What look like animated illustrations that could easily spring from a child’s imagination are actually newly unveiled artificial cells under a microscope.
Biophysicists at Germany’s Technical University of Munich along with an international team developed simple self-propelled biomachines in a quest to create cell models that display biomechanical functions.
The researchers say their work represents the first time a movable cytoskeleton membrane has been fabricated.
In April 2015, a paper by Chinese scientists about their attempts to edit the DNA of a human embryo rocked the scientific world and set off a furious debate. Leading scientists warned that altering the human germ line without studying the consequences could have horrific consequences. Geneticists with good intentions could mistakenly engineer changes in DNA that generate dangerous mutations and cause painful deaths. Scientists — and countries — with less noble intentions could again try to build a race of superhumans.
How One Scientist Is Helping Plants Survive California’s Worst Drought
Every living thing has its own natural responses to stress.
When critical nutrients are in short supply, our bodies, for example, find ways to maintain normal function until those nutrients are replenished. Plants do the same. In drought conditions, natural processes kick in to keep them alive until they can be watered again.
When faced with a water shortage, plants produce a stress hormone known as abscisic acid (ABA), which signals the plant to consume less water. ABA binds to a specific protein receptor in the plant, signaling stomata—or unique guard cells—to close and reduce the amount of water lost. This receptor is so important that its discovery by UC Riverside’s Sean Cutler, his team and others was listed as one of 2009′s breakthroughs of the year by Science magazine.
To help plants survive extreme drought conditions, some have tried spraying ABA directly on crops during water shortages. The move can improve crop yields, but ABA is expensive to produce and breaks down easily, even before a plant can absorb and use it.
How Genetically Engineered Gardens Could Replace Airport Security Checkpoints
Fascinating article by Jason Koebler on motherboard about genetically engineered plants that could replace security checkpoints. Dr. June Medford, a pioneering synthetic biologist, already engineered a plant that changes color when it detects TNT or certain pollutants. Her vision:
“The way we screen airports to get on a plane is, everyone goes through detector systems and it’s slow. What would make much more sense, my vision is that you would walk through a garden-like setting, with a webcam looking down on plants, seeing if they detected anything.”
The plants could also be hooked up to internet-connected systems. Medford is certain, that a mass production is feasible within 5 years.
Enzymes that don’t exist in nature have been made from genetic material that doesn’t exist in nature either, called XNA, or xeno nucleic acid.
It’s the first time this has been done and the results reinforce the possibility that life could evolve without DNA or RNA, the two self-replicating molecules considered indispensible for life on Earth.
“Our work with XNA shows that there’s no fundamental imperative for RNA and DNA to be prerequisites for life,” says Philipp Holliger of the Laboratory of Molecular Biology in Cambridge, UK, the same laboratory where the structure of DNA was discovered in 1953 by Francis Crick and James Watson.
Bacteriophages: Antibiotic Alternative or Just a Phase?
It is now clear that we are rapidly approaching a post-antibiotic
era, and the need for an alternative is more vital than ever. The CDC estimates
that approximately 2 million people are infected with antibiotic resistant
bacteria each year, and of that 23 000 of them die as a result of the infection
. Our antibiotic pipeline is drying
up and the development of new antibiotics is both slow and expensive, making
antibiotics unappealing investments for pharmaceutical companies. Although
alternatives to antibiotics are far from the market, the field is slowly expanding.
Amongst the alternatives, bacteriophages (phages) are a potential candidate for
both diagnostic and therapeutic medicine.
Quite simply, phages are viruses that infect bacteria. These
are the most abundant biological entity on the planet and are thought to
outnumber bacteria 10:1. Their sheer abundance has led to a vast diversity that
has yet to be exploited by modern medicine. This is in part due to a number of
problems with phages that haven’t made them ideal candidates for therapy. This
article seeks to look at some of the problems with phages, and what steps are
being taken to improve them for application in humans.
Rapid clearance from the host:
Delivery systems for phages have not been thoroughly assessed for systemic phage application. In other words we are still lacking a way of delivering a bacteriophage drug intravenously to ensure that phages have the maximal effect on the patient. Annoyingly, our immune systems are great at rapidly inactivating and removing them from our bodies , with animal studies showing that phage can be completely cleared within 24 hours . Early work carried out in germ-free mice in the 70s showed that phages are passively collected in the mononuclear phagocyte system (MPS), where they remain viable until inactivated by immune cells .
