The 2017 Blavatnik Science Symposium

From Microbial Immunity to Genome Editing

Much the way that rapid, affordable gene sequencing ushered in a new age of insight about genetic causes of disease, the advent of CRISPR-Cas9, the revolutionary genome editing technique, has opened avenues of possibility that were the stuff of science fiction just a decade ago. Blavatnik National Laureate Feng Zhang delivered the opening keynote of the 2017 Blavatnik Science Symposium with a recap of the brief history of CRISPR-Cas9, which he helped pioneer over the past six years, and an exciting preview of a new class of CRISPR-based diagnostics.

Zhang highlighted the advantages of CRISPR-Cas9 over previous gene-editing systems, which were clunky, imprecise, expensive, and time-consuming. Similar to the “find and replace” function in word processing software, the Cas9 protein can quickly and precisely seek out, cut, and if needed, replace a specific sequence of DNA embedded in human or animal cells.

Cas9 is just one of many enzymes that comprise the adaptive immune system of bacterial cells, and Zhang and his collaborators are probing the diversity of CRISPR systems with the hope of understanding how other enzymes may be tapped for biotechnological advances. Using computational approaches to scan bacterial genomes, they discovered numerous CRISPR-associated proteins. One protein, Cas13, drew attention for its unique ability to target and degrade RNA, rather than DNA. “We were very excited when we found these because it suggests that we can broaden the CRISPR system to achieve a whole different set of manipulations within the cell,” said Zhang.

Cas13, or C2c2, can be used to detect viral RNA by cleaving both the nucleic acid of the virus itself, as well as that of reporter RNA tagged with fluorescent proteins.

One of the most promising emerging applications for Cas13 comes in the form of a diagnostic technique that can detect viruses at attomolar sensitivities. Dubbed SHERLOCK, for Specific High Sensitivity Enzymatic Reporter Unlocking, the system takes advantage of the fact that while Cas13 specifically targets RNA, the RNA it targets is not always specific. Zhang explained that the protein is less discriminate than Cas9, which precisely cleaves the DNA sequences programmed by its RNA guide. Cas13, however, tends to cleave not only the targeted RNA, but also “collateral” RNA in the vicinity of the target. By adding fluorescent “reporter” RNAs to samples containing viruses such as Zika and dengue—RNAs that produce a detectable signal when snipped by Cas13—researchers can detect the presence of even a single viral particle.

SHERLOCK is particularly promising as a field-based or point-of-care diagnostic due to its adaptability—it can be designed as a paper-based diagnostic requiring no refrigeration—and its extraordinary sensitivity. Zhang and his collaborators, including fellow Blavatnik honoree Pardis Sabeti of Harvard, are working to refine SHERLOCK for use in epidemic outbreaks, especially in rural and resource-constrained settings.

Nanotechnology for Energy

“Energy storage is one of the most important missing links in the energy landscape,” said Blavatnik National Laureate Yi Cui, who is using nanotechnology to both improve current battery technologies and create new paradigms for powering the future. Cui discussed how two major shifts in the realm of electricity—the plummeting cost of power generated from renewable sources like solar and wind, along with the surge in manufacture and market share of electric cars— have upped the pressure on scientists and engineers to develop storage solutions for a new electricity economy. Integrating renewable energy into the electrical grid will require storage capacities impossible to support using today’s battery technologies. Likewise, the full environmental benefits of electric cars cannot be realized without considerable improvements in both vehicle cost and run-time on a single charge.

Cui is tackling both hurdles by merging nanotechnology with battery chemistry to safely boost capacity and performance. He described the tantalizing potential of wringing two or three times the energy density from lithium batteries by replacing traditional graphite anodes with silicon ones, or even achieving what he deems the “holy grail of batteries”—one with a lithium metal electrode. In both cases, nanostructures may be the key to a successful architecture. Silicon has more than ten times the storage capacity of graphite, but the material is prone to breakage as it expands and contracts with the flow of ions. Cui has developed nanoscale solutions to make silicon anodes a reality, including a technique that surrounds silicon nanoparticles with conductive, protective shells that allow for expansion and contraction. A similar shell-like protective structure may allow researchers to reap the benefits of lithium metal batteries, which can store more energy than silicon but are prone to cracks that can short-circuit the battery and cause fires.

The energy density of lithium batteries can be dramatically increased by using different materials for cathodes and anodes—silicon and sulfur each boast more than 10 times the storage capacity of more commonly used materials.

Such heavy reliance on lithium poses little concern in terms of supply—estimates of the global reserve of the easily minable element reveal enough material to make more than 10 billion Nissan Leaf cars—but Cui notes that most of the lithium on Earth is dissolved in ocean water. “We don’t need to worry about lithium supply right now, but that won’t be true forever,” he said. Cui’s lab has already pioneered a method for using nanomaterials to extract another valuable element—uranium—from seawater, and he sees a future role for similar materials in tapping the ocean’s nearly endless supply of lithium.

