Stanford bioengineers develop tool for reprogramming genetic code

Stanford bioengineers have developed a new tool that allows them to preferentially activate or deactivate genes in living cells. VITSTUDIO/SHUTTERSTOCK

Biology relies upon the precise activation of specific genes to work properly. If that sequence gets out of whack, or one gene turns on only partially, the outcome can often lead to a disease.

Now, bioengineers at Stanford and other universities have developed a sort of programmable genetic code that allows them to preferentially activate or deactivate genes in living cells. The work is published in the current issue of Cell, and could help usher in a new generation of gene therapies.

The technique is an adaptation of CRISPR, itself a relatively new genetic tool that makes use of a natural defense mechanism that bacteria evolved over millions of years to slice up infectious virus DNA.

Standard CRISPR consists of two components: a short RNA that matches a particular spot in the genome, and a protein called Cas9 that snips the DNA in that location. For the purposes of gene editing, scientists can control where the protein snips the genome, insert a new gene into the cut and patch it back together.

Inserting new genetic code, however, is just one way to influence how the genome is expressed. Another involves telling the cell how much or how little to activate a particular gene, thus controlling how much protein a cell produces from that gene and altering its behavior.

It's this action that Lei Stanley Qi, an assistant professor of bioengineering and of chemical and systems biology at Stanford, and his colleagues aim to manipulate.

Influencing the genome
In the new work, the researchers describe how they have designed the CRISPR molecule to include a second piece of information on the RNA, instructing the molecule to either increase (upregulate) or decrease (downregulate) a target gene's activity, or turn it on/off entirely.

Additionally, they designed it so that it could affect two different genes at once. In a cell, the order or degree in which multiple genes are activated can produce different metabolic products.

"It's like driving a car. You control the wheel to control direction, and the engine to control the speed, and how you balance the two determines how the car moves," Qi said. "We can do the same thing in the cell by up- or downregulating genes, and produce different outcomes."

As a proof of principle, the scientists used the technique to take control of a yeast metabolic pathway, turning genes on and off in various orders to produce four different end products. They then tested it on two mammalian genes that are important in cell mobility, and were able to control the cell's direction and how fast it moved.

Future therapies
The ability to control genes is an attractive approach in designing genetic therapies for complex diseases that involve multiple genes, Qi said, and the new system may overcome several of the challenges of existing experimental therapies.

"Our technique allows us to directly control multiple specific genes and pathways in the genome without expressing new transgenes or uncontrolled behaviors, such as producing too much of a protein, or doing so in the wrong cells," Qi said. "We could eventually synthesize tens of thousands of RNA molecules to control the genome over a whole organism."

Next, Qi plans to test the technique in mice and refine the delivery method. Currently the scientists use a virus to insert the molecule into a cell, but he would eventually like to simply inject the molecules into an organism's blood.

"That is what is so exciting about working at Stanford, because the School of Medicine's immunology group is just around the corner, and working with them will help us address how to do this without triggering an immune response," said Qi, who is a member of the interdisciplinary Stanford ChEM-H institute. "I'm optimistic because everything about this system comes naturally from cells, and should be compatible with any organism."

Source: Stanford university

Source of most cases of invasive bladder cancer identified

Philip Beachy and his team found a single type of cell in mice that gives rise to invasive bladder cancers. Credit: Steve Fisch

A single type of cell in the lining of the bladder is responsible for most cases of invasive bladder cancer, according to researchers at the Stanford University School of Medicine.

Their study, conducted in mice, is the first to pinpoint the normal cell type that can give rise to invasive bladder cancers. It's also the first to show that most bladder cancers and their associated precancerous lesions arise from just one cell, and explains why many human bladder cancers recur after therapy.

"We've learned that, at an intermediate stage during cancer progression, a single cancer stem cell and its progeny can quickly and completely replace the entire bladder lining," said Philip Beachy, PhD, professor of biochemistry and of developmental biology. "All of these cells have already taken several steps along the path to becoming an aggressive tumor. Thus, even when invasive carcinomas are successfully removed through surgery, this corrupted lining remains in place and has a high probability of progression."

Although the cancer stem cells, and the precancerous lesions they form in the bladder lining, universally express an important signaling protein called sonic hedgehog, the cells of subsequent invasive cancers invariably do not -- a critical switch that appears vital for invasion and metastasis. This switch may explain certain confusing aspects of previous studies on the cellular origins of bladder cancer in humans. It also pinpoints a possible weak link in cancer progression that could be targeted by therapies.

"This could be a game changer in terms of therapeutic and diagnostic approaches," said Michael Hsieh, MD, PhD, assistant professor of urology and a co-author of the study. "Until now, it's not been clear whether bladder cancers arise as the result of cancerous mutations in many cells in the bladder lining as the result of ongoing exposure to toxins excreted in the urine, or if it's due instead to a defect in one cell or cell type. If we can better understand how bladder cancers begin and progress, we may be able to target the cancer stem cell, or to find molecular markers to enable earlier diagnosis and disease monitoring."

Beachy is the senior author of the study, which will be published online April 20 in Nature Cell Biology. He is the Ernest and Amelia Gallo Professor in the School of Medicine and a member of the Stanford Cancer Institute and the Stanford Institute for Stem Cell Biology and Regenerative Medicine. He is also a Howard Hughes Medical Institute investigator. Kunyoo Shin, PhD, an instructor at the institute, is the lead author.

Bladder cancer is the fourth most common cancer in men and the ninth most common in women. Smoking is a significant risk factor. There are two main types of the disease: one that invades the muscle around the bladder and metastasizes to other organs, and another that remains confined to the bladder lining. Unlike the more-treatable, noninvasive cancer -- which comprises about 70 percent of bladder cancers -- the invasive form is largely incurable. It is expensive and difficult to treat, and the high likelihood of recurrence requires ongoing monitoring after treatment.