There have been two solutions developed so far to amend this problem . The first was developed in the late 90s by the National Institute of Health in the US, which involved the serial passage of phage through a living organism. It was hypothesised that some phage would have mutations in their coat proteins that would give them increased protection from the natural filtration systems in the body over wild type phage  and by selecting for these phage, you could gradually produce a population of long-circulating phage. When applied, these phage would have longer circulation times, and therefore a greater chance of colliding with their target bacteria. Animal studies have shown far better recovery of animals given long-circulating strains of virus over wild type, when presenting symptoms of otherwise fatal bacteraemia .
Figure 1. Diagram showing a few of the possible receptors for Salmonella sp. phage 
Additionally, to prevent degradation or inactivation of phages, polymers can be added to the coatings of phages . The polymer polyethylene glycol (PEG) has been shown to increase systematic circulation and decrease T-helper cell activation in response to phage. It is likely that a combination of these two methods may improve delivery strategies in the future of phage therapeutics.
Altering host range and preventing resistance:
Unlike antibiotics, phages have incredibly refined, narrow host-ranges. This property is in reality a double edged sword: in many cases, phages are only able to target a few strains of a single species, whereas antibiotics relentlessly target multiple branches of the bacterial phylogenetic tree. Antibiotic treatment can lead to disruption of the host’s own microbiota which can permit the colonisation of nastier and less cooperative microorganisms.
In contrast, phages can target their host whilst leaving the surrounding organisms in relative peace. When a patient presents symptoms of infection, the particular species or strain causing the infection would be unknown. Identifying the culprit before selecting the right phage would take time a patient may not have.
Receptors on the bacterial cell surface are what determine which phage are able to bind to the cell. A wide variety of receptors are used by phage, but many still remain a mystery. To curtail these issues and ensure that as many receptors can be targeted for a particular bacterium, phage cocktails are used . These are mixtures containing a number of different phage strains. In theory, the cocktail should be designed so that the phages together should be able to target all the known clinically relevant strains of a particular species of bacteria.
Creating phage cocktails from natural sources can be laborious , however viral DNA provides a platform for genetically engineering phages with desired properties. Improving phage cocktails with modified phages expressing structures that could target a wide variety of receptors on a bacterial cell could ensure that a cocktail could target the maximum number of strains, whilst reducing the selection pressure on a sole receptor. Resistance to the phage cocktail would then also be avoided.
Much of this work looks at genetically engineering phage tail fibres [7, 8]. These ‘spider-leg’ like components regulate the initial binding step between a phage and a target cell. It has been shown by Mahichi et al, 2009 and Ando et al, 2015 that switching tail fibres between phages with different host ranges can confer host-range specificity from one phage to another. Hopefully, modular engineering of phages will push phage technology forwards, offering new strategies for developing phages for therapeutic purposes.
Figure 2. Diagram showing how the modular shuffling of tail fibres between viral strains can confer host range of parental strain .
Preventing the release of cellular toxins
A major health risk of phage, is that like β-lactam antibiotics, they interfere with the bacterial cell wall integrity and ultimately lead to cell lysis. Lysing cells prevents further replication, but also releases all the cell’s content. This may include but not be limited to superantigens and lipopolysaccharides (LPS) . These toxins will trigger the inflammatory response, and in extreme cases cause organ failure and death.
Phages have a simple dual-lysis system consisting of a holin and endolysin. The holin is a pore-forming membrane protein that creates an exit from the cytoplasm for the endolysin. The endolysin is then able to attack the peptidoglycan of the bacterial cell wall, resulting in its rupture. To generate phage incapable of lysing a cell, the dual lysis system simply needs to be inactivated.
To restore killing power to the phage in the absense of the dual lysis system, a bacterial toxin needs to be incorporated into the phage genome. Hagens et al, 2004 has shown that by engineering the filamentous phage M13 to encode a non-native restriction enzyme, antimicrobial activity can be restored through the generation of double stranded breaks in chromosomal DNA. Upon infecting Psuedomonas aeruginosa with this phage, there was a 99% drop in viable cell counts over the time course . Other research has looked into other uses for the non-lytic killing of bacteria, including proteins that interfere with regulatory systems and other bacterial toxins.
