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25

In 2010, Dr. Craig Venter actually used a bacterial shell and wrote DNA for it. Scientists have created the world's first synthetic life form in a landmark experiment that paves the way for designer organisms that are built rather than evolved. (Snip) The new organism is based on an existing bacterium that causes mastitis in goats, but at its ...


21

In principle it is possible. Life doesn’t contain some divine or intrinsically spiritual element that we would have to add to our artificial organism potion to breathe life into it. At this moment we are limited by gaps in our knowledge and by the current state of technology. We first have to better understand fundamental principles of life on a ...


15

I found an oldish paper on this topic (from 1994). Here's a summary: Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. by Chen, Bjerknes, Kumar, & Jay. Nucleic Acids Research. (1994) Experiment The authors constructed a series of synthetic RBS regions that ...


14

I would like to add a lecture on Synthetic Biology by Andrew Hessel, who introduces the open source synthetic biology field, compares it to computing, and gives an overview of what are its applications, like the creation of the first synthetic organism. I also stumbled upon a talk from the famous physicist Michio Kaku, who shares his vision about the world ...


10

Systems Biology Wingreen & Botstein who run the graduate systems biology course at Princeton wrote a paper about how to teach the subject (Wingreen & Botstein, 2006). In the paper they highlight the key concepts they think are crucial to understanding modern systems biology, and they teach the course through discussion of seminal papers in the ...


9

This is a great question as I just made my own "homebrew" chemically competent cells. There are a vast variety of E. coli strains that are commonly used for cloning. They may be transformed chemically by heat shock method, or electrically by electroporation (a brief summary may be found here). These can be made in the lab manually, or purchased commercially ...


9

The posts above seem very thorough and complete, but I'd like to add by linking to this TED talk, as well as this one, for you to familiarize yourself with Craig Venter's work on synthetic life. Enjoy!


6

I haven't tried Gibson Assembly myself, but I do know the Cambridge iGEM Team in 2010 and 2011 developed a web-based tool - Gibthon - for automatically generating primers for Gibson Assembly. You could try running your difficult sequences through their tool to see what it suggests for primers. It apparently gives you a "value for the Gibbs free energy of ...


6

I have heard that Epi300 electrocompetent cells (1) from Epicentre are very efficient: > 1 x 1010 cfu/µg of pUC19. Dan Gibson used them in his paper for the synthesis of the mitochondrial genome (2). We were also thinking of using them for our assemblies, but they are pretty expensive. 1. TransforMax™ EPI300™ Electrocompetent E. coli 2. Chemical synthesis ...


6

The problem is of course very complex so take my answers as simplifications. Most transgenesis so far has been done on unicellular beings (bacteria, yeast), which we can change as much as we want fairly "easily", plants, insects and some mammals. Notably, for the latter case, mice are the species which has been used the most for transgenesis, as they are ...


5

It seems to me that the difference is mainly semantic, although the aims of synthetic biology are undoubtedly more ambitious than those of genetic engineering in, say, the 80s and 90s. The Wikipedia page on genetic engineering has this definition of the difference: Synthetic biology is an emerging discipline that takes genetic engineering a step ...


5

I have a similar background (CS switching to systems biology) and I learned a great deal by reading "Systems Biology: A Textbook" by Edda Klipp et al [1]. It's a very good overview of different sub-areas and it's written in a way that's friendlier to a technical mind than most other bio-related books (i. e. concise, to the point, not shy with formulas). The ...


5

By looking at the sequence only? This is an unsolved problem. Its not clear to me exactly what you are looking for, but here are some thoughts... On a relatively narrow question as to whether any gene you plug into a bacterium, yeast, mouse, goat or other transgenic organism - the rna may not translate into protein in detectable levels or at high enough ...


5

I'm afraid there's not much of answer but back to the bench with you! (That's why it's called re-search). There are several factors that could be playing a role here. You could have transcriptional or translational read through. You should check your sequence and the cells you are going into to make sure you aren't getting Amber (UAG) suppression. ...


4

Are you working in academia? It might be worthwhile to call the companies directly and see if there is a discounted rate for your institution (another lab or department may have already set something up). You won't be able to get information on the different algorithms if they are proprietary. However considering that codon usage data is public and shared ...


4

You might want to read Gibson's paper on the step-wise assembly of the mouse mitochondrial genome (1): He started with 60b long oligos with 20b overlap, as he assembled 5 of those 60-mers into a backbone, obtaining 384b fragments. On the next step, he joined 5 of those 384mers, obtaining 1.2kb constructs. You can do the same, but on the second step use 2x ...


