Tag Archives: biotechnology

This bacterium shoots wires out of its body to power itself

This bacterium has a lot in common with power companies. Power companies use copper wires to channel electricity (and therefore, electrons), and this bacterium developed a mechanism to do something similar: in the absence of oxygen, it grows nanowires from its own body through which it pushes electrons to nearby rocks.

nanowire bacteria

This is how it obtains energy, as opposed to almost all organisms, which use internal processes to produce their energy.

This being said though, researchers have long known that bacteria can swap electrons with minerals, but the details and specific cases were quite rare. Even visualizing bacteria ripping out material from itself to create nanowires to power itself up. But now, one team of physicists and biologists has imaged Shewanella oneidensis, a soil bacteria growing nanowires live – they actually caught them in the act.

Interestingly enough, the bacteria’s wires are actually formed from the bacteria’s outer membranes.

“What the cell is doing is actually morphing a little bit,” Mohamed El-Naggar, a physicist at the University of Southern California who led the new study, tells Popular Science. “It’s extending its outer membrane in the shape of a long tube.”

Previously, due to the lack of directly observed information, scientists believed that the nanowires were made out of cili – hair-like appendages that are common on single-celled organisms.

“This solves a long-standing mystery about how exactly does the charge move on these structures,” El-Naggar says. Bacterial cell membranes have proteins embedded in them called cytochromes, which—ta-da!—are known to pass electrons to one another. Pili don’t have cytochromes.

But studying this type of bacteria is not just about observing one of nature’s most curious behaviors; one day, the research could lead to the mixing of silicon components to biological ones, creating “cyborg” circuits. After all, if the bacteria can use their own biological matter to send electricity to rocks, they could certainly do the same thing with silicone circuits. Engineers are also trying to incorporate nanowire-making bacteria into fuel cells.

However, there’s still plenty of work to do on both fields – and there is no guarantee that the result would be more efficient than today’s options. But it is efficient for bacteria – and that gives researchers hopes; at the very least, they could learn from this interaction.

 “You kind of end up getting the best of both worlds,” El-Naggar says.

Indeed, at the very least, you could create components that fix themselves and replicate themselves (from the bacteria) but still have the precise characteristics of human components

MIT cell circuit has its own memory

MIT engineers have created genetic circuits in bacterial cells that not only perform logic functions, but also remember the results, encode them in the cell’s DNA and pass it on for generations to come.

Biotechnology

cell circuit

The circuits, which are described in Nature Biotechnology could have a swarm of appplications, most notably long-term environmental sensors, efficient controls for biomanufacturing, or to program stem cells to differentiate into other cell types; but really, the sky’s the limit when it comes to this type of research.

“Almost all of the previous work in synthetic biology that we’re aware of has either focused on logic components or on memory modules that just encode memory. We think complex computation will involve combining both logic and memory, and that’s why we built this particular framework to do so,” says Timothy Lu, an MIT assistant professor of electrical engineering and computer science and biological engineering and senior author of the Nature Biotechnology paper.

Biologists working on this type of research often use interchangeable genetic parts to design circuits that perform a specific function, for example detecting a specific chemical element; the result of this would generate a specific response, such as production of green fluorescent protein (GFP). However, circuits could also be designated for any boolean (yes or no) function, as well as “and” and “or” functions – this means that it can use multiple inputs.

Lu and his colleagues designed a circuit that would be irreversibly altered by the original stimulus, creating a permanent memory of the event. The circuits they used (relying on previous research from 2009) depend on enzymes known as recombinases, which can cut out stretches of DNA, flip them, or insert them. Basically, sequential activation of the genes allows a count of these events.

But taking things even further, Lu designed the new circuits so that the memory function is built into the logic gate itself.

[in] the new circuits, the inputs stably alter regions of DNA that control GFP production. These regions, known as promoters, recruit the cellular proteins responsible for transcribing the GFP gene into messenger RNA, which then directs protein assembly.

The thing is, once the DNA terminator sequences are flipped, they can’t return to their original state — the memory of the logic gate activation is permanently stored in the DNA sequence; this may actually be a good thing: the information is transmitted forward up to 90 generations.

Uses… uses everywhere!

