SynBioFromLeukipposInstitute

*Can You Feel Me Now*? *The Sensational Rise of Haptic Interfaces*

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BY NATHAN HURST

"Your first experience with haptics was probably your phone vibrating in your pocket. Or maybe it was the rumble pack on your N64 controller. But whatever the case, you probably didn’t know it as a haptic interface.

Haptics is to touch the way optics is to sight. It's a user interface that circumvents the cluttered inputs of sight and sound, and it's appearing in an increasing number of objects we interact with daily. Vibration is just the beginning.

......

Unlike the feedback-based, interactive vibrations from Surround Haptics, Cadillac, and RISR, the vibrating insoles Jim Collins is working on don't impart information to the user — at least not consciously. Collins — a bioengineer at Boston University and the Wyss Institute at Harvard — found that random vibrations introduced in the feet of participants helped them sway less, or keep their balance better. "It's not a feedback-based system," says Collins, who has been studying the effect for almost 20 years. "What we're doing is introducing a bias signal, to their sensory neurons, which is basically serving as a pedestal or booster for the signals they normally would detect." That is, small vibrations in the feet cause heightened nerve sensitivity, and thus users — including stroke victims, diabetics, the elderly, but also the young and fit — detect signals they would normally miss. The insoles aren't on the market yet, but Collins envisions additional future applications in sports equipment, like ski boots and golf shoes...."

http://bit.ly/YpWVH7

by
Pankaj K Mandal& Derrick J Rossi

"Induced pluripotent stem (iPS) cells hold the potential to revolutionize regenerative medicine through their capacity to generate cells of diverse lineages for future patient-specific cell-based therapies. To facilitate the transition of iPS cells to clinical practice, a variety of technologies have been developed for transgene-free pluripotency reprogramming. We recently reported efficient iPS cell generation from human fibroblasts using synthetic modified mRNAs. Here we describe a stepwise protocol for the generation of modified mRNA-derived iPS cells from primary human fibroblasts, focusing on the critical parameters including medium choice, quality control, and optimization steps needed for synthesizing modified mRNAs encoding reprogramming factors and introducing these into cells over the course of 2-3 weeks to ensure successful reprogramming. The protocol described herein is for reprogramming of human fibroblasts to pluripotency; however, the properties of modified mRNA make it a powerful platform for protein expression, which has broad applicability in directed differentiation, cell fate specification and therapeutic applications."
http://bit.ly/Wb3d0X

Professor Rahul Sarpeshkar

"We create (1) novel DNA and protein circuits for systems and synthetic biology; (2) implantable medical devices such as cochlear implants and brain-machine interfaces; (3) ultra-energy-efficient, ultra-low-power, and energy-harvesting systems; and, (4) biological and bio-inspired supercomputers. The common theme in all of our work is analog circuit design."
 http://bit.ly/WX5Rps

BY ANDREW MYERS

"Stanford researchers are the first to demonstrate that sophisticated light resonators can be inserted inside living cells without damage to the cell. The development marks a new age in which tiny lasers and light-emitting diodes yield new avenues in the study of living cells.If engineers at Stanford have their way, biological research may soon be transformed by a new class of light-emitting probes small enough to be injected into individual cells without harm to the host.

 Welcome to biophotonics, a discipline at the confluence of engineering, biology and medicine in which light-based devices – lasers and light-emitting diodes (LEDs) – are opening up new avenues in the study and influence of living cells. The team described their probe in a paper published online Feb. 13 by the journal Nano Letters. It is the first study to demonstrate that tiny, sophisticated devices known as light resonators can be inserted inside cells without damaging the cell. Even with a resonator embedded inside, a cell is able to function, migrate and reproduce as normal."

http://stanford.io/13gA8P8

by
Yen-Hsiang Wang, Kathy Y. Wei, Christina D. Smolke

"A major objective of synthetic biology is to make the process of designing genetically encoded biological systems more systematic, predictable, robust, scalable, and efficient. Examples of genetic systems in the field vary widely in terms of operating hosts, compositional approaches, and network complexity, ranging from simple genetic switches to search-and-destroy systems. While significant advances in DNA synthesis capabilities support the construction of pathway- and genome-scale programs, several design challenges currently restrict the scale of systems that can be reasonably designed and implemented. Thus, while synthetic biology offers much promise in developing systems to address challenges faced in the fields of manufacturing, environment and sustainability, and health and medicine, the realization of this potential is currently limited by the diversity of available parts and effective design frameworks. As researchers make progress in bridging this design gap, advances in the field hint at ever more diverse applications for biological systems."

http://bit.ly/WLS7fN

Illustration http://en.wikipedia.org/wiki/Biological_systems

*Engineering cells for more efficient biofuel production*

by
Anne Trafton

"In the search for renewable alternatives to gasoline, heavy alcohols such as isobutanol are promising candidates. Not only do they contain more energy than ethanol, but they are also more compatible with existing gasoline-based infrastructure. For isobutanol to become practical, however, scientists need a way to reliably produce huge quantities of it from renewable sources. 