In 2011, Shin and Beachy and their colleagues identified a cell type in the bladder that is capable of completely replacing the lining of the organ after infection or damage. The fact that it could give rise to multiple cell types (even forming small, multilayered, bladder-like spheres when cultured in vitro), and also self-renew, showed that it was a bladder stem cell. 

They found that the cell, which came from the basal layer of the bladder epithelium, used a protein called sonic hedgehog to "talk" to other cells in the bladder and stimulate proliferation and specialization into other cell types. (Beachy identified the first hedgehog protein in fruit flies in 1992; the hedgehog signaling pathway has since been shown to play a vital role in embryonic development and in many types of cancers.)

Many animal models of cancer rely on prior knowledge or hunches as to what genes or cell types are involved. Researchers may genetically alter an animal, or a certain cell type, to induce the overexpression of a gene known to be involved in tumorigenesis, for example, or block the expression of a gene that inhibits cancer development.

Although prior work suggested that basal cells may play a role in bladder cancer, the researchers chose an unbiased approach when developing their mouse model that more closely mimicked what happens in humans: They put a chemical compound called N-butyl-N-4-hydroxybutyl nitrosamine, or BBN, in the mice's drinking water and watched the animals over a period of months.

Nitrosamines are carcinogens found in cigarette smoke; BBN is a form of the chemical that is specifically activated in the bladder. After four months, many of the animals had developed precancerous lesions, or carcinomas in situ, in their bladders that very closely resemble those seen in human patients. By six months, all of the animals had developed invasive bladder cancers.

With their model in place, the researchers then conducted two main experiments in the mice: In the first experiment, they looked to see what would happen in animals exposed to BBN when the sonic-hedgehog-expressing cells were marked with a distinctive fluorescent color. In the second, they used genetic techniques to selectively kill those same cells in animals prior to exposure with BBN.

In the first case, they saw something startling: After just a few months of BBN exposure, nearly the entire lining of the bladder was labeled with the fluorescent green marker that indicated the cells had arisen from the sonic-hedgehog-expressing basal stem cells. When transplanted into other mice, those labeled cells were able to give rise to bladder cancers, but cells not expressing sonic hedgehog did not.

In the second case, no tumors grew in the animals in which the stem cells had been selectively killed -- although the bladder architecture became severely compromised in the absence of stem cells to regenerate cells lost during the normal course of bladder function.

"So now we have two lines of evidence indicating that the bladder stem cells are solely responsible for tumorigenesis," Shin said. "When we mark the bladder stem cells, the tumors are also marked. When we remove, or ablate, the stem cells, no tumors arise after BBN treatment."

Next the researchers tackled the question of whether bladder cancers arise as the result of genetic changes to one or more of these bladder stem cells. To do so, they used a genetically engineered mouse with cells that fluoresce green, but which can be triggered to randomly fluoresce one of three other colors: red, blue or yellow. Known as a "rainbow mouse," the animal allows researchers to more precisely determine the origin of groups of cells. If all cells in a tumor are red, for example, it is much more likely that they originated from a single cell.

"After four months of BBN treatment," Beachy said, "we'd most often see just one color dominating the entire epithelium. This clearly indicates that a single cell has taken over the lining of the entire bladder, elbowing out its neighbors in a way that's not been seen in other organs."

Further studies showed that, surprisingly, none of the cells in the most advanced, invasive carcinomas in the BNN-treated animals expressed sonic hedgehog -- despite the fact that only sonic-hedgehog-expressing cells are able to give rise to the earlier stages of bladder cancer. One obvious implication of the lack of sonic hedgehog expression in these cells is that the hedgehog pathway somehow inhibits steps required for tissue invasion or metastasis.

"We know that the hedgehog pathway is widely used throughout the animal kingdom to tightly regulate cellular and tissue differentiation," Hsieh said. "So its loss could make sense in this context because cancer is essentially a loss of normal regulation."

"One really important lesson from this study," Beachy said, "is the idea that, by the time you get to a full-blown tumor, the properties of the cells in that tumor may have changed quite significantly from the cell type that gives rise to the tumors. This can complicate understanding how human tumors arise, because even if you identify the tumor-propagating cells within a mature tumor, conclusions about the origins of a cancer based on properties of these cells may be inaccurate."

Source: Stanford University Medical Center

Special delivery: Hitchhiking microparticles deliver drugs directly

Disc-shaped microparticles use monocytes to get to their destination. Credit: Peter Allen illustration

Inflammation is a normal and often beneficial response to injury or infection. The swelling, heat and even pain are the body's attempts to protect its soft tissue, remove offending objects, substances or microbes and initiate healing. However, persistent inflammation is often indicative of more serious conditions and can lead to problems of its own, including impaired healing, loss of function or even tissue death.

"Many diseases result in inflammation," said Samir Mitragotri, professor of chemical engineering at UC Santa Barbara and director of the campus's Center for Bioengineering. Whether inflammation is a byproduct of the disease or the inflammation is the disease, it is a common indicator of a problem with the system. "If we could target the common denominator, whether the inflammation is coming from cancer or arthritis, we could deliver the drug there," said Mitragotri, who specializes in targeted drug delivery.

By taking advantage of natural body processes, researchers at UC Santa Barbara and MIT have developed a method of targeting inflamed tissues, creating a way to treat both the inflammation and its underlying cause.

"It's a cell-mediated approach to targeted drug delivery," said UCSB grad student researcher Aaron Anselmo, lead author of a study in the current issue of the Journal of Controlled Release.

Key to this technology is the utilization of monocytes, the type of white blood cell known for its ability to penetrate into deep sections of tissue. Under normal circumstances, the job of these monocytes is to circulate in the blood and respond to biochemical signals that indicate inflammation -- a sign of injury or infection. Once at the site, these monocytes transform into macrophages, cells that reside in the affected tissues to engulf and digest foreign material.

