Showing posts with label synthetic biology. Show all posts
Showing posts with label synthetic biology. Show all posts
Monday, October 24, 2011
Try this at home by Daniel Grushkin
The next big scientific breakthrough may come from a garage, not a lab, with do-it-yourself biologists popping up everywhere. Genetic tinkerer Daniel Grushkin has a message for the curious: go ahead, try this at home.
In the scientific journals, we’ve been labeled biotech hobbyists, citizen scientists, even biohackers.Last December, seven of us opened the first community lab, called Genspace. Though it’s a fully functional lab, it has a decidedly hacked-together aesthetic. We built it in a Brooklyn, N.Y., warehouse that was converted into a workspace for architects and designers. At the center of the floor sits a glass cube made of found objects. The walls are created from windows and sliding glass doors saved from demo sites. The lab benches are stainless steel tables salvaged from industrial kitchens. Most of the equipment was donated by a biotech company that downsized during the economic crisis.We incorporated Genspace as a nonprofit to serve as a shared lab, a nursery for biotech tinkerers. Our members include an entrepreneur with great ideas but a miniscule budget, an artist employing single-celled organisms for an experimental design palette, a molecular biologist with a penchant for mentorship, and folks like me, who want to learn by creating novel organisms.
Wednesday, October 12, 2011
The Pearl Gel Box and Creative Commons
Open Hardware for Molecular Biology Experiments
Sure it takes years of training to become a world class biologist, but now you can have fun with their equipment without slaving away in academia. Pearl Biotech is selling an electrophoresis gel box, an instrument used in the separation and characterization of DNA online. Electrophoresis is a safe procedure that is useful to molecular biologists but can be enjoyed by anyone. It’s a standard experiment in high school labs. The Pearl Gel Box is an open hardware device which means that anyone is free to build or adapt it as along as they share their modifications in a similar manner. Pearl Biotech sells a fully assembled version for $200. By providing a cheap entry level tool for genetics Pearl is helping generate interest in the field and supporting the do it yourself community.
Mammalian synthetic biology: engineering of sophisticated gene networks
J Biotechnol. 2007 Jul 15;130(4):329-45. Epub 2007 May 24.
(Must subscribe to see full text)
(Must subscribe to see full text)
Abstract:
With the recent development of a wide range of inducible mammalian transgene control systems it has now become possible to create functional synthetic gene networks by linking and connecting systems into various configurations. The past 5 years has thus seen the design and construction of the first synthetic mammalian gene regulatory networks. These networks have built upon pioneering advances in prokaryotic synthetic networks and possess an impressive range of functionalities that will some day enable the engineering of sophisticated inter- and intra-cellular functions to become a reality. At a relatively simple level, the modular linking of transcriptional components has enabled the creation of genetic networks that are strongly analogous to the architectural design and functionality of electronic circuits. Thus, by combining components in different serial or parallel configurations it is possible to produce networks that follow strict logic in integrating multiple independent signals (logic gates and transcriptional cascades) or which temporally modify input signals (time-delay circuits). Progressing in terms of sophistication, synthetic transcriptional networks have also been constructed which emulate naturally occurring genetic properties, such as bistability or dynamic instability. Toggle switches which possess "memory" so as to remember transient administered inputs, hysteric switches which are resistant to stochastic fluctuations in inputs, and oscillatory networks which produce regularly timed expression outputs, are all examples of networks that have been constructed using such properties. Initial steps have also been made in designing the above networks to respond not only to exogenous signals, but also endogenous signals that may be associated with aberrant cellular function or physiology thereby providing a means for tightly controlled gene therapy applications. Moving beyond pure transcriptional control, synthetic networks have also been created which utilize phenomena, such as post-transcriptional silencing, translational control, or inter-cellular signaling to produce novel network-based control both within and between cells. It is envisaged in the not-too-distant future that these networks will provide the basis for highly sophisticated genetic manipulations in biopharmaceutical manufacturing, gene therapy and tissue engineering applications.