Gene Regulation in Fragile X

Fragile X is the most common inherited cause of both intellectual disability and autism. Instantly recognizable as a visible structural change on the X chromosome, the disorder is also characterized by a novel mutation—a trinucleotide repeat expansion in a gene known as FMR1, which codes for the FMRP protein.  Blavatnik alumnus Samie Jaffrey explained that while a person with a typical FMR1 gene may have 30-50 repeats of a CGG sequence, those with Fragile X often have several hundred, and in such individuals, the FMR1 gene is switched off. However, the gene is not born silent, said Jaffrey, describing what he calls “a massive epigenetic silencing” that occurs during gestation in individuals who will ultimately have Fragile X. “These fetuses make FMRP in utero for the first 10.5 weeks of gestation, but then something happens around 11 weeks—there’s a sensor that detects this long string of repeats and switches the gene off,” he said.

Uncovering the mechanism of this epigenetic silencing has led to a deeper understanding of the role RNA can play in gene regulation, and is advancing the development of therapies that may eventually “unsilence” the FMR1 gene and restore protein production.

In experiments, Jaffrey and his collaborators recapitulated the gestational process using embryonic stem cells affected by Fragile X, along with control cell lines. “Before they differentiate, Fragile X stem cells make the FMRP protein normally,” said Jaffrey, noting that the FMR1 gene is only silenced when cells are coaxed to differentiate, at which point Fragile X-affected cells lose active histone marks—indicators of a functional gene—and acquire repressive ones.

By day 60, neurons differentiated from Fragile X stem cells no longer produce the FMRP protein.

Previous research showed that the trinucleotide repeat expansion unique to Fragile X is present in both DNA as well as RNA, and researchers had long hypothesized that mRNA may play a role in silencing the FMR1 gene. Jaffrey discovered that the silencing of FMR1, at roughly 45 days of gestation, coincides with the formation of a FMR1 mRNA/DNA duplex at the site of the trinucleotide repeat expansion that effectively shuts down the FMR1 promoter. These findings have led to a partnership with fellow Blavatnik honoree Matthew Disney, of Scripps Florida, who develops small molecules that preferentially bind to RNA motifs. The researchers identified a compound that selectively binds to the shape made by CGG repeat RNA sequences. As Jaffrey said, “If we can find a drug to bind the FMR1 RNA and lock it into place, we can prevent this RNA/DNA duplex from forming.” While experiments have been limited to neurons thus far, the results are promising: Jaffrey reports that cells treated with the RNA-binding compound are spared the epigenetic silencing of FMR1.

Earth’s climate is undeniably changing. From unprecedented flooding to devastating drought and including periods of record heat and unseasonable cold, climate change is impacting the ecosystems that support life on Earth in ways that are not yet understood. William Anderegg began a series of presentations and discussion about scientists’ efforts to glean insight about the potential impacts of climate change both by searching for clues in the past, and applying cutting-edge computational and modeling techniques to prepare for the future.

Models predicting the impact of climate shifts on the Earth’s forests are widely divergent, highlighting the need for more precise forecasting methods.

Anderegg’s work seeks to uncover the mechanisms that govern trees’ response to drought stress—a core concept in modeling the impact of climate change on forest ecosystems. “Forests stand at an interesting tension point,” said Anderegg. “On one hand, rising carbon dioxide levels largely benefit plants, but on the other hand, consequences of climate change, such as drought and hotter temperatures, are largely harmful to them.” Determining where and when each of these effects may dominate is a fundamental challenge of predicting forest fate for the remainder of this century and beyond.

Present-day models of the impact of climate change on trees diverge wildly, a fact Anderegg attributes in part to a lack of mechanistic knowledge about one of the most basic functions of plants—their use of stomata, or leaf pores, to maximize photosynthesis and minimize water loss. Understanding the strategies plants use to boost survival, particularly in stress conditions, could contribute significantly to efforts to improve forecasting models, explained Anderegg. Prevailing theories of stomatal conductance largely treat trees as singular entities with a fixed potential for photosynthesis and a finite amount of moisture to retain or lose based on environmental conditions. Upending those long-held beliefs, Anderegg introduced a new notion of stomatal function based on game theory, stating that “plants don’t operate individually—roots overlap and they regularly steal each other’s water, so the plant that’s best at stealing water maximizes its profits and wins.” Forecasting models rooted in this new approach offer less divergent predictions of the impacts of environmental stresses like drought and heat on stomatal conductance, especially at longer timescales. “It’s useful because this is what we want to be able to predict—when and where these tipping points may happen and when ecosystems may crash,” Anderegg said.

Sea level rise is another area of predictive interest for those who study climate change. Efforts to model the amount of sea level rise that can be expected over the next two centuries requires consideration of far longer timescales, explained geologist Nicolás Young, who is pioneering new techniques to better understand how the growth and retreat of glaciers and ice sheets over the past several million years may help predict future changes.