Working with the expertise of chemical engineering and materials science researchers at MIT, including graduate researcher Jonathan Gilbert and professors Robert Cohen and Michael Rubner, the UCSB researchers developed an approach based on "cellular backpacks" -- flat, disc-shaped polymeric particles that could, in the near future, hold therapeutic agents that can be released at the site of the inflammation. These polymeric discs are coated on one side with a single layer of an antibody that can bind to receptors on the monocyte's surface.

To prevent the cellular backpack from being engulfed and devoured by the very cell that is transporting it, the researchers chose a flexible particle that is nonspherical in shape, which, according to the study, has proved to be more durable and resistant to phagocytosis than a rigid spherical particle. The shape and flexibility gives the backpack the ability to bind strongly while resisting phagocytosis to hitchhike onto monocytes and reach the inflamed tissue.

In-vitro and in-vivo tests have proved that cellular backpacks are successful in attaching to and being transported by monocytes to target areas without impairing the monocytes' natural functions, said Anselmo. Further studies will include research into how much drug can be loaded into the cellular backpacks. Ideally, Anselmo said, the cellular backpacks loaded with drugs would be injected into the bloodstream, whereupon they would attach to these traveling monocytes and hitchhike to the target region. At the inflamed site, the particles would simultaneously degrade and release their drugs.

The development of effective cellular backpacks has broad potential, say the researchers.
"Basically the main benefit is that you can deliver the drug in a more effective dose," Mitragotri said. Take for example the case of chemotherapy, which often has a narrow therapeutic range: Too little and the treatment is not effective, too much and it can be lethal. 
Because chemo travels through the bloodstream and affects all the tissues it comes in contact with, dosages are restricted at least in part based on the deleterious effect it has on other, unafflicted organs and their functions. Not only can targeted therapy ensure other body systems remain unaffected, Mitragotri explained, but it could allow for higher doses of drug to the site, which could decrease treatment time.

Source: University of California - Santa Barbara

Scientists grow cartilage to reconstruct nose

Made from a probe of the nasal septum: white, glossy cartilage was made in the laboratory.
Credit: Department of Biomedicine at the University of Basel

Scientists at the University of Basel report first ever successful nose reconstruction surgery using cartilage grown in the laboratory. Cartilage cells were extracted from the patient's nasal septum, multiplied and expanded onto a collagen membrane. The so-called engineered cartilage was then shaped according to the defect and implanted. The results will be published in the current edition of the academic journal The Lancet.

A research team from the University of Basel in Switzerland has reported that nasal reconstruction using engineered cartilage is possible. They used a method called tissue engineering where cartilage is grown from patients' own cells. This new technique was applied on five patients, aged 76 to 88 years, with severe defects on their nose after skin cancer surgery. One year after the reconstruction, all five patients were satisfied with their ability to breathe as well as with the cosmetic appearance of their nose. None of them reported any side effects.

Cells from the nasal septum

The type of non-melanoma skin cancer investigated in this study is most common on the nose, specifically the alar wing of the nose, because of its cumulative exposure to sunlight. To remove the tumor completely, surgeons often have to cut away parts of cartilage as well. Usually, grafts for reconstruction are taken from the nasal septum, the ear or the ribs and used to functionally reconstruct the nose. However, this procedure is very invasive, painful and can, due to the additional surgery, lead to complications at the site of the excision.

Together with colleagues from the University Hospital, the research team from the Department of Biomedicine at the University of Basel has now developed an alternative approach using engineered cartilage tissue grown from cells of the patients' nasal septum. 

They extracted a small biopsy, isolated the cartilage cells (chondrocytes) and multiplied them. The expanded cells were seeded onto a collagen membrane and cultured for two additional weeks, generating cartilage 40 times the size of the original biopsy. The engineered grafts were then shaped according to the defect on the nostril and implanted.

New possibilities for facial reconstruction

According to Ivan Martin, Professor for Tissue Engineering at the Department of Biomedicine at the University and University Hospital of Basel, "The engineered cartilage had clinical results comparable to the current standard surgery. This new technique could help the body to accept the new tissue better and to improve the stability and functionality of the nostril. Our success is based on the long-standing, effective integration in Basel between our experimental group at the Department of Biomedicine and the surgical disciplines at the University Hospital. The method opens the way to using engineered cartilage for more challenging reconstructions in facial surgery such as the complete nose, eyelid or ear."

The same engineered grafts are currently being tested in a parallel study for articular cartilage repair in the knee. Despite the optimistic perspectives, the use of these procedures in the clinical practice is still rather distant. "We need rigorous assessment of efficacy on larger cohorts of patients and the development of business models and manufacturing paradigms that will guarantee cost-effectiveness," says Martin.

Source: University of Basel

First contracting human muscle grown in laboratory

This is a microscopic view of lab-grown human muscle bundles stained to show patterns made by basic muscle units and their associated proteins (red), which are a hallmark of human muscle.
Credit: Nenad Bursac, Duke University

In a laboratory first, Duke researchers have grown human skeletal muscle that contracts and responds just like native tissue to external stimuli such as electrical pulses, biochemical signals and pharmaceuticals.

The lab-grown tissue should soon allow researchers to test new drugs and study diseases in functioning human muscle outside of the human body.

The study was led by Nenad Bursac, associate professor of biomedical engineering at Duke University, and Lauran Madden, a postdoctoral researcher in Bursac's laboratory. It appears January 13 in the open-access journal eLife

"The beauty of this work is that it can serve as a test bed for clinical trials in a dish," said Bursac. "We are working to test drugs' efficacy and safety without jeopardizing a patient's health and also to reproduce the functional and biochemical signals of diseases -- especially rare ones and those that make taking muscle biopsies difficult."