These kind of circuits are commonly used to create a type of circuit known as a digital-to-analog converter; they take digital inputs (like the presence of a chemical) and convert them into analog output. If they have two such circuits, they can produce four different analog output levels. That type of circuit could offer better control over the production of cells that generate biofuels, drugs or other useful compounds. If you use them as environmental sensors, you get very precise long-term memory.

“You could have different digital signals you wanted to sense, and just have one analog output that summarizes everything that was happening inside,” Lu says.

This could also be useful in stem cells, allowing researchers to track their development as they become other cells. Michael Jewett, an assistant professor of chemical and biological engineering at Northwestern University, says the new design represents a “huge advancement in DNA-encoded memory storage”:

“I anticipate that the innovations reported here will help to inspire larger synthetic biology efforts that push the limits of engineered biological systems,” says Jewett, who was not involved in the research.

The research was funded by the Office of Naval Research and the Defense Advanced Research Projects Agency (DARPA).

Via MIT

magnetic beads

Micro-beads based system could allow for instant laboratory analysis

magnetic beadsHarnessing the oscillation of magnetic microscopic beads, MIT scientists have carried out experiments which show that it’s possible to develop a tiny device capable of diagnosing biological samples instantly. Such a tiny lab would allow for fast, compact and versatile medical-testing.

Tiny magnetic balls, in the micrometer scale or a millionth of a meter, embedded with biomolecules such as antibodies, allow for proteins or even cells to bind to them. An oscillating magnetic field makes the individual beads resonate. Since the measured frequency is proportional to the mass of the bead+bio-sample, its size can also be determined. This would provide a way to detect exactly how much of a target biomolecule is present in a sample, and in the process also provide an instant information readout, compared to days typically required in a conventional laboratory. This could, for example, lead to tests for disease agents that would need just a tiny droplet of blood and could deliver results instantly, instead of requiring laboratory analysis.

Other chip-based biomedical tests are currently used today, but using this technique, coupled magnetic tracks on a microchip surface, the MIT researchers are confident that results can be provided a lot faster, and at a much smaller required biological sample size. However, the team has yet to prove their system with bio-samples, instead their system was proven to detect magnetic beads of different sizes, corresponding to those between particles that are bound to biological molecules and those that are not. The next obvious step after this proof of concept is repeating the procedure using biological samples, as well.

“It is very interesting how the researchers combine technologies that are well understood for applications in computing and data storage, and apply them to something completely different,” said R. Sooryakumar, a professor of physics at Ohio State University who was not involved in this research. He adds, “These magnetic devices are potentially valuable tools that could go well beyond how one may normally expect them to be used. The ramifications, for example in food safety and health care, such as pathogen or cancer detection, are indeed exciting.”

Findings were reported in the journal Lab on a Chip.

[source]

 

Medusoid

Synthetic jellyfish made from rat heart cells can swim like the real deal

A team led by researchers at the California Institute of Technology (Caltech) and Harvard University have built this remarkable display of modern bioengineering – a completely engineered jellyfish that blends both living and non-living parts, masterfully fitted together. Called the medusoid, this cyborg jellyfish was created using silicone and muscle cells from a rat’s heart, and surprisingly, it can move and behave exactly like its living, biological counterpart, as seen in the video above.

“Morphologically, we’ve built a jellyfish. Functionally, we’ve built a jellyfish. Genetically, this thing is a rat,” says Kit Parker, a biophysicist at Harvard University in Cambridge, Massachusetts, who led the work.

MedusoidJellyfish are believed to be the oldest multi-organ animals in the world, possibly existing on Earth for the past 500 million years. They can swim with rhythmical contractions of the bell (muscles) that propel it with the force of the water pushed from inside the bell, sort of like jet propelling does with air jets, the action creates an equal and opposite reaction. This is very similar to how the human heart functions at a principle level, making it a viable candidate to model and analyze for tissue engineering purposes.

And Parker along with colleagues from the lab, where they work on creating artificial models of human heart tissues for regenerating organs and testing drugs, didn’t waste one moment after recognizing the jellyfish’s potential.