Today’s computer models predict degrees of sea level rise based on projected CO₂ emissions, but such simulations are imprecise. Young believes that the geologic record of the size of ice sheets provides the best point of comparison for improving models of future sea level rise, yet until now, scientists have only been able to determine how large ice sheets once were, not the reverse. “It’s very hard to reconstruct a smaller-than-present ice sheet,” said Young. “When a sheet grows, it leaves distinct clues on the landscape that mark its former position, and while smaller ice sheets leave the same clues, the evidence is smothered when the sheet expands again.”​

The Greenland ice sheet expands and contracts during glacial and interglacial periods, but determining the extent of ice sheet coverage over time is challenging.

Modern analytics have allowed scientists to analyze arctic ice cores from the 1990s that also contain samples of bedrock, which offer clues to the extent of ice sheet coverage over time. These bedrock samples are the key to new techniques for determining whether current ice-covered regions have experienced periods of melting and exposure. As Young explained, certain isotopes are measurable in bedrock, and such isotopes are only present in the absence of ice cover. “The only way those isotopes can get there is if there’s no ice covering the site. It’s an on/off signal, there’s no other way to do it,” he said. By analyzing the location of an isotope-containing core relative to the sheet today, it is possible to gauge the degree to which an ice sheet or glacier has expanded or contracted over time.

Such insights are critical to building the geological record and decreasing the variability in computer simulations of future sea-level rise due to ice melt, Young explained, and demonstrate that contrary to popular belief, the Greenland Ice Sheet is surprisingly dynamic, having undergone considerable shifts in size over the past two million years.

“All natural systems, whether ice sheets or trees in a forest, are racing toward equilibrium with a changing environment, and one of the big questions is, ‘when will we be at that equilibrium, and can we predict how close we are?” said Robert Anderson, turning the discussion to the impacts of climate change on the distribution patterns of animal species.

Land use changes and deforestation have long been threats to biodiversity. As the human population grows and resource demands increase, these threats become heightened, and along with the rising specter of climate change, compound the strain on wild animal communities. Improving predictive models of how such factors affect animals is of critical importance to understanding threats posed by invasive species and zoonotic diseases, as well as planning nature reserves and informing policy decisions.

Anderson explained that animal species respond to abiotic, biotic, and spatial factors, yet most current modeling schemes are not sufficient to account for the impacts of these factors on wild communities. While further development is needed in this area, Anderson reported on the early-stage development of a new species-niche modeling framework that allows for incorporation of all three classes of factors. It uses current and past biodiversity occurrence data, biological data about species functional traits, geography, and estimates of climate change and land use shifts to construct models that predict future movement and distribution.

The ability to design and tune new classes of polymers has allowed scientists to expand the application of these already ubiquitous materials in fields ranging from drug delivery and rehabilitative medicine to environmental cleanup and energy storage. Two Blavatnik honorees shared their research using unique and highly optimized polymers to achieve unprecedented performance and results in their respective fields.

Beta cyclodextrin, a cornstarch-based compound used in the odor-absorbing product Febreze, was the inspiration for a new class of polymers engineered by William Dichtel, who explained how a design tweak turned a common compound into a potentially game-changing tool for water purification. Beta cyclodextrin’s ability to bind organic particles is well documented, yet its solubility makes it impractical for many applications. By cross-linking beta cyclodextrin to a porous polymer, Dichtel created a novel material—an insoluble, high surface-area polymer capable of rapidly encapsulating micropollutants in water.

Tests of both porous and non-porous beta cyclodextrin polymers against activated carbon—the most common adsorbent material used in water purification—showed that the porous polymer outperformed both its non-porous counterpart and activated carbon in uptake of a common pollutant, bisphenol A (BPA). For Dichtel, this represents a potential opportunity to rid wastewater of micropollutants that may often evade treatment processes and may have negative environmental impacts. These include pharmaceuticals, pesticides, and personal care products.

A porous beta-cyclodextrin polymer, DFB-CDP, effectively eliminates the pollutant PFOA from water, outperforming both activated carbon and non-porous polymers.

Further trials testing the polymer’s performance against 83 micropollutants at environmentally-relevant concentrations showed widespread, strong affinity for many compounds not bound by activated carbon, along with a weak affinity for one prevalent and environmentally persistent pollutant, perflouorooctanoic acid, or PFOA. Dichtel tuned the polymer’s structure to increase affinity for PFOA, ultimately yielding a polymer capable of quickly removing even trace amounts of the pollutant from water. “There’s a lot of play in the design of the material, and many other potential cross-linkers to tailor these adsorbents for performance,” said Dichtel. “Another nice thing is that these materials are not intended to be used and disposed of—you can wash pollutants out of them and reuse them.”