4

My understanding is that synthetic biology is genetic engineering 2.0. The difference is in the approach. Whereas genetic engineering projects are usually ad hoc, synthetic biology aims to apply proper engineering principles such as standardisation, modularisation, and reusability. Synthetic biologists create and use libraries of standard parts that are ...


4

The "...in large enough amounts to enable 3D printing?" part of your question is, I think, still unknown, but spider silk has been being synthesized in transgenic goat milk for quite a long time already, and I suspect that it's now just a matter of time before the answer to your question is an unqualified "yes." See Macromolecules, 2011, 44 (5), pp ...


4

From my experience in the mammalian world (and this may apply to bacterial systems as well), it's not so much the number of genes in the plasmid as its actual size. The larger the construct is, the more difficult it will be to get it into your target cells in one piece, without degradation or shearing. Since the transformation efficiency is lower, you are ...


4

The amount of transfected plasmid does not correlate at all with the protein expression level. After transfction, usually each cell is going to get and keep only one copy of the plasmid. Once the plasmid is in the cell, it will be replicated and the cell will contain X copies of it, depending on the plasmid copy number. In general, plasmids with low copy ...


3

yDNA came first: Lee & Kool (2005) A New Four-Base Genetic Helix, yDNA, Composed of Widened Benzopyrimidine−Purine Pairs. J Am Chem. Soc. 127: 3332-3338 As seen in this Figure from the paper it is a DNA consisting of T and C substituted with yT and yC, widened analogues. xDNA came next (also from the Kool lab.): Lynch et al. (2006) Toward a ...


3

They seem to be practically the same, with the exception of the goals. Genetic Engineering is the direct modification of the genes of an organism which results in capabilities being added or taken away. Synthetic Biology aims to modify the behaviors of an organism or integrate the behaviors of multiple organisms into a singular whole. As is explained in ...


3

The following papers are a good starting point: René Thomas, Boolean formalization of genetic control circuits, Journal of Theoretical Biology, Volume 42, Issue 3, December 1973, Pages 563-585 <= A classic paper in the field. Thieffry D. Dynamical roles of biological regulatory circuits. Brief Bioinform. 2007 Jul;8(4):220-5. Remy E, Ruet P. From ...


3

There is a recent published book, from Garland Science for systems biology http://www.garlandscience.com/product/isbn/9780815344674 and a clasic textbook: Physical Biology of the Cell http://www.garlandscience.com/product/isbn/9780815341635


3

Amazingly, yes. See High level gene expression in mammalian cells by a nuclear T7-phage RNA polymerase. The authors recognize that the T7 RNA polymerase tends to work only in the cytoplasm thus is unable to transcribe genes in the nucleus. To remedy this limitation, the T7 polymerase was fused to a nuclear location signal peptide to localize the polymerase ...


3

The J. Craig Venter Institute recently has indeed created a synthetic, self-replicating cell (see the press release). So it's definitely not impossible to create completely synthetic cells for use in synthetic biology, but that doesn't mean it makes much sense to do so. E. coli in particular have been used as bench tools for decades: lots of protocols exist ...


3

Could be insert polymerization. If you have your stretch of DNA like this: (5')-AATTagctagcatcgtgatcgacg-(3') |||||||||||||||||||| (3')-tcgatcgtagcactagcagcGGCC-(5') And you take that, flip it around, it will ligate onto itself, like this: (5')-AATTagctagcatcgtgatcgacg-(3')(5')-CCGGcgacgatcacgatgctagct-(3') ...


3

I am also about to undertake some FRET studies (this week in fact). FRET linkers are a thing of tinkering, unfortunately. Förster resonance energy transfer, or FRET, is a phenomena that decays with $ 1/{r^6} $, the radius between the donor and acceptor. When constructing FRET reporters, there are a few things to keep in mind: Length of linker. The length ...


2

There is this guy, Martin Hanczyc, working on protocells to better understand how the beginning of life occurred. He makes synthetic protocells. They don't have any DNA in them but they are pretty cool and maybe the beginnings to making synthetic cells. Perhaps once science has figured out how cells began and their very minimal needs they can create ...


2

Here is a blog post from Ginkgo BioWorks that graphs the turn-times from 3 major suppliers: http://blog.ginkgobioworks.com/2012/01/14/commercial-gene-synthesis/



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