 MIT chemical engineers and biologists have now devised a way to dramatically boost isobutanol production in yeast, which naturally make it in small amounts. They engineered yeast so that isobutanol synthesis takes place entirely within mitochondria, cell structures that generate energy and also host many biosynthetic pathways. Using this approach, they were able to boost isobutanol production by about 260 percent. 

Though still short of the scale needed for industrial production, the advance suggests that this is a promising approach to engineering not only isobutanol but other useful chemicals as well, says Gregory Stephanopoulos, an MIT professor of chemical engineering and one of the senior authors of a paper describing the work in the Feb. 17 online edition of Nature Biotechnology...." 

http://bit.ly/Xmy8Ct

comment to:

*Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols*

by
José L Avalos,Gerald R Fink& Gregory Stephanopoulos

"Efforts to improve the production of a compound of interest in Saccharomyces cerevisiae have mainly involved engineering or overexpression of cytoplasmic enzymes. We show that targeting metabolic pathways to mitochondria can increase production compared with overexpression of the enzymes involved in the same pathways in the cytoplasm. Compartmentalization of the Ehrlich pathway into mitochondria increased isobutanol production by 260%, whereas overexpression of the same pathway in the cytoplasm only improved yields by 10%, compared with a strain overproducing enzymes involved in only the first three steps of the biosynthetic pathway. Subcellular fractionation of engineered strains revealed that targeting the enzymes of the Ehrlich pathway to the mitochondria achieves greater local enzyme concentrations. Other benefits of compartmentalization may include increased availability of intermediates, removing the need to transport intermediates out of the mitochondrion and reducing the loss of intermediates to competing pathways."

http://bit.ly/12HvL4b

by
Aunica L. Kane, Daniel R. Bond, and Jeffrey A. Gralnick

"Growth in three-electrode electrochemical cells allows quantitative analysis of mechanisms involved in electron flow from dissimilatory metal reducing bacteria to insoluble electron acceptors. In these systems, gold electrodes are a desirable surface to study the electrophysiology of extracellular respiration, yet previous research has shown that certain Shewanella species are unable to form productive biofilms on gold electrodes. To engineer attachment of Shewanella oneidensis to gold, five repeating units of a synthetic gold-binding peptide (5rGBP) were integrated within an Escherichia coli outer membrane protein, LamB, and displayed on the outer surface of S. oneidensis. Expression of LamB-5rGBP increased cellular attachment of S. oneidensis to unpoised gold surfaces but was also associated with the loss of certain outer membrane proteins required for extracellular respiration. Loss of these outer membrane proteins during expression of LamB-5rGBP decreased the rate at which S. oneidensis was able to reduce insoluble iron, riboflavin, and electrodes. Moreover, poising the gold electrode resulted in repulsion of the engineered cells. This study provides a strategy to specifically immobilize bacteria to electrodes while also outlining challenges involved in merging synthetic biology approaches with native cellular pathways and cell surface charge."


http://bit.ly/Y3UvOe

*Dan Rather Reports*, "*Cutting Edge*" *Synthetic Biology* 

"Dan Rather Reports, "Cutting Edge" Promo from AXS TV. Like this? Watch the latest episode of AXS TV on Blip! http://blip.tv/hdnet-news-and-documen... ;

 Synthetic biology is at the forefront of modern science, as researchers reinvent cells by manipulating DNA to solve some of the most important problems facing the world."

http://bit.ly/Zi3yzP

*Lipid Nanotechnology*

by
Mashaghi S, Jadidi T, Koenderink G, Mashaghi A.

"Nanotechnology is a multidisciplinary field that covers a vast and diverse array of devices and machines derived from engineering, physics, materials science, chemistry and biology. These devices have found applications in biomedical sciences, such as targeted drug delivery, bio-imaging, sensing and diagnosis of pathologies at early stages. In these applications, nano-devices typically interface with the plasma membrane of cells. On the other hand, naturally occurring nanostructures in biology have been a source of inspiration for new nanotechnological designs and hybrid nanostructures made of biological and non-biological, organic and inorganic building blocks. Lipids, with their amphiphilicity, diversity of head and tail chemistry, and antifouling properties that block nonspecific binding to lipid-coated surfaces, provide a powerful toolbox for nanotechnology. This review discusses the progress in the emerging field of lipid nanotechnology.

