Solving the world’s problems with new biotechnology

The ability to isolate, create, synthesize, or artificially evolve living organisms towards desirable phenotypes may be increasingly important for solving many of the problems the world is facing. Such problems may include creating renewable energy using biowaste, finding biocontrol products that kill food-spoiling fungi “organically”, or assaying pathogens in the field using synthetic biological detection systems. With the arrival of synthetic biology, “it is possible to design and assemble chromosomes, genes and gene pathways, and even whole genomes”, according to the J. Craig Venter Institute. That is, if you know which genes or gene pathways you would need to put into the synthetic genome that would lead to the desired traits. So far, most published synthetic biology work involves bringing in transcription factors from a non-host source to set up an artificial network like circadian oscillators, showing that it can be done and it is interesting.

Through the process of evolution biological systems aptly self-engineer favorable traits in order to survive, but these changes require millions of years to manifest. However, there are quicker adaptations to environmental cues, such as developing antibiotic resistance, which can be achieved through a small number of mutations in hundreds or even dozens of generations. The question is how to harness this kind of adaptation for new strains that can be used as products with defined purposes? As a first requirement, you must have an assay for identifying the wanted mutants or method for augmenting their subpopulation, which is not necessarily easy and normally takes some clever designs to establish. Since evolutionary success in nature results from continuous “rounds” of gene mutagenesis, expression and selection, an evolution in the lab should ideally proceed with continuity. Previously, each round of mutation and selection takes a few days to complete. Recently, Esvelt et al. in David Liu’s lab at Harvard demonstrated one way of doing in vitro continuous evolution, by creating a lagoon of mixed E. coli and phages. By continuous dilution of the phage population through outflow, those phages that remain in the pool with properties that help them propagate in the host bacteria will have a better chance to regenerate and accumulate mutations towards the design of the assay [1].

Another aspect of natural evolution is that it occurs in a heterogeneous environment separated into niches of subpopulations with uneven stress levels. Although most evolutions with human intervention were conducted in a homologous population under the same stress and selection, a spatially complex environment may speed up evolution. This may not be easy to imagine, but if a mutant acquires some level of resistance to its environmental stress level and has a chance to move to join a population under higher stress, its relative fitness will likely increase. In addition, in a smaller population in the niche under higher stress, the mutant with marginally beneficial properties acquired under lower pressure can take over more quickly. This was demonstrated by Zhang et al. who showed that with a gradient of antibiotics applied to an array of microwells interconnected through tiny channels, new resistant strains can evolve in less than a day. Without the gradient, or separate the interconnected niches into discrete wells, no resistant populations could be obtained [2].

With more understandings like these and equipped with large scale gene synthesis, chromosome assembly, and deep sequencing technologies, we should see increasing numbers of human-made organisms serving special needs for food, health, energy, and the environment. Synthetic biology or artificial evolution won’t solve all the world’s problems, but if applied effectively and diligently, they can certainly help with many critical aspects as the technology “coevolves” with the environment.

[1] Kevin M. Esvelt, Jacob C. Carlson, & David R. Liu. “A system for the continuous directed evolution of biomolecules” Nature 499, 2011.
Qiucen Zhang, Guillaume Lambert, David Liao, Hyunsung Kim, Kristelle Robin, Chih-kuan Tung, Nader Pourmand, Robert H. Austin. “Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments” Science 333, 2011.

New Products of the week: Modified UTP (Pseudouridine-5´-triphosphate), and Modified CTP (Methylcytidine-5´-triphosphate) for in vitro transcription of mRNA.

Promotion of the week: Friday special this week, buy 2 GFP-Trap get 1 free. Email the code “2+1GFPTrap” after placing your order of 2 GFP-Trap beads (0.25ml or 0.5ml scales only).

Tags: biocontrol, bioenergy, biofuel, biowaste, chromosome assembly, deep sequencing, food fungus, green energy, in vitro evolution, microenvironment, next generation sequencing, synthetic biology

New SurfaceBind gDNA Isolation and Purification

Allele Biotech’s SurfaceBind Genomic DNA Pu¬rification Kit is designed for fast, easy, and high-throughput gDNA isolation and purification for lysate obtained through the use of Allele-in-One Mouse Tail Direct Lysis Buffer. Based on our Solid Surface Revers¬ible Binding (SSRB) technology the SurfaceBind system utilizes a plastic tube with its surface coated with proprietary turbo-binders acting to selectively capture and efficiently bind DNA mol¬ecules from reaction mixtures. After lysis of cells, gDNA molecules will specifically interact with the turbo binders and bind to the surface of the tube in the presence of the binding buffer, while pro¬teins and other contaminants will remain in solu¬tion. The DNA can be eluted with as little as 10 microliters of water or buffer for the next application, allowing for a highly concentrated solution.

The entire process of recovery takes less than 10 minutes with only 1 centrifugation step, making it fast and easy. SSRB technology also provides for maxi¬mum DNA capture and release with limited sam¬ple input, without the DNA loss associated with membrane and bead-based technologies.

This is a newly developed product particularly for the Allele Biotech’s customers who use the All-in-One mouse tail genotyping kits: get purified genomic DNA using the same lysate you generated for a quick PCR. The yield and purity will enable direct applications to chip assays, sequencing, Southern blotting, etc.Next time you use Allele-in-One Mouse Tail Direct Lysis Buffer be sure to try our SurfaceBind gDNA Purification kit.

mWasabi-GFP Expression vector with IRES for co-expression. Cat # ABP-FP-WIRES10. email FP@allelebiotech.com for more FP IRES-containing plasmids.

10% off all mTFP1-expressing plasmids this week, check out the vectror you like at shop.allelebiotech.com

Tags: DNA purification, genomic DNA, microarray DNA, mouse tail genotyping, next generation sequencing, one step PCR, Southern Blot