Category: bioengineering

Scientists Just Successfully Programmed Bacteria Using Synthetic Genes

Bacteria Growth

Nature is, perhaps, the most efficient builder there is. Since life began, examples of inorganic components working with organic material to make material composites abound. Now, scientists from Duke University have effectively harnessed nature’s construction abilities to develop 3D materials. In a study published in the journal Nature Biotechnology, the researchers prove it’s possible to program bacteria to build a device that functions as a pressure sensor.

Growing materials using cellular or bacterial process isn’t new, but the way the Duke researchers harnessed this incredible ability is quite novel. Previous attempts were limited to just 2D structures and depended heavily on external control to make bacteria grow. The new research, however, showed that its entirely possible to let nature do its thing.

“Nature is a master of fabricating structured materials consisting of living and non-living components,” researcher Lingchong You, a Paul Ruffin Scarborough Associate Professor of Engineering at Duke, said in a press release. “But it is extraordinarily difficult to program nature to create self-organized patterns. This work, however, is a proof-of-principle that it is not impossible.”

Basically, You’s team programmed a genetic circuit (or a biological package of instructions) into the bacteria’s DNA. This produced a protein that allowed its own expression in a positive feedback loop, causing it to grow into a dome-shaped bacterial colony until it ran out of food. The bacteria also released small molecules that worked as messengers, which were capable of diffusing into the environment. Once the bacterial colony reached its critical threshold, it began producing two more proteins — one stopped growth, while the other worked as a biological Velcro that could latch into inorganic materials.

Biological Devices

You’s team managed to turn their hybrid structure into a pressure sensor. They let the bacteria’s biological Velcro proteins latch onto gold nanoparticles that formed a shell as big as the average freckle. They then connected LED lights via copper wiring on identical dome structures, which were placed opposite each other, sandwiched between separate membranes. When pressed, a deformation increased the conductivity of the domes and lit the LEDs.

synthetic-bacteria-programming
Image credit: Will (Yangxiaolu) Cao, Kara Manke, Duke University

“In this experiment we’re primarily focused on the pressure sensors, but the number of directions this could be taken in is vast,” first author Will (Yangxiaolu) Cao explained. “We could use biologically responsive materials to create living circuits. Or if we could keep the bacteria alive, you could imagine making materials that could heal themselves and respond to environmental changes.” A number of other studies have shown that it’s quite possible to program cellular DNA, the most popular of these have allowed for the development of DNA computers and storage devices that use genetic material. You’s team, however, showed that it’s possible to develop 3D materials using an entirely natural process. At the very least, this could become a more efficient and cost-effective fabrication method. The size and shape of the bacterial dome can also be controlled by altering the properties of the porous membrane where they are grown.

“We’re demonstrating one way of fabricating a 3-D structure based entirely on the principal of self-organization,” researcher Stefan Zauscher said in the press release. “That 3-D structure is then used as a scaffold to generate a device with well-defined physical properties. This approach is inspired by nature, and because nature doesn’t do this on its own, we’ve manipulated nature to do it for us.”

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A New Gene Engineering Method Could Allow Us to Grow Organs for Transplants

A Chemical Approach

Making an organism’s genome — its entire genetic structure, from scratch — is already possible, but so far it’s only been successful in tiny bacterial genomes and in a portion of a yeast genome. Several researchers are working on synthesizing the entire human genome, but our current methods are limited because of their dependence on enzymes.

Now, a team of researchers from the University of Southampton in the U.K., working with colleagues from the University of Oxford and DNA synthesis firm ATDBio (based in Southampton and Oxford), propose a new method that could surpass these limitations.

In a study published in the journal Nature Chemistry, the researchers showcased a purely chemical technique for gene assembly. It uses an efficient and rapid-acting chemical reaction called click chemistry that puts together multiple modified DNA fragments into a gene — a process called click DNA ligation.

