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Questions tagged [synthetic-biology]

Synthetic biology is an approach to engineer biology. Core to the discipline is genetic engineering, which is made more akin to engineering by adding the levels of standardization, automation, and abstraction.

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Replacing, instead of repairing, DNA

I've been doing some light reading on DNA damage theory of aging. One of the main ideas from that theory that I got is that the accumulation of damage in our DNA is one of the biggest causes of why we ...
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Storage of bacteria

Why are strains of bacteria stored when they are inactive (frozen)? What is the problem with storing growing cultures for long periods?
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Difference between genetic engineering and synthetic biology

I've recently seen the term synthetic biology being used to describe research involving genetic modification of organisms. What is the difference between synthetic biology and genetic engineering? Is ...
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Will new proteins incorporating new amino acids trigger an immune response?

This article reported that scientists have succeeded in adding two new bases to the quartet of A, C, G and T, resulting in non-canonical amino acid. Additionally, the bacteria in which this was done ...
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What are low-accumulating genotypes? [closed]

What are low-accumulating genotypes? And how does it differ from high-accumulating genotypes?
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What can cause incompatible sticky ends to be ligated?

Actual question I have reason to believe (details see below) that in a ligation I carried out, an EcoRI sticky end (EcoRI: G'AATT_C) and an XmaI sticky end (XmaI: C'CCGG_G) were somehow ligated ...
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702 views

Ribosomal Turing Machines, DNA/RNA computation

I'm a computer science guy, recently crossing over to do some research in computational biology on RNA secondary structure prediction. While looking through the materials I got a crazy idea, what if ...
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101 views

What is the purpose of the AraC gene in pGLO?

The AraC gene activates in pGLO from my understanding in the presence of arabinose. Arabinose is present as a metabolite from other metabolic in the e.coli cell. Is it that there's no termination ...
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Papers where protein oligomerization has been engineered away

I have a protein that acts as a monomer, but appears to have a relatively high self-affinity in vivo (measured using transient transfection of a plasmid coding for the protein), which is annoying ...
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Dealing with Repetitive Bases in DNA?

I have been given a project involving a plasmid that contains long stretches of Adenine (60 or 120 bases each). These PolyA stretches are interrupted by the occasional G or C. I understand that ...
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A synthetic sieve organ known as kliver?

in this video at 5:28, the narrator talks about a "vat-grown all-purpose sieve organ" called Kliver that would do away with both liver and kidney transplant. But i don't seem to find online resources ...
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Can scientists create totally synthetic life?

This particular question has been of a great deal of interest to me, especially since it dives at the heart of abiogenesis.
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Forum on synthetic biology and hypothetical biology? [closed]

I am interested in synthetic biology, but not a scientist, and would like some advice on where to look for an online forum on synthetic biology and creating fictional species and animals or if someone ...
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What's the state of the art in designing and creating your own life forms?

What's the state of the art for solving the following problem. You imagine a set of features that you want a life-form to have. Just to take an arbitrary example, say you want your life-form to have a)...
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Why we utilize dextro glucose and levo amino acids?

Our body only digest dextro(Right handed) glucose and levo(Left handed) proteins and can't digest Levo glucose and dextro proteins. Why? Our body synthesis levo proteins. What is the reason?
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Introductory literature for synthetic / systems biology

I am a computer engineer (MSc in Computer Engineering) who's looking to switch into the field of synthetic / systems biology. I have a comprehensive layman's understanding of evolution, genetics, ...
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77 views

MIT's Programming Language for Cells

I have read a lot about the programming language, Cello, that MIT created to program DNA; however, I cannot seem to find any sources online that shows you how to program with Cello. Are there any good ...
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Could the protein dystrophin be artificially synthesised?

Could the protein dystrophin be artificially synthesised and if so could patients with DMD (Duchenne Muscular Dystrophy) benefit from it? //Now I don't have much scientific background other than a ...
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Assay for Glycosyltransferase

I want to do an assay to see, if an ordered enzyme is active or not. It's a glucosyltransferase from S. mutans which hydrolyses sucrose into fructose and glucose. It then connects the glucose-monomers ...
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How would you effect bulk DNA gene therapy for a human?

Let's imagine that we understood DNA programming and our genome very well and realized that there were some significant flaws (we die, we need sleep, etc.) And let's imagine that we understand how to ...
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How does a bacterium age without cell division?

If somehow a bacterium, let's say E. coli, is engineered in such a way that it loses the formation of ftsZ ring (or other ways that inhibit cell division), and if other conditions are optimal for ...
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3answers
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What does it mean to “write an image and GIF into the DNA of bacteria”?

BBC News recently published an article saying that: An image and short film has been encoded in DNA, using the units of inheritance as a medium for storing information ... The team sequenced the ...
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Can spider silk be synthesized to be used for 3D printing?

With the recent rise in 3D printing, I keep hearing about more novel ways to use the technology: cell 3D printing, liquid aluminum or plastic 3D printing. For example, this Ted talk deals with ...
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What happens when you tag a protease with its own degradation tag?

I've been learning about the ClipXP, ClipAP, and Lon proteases. They are proteases from the AAA+ family, which seek out proteins tagged with certain peptide sequences, unfold them, and chop them up. ...
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What's the difference between prions and prion-like proteins?

If I added a prion domain to a protein, does that make the protein a prion-like protein or would it be considered a prion at that point? I'm trying to understand what prions are, how they aggregate ...
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Is cell-free Life possible? [closed]

I think most of the people on this site know about the famous Baltimore paper describing the ability of the poliovirus to replicate itself without the need of cells but I want to expand on the issue ...
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Is it possible to synthesize chiral version of an organism (incompatible with our pathogens)?

