"Research approaches to developing biofuel processes involve the integration of different aspects of biology, chemistry, and engineering. Recent developments in knowledge and technology have enabled a shift away from discovery-based, trial-and-error design to a more directed prospective design process. Systems biology and synthetic biology have contributed to this shift in methodologies in complementary ways. Systems biology provides much of the knowledge background and whole-cell modeling methods to enable cellular-level design. Synthetic biology provides DNA-level detail to design strategies and the experimental methods to directly implement proposed designs. Application of methodologies from these two fields provides a strong framework for cellular and molecular biological engineering."
Venken, Lyn, IM Thijs, Inge, Eberle, W,, De Keersmaecker, Sigrid, Marchal, Kathleen, Vanderleyden, Jos
"Synthetic biology is an emerging discipline in biological research that aims to create novel behavior in organisms by applying engineering principles to biological systems. The synthetic biology approach for the engineering of micro-organisms relies on assembling biological parts each performing a specific biological function into a new biological circuit. Synthetic biology is expected to have a great impact which is demonstrated by recently developed alternative energy resources and novel therapeutics, both based on the engineering of micro-organisms. Developments along the synthetic biology approach will also give rise to new whole-cell biosensors based on cells with new detection circuits, transduction circuits and reporter genes. In addition, the multidisciplinarity of synthetic biology can be further exploited by combining the synthetic biology approach with the features of microelectronics and microfluidics, which will give rise to new miniaturized biosensor devices.
In this project, we aim to illustrate the potential of integrating microbiology with microdevices by discussing the development of a new biological part that allows transfer of information from bacteria to microchips by means of electrical signalling. In order to obtain electrical signalling between bacteria and micro-electronic devices, we exploit the redox cycling behaviour of electron shuttles. In the first stage of this project, pyocyanin, an electron shuttle produced by Pseudomonas aeruginosa, was selected as an appropriate electron signal to establish the electrical connection between bacteria and microchips. Since it’s possible to detect pyocyanin in bacterial cultures in a quantitative manner with microchip-based cyclic voltammetry. By introducing the biosynthesis pathway of pyocyanin in Escherichia coli, bacterial biosensor cells are capable of producing pyocyanin in response to the detection of a specific component. In order to characterize and optimize pyocyanin production by E. coli, we tested pyocyanin production with a fully characterized detection mechanism, e.g. the arabinose inducible promoter. As a result, E. coli was able to produce pyocyanin in a dose-reponsive manner when induced with different concentrations of arabinose. When pyocyanin production by E. coli and pyocyanin detection with the micro-electronic system is fully characterized, pyocyanin can be exploited as a new reporter molecule in bacterial biosensors and used to develop novel microchip-based biosensors." http://bit.ly/SAXqsM
Sequencing, splicing and expressing DNA may seem to be the quintessence of cutting-edge science—indeed DNA manipulation has revolutionized fields such as biofuels, chemicals and medicine.
The methods used by cells to perform complex calculations will have a big impact on electronics design. By David Boothroyd. Carver Mead – a true electronics visionary – once created a field of research that he called neuromorphic electronics. The name reflected the fact that the whole approach was inspired by how brain cells, or neurons, work. Now, one of his former students is trying to do something similar. But instead of brain cells, his strategy is to mimic cells in general – and the results could be revolutionary. Rahul Sarpeshkar, Associate Professor of Electrical Engineering and Computer Science at MIT’s Research Laboratory of Electronics (RLE), calls his approach cytomorphic electronics – ‘cyto’ pertains to cells as ‘neuro’ does to neurons. “I am stepping back and looking at how the DNA protein networks function inside a cell – whether neuron, liver or any other kind of cell. In many ways, this is more fundamental – the basic units in biology are DNA- protein and protein-protein computation. Even neurons performing sophisticated learning operations work this way.”