“It occurred to me in 2007 that we might have failed to understand the fundamental laws of muscular pumps,” says Kevin Kit Parker, Tarr Family Professor of Bioengineering and Applied Physics at Harvard and a coauthor of the study. “I started looking at marine organisms that pump to survive. Then I saw a jellyfish at the New England Aquarium, and I immediately noted both similarities and differences between how the jellyfish pumps and the human heart. The similarities help reveal what you need to do to design a bio-inspired pump.”

The scientists enlisted Caltech biotechnology researcher Janna Nawroth  for their jellyfish-emulating cause.  Nawroth performed most of the experiments, including the mapping of every cell in the bodies of juvenile moon jellies (Aurelia aurita), indispensable to understanding the animal’s propulsion system.

The team looked at an array of possible materials they could use to fashion their synthetic jellyfish; eventually they settled for a silicone polymer that makes up the body of the Medusoid into a thin membrane that resembles a small jellyfish, with eight arm-like appendage. The scientists then grew and applied  a single layer of rat heart muscle on the patterned sheet of silicone.

The swimming behaviour of the Medusoid closely mimics that of the real thing

The swimming behaviour of the Medusoid closely mimics that of the real thing

The medusoid was inserted in an electrically conducting container of fluid and  placed between two electrodes. The current was oscillated  from zero volts to five volts, and the medusoid began to swim with synchronized contractions that mimic those of real jellyfish.

“I was surprised that with relatively few components—a silicone base and cells that we arranged—we were able to reproduce some pretty complex swimming and feeding behaviors that you see in biological jellyfish,” says John Dabiri, a bioengineer who studies biological propulsion at the California Institute of Technology (Caltech) in Pasadena. “I’m pleasantly surprised at how close we are getting to matching the natural biological performance, but also that we’re seeing ways in which we can probably improve on that natural performance. The process of evolution missed a lot of good solutions.”

Parker says his team is taking synthetic biology to a new level. “Usually when we talk about synthetic life forms, somebody will take a living cell and put new genes in. We built an animal. It’s not just about genes, but about morphology and function.”

The team’s next goal is to design a completely self-contained system that is able to sense and actuate on its own using internal signals, as human hearts do. “You’ve got a heart drug?” says Parker. “You let me put it on my jellyfish, and I’ll tell you if it can improve the pumping.”

The findings were reported in the journal Nature Biotechnology.

Protein re-assembly

New method allows visualizing of protein self-assembly – paves way for nanotech against diseases

Be it a bacteria or a fully complex being, say a human, all living, biological organisms undergo lighting fast protein structure reassembly in response to environmnetal stimuli. For instance,  receptor proteins in the sinus are stimulated by various odor molecules, basically telling the organism that there’s food nearby or it’s in the vicinity of danger (sulphur, methane, noxious fumes). By studying these mechanisms, scientists can better understand these process. A great leap further in the field was achieved by researchers at  the University of Montreal, who’ve managed to image how proteins self-assemble.

Protein re-assembly

Here shown are two different assembly stages (purple and red) of the protein ubiquitin and the fluorescent probe used to visualize these stage (tryptophan: see yellow). Credit: Peter Allen.

Understanding and mapping these process helps pave a broader, more plastic picture of how organisms function from a molecular assembly mechanism point of view, but maybe most importantly aids in pinpointing assembly errors. Both Alzheimer’s and Parkinson’s, two of the most devastating neural degenerative disease currently plaguing mankind, are caused by errors in molecular assembly. According to Professor Stephen Michnick, the research is expected to help bioengineers design new molecular machines for nanotechnology applications which might fight these diseases.

“In order to survive, all creatures, from bacteria to humans, monitor and transform their environments using small protein nanomachines made of thousands of atoms,” explained Michnick.

Proteins are composed of linear structural chains of amino acids, which have the capability to self assemble at the rate of thousandth of a second into a nanomachine by virtue of millions of years of evolution. Determining how these proteins self-assemble is a crucial goal in biotechnology at the moment, however, this extremely fast assembly velocity, as well as the numerous possible combinations, makes it extremely difficult.

“One of the main challenges for biochemists is to understand how these linear chains assemble into their correct structure given an astronomically large number of other possible forms,” Michnick said.

Researcher Dr. Alexis Vallée-Bélisle expressed similar sentiments.

