The programmable and reliable hybridization of DNA strands has enabled the preparation of a wide variety of structures. This Review discusses how, in addition to these static assemblies, the process of displacing — and ultimately replacing — strands also makes possible the construction of dynamic systems such as logic gates or autonomous walkers.

/pdf/dynamic-dna-nanotechnology-using-strand-displacement-3n3nflfseh.pdf

Dynamic DNA nanotechnology using strand-displacement reactions

Engineered biological systems have been used to manipulate information, construct materials, process chemicals, produce energy, provide food, and help maintain or enhance human health and our environment. Unfortunately, our ability to quickly and reliably engineer biological systems that behave as expected remains quite limited. Foundational technologies that make routine the engineering of biology are needed. Vibrant, open research communities and strategic leadership are necessary to ensure that the development and application of biological technologies remains overwhelmingly constructive.

http://icampus.mit.edu/files/2011/11/iGem-Nature-Review-Foundns.pdf

Foundations for engineering biology

Keywords: Spin-Valve Sensors ; Cell Tracking Velocimetry ; On-A-Chip ; Polymerase-Chain-Reaction ; Total Analysis Systems ; Iron-Oxide Nanoparticles ; Field-Flow Fractionation ; Cross-Coupling Reactions ; Circulating Tumor-Cells ; Mode Magnetophoretic Microseparator Reference LMIS2-ARTICLE-2010-004doi:10.1021/cr9001929View record in Web of Science Record created on 2010-01-20, modified on 2016-08-08

Microfluidic applications of magnetic particles for biological analysis and catalysis.

Increasing our understanding of Earth’s biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet’s organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth’s eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project’s goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.

https://www.pnas.org/content/pnas/115/17/4325.full.pdf

Earth BioGenome Project: Sequencing life for the future of life.

This article reviews the application of electric circuit methods for the analysis of pressure-driven microfluidic networks with an emphasis on concentration- and flow-dependent systems. The application of circuit methods to microfluidics is based on the analogous behaviour of hydraulic and electric circuits with correlations of pressure to voltage, volumetric flow rate to current, and hydraulic to electric resistance. Circuit analysis enables rapid predictions of pressure-driven laminar flow in microchannels and is very useful for designing complex microfluidic networks in advance of fabrication. This article provides a comprehensive overview of the physics of pressure-driven laminar flow, the formal analogy between electric and hydraulic circuits, applications of circuit theory to microfluidic network-based devices, recent development and applications of concentration- and flow-dependent microfluidic networks, and promising future applications. The lab-on-a-chip (LOC) and microfluidics community will gain insightful ideas and practical design strategies for developing unique microfluidic network-based devices to address a broad range of biological, chemical, pharmaceutical, and other scientific and technical challenges.

Design of pressure-driven microfluidic networks using electric circuit analogy

1091 Recent work at the J. Craig Venter Institute (JCVI; Rockville, MD, USA) has resulted in relatively painless assembly of a 580-kb microbial genome from 101 pieces of starting material each 5–6 kb in length1. That this technique makes use of native recombination mechanisms in yeast suggests that it can be implemented in just about any laboratory that takes the time to learn the recipe. Combined with an existing widespread industry that regularly supplies synthetic DNA fragments of 5–10 kb in length, assembly in yeast will put the ability to build a wide range of DNA genomes in the hands of scientists, entrepreneurs and other interested parties worldwide. Single-step DNA assembly in yeast should prove useful as a tool to rapidly assemble metabolic pathways from many short DNA sequences. Shao and Zhao2 demonstrated precisely this sort of application in early 2009 by assembling functional metabolic pathways as these DNA synthesis companies face the commoditization of their product, the commercial sector that focuses on assembling and engineering genomes (or at least chromosomes) to create novel products for use in the medical, energy or industrial sectors is likely to become increasingly profitable. Demand for synthetic DNA will consequently spread around the globe as organizations of all sizes exploit biological technologies for many different aims. That some of those aims may be less appealing than others is already prompting calls to regulate synthesis in one way or another. But the global proliferation of demand is likely to limit the effectiveness of regulations implemented on the grounds of improving safety and security.

The changing economics of DNA synthesis

Thin polydimethylsiloxane (PDMS) films are frequently used in “lab on a chip” devices as flexible membranes. The common solvent used to dilute the PDMS for thin films is hexane, but hexane can swell the underlying PDMS substrate. A better solvent would be one that dissolves uncured PDMS but doesn't swell the underlying substrate. Here, we present protocols and spin curves for two alternatives to hexane dilution: longer spin times and dilution in tert-butyl alcohol. The thickness of the PDMS membranes under different spin speeds, spin times, and PDMS concentrations was measured using an optical profilometer. The use of tert-butyl alcohol to spin thin PDMS films does not swell the underlying PDMS substrate, and we have used these films to construct multilayer PDMS devices.

/pdf/thin-pdms-films-using-long-spin-times-or-tert-butyl-alcohol-qor90x1o3m.pdf

Thin PDMS Films Using Long Spin Times or Tert-Butyl Alcohol as a Solvent

THE ADVENT OF THE home molecular biology laboratory is not far off. While there is no Star Trek “Tricorder” in sight, the physical infrastructure of molecular biology is becoming more sophisticated and less expensive every day. Automated commercial instrumentation handles an increasing fraction of laboratory tasks that were once the sole province of doctoral level researchers, reducing labor costs and increasing productivity. This technology is gradually moving into the broader marketplace as laboratories upgrade to new equipment. Older, still very powerful instruments are finding their way into wide distribution, as any cursory tour of eBay will reveal.1 These factors are contributing to a proliferation that will soon put highly capable tools in the hands of both professionals and amateurs worldwide. There are obvious short term risks from increased access to DNA synthesis and sequencing technologies, and the general improvement of technologies used in measuring and manipulating molecules will soon enable a broad and distributed enhancement in the ability to alter biological systems. The resulting potential for mischief or mistake causes understandable concern—there are already public calls by scientists and politicians alike to restrict access to certain technologies, to regulate the direction of biological research, and to censor publication of some new techniques and data. It is questionable, however, whether such efforts will increase security or benefit the public good. Proscription of information and artifacts generally leads directly to a black market that is difficult to monitor and therefore difficult to police. A superior alternative is the deliberate creation of an open and expansive research community, which may be better able to respond to crises and better able to keep track of research whether in the university or in the garage.

The pace and proliferation of biological technologies.

Evidence indicates that, despite some critical successes, current conservation approaches are not slowing the overall rate of biodiversity loss. The field of synthetic biology, which is capable of altering natural genomes with extremely precise editing, might offer the potential to resolve some intractable conservation problems (e.g., invasive species or pathogens). However, it is our opinion that there has been insufficient engagement by the conservation community with practitioners of synthetic biology. We contend that rapid, large-scale engagement of these two communities is urgently needed to avoid unintended and deleterious ecological consequences. To this point we describe case studies where synthetic biology is currently being applied to conservation, and we highlight the benefits to conservation biologists from engaging with this emerging technology.

https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=2884&context=icwdm_usdanwrc

Is It Time for Synthetic Biodiversity Conservation

US biotech sector revenue is estimated to have grown on average >10% each year over the past decade—much faster than the rest of the economy. A more comprehensive assessment of biotech's economic contribution, however, will require improved data collection, classification and analysis.

Robert Carlson

Papers

The changing economics of DNA synthesis

Thin PDMS Films Using Long Spin Times or Tert-Butyl Alcohol as a Solvent

The pace and proliferation of biological technologies.

Is It Time for Synthetic Biodiversity Conservation

Estimating the biotech sector's contribution to the US economy.