Phage therapy has shown promise in recent years as being a good candidate for either working in synergy with or replacing antibiotics. The appalling lack of human based clinical trials haven’t helped to expose their potential for human use. Although this is the case, a significant amount of work has been done on improving phage therapy in preparation for further studies with human application. The past 15 years have seen an improved outcome for this technology as obstacles with phages are gradually manoeuvred by intelligent reengineering. With hindsight we have now acquired through our experiences with antibiotics, hopefully we will not make the same mistakes with phages as we have done with antibiotics.
1. CDC (2013) Antibiotic resistance threats. US Dep Heal Hum Serv 22–50
2. Lu TK, Koeris MS (2011) The next generation of bacteriophage therapy. Curr Opin Microbiol 14:524–531
3. Carlton RM (1999) Phage therapy: past history and future prospects. Arch Immunol Ther Exp (Warsz) 47:267–274
4. Merril CR, Biswas B, Carlton R, Jensen NC, Creed GJ, Zullo S, Adhya S (1996) Long-circulating bacteriophage as antibacterial agents. Proc Natl Acad Sci U S A 93:3188–3192
5. Chaturongakul S, Ounjai P (2014) Phage host interplay: examples from tailed phages and Gram-negative bacterial pathogens. Front Microbiol 5:1–8
6. Moradpour Z, Ghasemian A (2011) Modified phages: Novel antimicrobial agents to combat infectious diseases. Biotechnol Adv 29:732–738
7. Ando H, Lemire S, Pires DP, Lu TK (2015) Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing. Cell Syst 1:187–196
8. Mahichi F, Synnott AJ, Yamamichi K, Osada T, Tanji Y (2009) Site-specific recombination of T2 phage using IP008 long tail fiber genes provides a targeted method for expanding host range while retaining lytic activity. FEMS Microbiol Lett 295:211–217
9. Hagens S, Habel A, Ahsen U Von, Gabain A Von (2004) Therapy of Experimental Pseudomonas Infections with a Nonreplicating Genetically Modified Phage Therapy of Experimental Pseudomonas Infections with a Nonreplicating Genetically Modified Phage. Antimicrob Agents Chemother 46:3817–3822
Many technological advancements are created for current use, such as smart phones or virtual reality goggles, but there are an equal number of these advancements which are more likely to be used in the future (whether near or distant).
Royal College of Art graduate Julian Melchiorri has created a synthetic biological leaf which can actually absorb “water and carbon dioxide to produce oxygen just like a plant”, which Melchiorri suggests could be used by NASA for potential long-term space exploration.
“Plants don’t grow in zero gravity…NASA is researching different ways to produce oxygen for long-distance space journeys to let us live in space. This material could allow us to explore space much further than we can now.”
The leaves are made of chloroplasts which are placed in a silk protein matrix. Though not technically a real plant, the synthetic leaves do need light and water to survive. Most importantly, they can actually create oxygen. As Melchiorri states, the outcome of his experiments gave him “the first photosynthetic material that was working and breathing as a leaf does”.
Perhaps this technology could be used closer to home too! A large amount of these synthetic biological leaves could help produce oxygen in congested cities, but imagining them on spaceships or even different planets is pretty cool too!
An infographic exploration of animal longevity, from hare-today-gone-tomorrow to near-eternal-tortoises. What do you think makes some animals live longer than others, predators notwithstanding? Google that and let me know what you find, science detectives.
As for what it means for the future longevity of humans, check out these links:
Finally, a thought experiment: If our cells can become somewhat “immortal” in diseases like cancer, what’s to say that we can’t harness some of that biology and apply it to extending human lives without disease?
The new synthetic polymer material creates an instant scaffold, sort of like stacked gumballs, that allows new tissue to latch on and grow within the cavities formed between linked spheres of gel.
Conventionally, ointments and other hydrogel dressings have been used to fill in wounds to keep the areas moist and accelerate healing. But none of the materials used now provide a scaffold to allow new tissue to grow while the dressing itself degrades. As a result, the new tissue growth is relatively slow and fragile.
So bringing about an injectable biomaterial that promotes rapid regeneration of tissue has been a “holy grail” in the field of tissue engineering, said co-principal investigator Dino Di Carlo.
They envision the material being useful for a wide variety of wound application, including lacerations to large-area burns.
UC Berkeley researchers have also been developing new approaches to tissue engineering. Last March, their advancement in “herding cells” marked a new direction for smart bandages.