"A remarkable feature of modern silicon electronics is its ability to remain physically invariant, almost indefinitely for practical purposes. Although this characteristic is a hallmark of applications of integrated circuits that exist today, there might be opportunities for systems that offer the opposite behavior, such as implantable devices that function for medically useful time frames but then completely disappear via resorption by the body. We report a set of materials, manufacturing schemes, device components, and theoretical design tools for a silicon-based complementary metal oxide semiconductor (CMOS) technology that has this type of transient behavior, together with integrated sensors, actuators, power supply systems, and wireless control strategies. An implantable transient device that acts as a programmable nonantibiotic bacteriocide provides a system-level example." http://bit.ly/Sry8Sb
"Digital information is accumulating at an astounding rate, straining our ability to store and archive it. DNA is among the most dense and stable information media known. The development of new technologies in both DNA synthesis and sequencing make DNA an increasingly feasible digital storage medium. We developed a strategy to encode arbitrary digital information in DNA, wrote a 5.27-megabit book using DNA microchips, and read the book by using next-generation DNA sequencing." http://bit.ly/Pf4vyV
Charles A. Easley, Bart T. Phillips, Megan M. McGuire, Jennifer M. Barringer, Hanna Valli, Brian P. Hermann, Calvin R. Simerly, Aleksander Rajkovic, Toshio Miki, Kyle E. Orwig, Gerald P. Schatten
"Highlights In vitro culture induces germ cell differentiation of hPSCs hPSCs differentiate into spermatogonia, spermatocytes, and haploid spermatids Haploid spermatids have uniparental imprints similar to fertile human sperm Summary
Human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) have been shown to differentiate into primordial germ cells (PGCs) but not into spermatogonia, haploid spermatocytes, or spermatids. Here, we show that hESCs and hiPSCs differentiate directly into advanced male germ cell lineages, including postmeiotic, spermatid-like cells, in vitro without genetic manipulation. Furthermore, our procedure mirrors spermatogenesis in vivo by differentiating PSCs into UTF1-, PLZF-, and CDH1-positive spermatogonia-like cells; HIWI- and HILI-positive spermatocyte-like cells; and haploid cells expressing acrosin, transition protein 1, and protamine 1 (proteins that are uniquely found in spermatids and/or sperm). These spermatids show uniparental genomic imprints similar to those of human sperm on two loci: H19 and IGF2. These results demonstrate that male PSCs have the ability to differentiate directly into advanced germ cell lineages and may represent a novel strategy for studying spermatogenesis in vitro." http://bit.ly/TOIGh5
Dissolution of a transient electronic circuit by falling droplets of water. Biodegradable electronic implants that can be reabsorbed by the body have been us...
The misfits. The rebels. The troublemakers. The round pegs in the square holes. The once who see things differently. They are not found of rules and they have no respect for the status quo. You can quote them, disagree with them, glorify or vilify them. But the only thing you can't do is ignore them. Because they change things. They push the human race forward. And while some may see them as the crazy ones, we see genius. Because the people who are crazy enough to think they can change the world, are the ones who do. Think different!"
'We are our narratives, and what made Da Vinci and other human geniuses relatively creative and intelligent, is that they did not divide reality into the contemporary hegemonic narratives. Free to invent their world, they just played around with the impossible, the adjacent possible, and playfully composed the future of our species.'
'Possessing the same stock of cortical neurons, every healthy human brain is born with a potential to produce whatever a human brain has produced in the past and will produce in the future. This immense capacity remains practically unexploited, subordinated under the hegemony; social norms and cultural operating systems that reduce our narratives and dialogue to only that which is valued by the hegemony.'
'One of the things I mentioned to Jakob that I feel is useful in gaining perspective is to see money as a media technology and economics as an information system. If we realize that fundamentally we are dealing with information, it doesn’t matter what resources are being allocated, what matters is that each “thing” has a value, a significance. Values are intersubjective agreements, they can only be established through dialogue, through conversation and ritual – this is how cultures evolve and propagate themselves. Capitalism for example is not just a mode of production, it’s also a cultural operating system that reduces dialogue to that which can be expressed through the medium of money. Anything outside of that is not valued, it’s invisible and there lies many a problem.'