“To understand how a protein goes from a linear chain to a unique assembled structure, we need to capture snapshots of its shape at each stage of assembly,” Vallée-Bélisle noted.

The researchers sought to overcome these setbacks, and successfully established a new method for visualizing the process of protein assembly by attaching fluorescent probes at all points on the linear protein chain.

“The problem is that each step exists for a fleetingly short time and no available technique enables us to obtain precise structural information on these states within such a small time frame. We developed a strategy to monitor protein assembly by integrating fluorescent probes throughout the linear protein chain so that we could detect the structure of each stage of protein assembly, step by step to its final structure.”

However, Vallée-Bélisle emphasized that the protein assembly process “is not the end of its journey,” as a protein can change, via chemical modifications or with age, to take on different forms and functions.

“Understanding how a protein goes from being one thing to becoming another is the first step towards understanding and designing protein nanomachines for biotechnologies such as medical and environmental diagnostic sensors, drug synthesis of delivery,” he added.

The research is funded by Le fond de recherché du Québec, Nature et Technologie and the Natural Sciences and Engineering Research Council of Canada. The findings were published in the journal Nature Structural & Molecular Biology.’

source: U Montreal.

These aren't gummy bears, but smart, self-healing hydrogels that might become extensively used for internal medical sutures. (c) Joshua Knoff, UC San Diego Jacobs School of Engineering.

Self-healing hydrogels open a new realm of bioengineering possibilities

Scientists at University of California have successfully managed to engineer a new kind of hydrogels, capable of self-healing, which can bind to each other in acidic conditions within seconds, forming a strong bond that allows for repeated streathching, similar to organic tissue, like the human skin.

These aren't gummy bears, but smart, self-healing hydrogels that might become extensively used for internal medical sutures. (c) Joshua Knoff, UC San Diego Jacobs School of Engineering.

These aren't gummy bears, but smart, self-healing hydrogels that might become extensively used for internal medical sutures. (c) Joshua Knoff, UC San Diego Jacobs School of Engineering.

Hydrogels are made out of a network of hydrophilic polymer chains and are highly absorbent. They also possess a degree of flexibility similar to human tissue, making them particularly useful in biomedical research. Their current applications range from cell culturing, to sustained-release drug delivery, to specific pH sensors, to contact lenses. However, when a hydrogel is cut or ruptured in some way, the material becomes permanently severed. A solution to this problem was sought, and eventually a team of University of California researchers, lead by Dr. Shyni Varghese, managed to overcome it after adding “dangling side chain” molecules to the primary structure of the hydrogel which under special conditions adhere to one another, just like fingers on a hand would grasp one another. This allowed the hydrogel structure to bind back after it was cut or suffered a shock.

Before they practically created the self-healing hydrogels, the reseachers first performed a computer simulation. They learned that for the hydrogel structure to be capable of self-healing, a certain side chain molecules length was needed. After dwelling deeper, they found that there was an optimal length which allowed for the strongest binding, and used that.

Here’s where it gets very interesting – the researchers put two pieces of the new self-healing hydrogels in a solution. When the solution was low pH (acidic), the two chunks merged together instantly, forming a strong bond. When the solution was turned to high pH, the chunks separated. According to the researchers, this would make them an ideal adhesive to heal stomach perforations or for controlled drug delivery to ulcers.

Other applications for the self-healing hydrogels include sealing leakages from containers containing corrosive acids, energy conservation and recycling. The University of California researchers now look to develop hydrogels that self-heal at different pH levels.

The findings were published in the journal Proceedings of the National Academy of Sciences.

Source via Physorg

Nottingham University synthetic biology

Cellular operating system set to revolutionize synthetic biology

Nottingham University synthetic biology

University of Nottingham researchers are currently involved in synthetic biology project, whose scope and prospects are so ambitious, that if successful it will completely revolutionize the field of science. Their aim – developing programmable cellular life which can work as an “operating system.”

Currently, scientists are looking studying how to make the E. coli bacteria programmable, and if their trials provide to be successful, then it means they’ll be able to easily and quickly configure other cells to perform various tasks. The E. coli bacteria has been used by British scientists from London’s Imperial College to create a bio-transistor. They can also make new life forms altogether, which currently do not exist in nature to fit a certain purpose. This particular aspect of synthetic biology has earned its practitioners a bad reputation among creationalists, who dub their work “playing God”.