Bursac and Madden started with a small sample of human cells that had already progressed beyond stem cells but hadn't yet become muscle tissue. They expanded these "myogenic precursors" by more than a 1000-fold, and then put them into a supportive, 3D scaffolding filled with a nourishing gel that allowed them to form aligned and functioning muscle fibers.

"We have a lot of experience making bioartifical muscles from animal cells in the laboratory, and it still took us a year of adjusting variables like cell and gel density and optimizing the culture matrix and media to make this work with human muscle cells," said Madden.

Madden subjected the new muscle to a barrage of tests to determine how closely it resembled native tissue inside a human body. She found that the muscles robustly contracted in response to electrical stimuli -- a first for human muscle grown in a laboratory. She also showed that the signaling pathways allowing nerves to activate the muscle were intact and functional.

To see if the muscle could be used as a proxy for medical tests, Bursac and Madden studied its response to a variety of drugs, including statins used to lower cholesterol and clenbuterol, a drug known to be used off-label as a performance enhancer for athletes.

The effects of the drugs matched those seen in human patients. The statins had a dose-dependent response, causing abnormal fat accumulation at high concentrations. Clenbuterol showed a narrow beneficial window for increased contraction. Both of these effects have been documented in humans. Clenbuterol does not harm muscle tissue in rodents at those doses, showing the lab-grown muscle was giving a truly human response.

"One of our goals is to use this method to provide personalized medicine to patients," said Bursac. "We can take a biopsy from each patient, grow many new muscles to use as test samples and experiment to see which drugs would work best for each person."

This goal may not be far away; Bursac is already working on a study with clinicians at Duke Medicine -- including Dwight Koeberl, associate professor of pediatrics -- to try to correlate efficacy of drugs in patients with the effects on lab-grown muscles. Bursac's group is also trying to grow contracting human muscles using induced pluripotent stem cells instead of biopsied cells.

"There are a some diseases, like Duchenne Muscular Dystrophy for example, that make taking muscle biopsies difficult," said Bursac. "If we could grow working, testable muscles from induced pluripotent stem cells, we could take one skin or blood sample and never have to bother the patient again."

Other investigators involved in this study include George Truskey, the R. Eugene and Susie E. Goodson Professor of Biomedical Engineering and senior associate dean for research for the Pratt School of Engineering, and William Krauss, professor of biomedical engineering, medicine and nursing at Duke University.

The research was supported by NIH Grants R01AR055226 and R01AR065873 from the National Institute of Arthritis and Musculoskeletal and Skin Disease and UH2TR000505 from the NIH Common Fund for the Microphysiological Systems Initiative.

Source: Duke University

Synthetic biology for space exploration

Microbial-based biomanufacturing could be transformative once explorers arrive at an extraterrestrial site. Credit: Image courtesy of Royal Academy Interface

Does synthetic biology hold the key to manned space exploration of the Moon and Mars? Berkeley Lab researchers have used synthetic biology to produce an inexpensive and reliable microbial-based alternative to the world's most effective anti-malaria drug, and to develop clean, green and sustainable alternatives to gasoline, diesel and jet fuels. In the future, synthetic biology could also be used to make manned space missions more practical.

"Not only does synthetic biology promise to make the travel to extraterrestrial locations more practical and bearable, it could also be transformative once explorers arrive at their destination," says Adam Arkin, director of Berkeley Lab's Physical Biosciences Division (PBD) and a leading authority on synthetic and systems biology.

"During flight, the ability to augment fuel and other energy needs, to provide small amounts of needed materials, plus renewable, nutritional and taste-engineered food, and drugs-on-demand can save costs and increase astronaut health and welfare," Arkin says. "At an extraterrestrial base, synthetic biology could make even more effective use of the catalytic activities of diverse organisms."

Arkin is the senior author of a paper in the Journal of the Royal Society Interface that reports on a techno-economic analysis demonstrating "the significant utility of deploying non-traditional biological techniques to harness available volatiles and waste resources on manned long-duration space missions." The paper is titled "Towards Synthetic Biological Approaches to Resource Utilization on Space Missions." The lead and corresponding author is Amor Menezes, a postdoctoral scholar in Arkin's research group at the University of California (UC) Berkeley. Other co-authors are John Cumbers and John Hogan with the NASA Ames Research Center.

One of the biggest challenges to manned space missions is the expense. The NASA rule-of-thumb is that every unit mass of payload launched requires the support of an additional 99 units of mass, with "support" encompassing everything from fuel to oxygen to food and medicine for the astronauts, etc. Most of the current technologies now deployed or under development for providing this support are abiotic, meaning non-biological. Arkin, Menezes and their collaborators have shown that providing this support with technologies based on existing biological processes is a more than viable alternative.

"Because synthetic biology allows us to engineer biological processes to our advantage, we found in our analysis that technologies, when using common space metrics such as mass, power and volume, have the potential to provide substantial cost savings, especially in mass," Menezes says.

In their study, the authors looked at four target areas: fuel generation, food production, biopolymer synthesis, and pharmaceutical manufacture. They showed that for a 916 day manned mission to Mars, the use of microbial biomanufacturing capabilities could reduce the mass of fuel manufacturing by 56-percent, the mass of food-shipments by 38-percent, and the shipped mass to 3D-print a habitat for six by a whopping 85-percent. In addition, microbes could also completely replenish expired or irradiated stocks of pharmaceuticals, which would provide independence from unmanned re-supply spacecraft that take up to 210 days to arrive.

"Space has always provided a wonderful test of whether technology can meet strict engineering standards for both effect and safety," Arkin says. "NASA has worked decades to ensure that the specifications that new technologies must meet are rigorous and realistic, which allowed us to perform up-front techno-economic analysis."

The big advantage biological manufacturing holds over abiotic manufacturing is the remarkable ability of natural and engineered microbes to transform very simple starting substrates, such as carbon dioxide, water biomass or minerals, into materials that astronauts on long-term missions will need. This capability should prove especially useful for future extraterrestrial settlements.