Image Credit: US Department of Energy

“Our approach is a significant breakthrough in gene synthesis,” University of Southampton Chemical Biology Professor and Lead Researcher Ali Tavassoli said in a press release. “Not only have we demonstrated assembly of a gene using click-chemistry, we have also shown that the resulting strand of DNA is fully functional in bacteria, despite the scars formed by joining fragments.”

Human Genome Synthesis

Although plans to synthesize the human genome from scratch have been received with mixed feelings and ethical considerations, its appeal comes from the possibilities it has to offer. According to GP-write, an international effort working on engineering large genomes, applications of DNA synthesis include growing transplantable human organs from scratch, engineering viral immunity and cancer resistance, and even allowing for more efficient and cost-effective drug development and testing.

Ethical quandaries notwithstanding, synthetic DNA is promising. With it, we could be looking at better ways to treat DNA-based diseases, or edit them out altogether — ultimately, extending human life or even potentially creating it from scratch, so to speak. “Genome synthesis will play an increasingly important role in scientific research,” Tavassoli explained. He believes their approach will make it more possible.

A shortcoming of current methods involves the extensive use of enzymes, which can’t be incorporated into certain sites that control the expression (i.e., the switching “on” or “off”) of genes. This so-called epigenetic information can be crucial to better understand biological processes, e.g., cancer, which couldn’t be cured too soon.

“The synthesis of chemically modified genes, which we have achieved by a radical new approach, will become ever more important as the effects of epigenetically modified DNA on gene expression become clear,” study co-author Tom Brown said in the press release.

Furthermore, the chemical method could also greatly accelerate the synthesis of larger DNA strands, producing larger quantities of a single gene. “We believe our purely chemical approach has the potential to significantly accelerate efforts in this vitally important area, and ultimately lead to a better understanding of biological systems,” Tavassoli added.

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Can the Human Eye Detect Single Photons?

Seeing Single Photons

Physicists already know that the rods at the back of the human eye are sensitive enough to light that they can be stimulated by a single photon. However, whether or not this sensitivity carries through the visual and cognitive systems of the brain and triggers perception is a different question entirely. Testing this query has demanded technology that was unavailable until recently. Now, physicists can produce pairs of photons using photon guns that work reliably and on demand.

The simple experiment to test the human ability to perceive a lone photon involves firing one into a human eye and determining if the subject observed it. Pairs of photons are important to the setup of this experiment because they ensure that the researchers can monitor when the photon gun was actually triggered each time. However, it’s not easy to get good results despite this simple structure, because human observers are unreliable and a statistically significant result requires a high number of trials.

Last month, researchers from the University of Vienna in Austria published findings from their own experiment, which was similar. Their version made itself unique by asking subjects to record the confidence of their observation. The subjects correctly observed single photons just over half of the time, at 51.6 percent. This led the team to conclude: “Humans can detect a single-photon incident on the cornea with a probability significantly above chance.”

Image Credit: Tinsley, et al./Nature Communications
Image Credit: Tinsley, et al./Nature Communications

However, researchers a the University of Illinois at Urbana-Champaign question have questioned that conclusion, saying that the data does not support it, and arguing that the experiment lacks sufficient statistical significance. The University of Illinois team has conducted its own research in human vision, so they have expertise in the field.

Our Powerful Senses

So, why does this matter? To begin with, the ability to detect such a minuscule amount of energy would define the physical limits of biology expressed in the workings of the human brain — a “machine” functioning in a wet environment plagued by constant noise. If our eyes could pick up on single photons, measuring around 10 to 19 Joules each, it would paint a compelling picture of the power of human biological senses.

Engineers and physicists aspire to achieve that kind of precision and sensitivity with their own machines in wet, warm environments, so modeling our machines after our own senses could allow us to reach higher goals. As we reveal our own sensory limits to ourselves, we can expect to see more impressive technological advances.

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Scientists Are Close to Creating a Fully Synthetic Genome

More Than Bread and Beer

Humans have found a friend in yeast. The single-celled eukaryotes are used by humans for a wide variety of applications, such as making alcoholic beverages and baking, among others. Scientists are heading toward a breakthrough in bioengineering that could create synthetic organisms that will help make new kinds of drugs and fuels.