With the recent development of a wide range of inducible mammalian transgene control systems it has now become possible to create functional synthetic gene networks by linking and connecting systems into various configurations. The past 5 years has thus seen the design and construction of the first synthetic mammalian gene regulatory networks. These networks have built upon pioneering advances in prokaryotic synthetic networks and possess an impressive range of functionalities that will some day enable the engineering of sophisticated inter- and intra-cellular functions to become a reality. At a relatively simple level, the modular linking of transcriptional components has enabled the creation of genetic networks that are strongly analogous to the architectural design and functionality of electronic circuits. Thus, by combining components in different serial or parallel configurations it is possible to produce networks that follow strict logic in integrating multiple independent signals (logic gates and transcriptional cascades) or which temporally modify input signals (time-delay circuits). Progressing in terms of sophistication, synthetic transcriptional networks have also been constructed which emulate naturally occurring genetic properties, such as bistability or dynamic instability. Toggle switches which possess "memory" so as to remember transient administered inputs, hysteric switches which are resistant to stochastic fluctuations in inputs, and oscillatory networks which produce regularly timed expression outputs, are all examples of networks that have been constructed using such properties. Initial steps have also been made in designing the above networks to respond not only to exogenous signals, but also endogenous signals that may be associated with aberrant cellular function or physiology thereby providing a means for tightly controlled gene therapy applications. Moving beyond pure transcriptional control, synthetic networks have also been created which utilize phenomena, such as post-transcriptional silencing, translational control, or inter-cellular signaling to produce novel network-based control both within and between cells. It is envisaged in the not-too-distant future that these networks will provide the basis for highly sophisticated genetic manipulations in biopharmaceutical manufacturing, gene therapy and tissue engineering applications.
Tuesday, October 11, 2011
Synthetic biology: new engineering rules for an emerging discipline
From the Caltech Synthetic Biology Journal Club papers, I found this Nature Review:
Abstract
Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.
Abstract
Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.
Registry of Standard Biological Parts
The Registry is a continuously growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems. Founded in 2003 at MIT, the Registry is part of the Synthetic Biology community's efforts to make biology easier to engineer. It provides a resource of available genetic parts to iGEM teams and academic labs. You can register a new lab here.
The Registry sponsors international undergraduate teams (iGEM) to compete in building synthetic biology machines. This could be a good cause to make a group at university. It's another chance to boost a university's prestige and fame.
The Registry sponsors international undergraduate teams (iGEM) to compete in building synthetic biology machines. This could be a good cause to make a group at university. It's another chance to boost a university's prestige and fame.
Introduction
The aim of this blog is to be an account of a journey to understand biology, not for passing a scantron test, but for actually figuring out how nature works.
Yesterday, I first learned about a movement called DIY Bio (Do-It-Yourself Biology) by reading this article. It immediately appealed to me. Gregor Mendel's hobby contributed vastly to our knowledge of genetics, although he knew nothing about what a gene actually was. Santiago Ramon y Cajal was a painter, who turned his attention to the nervous system with the aid of accessible devices and his inventive methods. Charles Darwin sailed the world, and collected specimens before writing down his revolutionary ideas in the Origin of Species. However, I was always jealous of these scientists because they did not need a bachelor's degree, Ph.D., government grant, or corporate lab to contribute in a major way to science. Now, it seemed to me, all or most of these things were required.
With my personal discovery of DIY Bio, I hope I can actually do science here in Miami without having to wait to get an advanced degree. Of course, I am financially extremely limited, and am ignorant of the most powerful methods of study. However, I plan to overcome these obstacles in ways I have already planned.
I will post my progress and some articles on this blog. I welcome any feedback on tips, advice, and interest in the subject, too. All advancement in learning and understanding is a group effort. With this I begin...
Yesterday, I first learned about a movement called DIY Bio (Do-It-Yourself Biology) by reading this article. It immediately appealed to me. Gregor Mendel's hobby contributed vastly to our knowledge of genetics, although he knew nothing about what a gene actually was. Santiago Ramon y Cajal was a painter, who turned his attention to the nervous system with the aid of accessible devices and his inventive methods. Charles Darwin sailed the world, and collected specimens before writing down his revolutionary ideas in the Origin of Species. However, I was always jealous of these scientists because they did not need a bachelor's degree, Ph.D., government grant, or corporate lab to contribute in a major way to science. Now, it seemed to me, all or most of these things were required.
With my personal discovery of DIY Bio, I hope I can actually do science here in Miami without having to wait to get an advanced degree. Of course, I am financially extremely limited, and am ignorant of the most powerful methods of study. However, I plan to overcome these obstacles in ways I have already planned.
I will post my progress and some articles on this blog. I welcome any feedback on tips, advice, and interest in the subject, too. All advancement in learning and understanding is a group effort. With this I begin...
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