These are all pages which were linked to at some point for reference purposes or proof of theory. There are also some in here which are points of interest to me.
“Cell-compressing technique a new path in immunotherapy”
Cell-based immunotherapies, which often involve engineering cells to activate or suppress the immune system, have delivered some dramatic results to cancer patients with few other options. But the complex process of developing these therapies has limited a field that many believe could be a powerful new frontier in medicine.
Using a proprietary platform and an unconventional approach, startup SQZ Biotech is trying to expand immunotherapy impact by simplifying the process of engineering immune cells, thus unlocking a slew of new applications for the technology.
SQZ co-founder and CEO Armon Sharei SM ’13 Ph.D. ’13 says his company leverages a simple process—squeezing cells so they can be penetrated by specific molecules—to engineer a broader suite of cell functions than has been possible with the gene therapy approaches that have attracted the bulk of the investments in the field.
In the middle of next year, backed by over $100 million in funding and a collaboration with Roche that could net SQZ over $1 billion in drug development milestone payments, the startup is aiming to begin clinical trials on a treatment targeting human papillomavirus (HPV)-positive tumors. The company’s next potential therapy is aimed at autoimmune diseases including Type 1 diabetes.
Clinical trials will be the true test for a technology that Sharei believes can have a life-altering impact across a variety disease types.
“There’s many things SQZ can do,” Sharei says. “We think [these two clinical programs] are just the beginning.”
A novel approach
CAR T-cell therapies were approved by the U.S. Food and Drug Administration in 2017. They work by extracting a patient’s T cells, known as the soldiers of the immune system, and genetically engineering them to attack cancer cells. The engineered T cells are then injected back into the patient. The process has demonstrated the remarkable potential of immunotherapy, but it is still being refined, has certain limitations, and can be prohibitively expensive.
SQZ’s lead programs avoid genetic engineering to modulate long-term immune responses. The company’s current focus in oncology is on a broad class of cells known as antigen presenting cells, or APCs, which Sharei describes as the “generals of the immune system.” APCs can instruct a patient’s T cells to attack cancerous cells by presenting the right antigens on their surface in a function of the immune system that occurs naturally.
Engineering APCs to drive specific immune responses has been a struggle for researchers to date, but SQZ has shown that their platform offers a simple, scalable way to tackle the issue. The platform works by squeezing a patient’s immune cells through narrow channels on a microfluidic chip, making the cell membranes temporarily open up. Tumor-associated antigens are inserted into the cells and then naturally present on the cell’s surface, creating an APC. The engineered APCs can then be given back to the patient, where they can instruct the patient’s T cells as they naturally would, offering a relatively simple way to train T cells to attack cancer cells.
Conversely, when SQZ’s technology is used to target autoimmune diseases, red blood cells can be squeezed and manipulated to suppress an immune response, which Sharei says could lead to an innovative approach to treating chronic auto-immune diseases such as Type 1 diabetes.
An unexpected breakthrough
The technology behind SQZ was discovered out of exasperation as much as innovation. It began as a research project in the lab of Klavs Jensen, the Warren K. Lewis Professor of Chemical Engineering and a professor of materials science and engineering at MIT.
For over three years, researchers on the project attempted to shoot materials into cells using a microfluidic device and a jet. The cells proved to be difficult to penetrate, often deflecting away from the jet’s stream, so the team started forcing the cells toward the jet by constricting the cells through smaller channels within the chip. Eventually the project started to yield limited, often uncontrollable, results.
“It was a rough project,” remembers Sharei, who joined the project as a Ph.D. candidate when it was roughly two years old, while being co-advised by Jensen and Robert Langer, the David H. Koch Institute Professor. “There was quite a while when nothing was happening. We kept banging our head against the wall with the jet technique.”
One day the team decided to run the cells through the system without the jet and found that biomaterials in the fluid still entered the cells. That’s when they realized that constricting, or squeezing, the cell was opening up holes in the cell membranes.
The discovery set off a string of experiments to improve the process. In 2013, Sharei, Jensen, and Langer founded SQZ Biotech to share the cell squeezing technology with other research groups. But those collaborations didn’t produce the kind of groundbreaking experiments Sharei and his team were hoping for.
“Companies and academics weren’t really using SQZ for the new things it could do,” Sharei says. “They were using it for the things they could already do, just to do them better. That wasn’t going to have the game changing impact we envisioned for it.”
So SQZ pivoted from providing a lab tool to developing new therapies. Sharei, whose undergraduate work in organic electronics had made him an unlikely participant in the original research project to begin with, found himself with his first full-time job running a company with a unique strategy.
“At the time, the cell therapy industry was very focused on CAR T-cell therapy and gene editing,” Sharei says. “We thought there were much more powerful and simple concepts to implement [with SQZ], and you could hit a lot more diseases. This was an initially difficult message to convey to the field.”