"The mineral and carbon composition of other celestial bodies is different from the bulk of Earth, but the earth is diverse with many extreme environments that have some relationship to those that might be found at possible bases on the Moon or Mars," Arkin says. "Microbes could be used to greatly augment the materials available at a landing site, enable the biomanufacturing of food and pharmaceuticals, and possibly even modify and enrich local soils for agriculture in controlled environments."

The authors acknowledge that much of their analysis is speculative and that their calculations show a number of significant challenges to making biomanufacturing a feasible augmentation and replacement for abiotic technologies. However, they argue that the investment to overcome these barriers offers dramatic potential payoff for future space programs.

"We've got a long way to go since experimental proof-of-concept work in synthetic biology for space applications is just beginning, but long-duration manned missions are also a ways off," says Menezes. "Abiotic technologies were developed for many, many decades before they were successfully utilized in space, so of course biological technologies have some catching-up to do. However, this catching-up may not be that much, and in some cases, the biological technologies may already be superior to their abiotic counterparts."

This research was supported by the National Aeronautics and Space Administration (NASA) and the University of California, Santa Cruz.

Source: DOE/Lawrence Berkeley National Laboratory

Revolutionizing genome engineering

Streptococcus pyogenes is one of the bacteria in which the HZI scientists have studied the CRISPR-Cas system. Credit: © HZI / M. Rohde

Genome engineering with the RNA-guided CRISPR-Cas9 system in animals and plants is changing biology. It is easier to use and more efficient than other genetic engineering tools, thus it is already being applied in laboratories all over the world just a few years after its discovery. This rapid adoption and the history of the system are the core topics of a review published in the journal Science. The review was written by the discoverers of the system Prof. Emmanuelle Charpentier, who works at the Helmholtz Centre for Infection Research (HZI) and is also affiliated to the Hannover Medical School and Umeå University, and Prof. Jennifer Doudna from the University of California, Berkeley, USA.

Many diseases result from a change of an individual's DNA -- the letter code that genes consist of. The defined order of the letters within a gene usually codes for a protein. Proteins are the workforce of our body and responsible for almost all processes needed to keep us running. When a gene is altered, its protein product may lose its normal function and disorders can result. "Making site-specific changes to the genome therefore is an interesting approach to preventing or treating those diseases," says Prof Emmanuelle Charpentier, head of the HZI research department "Regulation in Infection Biology." Due to this, ever since the discovery of the DNA structure, researchers have been looking for a way to alternate the genetic code.

First techniques like zinc finger nucleases and synthetic nucleases called TALENs were a starting point but turned out to be expensive and difficult to handle for a beginner. "The existing technologies are dependent on proteins as address labels and customizing new proteins for any new change to introduce in the DNA is a cumbersome process," says Charpentier. In 2012, while working at Umeå University, she described what is now revolutionising genetic engineering: the CRISPR-Cas9 system.

It is based on the immune system of bacteria and archaea but is also of value in the laboratory. CRISPR is short for Clustered Regularly Interspaced Palindromic Repeats, whereas Cas simply stands for the CRISPR-associated protein. "Initially we identified a novel RNA, namely tracrRNA, associated to the CRISPR-Cas9 system, which we published in 2011 in Nature. We were excited when Krzysztof Chylinski from my laboratory subsequently confirmed a long term thinking: Cas9 is an enzyme that functions with two RNAs," says Charpentier.

Together the system has the ability to detect specific sequences of letters within the genetic code and to cut DNA at a specific point. In this process the Cas9 protein functions as the scissors and an RNA snippet as the address label ensuring that the cut happens in the right place. In collaboration with Martin Jinek and Jennifer Doudna, the system could be simplified to use it as a universal technology. Now the user would just have to replace the sequence of this RNA to target virtually any sequence in the genome.

After describing the general abilities of CRISPR-Cas9 in 2012 it was shown in early 2013 that it works as efficiently in human cells as it does in bacteria. Ever since, there has been a real hype around the topic and researchers from all over the world have suggested new areas in which the new tool can be used. The possible applications extend from developing new therapies for genetic disorders caused by gene mutations to changing the pace and course of agricultural research in the future all the way to a possible new method for fighting the AIDS virus HIV.

"The CRISPR-Cas9 system has already breached boundaries and made genetic engineering much more versatile, efficient and easy," Charpentier says. "There really does not seem to be a limit in the applications."

Source: Helmholtz Centre for Infection Research

Squid supplies blueprint for printable thermoplastics

This is a whimsical image of a squid creating 3-D printed devices. Credit: Adriás Bago

Squid, what is it good for? You can eat it and you can make ink or dye from it, and now a Penn State team of researchers is using it to make a thermoplastic that can be used in 3-D printing.

"Most of the companies looking into this type of material have focused on synthetic plastics," said Melik C. Demirel, professor of engineering science and mechanics. "Synthetic plastics are not rapidly deployable for field applications, and more importantly, they are not eco-friendly."

Demirel and his team looked at the protein complex that exists in the squid ring teeth (SRT). The naturally made material is a thermoplastic, but obtaining it requires a large amount of effort and many squid.

"We have the genetic sequence for six squid collected around the world, but we started with the European common squid," said Demirel, who with his team collected the cephalopods.

The researchers looked at the genetic sequence for the protein complex molecule and tried synthesizing a variety of proteins from the complex. Some were not thermoplastics, but others show stable thermal response, for example, the smallest known molecular weight SRT protein was a thermoplastic. The results of their work were published in today's (Dec. 17) issue of Advanced Functional Materials and illustrates the cover.

Most plastics are currently manufactured from fossil fuel sources like crude oil. Some high-end plastics are made from synthetic oils. Thermoplastics are polymer materials that can melt, be formed and then solidify as the same material without degrading materials properties.

This particular thermoplastic can be fabricated either as a thermoplastic, heated and extruded or molded, or the plastic can be dissolved in a simple solvent like acetic acid and used in film casting. The material can also be used in 3D printing machines as the source material to create complicated geometric structures.

To manufacture this small, synthetic SRT molecule, the researchers used recombinant techniques. They inserted SRT protein genes into E. coli, so that this common, harmless bacteria could produce the plastic molecules as part of their normal activity and the thermoplastic was then removed from the media where the E. coli lived. Wayne Curtis, professor of chemical engineering and Demirel collaborating on this project together with their students worked on this aspect of the project.

"The next generation of materials will be governed by molecular composition -- sequence, structure and properties," said Demirel.

The thermoplastic the researchers created is semi-crystalline and can be rigid or soft. It has a very high tensile strength and is a wet adhesive; it will stick to things even if it is wet.

This thermoplastic protein has a variety of tunable properties, which can be adjusted to individual requirements of manufacturing. Because it is a protein, it can be used for medical or cosmetic applications.

"Direct extraction or recombinant expression of protein based thermoplastics opens up new avenues for materials fabrication and synthesis, which will eventually be competitive with the high-end synthetic oil based plastics," the researchers report.

Source: Penn State

Visualizing DNA double-strand break process for the first time

The enzyme I-DmoI (purple) is specifically associated to the double strand of DNA (yellow and green). Credit: CNIO

Scientists from the Spanish National Cancer Research Centre (CNIO), led by Guillermo Montoya, have developed a method for producing biological crystals that has allowed scientists to observe --for the first time-- DNA double chain breaks. They have also developed a computer simulation that makes this process, which lasts in the order of millionths of a second, visible to the human eye. The study is published today by the journal Nature Structural & Molecular Biology.

"We knew that enzymes, or proteins, endonucleases, are responsible for these double strand breaks, but we didn't know exactly how it worked until now," said Montoya. "In our study, we describe in detail the dynamics of this basic biological reaction mediated by the enzyme I-Dmol. Our observations can be extrapolated to many other families of endonucleases that behave identically."

DNA breaks occur in several natural processes that are vital for life: mutagenesis, synthesis, recombination and repair. In the molecular biology field, they can also be generated synthetically. Once the exact mechanism that produces these breaks has been uncovered, this knowledge can be used in multiple biotechnological applications: from the correction of mutations to treat rare and genetic diseases, to the development of genetically modified organisms.

Slow-motion reaction

Enzymes are highly specialised dynamic systems. Their nicking function could be compared, said Montoya, to a specially designed fabric-cutting machine that "it would only make a cut when a piece of clothing with a specific combination of colours passed under the blade."

In this case, researchers concentrated on observing the conformational changes that occurred in the I-Dmol active site; the area that contains the amino acids that act as a blade and produces DNA breaks.

By altering the temperature and pH balance, the CNIO team has managed to delay a chemical reaction that typically occurs in microseconds by up to ten days. Under those conditions, they have created a slow-motion film of the whole process.

"By introducing a magnesium cation we were able to trigger the enzyme reaction and subsequently to produce biological crystals and freeze them at -200ºC," said Montoya. "In that way, we were able to collect up to 185 crystal structures that represent all of the conformational changes taking place at each step of the reaction."

Finally, using computational analysis, the researchers illustrated the seven intermediate stages of the DNA chain separation process. "It is very exciting, because the elucidation of this mechanism will give us the information we need to redesign these enzymes and provide precise molecular scissors, which are essential tools for modifying the genome," he concluded.

Source: Centro Nacional de Investigaciones Oncologicas (CNIO)

Controlling genes with your thoughts

Thoughts control a near-infrared LED, which starts the production of a molecule in a reaction chamber. Credit: Martin Fussenegger et al., Copyright ETH Zurich

It sounds like something from the scene in Star Wars where Master Yoda instructs the young Luke Skywalker to use the force to release his stricken X-Wing from the swamp: Marc Folcher and other researchers from the group led by Martin Fussenegger, Professor of Biotechnology and Bioengineering at the Department of Biosystems (D-BSSE) in Basel, have developed a novel gene regulation method that enables thought-specific brainwaves to control the conversion of genes into proteins -- called gene expression in technical terms.

"For the first time, we have been able to tap into human brainwaves, transfer them wirelessly to a gene network and regulate the expression of a gene depending on the type of thought. Being able to control gene expression via the power of thought is a dream that we've been chasing for over a decade," says Fussenegger.

A source of inspiration for the new thought-controlled gene regulation system was the game Mindflex, where the player wears a special headset with a sensor on the forehead that records brainwaves. The registered electroencephalogram (EEG) is then transferred into the playing environment. The EEG controls a fan that enables a small ball to be thought-guided through an obstacle course.

Wireless Transmission to Implant

The system, which the Basel-based bioengineers recently presented in the journal Nature Communications, also makes use of an EEG headset. The recorded brainwaves are analysed and wirelessly transmitted via Bluetooth to a controller, which in turn controls a field generator that generates an electromagnetic field; this supplies an implant with an induction current.

A light then literally goes on in the implant: an integrated LED lamp that emits light in the near-infrared range turns on and illuminates a culture chamber containing genetically modified cells. When the near-infrared light illuminates the cells, they start to produce the desired protein.

Thoughts Control Protein Quantity

The implant was initially tested in cell cultures and mice, and controlled by the thoughts of various test subjects. The researchers used SEAP for the tests, an easy-to-detect human model protein which diffuses from the culture chamber of the implant into the mouse's bloodstream.

To regulate the quantity of released protein, the test subjects were categorised according to three states of mind: bio-feedback, meditation and concentration. Test subjects who played Minecraft on the computer, i.e. who were concentrating, induced average SEAP values in the bloodstream of the mice. When completely relaxed (meditation), the researchers recorded very high SEAP values in the test animals. For bio-feedback, the test subjects observed the LED light of the implant in the body of the mouse and were able to consciously switch the LED light on or off via the visual feedback. This in turn was reflected by the varying amounts of SEAP in the bloodstream of the mice.

New Light-sensitive Gene Construct

"Controlling genes in this way is completely new and is unique in its simplicity," explains Fussenegger. The light-sensitive optogenetic module that reacts to near-infrared light is a particular advancement. The light shines on a modified light-sensitive protein within the gene-modified cells and triggers an artificial signal cascade, resulting in the production of SEAP. Near-infrared light was used because it is generally not harmful to human cells, can penetrate deep into the tissue and enables the function of the implant to be visually tracked.

The system functions efficiently and effectively in the human-cell culture and human-mouse system. Fussenegger hopes that a thought-controlled implant could one day help to combat neurological diseases, such as chronic headaches, back pain and epilepsy, by detecting specific brainwaves at an early stage and triggering and controlling the creation of certain agents in the implant at exactly the right time.

Source: ETH Zurich

Making lab-grown tissues stronger

Connective tissues like cartilage are made of cross-linked bundles of collagen fibers. UC Davis biomedical engineers have discovered that reducing oxygen or adding an enzyme called LOX can make these bundles stronger. The technique can be used to strengthen both natural cartilage kept in the lab for transplant, and artificial cartilage grown in culture. Credit: Eleftherios Makris and Kyriacos Athanasiou, UC Davis

Lab-grown tissues could one day provide new treatments for injuries and damage to the joints, including articular cartilage, tendons and ligaments.

Cartilage, for example, is a hard material that caps the ends of bones and allows joints to work smoothly. UC Davis biomedical engineers, exploring ways to toughen up engineered cartilage and keep natural tissues strong outside the body, report new developments this week in the journal Proceedings of the National Academy of Sciences.

"The problem with engineered tissue is that the mechanical properties are far from those of native tissue," said Eleftherios Makris, a postdoctoral researcher at the UC Davis Department of Biomedical Engineering and first author on the paper. Makris is working under the supervision of Professor Kyriacos A. Athanasiou, a distinguished professor of biomedical engineering and orthopedic surgery, and chair of the Department of Biomedical Engineering.

While engineered cartilage has yet to be tested or approved for use in humans, a current method for treating serious joint problems is with transplants of native cartilage. But it is well known that this method is not sufficient as a long-term clinical solution, Makris said.
The major component of cartilage is a protein called collagen, which also provides strength and flexibility to the majority of our tissues, including ligaments, tendons, skin and bones. Collagen is produced by the cells and made up of long fibers that can be cross-linked together.

Engineering new cartilage

Researchers in the Athanasiou group have been maintaining native cartilage in the lab and culturing cartilage cells, or chondrocytes, to produce engineered cartilage.

"In engineered tissues the cells produce initially an immature matrix, and the maturation process makes it tougher," Makris said.

Knee joints are normally low in oxygen, so the researchers looked at the effect of depriving native or engineered cartilage of oxygen. In both cases, low oxygen led to more cross-linking and stronger material. They also found that an enzyme called lysyl oxidase, which is triggered by low oxygen levels, promoted cross-linking and made the material stronger.

"The ramifications of the work presented in the PNAS paper are tremendous with respect to tissue grafts used in surgery, as well as new tissues fabricated using the principles of tissue engineering," Athanasiou said. Grafts such as cadaveric cartilage, tendons or ligaments -- notorious for losing their mechanical characteristics in storage -- can now be treated with the processes developed at UC Davis to make them stronger and fully functional, he said.
Athanasiou also envisions that many tissue engineering methods will now be altered to take advantage of this strengthening technique.

Source: University of California - Davis

First step: From human cells to tissue-engineered esophagus

This images shows a tissue-engineered esophagus. Credit: The Saban Research Institute

In a first step toward future human therapies, researchers at The Saban Research Institute of Children's Hospital Los Angeles have shown that esophageal tissue can be grown in vivo from both human and mouse cells. The study has been published online in the journal Tissue Engineering, 
Part A.

The tissue-engineered esophagus formed on a relatively simple biodegradable scaffold after the researchers transplanted mouse and human organ-specific stem/progenitor cells into a murine model, according to principal investigator Tracy C. Grikscheit, MD, of the Developmental Biology and Regenerative Medicine program of The Saban Research Institute and pediatric surgeon at Children's Hospital Los Angeles.

Progenitor cells have the ability to differentiate into specific types of cell, and can migrate to the tissue where they are needed. Their potential to differentiate depends on their type of "parent" stem cell and also on their niche. The tissue-engineering technique discovered by the CHLA researchers required only a simple polymer to deliver the cells, and multiple cellular groupings show the ability to generate a replacement organ with all cell layers and functions.

"We found that multiple combinations of cell populations allowed subsequent formation of engineered tissue. Different progenitor cells can find the right 'partner' cell in order to grow into specific esophageal cell types -- such as epithelium, muscle or nerve cells -- and without the need for exogenous growth factors. This means that successful tissue engineering of the esophagus is simpler than we previously thought," said Grikscheit.

She added that the study shows promise for one day applying the process in children who have been born with missing portions of the organ, which carries food, liquids and saliva from the mouth to the stomach. The process might also be used in patients who have had esophageal cancer -- the fastest growing type of cancer in the U.S. -- or otherwise damaged tissue, for example from accidentally swallowing caustic substances.

"We have demonstrated that a simple and versatile, biodegradable polymer is sufficient for the growth of tissue-engineered esophagus from human cells," added Grikscheit. "This not only serves as a potential source of tissue, but also a source of knowledge, as there are no other robust models available for studying esophageal stem cell dynamics. Understanding how these cells might behave in response to injury and how various donor cell types relate could expand the pool of potential donor cells for engineered tissue."

Additional contributors include first author Ryan G. Spurrier, MD, Allison L. Speer, MD, Xiaogang Hou, PhD and Wael N. El-Nachef, MD, of The Saban Research Institute of Children's Hospital Los Angeles. The study was supported by grants from the California Institute for Regenerative Medicine.

Source: Children's Hospital Los Angeles Saban Research Institute

Genetically identical ants help unlock the secrets of larval fate

Cerapachys biroi ants, native to Asia and introduced globally on tropical and subtropical islands, have no queens and have minimal genetic variation, making them ideal for research on social behavior. Credit: Image courtesy of Rockefeller University

A young animal's genes are not the only genes that determine its fate. The genetic identity of its caretakers matters too. Researchers suspect the interaction between the two can sway the fate of the young animal, but this complex dynamic is difficult to pin down in lab experiments.

However, social insect researchers have found a solution. Rockefeller University's Daniel Kronauer, head of the Laboratory of Insect Social Evolution, and his colleagues are developing a species of small raider ants as a model organism in order to ask questions about the relationships between genes, social behavior and evolution.

In a pair of recent papers, the researchers first explain the unique, and potentially useful, biology of this 2.5-millimeter-long ant. Then, in work with collaborators at the University of Paris 13, they put it to work exploring the interaction between the larvae and their nursemaids, and the influence on the young ants' reproductive success as adults.

Clonal raider ants, the species Cerapachys biroi, reproduce by cloning, and they live in colonies of as many as a few hundred nearly genetically identical workers. This makes these ants ideal for studies testing how a particular genetic makeup responds to different conditions, the researchers write in Current Biology. With the help of collaborators at BGI China, researchers in Kronauer's lab have sequenced the clonal raider ant's genome. This is an important step toward using the ant in the sorts of experiments conducted for years in traditional model organisms, such as mice and fruit flies.

"We have shown that colony mates are extremely closely related to one another, with all of the individuals in a colony being essentially genetically identical. This gives us precise control in experiments because we don't need to account for individual genetic variation," says Peter Oxley, a postdoc in the laboratory who led work establishing the clonal raider ant as a promising new model organism.

In the second study, one of the first to make use of the clonal raider ant, a team led by Serafino Teseo of the University of Paris 13 used the unique aspects of the ants' biology to test the indirect role genes play in shaping the future identity of larvae and whole colonies by looking at the interaction between larvae and adults. They did so by observing the success of two ant clones, A and B, in pure colonies or mixed together into chimeric colonies. They also swapped broods, so A adults raised B larvae and vice versa.

It turned out that A and B larvae developed differently depending on whether A or B nurses raised them. Left alone, pure A colonies produced the most young after six generations, making them more successful than B. However, in mixed colonies, B did better because its larvae more frequently turned into large adults that specialize in egg-laying rather than smaller, foraging-focused individuals.

The researchers suspect an indirect genetic effect -- specifically, a social influence. To begin to tease apart the dynamic, they had adults from one clone raise larvae from the other. Again, B did better when raised by A nurses than any of the other combinations. The results were published in Nature Communications.

The B colony's strategy of favoring reproduction over foraging when raised by A colony nurses smacks of social parasitism, in which one organism exploits another's social behavior for its own benefit. "This doesn't mean B is a parasite in the making, just that uncoupling the normal interaction between larvae and their nearly identical adult nursemaids reveals the presence of this mechanism," Kronauer says.

The study shows that, in social species, genetic makeup alone does not provide enough information to predict social behavior. Instead, interactions between social partners, such as larvae and their caregivers, are crucial determinants and can lead to surprising outcomes.

Source: Rockefeller University

Advanced biological computer developed

Microprocessor with DNA (illustration). Scientists have developed and constructed an advanced biological transducer, a computing machine capable of manipulating genetic codes, and using the output as new input for subsequent computations Credit: © Giovanni Cancemi / Fotolia

Using only biomolecules (such as DNA and enzymes), scientists at the Technion-Israel Institute of Technology have developed and constructed an advanced biological transducer, a computing machine capable of manipulating genetic codes, and using the output as new input for subsequent computations. The breakthrough might someday create new possibilities in biotechnology, including individual gene therapy and cloning.

The findings appear today (May 23, 2013) in Chemistry & Biology (Cell Press).
Interest in such biomolecular computing devices is strong, mainly because of their ability (unlike electronic computers) to interact directly with biological systems and even living organisms. No interface is required since all components of molecular computers, including hardware, software, input and output, are molecules that interact in solution along a cascade of programmable chemical events.

"Our results show a novel, synthetic designed computing machine that computes iteratively and produces biologically relevant results," says lead researcher Prof. Ehud Keinan of the Technion Schulich Faculty of Chemistry. "In addition to enhanced computation power, this DNA-based transducer offers multiple benefits, including the ability to read and transform genetic information, miniaturization to the molecular scale, and the aptitude to produce computational results that interact directly with living organisms."

The transducer could be used on genetic material to evaluate and detect specific sequences, and to alter and algorithmically process genetic code. Similar devices, says Prof. Keinan, could be applied for other computational problems.

"All biological systems, and even entire living organisms, are natural molecular computers. Every one of us is a biomolecular computer, that is, a machine in which all components are molecules "talking" to one another in a logical manner. The hardware and software are complex biological molecules that activate one another to carry out some predetermined chemical tasks. The input is a molecule that undergoes specific, programmed changes, following a specific set of rules (software) and the output of this chemical computation process is another well defined molecule."

Also contributing to the research were postdoctoral fellows Dr. Tamar Ratner and Dr. Ron Piran of the Technion's Schulich Faculty of Chemistry, and Dr. Natasha Jonoska of the Department of Mathematics at the University of South Florida.

Source:  American Technion Society