"The mechanisms which impact aging and aging-related diseases are complex and challenging to study. Systems-biology studies have mapped out aging-related genetic networks, but these top-down approaches are complicated by the difficulty of distinguishing correlations from causality. Genome-wide knockout or overexpression studies have identified single genetic factors that are involved in aging; however, single-factor studies cannot easily access complex phenotypes which emerge from complex networks. Studying these complex networks is challenging due to the potentially massive number of interactions between components that may be involved in aging. Moreover, it is difficult to study the history of single cells as they age due to the lack of high-throughput techniques for marking and tracking single-cells over time. This is important because cumulative environmental conditions and genetic changes are likely to be involved in the complex phenomenon of aging....."
"Research examines how to control spatial distribution of cells in microenvironments. Living systems are made of complex architectural organization of various cell types in defined microenvironments. The intricate interactions between different cell types control the specific functions of the associated tissues, such as the functions of native liver and cardiac tissues, metastasis and invasion of tumors, and embryonic development...." http://bit.ly/QHsXxi
*Ultra Low Power Bioelectronics*: *Fundamentals, Biomedical Applications, and Bio-inspired Systems*
by Rahul Sarpeshkar
"This book provides, for the first time, a broad and deep treatment of the fields of both ultra low power electronics and bioelectronics.
It discusses fundamental principles and circuits for ultra low power electronic design and their applications in biomedical systems. It also discusses how ultra-energy-efficient cellular and neural systems in biology can inspire revolutionary low power architectures in mixed-signal and RF electronics. A wealth of insights and examples from brain implants, cochlear implants, bio-molecular sensing, cardiac devices, and bio-inspired systems make the book useful and engaging for students and practicing engineers.
The book presents a unique, unifying view of ultra low power analog and digital electronics and emphasizes the use of the ultra-energy-efficient subthreshold regime of transistor operation in both. Chapters on batteries, energy harvesting, and the future of energy provide an understanding of fundamental relationships between energy use and energy generation at small scales and at large scales.
This book is based on a course taught at MIT for 10 years and was the best seller at the ISSCC 2010 conference. "
"A number of molecular biology techniques are available to generate variants from a particular start gene for eventual protein expression. We discuss the basic principles of these methods in a repertoire that may be used to achieve the elemental steps in protein engineering. These include site-directed, deletion and insertion mutagenesis. We provide detailed case studies, drawn from our own experiences, packaged together with conceptual discussions and include an analysis of the techniques presented with regards to their uses in protein engineering."
"The emergence of citizen biotech must be seen within the broader context of advanced technologies becoming ever more readily available to individuals and groups. With that availability, comes enhanced opportunities to develop new ideas. We have produced the first full-scale synthetic biological chair entitled; Genetic Generation Seat or Gen2Seat. At IGEM (International Genetically Engineered Machines) competition, we have genetically engineered the naturally occurring bacterium Acetobacter xylinum. This bacterium secretes copious amounts of cellulose, which can then be harvested and used directly as a building material. Alternatively, our goal is to create a novel strain that can also secrete the biopolymer chitin, which is normally produced by arthropods, such as insects and crustaceans. In addition, we fused mycelium blocks with the modified acetobactor to create a new biopolymer. Applying the tools of synthetic biology, alongside other biological disciplines, such as microbiology and tissue engineering, will allow us to create products more organically, with minimal waste and energy expenditure...."
"During development, diverse cellular identities are established and maintained in the embryo. Although remarkably robust in vivo, cellular identities can be manipulated using experimental techniques. Lineage reprogramming is an emerging field at the intersection of developmental and stem cell biology in which a somatic cell is stably reprogrammed into a distinct cell type by forced expression of lineage-determining factors. Lineage reprogramming enables the direct conversion of readily available cells from patients (such as skin fibroblasts) into disease-relevant cell types (such as neurons and cardiomyocytes) or into induced pluripotent stem cells. Although remarkable progress has been made in developing novel reprogramming methods, the efficiency and fidelity of reprogramming need to be improved in order increase the experimental and translational utility of reprogrammed cells. Studying the mechanisms that prevent successful reprogramming should allow for improvements in reprogramming methods, which could have significant implications for regenerative medicine and the study of human disease. Furthermore, lineage reprogramming has the potential to become a powerful system for dissecting the mechanisms that underlie cell fate establishment and terminal differentiation processes. In this review, we will discuss how transcription factors interface with the genome and induce changes in cellular identity in the context of development and reprogramming...."
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