Matthew Becker has designed a novel polymer to address a gruesome and growing problem—blast injuries suffered during military combat. Interest in new techniques for limb salvage has boomed over the past 15 years, driven both by a surge in blast injuries from improvised explosive devices as well as a lack of surgical and rehabilitative strategies to minimize disability and restore function. Becker’s proposed solution for healing segmental bone injuries is the result of more than a decade of research developing a unique biodegradable polymer shell that, when implanted at wound sites has the ability to bridge bone lost to injury, yielding unprecedented performance and healing in more than 1,000 experiments in five animal species.

Weeks after a simulated blast injury, a sheep femur patched with a polymer implant shows normal bone regrowth and callous formation.

The path from idea to implementation has been complex, Becker relayed, explaining the strict design parameters imposed for medical technologies designed to treat battle wounds. “This needed to be something that could be done in a single surgery, with no metal or other hardware, it had to be completely customizable to suit a range of injuries, and it had to be strong and resorbable,” Becker said. A novel amino-acid based polymer that can be quickly 3-D printed to form custom shells proved to be the ideal material for the job, combining remarkable strength—supporting up to 2500 pounds per square inch in a 4-point bending test—with a metabolic compatibility that results in less inflammation and swelling at the implant site. “The design is based on plumbing pipes, and in the surgery, the whole thing comes together like Legos,” joked Becker, simplifying a technique that has shown to promote a normal pattern of bone regeneration with typical callous formation, a significant feat compared to traditional approaches. “We’re not doing anything to induce bone to heal, but perhaps for the first time, we’re looking at strategies for not getting in the way of healing,” he said.

“If you want to have every object on Earth connected to the internet, how do you do that?” asked Mark Hersam, who kicked off a series of presentations on nanotechnology applications for electronics and energy. The notion of an entirely connected planet is not as far-fetched as it seems, he explained, noting the remarkable growth of internet-connected devices from 12.5 billion in 2010 to a projected 50 billion by 2020. Accompanying that boom is the surging electrical demand of so many devices, a fact that highlights the need to develop solutions that improve both energy sourcing and device efficiency.

Hersam believes that ubiquitous electronics must take their cue from the bar and QR codes of retail shopping, which rely on printing for low -cost production and ease of distribution. “In the future, we’ll need ultra-cheap, printable electronics, scalable production of electronic inks, seamless integration into manufacturing, and new power management schemes,” he said.

Solution-processed nanomaterials can be separated to form pure nanotube inks with specific properties.

Hersam’s lab has engineered pure electronic inks by solution-processing various nanoelectronic materials, then isolating them to yield low-cost inks with both electrically conductive and insulating properties. Such electronic inks, whether comprised of carbon nanotubes, graphene, boron nitride, or other materials, are water-based, and thus incompatible with current printing technologies. Yet by tuning the ink’s viscosity through the addition of plant-based polymers, they can be made compatible with all printing techniques, explained Hersam.

Creating printed circuitry took more than a decade of tweaking, but carbon nanotube-based integrated circuits are not only a reality, they are fully functional and consume up to 100-fold less power than current electronics. The next generation of printed circuitry, comprised of single-layer memristors, promise to be “closer to brain-like computing” in their capacity to process information at very low power.

A simple glass of water drives a new class of engines developed by Xi Chen, who is tapping into one of the most underestimated forms of energy—evaporation—as a next-generation power source. Harnessing the slow but powerful force of evaporation requires a unique, water-responsive medium, and for that, Chen and his collaborators turned to a harmless, ubiquitous bacterial spore that expands and contracts in response to changes in relative humidity. “Bacillus spores are rigid, and they produce a significant amount of energy as they shrink and swell,” said Chen, who noted that a study of the energy density of these spores revealed that, “with one pound of dry spore and moisture from water, you can lift a car one meter off the ground.”

A single layer of bacterial spores on a thin film swell and contract in response to changes in humidity, producing enough force to bend the film.

Transforming these mighty yet microscopic structures into a functional application is a work in process, and Chen showed the results of experiments with various evaporation-driven machines. By depositing a layer of spores on thin plastic, then adjusting the relative humidity, Chen and his collaborators created actuating films that can be linked to open and close a set of shutters on a small evaporation engine, or to turn a rotary wheel and even power a toy car. “These machines will run until the water dries out,” said Chen, “and it can be any kind of water—clean water, wastewater, sea water.”

Chen believes that evaporation-driven generators have the potential to become a major source of renewable energy in the future—he envisions large-scale, spore-layered films floating atop a reservoir— and could ultimately produce as much energy as solar and wind. “But this method is one hundred times cheaper,” he noted.

The sun is one of the most accessible, plentiful sources of renewable energy on the planet, yet solar energy represents less than one percent of total consumption in the United States. Tomoyasu Mani attributes this surprisingly low number to two simple facts. Number one, “[w]e still don’t have great means to convert solar energy into usable electricity,” he said, explaining that despite improved efficiencies over the past decade, photovoltaic cells are still largely inefficient. And secondly, even after twenty years of intensive research, many questions remain about precisely how and why photovoltaic cells work.