A lot of proposed synthetic biology applications can seem pretty out there, but some are really out there. NASA is currently advertising open postdoctoral positions in synthetic biology, with particular emphasis on food production in space. Engineered organisms have the potential to do lots of things that would be useful for space colonists, from producing food and fuel to treating wastewater. Because organisms replicate themselves, future astronauts would only have to bring some spores and seeds and empty bioreactors, the organisms would do the rest of the work. […]
Researchers have developed a new kind of synthetic creature, using the heart cells of a rat to make a robotic stingray that follows light.
While the rat-ray hybrid certainly sounds like a bit of a Frankenstein mish-mash, it’s serious research that could help pave the way for a greater understanding of how hearts pump blood around the body – in addition to leading to new kinds of more sophisticated synthetic robots.
Zachary Copfer self-coined the above photos as bacteriography. By growing genetically altered bacteria in a petri dish as his photographic film and then exposing parts to UV radiation as his light. Through this method he can literally grow the photograph. Copfer then refrigerates the bacteriograph, uses another blast of radiation treatment to kill any microbes, and then seals it with a layer of acrylic to fix and preserve the image.
Check out his work here and read more about bacteriography here and here.
Towards a Minimal Cell A Gallery of Giant Liposomes by Jorge Bernardino de la Serna University of Southern Denmark
One of the most ambitious endeavors of synthetic biology is creating “minimal cells” that fully recapitulate the functions of a natural cell—they capture energy, maintain ion gradients, store information, and mutate.
Although such technologies are still far on the horizon, researchers have made great progress in creating “semi-synthetic cells” that can mimic specific cellular tasks, such as protein production and synthesis of lipid membranes.
Many of these artificial cells reside inside liposomes, artificial vesicles each comprised of a lipid bilayer.
Technical Details Each micrograph shows a giant liposome ~20-50µm in diameter comprised of fats and proteins from the surface of the mammalian lung alveoli without any chemical treatment. The liposomes are directly isolated from a lung lavage.
Each micrograph was acquired at a different temperature or has varying composition of native fats and proteins.
Images obtained with a Laser Scanning Confocal inverted microscope with either conventional fluorescent excitation or two-photon excitation.
The DNA double helix that we’re all familiar with is a molecular ladder made of three key parts. The backbone of phosphates that tie everything together up and down, the sugar rings (“deoxyribose”) that serve as rungs, and the bases (A, C, G, T) that invisibly bond the two strands of the helix together, head to toe.
But that helix can be broken or mutated in nature, leading to mutations. And out of all the compounds in the world that could have evolved to carry our information, why just DNA and its cousin RNA? To answer that question, Vitor Pinheiro’s team created a completely new set of information molecules called XNA.
XNA replaces the deoxyribose sugar ring with other chemical rings like threose and cyclohexane. By evolving an enzyme that could read these funny bases, they were able to read DNA into XNA as well as the reverse. Plus it’s super-strong and resistant to breaking or cleaving.
Molecules like XNA could expand the information code for synthetic biology as well as help us answer the ultimate question about DNA: Why that, and not something else? Ed Yong has more great detail here.
When it comes to liquid fuels, the market is dominated by gasoline, diesel and jet fuel—all compounds derived from crude oil. These fuels are highly energy dense, cheap and (for now) abundant.
But for years, scientists have been working toward a secure and sustainable alternative to fossil fuels.
Ethanol, one of the earliest biofuel that’s largely derived from corn, hasn’t been able to compete with liquid fossil fuels. It isn’t particularly energy-dense and you need special modifications on your car to use ethanol or similar biofuels.
But researchers at UCLA are working on the next generation of advanced biofuels like Isobutanol.
“We try to produce branched-chain alcohols, that are a little larger, more energy dense and burn more like real gasoline,” explains UCLA researcher David Wernick.
Unlike ethanol, these biofuels are compatible with current fuel infrastructure, which means that you could use them with your current car.
By engineering bacteria (Bacillus subtilis), Wernick and his UCLA cohorts have enabled these tiny organisms to break down manure and other protein-rich waste like wastewater algae and byproducts from fermenting wine and beer.
Once the protein is broken down, the bacteria convert it into biofuel and ammonia, which can be used for fertilizer. The next step is scaling up the process and improving the amount of biofuel produced.
Learn more about the lab and their process of transforming poop and protein waste into fuel: