Tag Archives: bioengineering

Goodbye Poppy. Hello Narco-Yeast

S_cerevisiaeBioengineers have been successfully encoding and implanting custom genes into viruses, bacteria and yeast for a while now. These new genes usually cause these organisms to do something different, such as digest industrial waste, kill malignant hosts and manufacture useful chemicals.

So, it should come as no surprise to see the advent — only in the laboratory at the moment — of yeast capable of producing narcotics. There seems to be no end to our inventiveness.

Personally, I’m waiting for a bacteria that can synthesize Nutella and a fungus that can construct corporate Powerpoint presentations.

From the NYT:

In a widely expected advance that has opened a fierce debate about “home-brewed heroin,” scientists at Stanford have created strains of yeast that can produce narcotic drugs.

Until now, these drugs — known as opioids — have been derived only from the opium poppy. But the Stanford lab is one of several where researchers have been trying to find yeast-based alternatives. Their work is closely followed by pharmaceutical companies and by the Drug Enforcement Administration and Federal Bureau of Investigation.

Advocates of the rapidly advancing field of bioengineering say it promises to make the creation of important chemicals — in this case painkillers and cough suppressants — cheaper and more predictable than using poppies.

In one major advance more than a decade ago scientists in Berkeley added multiple genes to yeast until it produced a precursor to artemisinin, the most effective modern malaria drug, which previously had to be grown in sweet wormwood shrubs. Much of the world’s artemisinin is now produced in bioengineered yeast.

But some experts fear the technology will be more useful to drug traffickers than to pharmaceutical companies. Legitimate drug makers already have steady supplies of cheap raw materials from legal poppy fields in Turkey, India, Australia, France and elsewhere.

For now, both scientists and law-enforcement officials agree, it will be years before heroin can be grown in yeast. The new Stanford strain, described Thursday in the journal Science, would need to be 100,000 times as efficient in order to match the yield of poppies.

It would take 4,400 gallons of yeast to produce the amount of hydrocodone in a single Vicodin tablet, said Christina D. Smolke, the leader of the Stanford bioengineering team.

For now, she said, anyone looking for opioids “could buy poppy seeds from the grocery store and get higher concentrations.”But the technology is advancing so rapidly that it may match the efficiency of poppy farming within two to three years, Dr. Smolke added.

Read the story here.

Image: Saccharomyces cerevisiae cells in DIC microscopy. Public Domain.

Crispr – Designer DNA

The world welcomed basic genetic engineering in the mid-1970s, when biotech pioneers Herbert Boyer and Stanley Cohen transferred DNA from one organism to another (bacteria). In so doing they created the first genetically modified organism (GMO). A mere forty years later we now have extremely powerful and accessible (cheap) biochemical tools for tinkering with the molecules of heredity. One of these tools, known as Crispr-Cas9, makes it easy and fast to move any genes around, within and across any species.

The technique promises immense progress in the fight against inherited illness, cancer treatment and viral infection. It also opens the door to untold manipulation of DNA in lower organisms and plants to develop an infection resistant and faster growing food supply, and to reimagine a whole host of biochemical and industrial processes (such as ethanol production).

Yet as is the case with many technological advances that hold great promise, tremendous peril lies ahead from this next revolution. Our bioengineering prowess has yet to be matched with a sound and pervasive ethical framework. Can humans reach a consensus on how to shape, focus and limit the application of such techniques? And, equally importantly, can we enforce these bioethical constraints before it’s too late to “uninvent” designer babies and bioweapons?

From Wired:

Spiny grass and scraggly pines creep amid the arts-and-crafts buildings of the Asilomar Conference Grounds, 100 acres of dune where California’s Monterey Peninsula hammerheads into the Pacific. It’s a rugged landscape, designed to inspire people to contemplate their evolving place on Earth. So it was natural that 140 scientists gathered here in 1975 for an unprecedented conference.

They were worried about what people called “recombinant DNA,” the manipulation of the source code of life. It had been just 22 years since James Watson, Francis Crick, and Rosalind Franklin described what DNA was—deoxyribonucleic acid, four different structures called bases stuck to a backbone of sugar and phosphate, in sequences thousands of bases long. DNA is what genes are made of, and genes are the basis of heredity.

Preeminent genetic researchers like David Baltimore, then at MIT, went to Asilomar to grapple with the implications of being able to decrypt and reorder genes. It was a God-like power—to plug genes from one living thing into another. Used wisely, it had the potential to save millions of lives. But the scientists also knew their creations might slip out of their control. They wanted to consider what ought to be off-limits.

By 1975, other fields of science—like physics—were subject to broad restrictions. Hardly anyone was allowed to work on atomic bombs, say. But biology was different. Biologists still let the winding road of research guide their steps. On occasion, regulatory bodies had acted retrospectively—after Nuremberg, Tuskegee, and the human radiation experiments, external enforcement entities had told biologists they weren’t allowed to do that bad thing again. Asilomar, though, was about establishing prospective guidelines, a remarkably open and forward-thinking move.

At the end of the meeting, Baltimore and four other molecular biologists stayed up all night writing a consensus statement. They laid out ways to isolate potentially dangerous experiments and determined that cloning or otherwise messing with dangerous pathogens should be off-limits. A few attendees fretted about the idea of modifications of the human “germ line”—changes that would be passed on from one generation to the next—but most thought that was so far off as to be unrealistic. Engineering microbes was hard enough. The rules the Asilomar scientists hoped biology would follow didn’t look much further ahead than ideas and proposals already on their desks.

Earlier this year, Baltimore joined 17 other researchers for another California conference, this one at the Carneros Inn in Napa Valley. “It was a feeling of déjà vu,” Baltimore says. There he was again, gathered with some of the smartest scientists on earth to talk about the implications of genome engineering.

The stakes, however, have changed. Everyone at the Napa meeting had access to a gene-editing technique called Crispr-Cas9. The first term is an acronym for “clustered regularly interspaced short palindromic repeats,” a description of the genetic basis of the method; Cas9 is the name of a protein that makes it work. Technical details aside, Crispr-Cas9 makes it easy, cheap, and fast to move genes around—any genes, in any living thing, from bacteria to people. “These are monumental moments in the history of biomedical research,” Baltimore says. “They don’t happen every day.”

Using the three-year-old technique, researchers have already reversed mutations that cause blindness, stopped cancer cells from multiplying, and made cells impervious to the virus that causes AIDS. Agronomists have rendered wheat invulnerable to killer fungi like powdery mildew, hinting at engineered staple crops that can feed a population of 9 billion on an ever-warmer planet. Bioengineers have used Crispr to alter the DNA of yeast so that it consumes plant matter and excretes ethanol, promising an end to reliance on petrochemicals. Startups devoted to Crispr have launched. International pharmaceutical and agricultural companies have spun up Crispr R&D. Two of the most powerful universities in the US are engaged in a vicious war over the basic patent. Depending on what kind of person you are, Crispr makes you see a gleaming world of the future, a Nobel medallion, or dollar signs.

The technique is revolutionary, and like all revolutions, it’s perilous. Crispr goes well beyond anything the Asilomar conference discussed. It could at last allow genetics researchers to conjure everything anyone has ever worried they would—designer babies, invasive mutants, species-specific bioweapons, and a dozen other apocalyptic sci-fi tropes. It brings with it all-new rules for the practice of research in the life sciences. But no one knows what the rules are—or who will be the first to break them.

In a way, humans were genetic engineers long before anyone knew what a gene was. They could give living things new traits—sweeter kernels of corn, flatter bulldog faces—through selective breeding. But it took time, and it didn’t always pan out. By the 1930s refining nature got faster. Scientists bombarded seeds and insect eggs with x-rays, causing mutations to scatter through genomes like shrapnel. If one of hundreds of irradiated plants or insects grew up with the traits scientists desired, they bred it and tossed the rest. That’s where red grapefruits came from, and most barley for modern beer.

Genome modification has become less of a crapshoot. In 2002, molecular biologists learned to delete or replace specific genes using enzymes called zinc-finger nucleases; the next-generation technique used enzymes named TALENs.

Yet the procedures were expensive and complicated. They only worked on organisms whose molecular innards had been thoroughly dissected—like mice or fruit flies. Genome engineers went on the hunt for something better.

As it happened, the people who found it weren’t genome engineers at all. They were basic researchers, trying to unravel the origin of life by sequencing the genomes of ancient bacteria and microbes called Archaea (as in archaic), descendants of the first life on Earth. Deep amid the bases, the As, Ts, Gs, and Cs that made up those DNA sequences, microbiologists noticed recurring segments that were the same back to front and front to back—palindromes. The researchers didn’t know what these segments did, but they knew they were weird. In a branding exercise only scientists could love, they named these clusters of repeating palindromes Crispr.

Then, in 2005, a microbiologist named Rodolphe Barrangou, working at a Danish food company called Danisco, spotted some of those same palindromic repeats in Streptococcus thermophilus, the bacteria that the company uses to make yogurt and cheese. Barrangou and his colleagues discovered that the unidentified stretches of DNA between Crispr’s palindromes matched sequences from viruses that had infected their S. thermophilus colonies. Like most living things, bacteria get attacked by viruses—in this case they’re called bacteriophages, or phages for short. Barrangou’s team went on to show that the segments served an important role in the bacteria’s defense against the phages, a sort of immunological memory. If a phage infected a microbe whose Crispr carried its fingerprint, the bacteria could recognize the phage and fight back. Barrangou and his colleagues realized they could save their company some money by selecting S. thermophilus species with Crispr sequences that resisted common dairy viruses.

As more researchers sequenced more bacteria, they found Crisprs again and again—half of all bacteria had them. Most Archaea did too. And even stranger, some of Crispr’s sequences didn’t encode the eventual manufacture of a protein, as is typical of a gene, but instead led to RNA—single-stranded genetic material. (DNA, of course, is double-stranded.)

That pointed to a new hypothesis. Most present-day animals and plants defend themselves against viruses with structures made out of RNA. So a few researchers started to wonder if Crispr was a primordial immune system. Among the people working on that idea was Jill Banfield, a geomicrobiologist at UC Berkeley, who had found Crispr sequences in microbes she collected from acidic, 110-degree water from the defunct Iron Mountain Mine in Shasta County, California. But to figure out if she was right, she needed help.

Luckily, one of the country’s best-known RNA experts, a biochemist named Jennifer Doudna, worked on the other side of campus in an office with a view of the Bay and San Francisco’s skyline. It certainly wasn’t what Doudna had imagined for herself as a girl growing up on the Big Island of Hawaii. She simply liked math and chemistry—an affinity that took her to Harvard and then to a postdoc at the University of Colorado. That’s where she made her initial important discoveries, revealing the three-dimensional structure of complex RNA molecules that could, like enzymes, catalyze chemical reactions.

The mine bacteria piqued Doudna’s curiosity, but when Doudna pried Crispr apart, she didn’t see anything to suggest the bacterial immune system was related to the one plants and animals use. Still, she thought the system might be adapted for diagnostic tests.

Banfield wasn’t the only person to ask Doudna for help with a Crispr project. In 2011, Doudna was at an American Society for Microbiology meeting in San Juan, Puerto Rico, when an intense, dark-haired French scientist asked her if she wouldn’t mind stepping outside the conference hall for a chat. This was Emmanuelle Charpentier, a microbiologist at Ume?a University in Sweden.

As they wandered through the alleyways of old San Juan, Charpentier explained that one of Crispr’s associated proteins, named Csn1, appeared to be extraordinary. It seemed to search for specific DNA sequences in viruses and cut them apart like a microscopic multitool. Charpentier asked Doudna to help her figure out how it worked. “Somehow the way she said it, I literally—I can almost feel it now—I had this chill down my back,” Doudna says. “When she said ‘the mysterious Csn1’ I just had this feeling, there is going to be something good here.”

Read the whole story here.

Growing a Brain Outside of the Body

‘Tis the stuff of science fiction. And, it’s also quite real and happening in a lab near you.

From Technology Review:

Scientists at the Institute of Molecular Biotechnology in Vienna, Austria, have grown three-dimensional human brain tissues from stem cells. The tissues form discrete structures that are seen in the developing brain.

The Vienna researchers found that immature brain cells derived from stem cells self-organize into brain-like tissues in the right culture conditions. The “cerebral organoids,” as the researchers call them, grew to about four millimeters in size and could survive as long as 10 months. For decades, scientists have been able to take cells from animals including humans and grow them in a petri dish, but for the most part this has been done in two dimensions, with the cells grown in a thin layer in petri dishes. But in recent years, researchers have advanced tissue culture techniques so that three-dimensional brain tissue can grow in the lab. The new report from the Austrian team demonstrates that allowing immature brain cells to self-organize yields some of the largest and most complex lab-grown brain tissue, with distinct subregions and signs of functional neurons.

The work, published in Nature on Wednesday, is the latest advance in a field focused on creating more lifelike tissue cultures of neurons and related cells for studying brain function, disease, and repair. With a cultured cell model system that mimics the brain’s natural architecture, researchers would be able to look at how certain diseases occur and screen potential medications for toxicity and efficacy in a more natural setting, says Anja Kunze, a neuroengineer at the University of California, Los Angeles, who has developed three-dimensional brain tissue cultures to study Alzheimer’s disease.

The Austrian researchers coaxed cultured neurons to take on a three-dimensional organization using cell-friendly scaffolding materials in the cultures. The team also let the neuron progenitors control their own fate. “Stem cells have an amazing ability to self-organize,” said study first author Madeline Lancaster at a press briefing on Tuesday. Others groups have also recently seen success in allowing progenitor cells to self-organize, leading to reports of primitive eye structures, liver buds, and more (see “Growing Eyeballs” and “A Rudimentary Liver Is Grown from Stem Cells”).

The brain tissue formed discrete regions found in the early developing human brain, including regions that resemble parts of the cortex, the retina, and structures that produce cerebrospinal fluid. At the press briefing, senior author Juergen Knoblich said that while there have been numerous attempts to model human brain tissue in a culture using human cells, the complex human organ has proved difficult to replicate. Knoblich says the proto-brain resembles the developmental stage of a nine-week-old fetus’s brain.

While Knoblich’s group is focused on developmental questions, other groups are developing three-dimensional brain tissue cultures with the hopes of treating degenerative diseases or brain injury. A group at Georgia Institute of Technology has developed a three-dimensional neural culture to study brain injury, with the goal of identifying biomarkers that could be used to diagnose brain injury and potential drug targets for medications that can repair injured neurons. “It’s important to mimic the cellular architecture of the brain as much as possible because the mechanical response of that tissue is very dependent on its 3-D structure,” says biomedical engineer Michelle LaPlaca of Georgia Tech. Physical insults on cells in a three-dimensional culture will put stress on connections between cells and supporting material known as the extracellular matrix, she says.

Read the entire article here.

Image: Cerebral organoid derived from stem cells containing different brain regions. Courtesy of Japan Times.

Printing Human Cells

The most fundamental innovation tends to happen at the intersection of disciplines. So, what do you get if you cross 3-D printing technology with embryonic stem cell research? Well, you get a device that can print lines of cells with similar functions, such as heart muscle or kidney cells. Welcome to the new world of biofabrication. The science fiction future seems to be ever increasingly close.

[div class=attrib]From Scientific American:[end-div]

Imagine if you could take living cells, load them into a printer, and squirt out a 3D tissue that could develop into a kidney or a heart. Scientists are one step closer to that reality, now that they have developed the first printer for embryonic human stem cells.

In a new study, researchers from the University of Edinburgh have created a cell printer that spits out living embryonic stem cells. The printer was capable of printing uniform-size droplets of cells gently enough to keep the cells alive and maintain their ability to develop into different cell types. The new printing method could be used to make 3D human tissues for testing new drugs, grow organs, or ultimately print cells directly inside the body.

Human embryonic stem cells (hESCs) are obtained from human embryos and can develop into any cell type in an adult person, from brain tissue to muscle to bone. This attribute makes them ideal for use in regenerative medicine — repairing, replacing and regenerating damaged cells, tissues or organs. [Stem Cells: 5 Fascinating Findings]

In a lab dish, hESCs can be placed in a solution that contains the biological cues that tell the cells to develop into specific tissue types, a process called differentiation. The process starts with the cells forming what are called “embryoid bodies.” Cell printers offer a means of producing embryoid bodies of a defined size and shape.

In the new study, the cell printer was made from a modified CNC machine (a computer-controlled machining tool) outfitted with two “bio-ink” dispensers: one containing stem cells in a nutrient-rich soup called cell medium and another containing just the medium. These embryonic stem cells were dispensed through computer-operated valves, while a microscope mounted to the printer provided a close-up view of what was being printed.

The two inks were dispensed in layers, one on top of the other to create cell droplets of varying concentration. The smallest droplets were only two nanoliters, containing roughly five cells.

The cells were printed onto a dish containing many small wells. The dish was then flipped over so the droplets now hung from them, allowing the stem cells to form clumps inside each well. (The printer lays down the cells in precisely sized droplets and in a certain pattern that is optimal for differentiation.)

Tests revealed that more than 95 percent of the cells were still alive 24 hours after being printed, suggesting they had not been killed by the printing process. More than 89 percent of the cells were still alive three days later, and also tested positive for a marker of their pluripotency — their potential to develop into different cell types.

Biomedical engineer Utkan Demirci, of Harvard University Medical School and Brigham and Women’s Hospital, has done pioneering work in printing cells, and thinks the new study is taking it in an exciting direction. “This technology could be really good for high-throughput drug testing,” Demirci told LiveScience. One can build mini-tissues from the bottom up, using a repeatable, reliable method, he said. Building whole organs is the long-term goal, Demirci said, though he cautioned that it “may be quite far from where we are today.”

[div class=attrib]Read the entire article after the leap.[end-div]

[div class=attrib]Image: 3D printing with embryonic stem cells. Courtesy of Alan Faulkner-Jones et al./Heriot-Watt University.[end-div]

Growing Complex Organs From Scratch

In early 2010 a Japanese research team grew retina-like structures from a culture of mouse embryonic stem cells. Now, only a year later, the same team at the RIKEN Center for Developmental Biology announced their success in growing a much more complex structure following a similar process — a mouse pituitary gland. This is seen as another major step towards bioengineering replacement organs for human transplantation.

[div class=attrib]From Technology Review:[end-div]

The pituitary gland is a small organ at the base of the brain that produces many important hormones and is a key part of the body’s endocrine system. It’s especially crucial during early development, so the ability to simulate its formation in the lab could help researchers better understand how these developmental processes work. Disruptions in the pituitary have also been associated with growth disorders, such as gigantism, and vision problems, including blindness.

The study, published in this week’s Nature, moves the medical field even closer to being able to bioengineer complex organs for transplant in humans.

The experiment wouldn’t have been possible without a three-dimensional cell culture. The pituitary gland is an independent organ, but it can’t develop without chemical signals from the hypothalamus, the brain region that sits just above it. With a three-dimensional culture, the researchers could grow both types of tissue together, allowing the stem cells to self-assemble into a mouse pituitary. “Using this method, we could mimic the early mouse development more smoothly, since the embryo develops in 3-D in vivo,” says Yoshiki Sasai, the lead author of the study.

The researchers had a vague sense of the signaling factors needed to form a pituitary gland, but they had to figure out the exact components and sequence through trial and error. The winning combination consisted of two main steps, which required the addition of two growth factors and a drug to stimulate a developmental protein called sonic hedgehog (named after the video game). After about two weeks, the researchers had a structure that resembled a pituitary gland.

[div class=attrib]Read the entire article here.[end-div]

[div class=attrib]New gland: After 13 days in culture, mouse embryonic stem cells had self-assembled the precursor pouch, shown here, that gives rise to the pituitary gland. Image courtesy of Technlogy Review / Nature.[end-div]