Mani described his efforts to improve fundamental understanding of charge separation and transport in photovoltaic cells, noting that from a chemistry standpoint, “photovoltaic cells shouldn’t work at all—these are charged particles in a non-polar environment.” By designing charged molecules in the lab and studying their vibrations, Mani has derived critical insights about electron behavior that may inform the design of next-generation molecules for use in photovoltaic solar cells.

Electron transport is also a dominant theme in Mohamed El-Naggar’s work, which focuses not on the movement of electrons in solid state materials, but rather on the flow of energy in living cells. While all eukaryotes and many bacteria require oxygen for respiration, El-Naggar explained that many other species of bacteria are capable of a unique form of respiration that relies not on intracellular transfer of electrons, but on extracellular transfer, where the acceptor is not oxygen, but redox-active minerals found in nature. El-Naggar’s studies of one such “rock breathing,” bacterium, Shewanella oneidensis, have illuminated the process by which these organisms form biological chains to transport electrons to inorganic surfaces, and inspired a new class of fuel cells based on this unique microbial metabolism.

In experiments, El-Naggar and others have successfully tricked Shewanella into transferring electrons to a favorably biased electrode, a feat that can be replicated to power devices. “A microbial fuel cell is very much like abiotic fuel cells, except that instead of a novel metal catalyst that’s driving oxidation of the fuel, it’s a living, eating, breathing organism on your electrode that we’re harvesting electrons from,” he said. The technology has been demonstrated on a relatively small scale, but El-Naggar believes it’s only a matter of time before such microbial fuel cells operate in a bigger arena, such as wastewater treatment devices that rely on microbial metabolism instead of external power.

Gleb Yushin characterizes his discovery of a fundamentally new method of synthesizing nanowires as a happy accident. Unlike traditional nanowire synthesis, which is prohibitively expensive, requires both specialized equipment and corrosive chemicals, and yields very little product relative to the amount of material used, Yushin’s technique involves little more than “putting some powder in a bucket, adding solvent, and collecting nanowires in just a few hours.”

The prospect of easy bulk synthesis of nanowires—one-dimensional structures that have applications in medical devices and sensors, electronics, and structural composites—is revolutionary, explained Yushin, who said that a 100-to-1000-fold reduction in cost is critical for nanowire technologies to become commercially feasible. His technique calls for combining a bimetallic alloy—of which one metal is reactive—with a common solvent (such as ethanol) at room temperature and relying on ambient pressure. As the reactive metal dissolves, elongated nanoparticles form. By varying the alloy, solvent, and temperature, the resulting nanowires can be tuned for specific properties, including diameter.

One application Yushin is particularly excited about is the potential for creating membranes made of ceramic nanowire for use as separators in lithium-ion batteries. “The polymer barriers we use today sometimes fail, especially at higher temperatures,” said Yushin. "You can heat ceramic nanowires to 1,000 degrees Celsius with no problem.”

With increasing utilization of nanomaterials and nanoparticles, Christy Haynes is less concerned with finding uses for these materials and more concerned with the potential implications for human and environmental health. Haynes recalled that the historical excitement over DDT and chlorofluorocarbons ultimately led to disaster due to unanticipated, negative environmental consequences, meaning that now is the time to advocate for proactive design of nanomaterials. “If we understand the molecular-level interactions between these particles and a biological system, we can think about how to achieve safe design,” she said.

Shewanella bacteria exposed to nickel manganese cobalt oxide nanoparticles show decreased respiration and reproduction.

Haynes described a test case of evaluating the safety of a common nanomaterial used in lithium ion batteries in relation to the same bacterium, Shewanella oneidensis, which was the focus of a previous presentation. “This is one of the most robust organisms we study,” said Haynes, introducing Shewanella and the nanoparticle of interest, nickel manganese cobalt oxide (NMC), which is used in electric car batteries. If estimates of electric car sales by 2020 prove accurate, roughly 10⁹ kg of NMC nanoparticles will be on the road in the coming years, with no infrastructure available for recycling the material and no information about potential safety issues once the particles are landfilled. “If these bacteria are impacted [by nanoscale NMC], we are going to have a bigger environmental issue,” she said.

Experiments in Haynes’ lab showed that Shewanella show reduced respiration and reproduction in the presence of NMC nanoparticles. Further exploration revealed that ion dissolution, specifically incongruously high dissolution of cobalt and nickel in relation to manganese and lithium, was especially toxic. Tuning the stoichiometry of the material—reducing the nickel and cobalt and increasing the percentage of manganese—resulted in an equally effective battery material with minimal toxicity.

Hidden within the genetic code is a remarkably complex network of regulatory elements that play critical roles in health and disease. The second day of the symposium began with a series of presentations describing some of these regulatory mechanisms and research efforts to harness them for therapeutic impact. Matthieu Gagnon opened the session with a discussion of the increasing threat of multidrug-resistant bacteria and the push to develop new antibiotics that are both effective and limit the potential for resistance.

More than half of all antibiotics target the bacterial ribosome, interrupting protein synthesis. Previous research has demonstrated that various classes of antibiotics bind to different functional centers of the ribosome, intervening differently in the translation process. Nature has its own version of these chemical interrupters, in the form of antimicrobial peptides—compounds produced by many plants, mammals, and insects that bind to bacterial ribosomes and protect the host from infection.

The antimicrobial peptide oncocin binds to a known site of antibiotic action, the peptide exit tunnel, blocking it completely.

Gagnon explained his work using x-ray crystallography to analyze the mechanisms of several antimicrobial peptides (AMPs), including onconin, which is produced by honey bees, and bactenecin derived from cows. Unlike many other antimicrobial peptides, which act through membrane lysis, this particular class of AMPs enters the cell and completely blocks the peptide exit tunnel. “What’s interesting is that these peptides overlap with the binding sites of several known antibiotics that are known to bind to the peptide exit tunnel,” said Gagnon. “By imaging these structures and understanding the mechanisms by which these antimicrobial peptides inhibit protein synthesis, we can begin to understand how these may provide leads for new drug candidates,” he explained.

Bradley Pentelute continued the theme of ribosome biology, but rather than analyzing its function, Pentelute and his collaborators are attempting to mimic it. “We’re not as good as a ribosome, yet, but we’re certainly trying to get there,” he quipped, introducing the concept behind a device of his own design—a fully automated, flow-based peptide synthesis machine fondly dubbed “The Amidator.” The dream of creating functional synthetic peptides as the basis for new drugs and vaccines is not a new one, but the ability to do so precisely, affordably, and at a speed that even approaches the remarkable pace at which nature bonds amino acids—up to 10 per second—has eluded scientists until now.

A fully automated peptide synthesis machine can bind amino acids in seconds and form functional synthetic proteins.

Over the course of several years, Pentelute has refined techniques for automated peptide synthesis, first by embracing a flow-based approach over batch synthesis, then building several generations of semi-automated machines capable of binding amino acids to build polypeptides at a rate of about three minutes per bond—far faster than manual synthesis, which requires up to 30 minutes per bond. Only a fully automated system that forms bonds in seconds could feasibly fill what Pentelute deems a “manufacturing gap” in developing next-generation peptide-based therapies, including personalized cancer vaccines. The latest version of the Amidator comes closest to realizing this goal, binding amino acids in just 30 seconds and giving scientists the ability to fully customize reagents, temperature, flow rates, and other factors to create custom polypeptides—and even small proteins.

Kate Meyer shifted the discussion from proteins to the steps that precede protein production—RNA transcription and gene regulation, specifically focusing on the mechanisms by which RNA modifications regulate gene expression. Recent studies have confirmed that RNA, much like DNA, is susceptible to reversible chemical modifications, and that these changes can have widespread impacts on gene expression. Meyer focused on one post-transcriptional modification called m6A, which results from methylation of adenosine residues in RNA. This modification eluded researchers’ efforts to identify and study it, but the advent of commercially available antibodies with sensitivity to m6A has facilitated studies of the influence of this surprisingly common mark. “About 25-33 percent of the genome at any time is encoding an RNA that gets methylated, and m6A is found in at least 20 percent of the transcriptome,” said Meyer.

Research on the location and function of m6A reveals that m6A-containing RNAs have a unique distribution, and are most prevalent within 3’ UTRs—a key region for RNA regulation—and near the stop codon. Meyer reports that determining the role of m6A-mediated changes in human health and disease is a rapidly growing field of research, particularly as these changes contribute to development and functioning of the nervous system, as brain tissues evidence high enrichment of m6A.

Computational tools can be a powerful complement to studies of biological systems, allowing researchers to create dynamic in-silico representations of physical processes, including cell and organ growth and regulatory processes. Celeste Nelson gave the first of two presentations on modeling biological systems. She described the impressive gas-exchange capabilities of healthy human lungs, as well as the devastating impacts of lung disease and disorders, particularly in newborn infants and those suffering from asthma and chronic obstructive pulmonary disease.

All lungs are not created equal, nor are they constructed through the same physical mechanisms, Nelson explained. By elucidating these developmental and morphological differences, as well as the physical forces that drive branched lung formation, she hopes to tap the evolutionary diversity of lung structures to create “a toolbox to engineer new organs in the future.”

Nelson reviewed the branching architecture of the embryonic chicken lung, illustrating the phenomenon known as apical constriction, which is responsible for effecting shape change in epithelial cells to facilitate branch formation. If this process is inhibited, branching too is inhibited. Computational models visualizing the primary chicken bronchus as a thick-walled tube provided the first confirmation that the physical force of apical constriction alone is adequate to generate branches.

Airway smooth muscle differentiates at the site of bifurcation during the development of mammalian lungs. The muscle provides critical support for the developing branches.

Branch formation in humans is more complex, as mammalian lung development follows a bifurcating branch pattern, where a parent branch splits into two daughter branches. This process, repeated eight million times in humans, is driven not by apical constriction, but by the concurrent differentiation of airway smooth muscle tissue at the site of each bifurcation. “This smooth muscle proliferates around the epithelium, cinching it in place like a corset,” said Nelson. “If we interfere with this process by speeding it up, we wrap the airways like a mummy, and if we prevent differentiation, the epithelium will fail to bifurcate—it just buckles.” she continued. Studies in mice show that this tendency to buckle via viscoelastic instability is restricted by forces from the smooth muscle that supports branches as they form in mammals.

Every time a cell completes a cycle of division, it faces a choice—enter the cycle again, or shift into a quiescent state. The signals that determine that course of action—to divide, or not to divide—were the subject of a presentation by Blavatnik National Finalist Benjamin Tu, who explained how studies of budding yeast cells have yielded surprising insights into the role of metabolites in regulating both healthy and malignant cell growth.

It has been well-documented that yeast cells grown in a chemostat undergo periods of oscillations in oxygen consumption. These robust changes in metabolism led Tu and his group to investigate potential changes in genetic expression during those cycles. They determined that yeast cells express distinct sets of genes associated with different phases of the cell cycle—specifically stress/survival, growth, and division— as their metabolic state changes. “We were especially interested in the genetic changes at the transition between the stress phase and the growth phase,” said Tu. “What signals the cell to make that transition?” he asked.

Levels of acetylated histones rise as yeast cells transition from a stress/survival phase into a growth phase.

Experiments show that glucose, acetate, lactate, and other products of glycolysis trigger cells to enter a growth phase, and Tu noted that these metabolites can all be converted to acetyl-CoA. When cells enter a growth phase, acetyl-CoA levels rise, as do the levels of acetylated histones in the genes associated with growth. “This molecule is a key gauge of the metabolic state of the cell— it’s like a gatekeeper that enables access to all these genes a cell can turn on in tune with its metabolic state,” he said.

Understanding the importance of acetyl-CoA for cell growth led to further studies of the role of metabolites in cancer cell growth. As cancer cells produce energy through aerobic glycolysis, Tu searched for an alternative pathway through which cancer cells might access acetyl-CoA for growth, ultimately returning to yeast cells for inspiration. He found that much like yeast, mammalian cancer cells make acetyl-CoA through the conversion of acetate via the enzyme acetyl-CoA synthetase (ACCS2). Experiments in animal models confirm the role of the enzyme in providing this key metabolite to malignant cells: mice with suppressed ACCS2 show increased resilience to cancer, while normal cell growth is unaffected. They also evidence resistance to obesity, even on a high-fat diet. “ACCS2 doesn’t seem to regulate typical growth and development,” said Tu, remarking that inhibition of this enzyme may have therapeutic potential.

The Zika Crisis

While diseases like Zika and Ebola are relatively recent additions to the news cycle, analysis of adaptive mutations in the human genome show that these viruses, among many others, are anything but new to humankind. Such insights are central to Pardis Sabeti’s efforts to transform how the scientific and medical communities respond to disease outbreaks. Genomic data, such as the kind Sabeti and her collaborators gathered in Nigeria amid an outbreak of Lassa fever, and in Sierra Leone as Ebola ran rampant through West Africa in 2014, provide unprecedented opportunities for real-time surveillance, tracking, diagnosis, and treatment of emerging infectious diseases.

“The most important thing genomic data can tell you is that we have to act fast—these diseases are moving targets,” Sabeti said, discussing the results of the rapid-fire sequencing of 99 genomes of the Ebola virus she and her colleagues at the Broad Institute published during the peak of the Ebola crisis in 2014. By making the viral genomes public, Sabeti and others working to contain the virus could analyze the evolution of the disease by tracking mutations as it adapted and spread through the population—information that informed both containment measures as well as efforts to create an Ebola vaccine. “These are all fundamentally driven by the genome of the virus, and if it changes, we have to change our approach too,” she said.

Sabeti also described her lab’s contributions to understanding the Zika virus. Drawing from patient samples collected in ten Zika-affected countries, the researchers created the first genomic family trees of the virus, tracing Zika’s path from Brazil to the Caribbean, and into the United States. These data revealed that Zika was circulating well before it was first detected, a phenomenon Sabeti sees in most infectious diseases she tracks. “This information tells us that our surveillance can be far better,” she said.