An international team of researchers has been able to devise a way to synthesize a large part of yeast’s genetic code. Prior to this announcement, the team had been able to completely synthesize one of yeast’s 16 chromosomes. Now, the team has published a series of papers in the journal Science showing that they have been able to add another five chromosomes, thus bringing their total to six. They say they’re on track to finish the remaining ten chromosomes to form a completely synthetic genome by the end of this year.

Zappys Technology Solutions/Flickr

From Yeast to Human Genomes

While the scientific community remains leery of synthetic genome creation, many have united in praising this project’s work. In an article accompanying the research, Daniel Gibson, vice president of DNA technologies at Synthetic Genomics, stated, “This is really going to allow us to understand how to design cells from the bottom up that can be reprogrammed for many applications.”

Some of those “many applications” are what worry bioethicists, biologists, and environmentalists, among others. Todd Kuiken from North Carolina State University’s Genetic Engineering and Society Center compares the potential accidental or purposeful release of synthetic organisms to the introduction of invasive species. “You can think of it of like introducing an invasive species into a different environment. It will have some type of impact to the system.”

The yeast project is operating under conditions emphasizing safety as well as ethics. “This is a whole new era where we’re moving beyond little edits on single genes to being able to write whatever we want throughout the genome,” says George Church, a prominent Harvard University geneticist. “The goal is to be able to change it as radically as our understanding permits.”

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Scientists Are Making a Fabric of “Biological Tissues”

Tough as Bone

The development of super materials is changing our world —from carbon nanotubes to graphene. Scientists and engineers the world over are continually developing newer ways to apply these materials. Researchers from the University of New South Wales (UNSW) in Australia are adding another material to this list, and it’s one of a biological origin.

UNSW researchers, in a paper published in the journal Scientific Reports, describe how it’s possible to craft advanced functional materials using “nature’s tissue weaving algorithms.” Specifically, they have engineered a “smart fabric” that mimics the sophisticated and complex properties of a bone tissue called periosteum. This tissue covers all the bones in the human body, except for the joints, and gives bones added strength to bear high impact loads. This resilience and durability come from periosteum’s complex collagen arrangements, elastin, and other structural proteins found within it.

The team mapped periosteum’s complex tissue architecture and modeled these in 3D. These computer models were used to scale up and produce fabric prototypes using a state-of-the-art computer-controlled Jacquard loom. “We then tested the feasibility of rendering periosteum’s natural tissue weaves using computer-aided design software,” said lead researcher Knothe Tate.

“The result is a series of textile swatch prototypes that mimic periosteum’s smart stress-strain properties,” Tate added. “We have also demonstrated the feasibility of using this technique to test other fibers to produce a whole range of new textiles.”

Periosteum's tissue fabric layer. Credits: Melissa Knothe Tate
Periosteum’s tissue fabric layer. Photo Credit: Melissa Knothe Tate

 

Weaving the Future of Joints

There was some challenge in retrieving a periosteum-based fiber from its 3D computer model into the weaving loom to become an actual material. “The challenge with using collagen and elastin is their fibers, that are too small to fit into the loom. So we used elastic material that mimics elastin and silk that mimics collagen,” Tate said.

With proof of concept tests completed, the team is now getting ready to produce fabric prototypes of this periosteum fabric. Patents for this super material are already pending in Australia, the United States, and in Europe. The materials’ applications are expected to range from advancing functioning medical materials, to improving safety and transport technology.

This material could even be used with ‘smart’ compression bandages that respond to the movement of patients with deep-vein thrombosis or similar ailments. It could help to develop protective suits that harden under high impact for extreme sports athletes, soldiers, or even astronauts. It could also be used for making safer steel belt radial tires.

While these applications are all great, the application intended by the UNSW researchers is more biological. “Our longer term goal is to weave biological tissues – essentially human body parts – in the lab to replace and repair our failing joints that reflect the biology, architecture and mechanical properties of the periosteum,” lead author Joanna Ng explained. The team is currently working towards this next stage, hoping to unlock the potential of this super material.

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