first book about something much more fundamental how the internet is transforming the nature of our collective intelligence and how we understand the world” (cover text)
|
Scoop.it!
Do it your self bio-engineering with designer Tuur van Balen. Presented at the Next Nature Power Show 2011 in Amsterdam.
Scoop.it!
Livre: Systems biology and synthetic biology of lactic acid fermentation in foods JEROEN Hugenholtz, EDDY J. "Fermented foods are produced all over the world. This book describes systems biology and synthetic biology approaches to improve food fermentation processes. It offers examples on how these approaches can be used to control and improve fermentation processes and to introduce new functionalities to fermented foods and beverages. The text also presents strategies to transfer antimicrobial-production to other strains and to combine production of several different antimicrobials in one lactic acid bacterium. In addition, the authors explain how the use of high-vitamin producing lactic acid bacteria can lead to fermented foods with increased and bioavailable vitamins."
Scoop.it!
"Signaling pathways lie at the heart of cellular responses to environmental cues. The ability to reconstruct specific signaling modules ex vivo allows us to study their inherent properties in an isolated environment, which in turn enables us to elucidate fundamental design principles for such motifs. This synthetic biology approach for analyzing natural, well-defined signaling modules will help to bridge the gap between studies on isolated biochemical reactions — which can provide great mechanistic detail but do not capture the complexity of endogenous signaling pathways — and those on entire networks of protein interactions — which offer a systems-level view of signal transduction but obscure the mechanisms that underlie signal transmission and processing. Additionally, minimal signaling modules can be tractably engineered to predictably alter cellular responses, opening up possibilities for creating biotechnologically and biomedically useful cellular devices."
Scoop.it!
Online-learning initiative’s first offering, ‘6.002x: Circuits and Electronics,’ accepting registrants now. - A great move! Thanks MIT! With such concepts MIT will survive the move into the digital age!
Scoop.it!
America's Woodrow Wilson centre has recommended a new system for monitoring the dangers of 'artificial life' laboratories around the world - highlighting the dangers of 'do it yourself' science. -------- Labs need to be monitored, says American institute -------- A system for keeping an eye on potentially dangerous 'artificial life' laboratories around the world is essential, say leading experts.
Scoop.it!
The possibilities of genetic manipulation through synthetic biology leading to unintended consequences or biological weapons. - Is this a real risk? How should we react? -
The World Economic Forum Global Risks Report is one of the most authoritative annual assessments of emerging issues surrounding risk currently produced.
Scoop.it!
"Elegant = Complex Many would say the opposite, elegance = simplicity. They have (classical) physics envy—for smooth, linear physics, and describably delicious four-letter words, like "F=ma". But modern science has moved on, embracing the complex. Occam now uses a web-enabled, fractal e-razor. Even in mathematics, stripped of awkward realities of non-ideal gases, turbulence, and non-spherical cows, simple statements about integers like Fermat’s an + bn = cnand wrangling maps with four colors take many years and pages (occasionally computers) to prove...."
Scoop.it!
"...information from SynBio.org (Cambridge synthetic biology resources) regarding a new web-based Synthetic Biology Scorecard project. This project is run by the Woodrow Wilson Center and is designed to track efforts to improve the governance of synthetic biology research and development so risks are minimized and broad social and economic benefits can be realised..."
Scoop.it!
"Nanoparticles disguised as red blood cells could be used to deliver anti-cancer drugs directly to a tumour. So say researchers at the University of California at San Diego, whose new technique is unique in its approach to harnessing nanoparticles..."
Scoop.it!
"Shortly after Craig Venter and his colleagues published their synthetic bacterial genome, US President Barack Obama asked the Presidential Commission for the Study of Bioethical Issues to look into the risks and benefits of synthetic biology. The committee came back in December 2010 with a list of recommendations. The Woodrow Wilson International Center for Scholars, a public-policy think tank, is monitoring the progress being made on those recommendations with a new scorecard, reports the Nature News Blog. "The Wilson centre's new scorecard makes it clear that progress implementing the commission's proposals — several of which are on an 18-month timeline — has been middling, if that," Nature writes."
Scoop.it!
"Synthetic Biology (SB) will be one of the dominant industries of the 21st century, serving as the foundation and manufacturing mechanism of new materials, industrial and consumer products, pollution control processes, vaccines, medical advances, and many more innovations. In short, an industry larger than that created by the information revolution.
|