Zika circulates for a short time and in low concentration in patients’ blood, making diagnosis challenging.  Improving diagnostic methods for Zika is a priority, especially for pregnant women, and Sabeti and her collaborators— Blavatnik National Laureate Feng Zhang among them—are addressing the challenge with their CRISPR-based diagnostic platform, SHERLOCK. Using CRISPR enzymes that search for RNA, rather than DNA, and cut not only targeted viral RNA but also red fluorescent “reporter” RNA, the researchers are testing an inexpensive, highly sensitive Zika assay that uses direct patient samples at room temperature.

While no one can pinpoint the site of the next infectious threat, Sabeti sees genomic data as the key to revolutionizing outbreak response. “We can create an end-to-end system where we get the genome sequence of a virus, immediately design assays to target it, and then test those primers and guides, and we can do it all in days,” she said. “This is what we’re most excited about.”

Tales of the Cosmos

For 400,000 years after the Big Bang, the universe was simple and uniform—an expanding medium of dark matter and just two gases, hydrogen and helium—according to Eli Visbal, who studies the formation of the earliest stars and the first supermassive black holes. Over the next billion years, the universe experienced changes that Visbal characterizes as an “immense transition from simplicity to complexity,” with the formation of stars, galaxies, and billion-solar mass black holes. Understanding the nature of this transition and developing theoretical frameworks to describe the forces that drove it are key not only to understanding the early universe, but to guiding the development of next-generation telescopes, which cosmologists hope will validate these frameworks.

Visbal reported on his work creating large-scale simulations of early star formation—the first to account for the fact that baryonic, or normal matter, and dark matter move through the universe at different speeds, and that this relative difference in velocity may suppress star formation. Through simulations of large regions of the early universe, Visbal and colleagues noted that in dense areas with increased relative velocity, star formation was likely strongly suppressed.

Simulations of overly dense areas have also led to a possible explanation for a quandary that has long puzzled cosmologists: evidence points to the existence of billion-solar mass black holes when the universe was roughly 800 million years old, yet traditionally, such supermassive black holes are thought to develop over billions of years. Visbal proposed a theory that may explain the rapid growth of these black holes, explaining that if an early galaxy was closely neighbored by a dense dark matter halo, radiation from the dark matter halo may be enough to “switch off” the galaxy’s ability to form stars, leading to a direct collapse and the formation of a larger-than-expected “seed” black hole. “Under very specific conditions—namely a high flux from a nearby source—it’s possible that instead of making stars, a galaxy becomes a massive black hole, which would give us a head-start in growing a supermassive black hole more quickly,” he said.

Frontiers in Materials Science

The symposium concluded with a review of the role of quantum materials and systems in transformative new technologies. Dmitri Talapin hailed a new era of materials and devices built with “designer atoms” rather than through traditional chemistry, which limits interactions between solids with different properties. As previous speakers noted, nanoscale materials allow for unprecedented tuning and optimization of electronic, magnetic, optical, and catalytic properties, and can be combined to form specialized, non-equilibrium materials. Talapin describes the field as “a very rich playground,” where solid materials with distinct functionalities come together to form the basis for next-generation devices including field-effect transistors, semiconductors, LED displays, and photovoltaic cells.

Direct optical lithography of functional inorganic materials, or DOLFIN, is a new technique that allows for nearly limitless patterning on nanocrystalline films.

Researchers have long appreciated the potential for nanomaterials to transform future devices, but building larger-scale, complex structures with nanocrystals has remained challenging. Enter DOLFIN, or Direct Optical Lithography of Functional Inorganic Materials, a technique Talapin and collaborators at Argonne National Laboratory pioneered to improve nanoscale manufacturing. In traditional transistor manufacturing, photolithography is used to build patterned circuitry onto silicon chips in sequential layers. The process is effective, but limited to select materials and application. DOLFIN instead relies on nanoscale materials with different properties suspended in an “ink,” which is then evaporated, resulting in nanocrystalline thin films with remarkable electron mobility. By adding light-responsive surface ligands and exposing them to ultraviolent light in a desired pattern, the researchers can bypass the traditional patterning process, making the technique useful for a wide range of applications. “This is an entirely new platform for designer functional materials,” said Talapin.

The symposium concluded with Alexander Pechen’s discussion of the second quantum revolution, which seeks to use the counterintuitive phenomena of quantum systems for a range of practical applications. While some technologies based on quantum systems already exist—including quantum communications networks—Pechen and others in the field believe the most exciting applications are yet to come. Quantum computers, which use quantum bits, or qubits, versus standard bits, have the potential to yield impossibly fast computational speeds due to the unique dual-state of the qubit. Similarly, quantum cryptography, which is already in use in key distribution networks, allows for nearly unhackable transmission of information; in quantum states, any observation or measurement of a system modifies that system, thus any attempt to intercept the message alters it. “It’s impossible to get information and be invisible at the same time,” Pechen said. He also reviewed the potential applications for quantum control systems and simulations.