..."

http://bit.ly/XTppH7

Interview: 
*Jason Silva* - *Synthetic Biology* 


http://bit.ly/13AxP9Y

via +Michal Galdzicki 

*5th International Workshop on Bio-Design Automation*

"About IWBDA The Fifth International Workshop on Bio-Design Automation (IWBDA) co-located with SB6.0 will bring together researchers from the synthetic biology, systems biology, and design automation communities. The focus is on concepts, methodologies and software tools for the computational analysis of biological systems and the synthesis of biological systems. Still in its early stages, the field of synthetic biology has been driven by experimental expertise; much of its success can be attributed to the skill of the researchers in specific domains of biology. There has been a concerted effort to assemble repositories of standardized components. However, creating and integrating synthetic components remains an ad hoc process. The field has now reached a stage where it calls for computer-aided design tools. The electronic design automation (EDA) community has unique expertise to contribute to this endeavor. This workshop offers a forum for cross-disciplinary discussion, with the aim of seeding collaboration between the research communities. Topics of interest include: Design methodologies for synthetic biology.Standardization of biological components.Automated assembly techniques.Computer-aided modeling and abstraction techniques.Engineering methods inspired by biology.Domain specific languages for synthetic biology.Data exchange standards and models for synthetic biology.Call for Abstracts Abstracts should be two pages long, following the ACM SIG Proceedings templates at http://www.acm.org/sigs/publications/proceedings-templates. Indicate whether you would like your abstract considered for a poster presentation, an oral presentation, or both. Include the full names, affiliations and contact information of all authors. Abstracts will be reviewed by the Program Committee. Those that are selected for oral and poster presentations will distributed to workshop participants and posted on the workshop website. The submission system will be opened shortly. Key Dates Call for participation published: TBDAbstract submission deadline: TBDAbstract acceptance notification: TBDWorkshop: July 12-13, 2013Dates and Venue The workshop will take place following BioBricks Foundation SB6.0: The Sixth International Meeting on Synthetic Biology at Imperial College, London, UK. Lodging during the conference will be available at Imperial College and at hotels close by. Agenda The conference program is current in development Organizing Committee Executive Committee General Chair - Jonathan Babb (jbabb@mit.edu)Finance Co-Chair - Aaron Adler (aadler at bbn dot com)Finance Co-Chair - Traci Haddock (tracihaddock@gmail.com)Program Committee Co-Chair - Leonidas Bleris (bleris@utdallas.edu)Program Committee Co-Chair - Ilias Tagkopoulos (iliast@cs.ucdavis.edu)Industry Liaison Chair - Jose Pacheco (jose@igem.org)Publication Chair - Michal Galdzicki (mgaldzic@uw.edu)Steering Committee Douglas Densmore (ougd@bu.edu)Soha Hassoun (soha@cs.tufts.edu)Natasa Miskov-Zivanov (nam66@pitt.edu)Marc Riedel (mriedel@umn.edu)Ron Weiss (rweiss@mit.edu)"
http://bit.ly/13p2WFj ;

by
NIC HALVERSON

"For children born with microtia, a congenital deformity of the external ear, reconstructive surgery solutions can involve long, painful operations or prosthetics that rarely resemble the real thing.

 However, Cornell bioengineers and physicians have offered new hope by using 3-D printing and injectable gel molds to create an artificial ear that looks, feels and functions like a natural one. Dr. Jason Spector, director of the Laboratory for Bioregenerative Medicine and Surgery and associate professor of plastic surgery at Weill Cornell Medical College, said this method is "absolutely" the best option reconstructive surgeons have for helping kids with microtia or those who've lost part of an ear to trauma or cancer...."

 http://bit.ly/12TxoMc

by
Binquan Luan

IBM computational biology center  

"Nanotechnology for DNA Sequencing

The information to produce many of the components of the cell such as RNAs and proteins is encoded in the sequence of nucleotides of a cell. Determining the DNA sequence is therefore fundamental to molecular biology and medicine. The most used technique for DNA sequencing has been the dideoxy termination method developed by F. Sanger in a Nobel Prize winning groundbreaking work. Through parallelization, automation and refinement of the established Sanger sequencing method, the Human Genome Project is estimated to have cost $3 billion. Much lower cost methods for DNA sequencing will be required to make genome sequencing feasible for routine healthcare practice.Many new generation sequencing methods have been developed during the last decade, which represent significant advances over the traditional Sanger sequencing. Amongst them, a method based on threading a DNA molecule through a pore of a diameter of a few nanometers to sequence this molecule while it translocates through the nanopore occupies a privileged place. DNA nanopore sequencing has the advantage of being a real-time single molecule DNA sequencing method with little to no sample preparation and inherently of low-cost.At least two technical roadblocks prevent implementations of DNA nanopore nucleotide identification by electrical sensor methods. 1) The absence of a reliable approach to control the translocation of DNA through the nanopore. 2) The technical difficulties in making sufficiently small sensors. Our work in this field focuses on solving the challenge of translocation control.To control the DNA translocation through the nanopore we have proposed a device consisting of a metal/dielectric/metal/dielectric/metal multilayer nano-structure built into the membrane that contains the nanopore. Voltage biases between the electrically addressable metal layers will modulate the electric field inside the nanopore. This device utilizes the interaction of discrete charges along the backbone of a DNA molecule with the modulated electric field to trap DNA in the nanopore with single-base resolution. By cyclically turning on and off these gate voltages, we showed theoretically, and we expect to be able prove experimentally, the plausibility to move DNA through the nanopore at a rate of one nucleotide per cycle. We call this device a DNA transistor, as a DNA current is produced in response to modulation of gate voltages in the device.The DNA transistor is then a DNA positional controlling platform with single-base-resolution, which could be used in combination with sensor measurements that are under development by us and other research groups. By providing enough dwell time for each DNA nucleotide at the electrodes constituting the sensor, the DNA transistor allows exploration of the best electrical sensor that can resolve the difference between the four DNA nucleotides. In that sense, the DNA transistor paves the way to nanopore-based nucleotide sequencing, and personalized "