Professor Natalio Krasnogor of the University’s School of Computer Science, who leads the Interdisciplinary Computing and Complex Systems Research Group, said: “We are looking at creating a cell’s equivalent to a computer operating system in such a way that a given group of cells could be seamlessly re-programmed to perform any function without needing to modifying its hardware.”

More importantly, if the researchers manage to pass the finish line with their project, the resulting in vivo biological cell-equivalent of a computer operating system will be able to generate a database of easy-to-implement cellular programs that would allow the entire field of synthetic biology to move exponentially faster toward discoveries rather than inch forward by trial and error, the rate at which is today. The Nottingham scientists are confident that this can be achievable in five years time.

Practical applications of this kind of bio-technology would be inestimable in their output value. Customized living cells could be tailored to clean up environmental disasters, scrub unwanted carbon from the air, pull pollutants from drinking water, attack pathogens inside the human body, protect food sources from agricultural pests, and so on. You get the picture, this is the kind of thing that can bring man into a golden age of science.

University of Nottingham press release via popular sci

 

Transistor gates created out of E. Coli bacteria – huge biocomputing leap forward!

Scientists at London’s Imperial College have successfully managed to create biological logic gates, indispensible for the production of electronical devices, simply our of bacteria and DNA. Though the research detailed in a recently published study in the journal Nature Communications was anything but simple, it provides an incredible advancement in the field of biotechnology.

“Logic gates are the fundamental building blocks in silicon circuitry that our entire digital age is based on,” said Richard Kitney co-author of the research project recently published in the journal nature Communications. “Without them, we could not process digital information. Now that we have demonstrated that we can replicate these parts using bacteria and DNA, we hope that our work could lead to a new generation of biological processors, whose applications in information processing could be as important as their electronic equivalents.”

Scientists have expermentally proven that their that their biological gates can replicate the process that is equivalent to an electronic transistor gate that can be switched on and off. In one experimental instance, the team made an AND gate from E Coli bacteria, a keyword most of us link with an impending pandemic (there are numerous variants of the strain, few are indeed dangerous), which had its DNA altered to perform a switch on/off action when interacting with a certain chemical.

While these are the most advanced biological gates created so far, Kitney and his team aknowledge that they’re still very far away from presenting to the world a reliable product. The future, however, seems to shine for bio technology. Such bio processing units could be streamed through one’s arteries and monitor various parameters through biosensors. In case of misbalanced parameters, the biodevice might then trigger medication to relieve the affected area. Cancer cells could be pounded imediately before they have the chance to spread. The potential applications are too many to ennounce here, albeit still very far away from reality.

The next step in the development are multiple gates in “more complex circuitry”, which could one day lead to building blocks for “microscopic biological computers,” like the ones listed in the potential applications above. One step at a time.

Existing Biotechnology Could Save Energy And Cut Carbon Dioxide By 100 Percent

carbon The carbon dioxide problem has been give much less attention than alternative fuel or biomass-derived energy production yet it is very important as chemical production creates billions of tons of carbon dioxide each year. But fear not – an analysis has concluded that use of existing biotechnology in the production of so-called bulk chemicals could reduce consumption of non-renewable energy and carbon emissions by 100 percent. B. G. Hermann and colleagues analyzed current and future technology routes leading to 15 bulk chemicals using industrial biotechnology, calculating their carbon emissions and fossil energy use. They have concluded that savings of about 500-1000 million tons per year are possible. The study, “Producing Bio-Based Bulk Chemicals Using Industrial Biotechnology Saves Energy and Combats Climate Change,” appeared in the Nov. 15 issue of ACS’ Environmental Science & Technology. Bulk chemicals like ethylene, butanol or acrylic acid are the basic raw materials used in the production of everything from plastics and fertilizers to electronic components and medicines. But even in these days bio-based bulk chemicals “offer clear savings in non-renewable energy use and green house gas emissions with current technology compared to conventional petrochemical production.”. Hopefully this study is not going to remain just a theory.