In theory, it should be possible to synthesize chiral (mirror image) version of some organism: with all molecules replaced with their enantiomers, e.g. L-sugars in place of our D-sugars. Direct ...
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DNA synthesis companies: cost per base, turn-around time, codon-optimization algorithms

I would like to synthesize a 3.4kb gene (originally isolated from soil bacteria) and transform it into E. coli. There are several companies (DNA2.0, GeneScript, BlueHeron) which will synthesize the ...
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Is it possible to have undamaged healthy cell, that is dead?

I am trying to clarify my understanding of how unicellular organisms are alive, given my existing background (computational modelling, unrelated to biology). During my thoughts on subject I have came ...
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104 views

Is it possible to create DNA of a species that could be any animal [closed]

I was thinking about a fiction world in which all animal (at least vertebrate) could crossbred because they share same number and layout of chromosome but differ in hereditary detail (like human skin ...
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435 views

Has synthetic biology created new plants or animals as of 2013?

I've seen a Ted.com talk where the speaker suggests that modern science can create new micro organisms, like bacteria with a pre- defined new set of traits. But has anyone create a new species of ...
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311 views

Is it possible to remove one strand of double stranded DNA in vivo?

Assume we do have a double stranded DNA sequence in human cells, say ...ATCGATATCGATATTGCAGAGCATAGCTATAA... ...TAGCTATAGCTATAAGCTCTCGTATCGATATT... Now I want to ...
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Molecular Logic GATE

Currently either PET-Fluorophore or FRET is used as output of the molecular/DNA-based logic gate. Likewise, in a logic gate, lets say YES GATE, you provide an input to the logic gate and in return you ...
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870 views

Why isn't there a standard unit of promoter strength?

Sometimes in synthetic biology, we need to know rates of transcription of one promoter in relation to others (particularly inducible vs constitutive) in order to perform tasks like balancing ...
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Barcode exchange between neighbouring cells

I am currently interested in equipping animal cells in a tissue with individual barcodes. These barcodes should get amplified in the cells (not to a cell degrading extent, of course), and also ...
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Why does pETDuet-1 only have one T7 terminator but two T7 promoters?

Why does pETDuet-1 only have one T7 terminator but two T7 promoters (vector map below)? Is there any advantage of having only one terminator? There are going to be two mRNAs transcribed from this ...
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What is the highest number of genes expressed under one T7 promoter?

What is the highest number of genes expressed under one T7 promoter? Also, what is the longest polycistronic mRNA? I am interested in the context of heterologously expressing biosynthetic gene ...
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In theory how fast could nerve signals travel if the nerve fibre was perfectly insulated?

My question is purely theoretical and my main aim is to find out the maximum speed that a nerve signal can travel within a nervous system and and whether this speed represents the physical limit of ...
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What prevent us from synthesizing a cell from “scratch”?

In this recent article "Design and synthesis of a minimal bacterial genome", they created a minimal cell with only 473 genes. However, they didn't synthesize all of the necessary components of the ...
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247 views

A career in synthetic biology [closed]

So I am thinking about a career in synthetic biology, but I am not sure what route should/needs to be taken. I don't want to do technician work--I want to be involved in the planning. Y'know, the ...
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331 views

Balanced vs Maximized Codon Optimization

I have worked with the optimization of several viral proteins, from different viruses/families, with different results. When Menzella, 2011 was published I tried that method. I found quite the ...
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Do DNA supply houses maintain a watch list for dangerous oligos (Anthrax, Smallpox, etc.)?

The recent work by DeLoache, et al. on a synthetic opiate-precursor production pathway in yeast has generated a lot of scare stories in the media about people homebrewing heroin as easily as they ...
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Colormetric assay for a phenol product?

I am working on an assay for phenol products created by a colony of bacteria. I have searched up a paper that involves gibbs reageant but the protocol is kind of unclear. Does any of you know where I ...
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199 views

“Antibiotic resistance” equivalent in archaea for selection during cloning

I'm beginning to work with halophilic archaea and I'm trying to figure out a good way to select for cells that have taken up a plasmid. Obviously, one can't use antibiotic resistance since they are ...
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How to secrete a recombinant protein from E. coli?

What are some secretory pathways that can be used to secrete a recombinant bacterial enzyme from E. coli? I have a recombinant protein (29kDa) that I will express in E. coli BL21 cells. For now I ...
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What is the spacing between stop codon and transcription terminator?

When one tries to express a protein from a synthetic plasmid in E. coli, how many base pairs should there be between stop codon and the transcription terminator site?
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1k views

T7 Tagging in Synthetic Biology

What is a T7 tag and can if be used to purify synthesized proteins? Is it charge based like a His tag?
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His Tag location in gene circuit

I am part of an undergraduate research group and we are trying to produce a protease in an E.coli gene circuit. We are not sure where to place the His tag in our circuit. The sequence is ...OmpA(gene)-...
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58 views

Will tagging a protease with HlyA for secretion inactivate the protease?

We are looking to secrete the protease proline iminopeptidase by attaching the secretion signal HlyA to the protease in a gene circuit. Since the natural HlyA secretion sequence in Escherichia coli ...
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Proline Iminopeptidase v Proline Aminopeptidase

We're an undergraduate independent research team and we are having trouble purchasing commercial proline iminopeptidase as it is unavailable on Sigma Aldrich and very expensive on other websites. We ...