http://bit.ly/TJ6h3c

Date: Friday, Feb. 22, 2013, 8 a.m. — Saturday, Feb. 23, noon Local
Location: The Charles Hotel, Harvard Square, One Bennett Street, Longfellow Room, Cambridge, MA, United States

EXPECTED OUTCOME

The goal of the SemiSynBio workshop is to identify future research directions for the semiconductor industry based on concepts and principles derived from Synthetic Biology (e.g. highly functional space-limited digital and analog systems that operate with extremely low energy consumption etc.).

http://bit.ly/YGv3wR

by
Stephen R. Munzer

"Two examples of research biobanks are discussed. The first is a set of stored blood samples taken from Havasupai Indians by scientists at Arizona State University (ASU). The second is a set of zinc finger proteins (ZFPs) and zinc finger nucleases (ZFNs) assembled by Sangamo BioSciences, Inc. of California. Both examples involve individual and group autonomy, informational asymmetries, and exchange. Both examples are controversial but for different reasons. In the Havasupai case, the Indians claimed that the scientists used the blood samples to analyze a Havasupai predisposition to diabetes, to which they consented, and to extract information about Havasupai inbreeding, schizophrenia, and geographical origins, to which the Indians did not consent. Eventually, ASU returned the blood samples and compensated the tribe and some individual members. Scrutiny shows that the Havasupai complaints were mainly justified. As to ZFPs and ZFNs, some lawyer-scientists contend that Sangamo’s preeminent patent and trade secret position unfairly hinders others from benefiting from Sangamo’s knowledge. Close examination shows no unfairness in the Sangamo case, for two reasons. First, the Zinc Finger Consortium provided an open access alternative to dealing with Sangamo. Second, under standard economic criteria Sangamo did not have a monopoly on zinc finger technology."
http://bit.ly/11STA9M

Illustration
http://en.wikipedia.org/wiki/Havasupai_people

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By Lisa M. Krieger

"Most people look at the cedar in Drew Endy's front yard and admire its graceful green boughs, heavy with needles, sap and cones.

Endy sees something much different: an industrial manufacturing platform, waiting to be exploited."I dream we could someday reprogram trees that could self-assemble a computer chip in your front yard," exudes the brilliant and intense Stanford University scientist, who has emerged as a leading evangelist in the new field of synthetic biology.One gene at a time, Endy and other elite teams of Bay Area scientists are striving to design and build organisms unlike anything made by Mother Nature.It's not yet possible to create artificial life from scratch. But it's getting closer, through projects that essentially swap out a cell's original operating system for a lab-designed one. These made-to-order creations then can be put to work.The Human Genome Project gave us the ability to read nature's instruction manual -- DNA -- like words in a book. But the real opportunities, scientists say, lie in our ability to not only read genetic code, but to write it, then build it using off-the-shelf chemical ingredients, strung together like holiday lights. It is the creation of new genomes -- and a new frontier in bioengineering.Synthetic biology works because biological creatures are, in essence, programmable manufacturing systems. The DNA instruction manual buried inside every cell -- its software, in a sense -- can be replaced with a man-made version, giving us the ability to tell it what to make.This presages the distant day when Endy's big Menlo Park cedar churns out computer chips, not cones. Or makes cancer-fighting drugs. Or fuels. Or building materials. Or anything else.There are concerns about safety and ethics. In the wrong hands, lone villains or rogue regimes could unleash dangerous life forms. A review in 2010 by a White House commission concluded the field needs monitoring, but the risks are still limited."

http://bit.ly/YzEQ87

*A cool bio art video*

by
björk

hollow

http://bit.ly/Zi8l48