But the broader perception of SQZ changed overnight when the startup signed a partnership with Roche toward the end of 2015, which marked Roche’s first investment in cell-based immunotherapies. Recently, after nearly three years of encouraging preclinical research, Roche announced a dramatic expansion of that partnership, to include more types of APCs in the upcoming clinical trials. The deal gives SQZ $125 million in upfront payments and near-term milestones. On top of that, SQZ may receive development milestone payments of over $1 billion from the pharmaceutical giant. The collaboration also stipulates the two companies could share certain commercial rights to approved products in the future.
The deal gives SQZ some spending power as it tries to strike a balance among pursuing research initiatives internally, partnering with other companies, and granting licenses to outside research groups.
For Sharei, the researcher-turned-CEO, the goal is finding the right path to turn SQZ’s potential into treatments that maximize impact for patients.
“The long-term vision is a company that’s creating many different cell-based therapeutics that have an impact across different disease areas,” Sharei says. “But getting there is all about seeing how these [early trials] do. And as those start to show proof, we can expand into different disease areas as well as broaden the footprint of our early trials.”
“First immunotherapy success for triple-negative breast cancer”
“New research led by Queen Mary University of London and St Bartholomew’s Hospital has shown that by using a combination of immunotherapy and chemotherapy the body’s own immune system can be tuned to attack triple-negative breast cancer, extending survival by up to ten months.
The research, which is published today in the New England Journal of Medicine and presented at the European Society for Medical Oncology 2018 Congress in Munich, also showed that the combined treatment reduced the risk of death or the cancer progressing by up to 40 per cent.
Triple-negative breast cancer often affects young women, with many people diagnosed in their 40s or 50s. The standard treatment is chemotherapy, which most patients quickly develop resistance to. If the disease spreads to other parts of the body, survival is often only 12 to 15 months.
The new treatment combines standard weekly chemotherapy with the immunotherapy medication atezolizumab which is given once every two weeks. The combination works by chemotherapy ‘roughening up’ the surface of the cancer, which enables the immune system to better recognise and therefore fight the cancer as a foreign object.
‘A massive step forward’
Author of the trial Professor Peter Schmid, Professor of Cancer Medicine at Barts Cancer Institute, Queen Mary University of London, and Clinical Director of the Breast Cancer Centre at St Bartholomew’s Hospital, explained: “These results are a massive step forward. We are changing how triple-negative breast cancer is treated in proving for the first time that immune therapy has a substantial survival benefit. In a combined treatment approach, we are using chemotherapy to tear away the tumour’s ‘immune-protective cloak’ to expose it as well as enabling people’s own immune system to get at it.
“Triple-negative breast cancer is an aggressive form of breast cancer; we have been desperately looking for better treatment options. It is particularly tragic that those affected are often young, with many themselves having young families. I’m thrilled that by using a combination of immunotherapy and chemotherapy we are able to significantly extend lives compared to the standard treatment of chemotherapy alone.”
Based on the results of this trial this new treatment is currently under review by health authorities and will hopefully become available in the NHS in the near future. In the interim, patients at St Bartholomew’s Hospital with triple-negative breast cancer are offered immunotherapy within ongoing trials.
“Tumor cell expansion challenges current physics”
A malignant tumor is characterized by the ability to spread. To do so, tumor cells stick to the surrounding tissue (mainly collagen) and use physical forces to propel themselves. A study published in Nature Physics by a team led by Xavier Trepat, lecturer at the Department of Biomedicine, University of Barcelona (UB), and Jaume Casademunt, professor of Physics at the UB, reveals the forces these tumor cells use to spread.
Researchers put breast tumor cells on a collagen-rich surface and observed how they expanded. The technology Trepat’s group developed allowed them to measure the physical forces used by the cells during the process, which has not been observed before. They report that tumor metastasis depends on a competition between forces: cells stick to each other and are kept together, and at the same time, they adhere to the environment in order to escape. Depending on the predominant force, the tumor will keep its spherical shape or it will spread around the tissue surface. “It is a similar process to placing a drop of water on a surface. In some surfaces, the drop will spread out, for example on a brick, while the drop will remain spherical on waterproof fabric, for example,” says Carlos Pérez, IBEC researcher, intern at ‘la Caixa’ and first author of the article.
Despite the similarities between tumors and liquids, the physics in these two phenomena are very different. “Wetting in surfaces is a core problem in classical physics we understand, but tumors seem to follow very different laws,” notes Ricard Alert, UB researcher, intern at ‘la Caixa’ and co-author of the article. Unlike passive fluids, cells can create forces and move on their own. This turns biological tissues into active fluids, and in particular, tumors into active drops. Therefore, understanding tumor expansion on a surface requires developing a new physical theory that researchers have named “active wetting.”
“When we think about states of matter, we usually think about solids, liquids or gases. Our results and other laboratory results point out that living cells do not fit into this scheme and behave like another state of matter, which we call active matter,” says Jaume Casademunt. When a tumor appears, cells accumulate mutations and their mechanical properties change. In general, tumor cells lose the connection between one another and join with their environment. During tumor growth, the own environment changes too, increasing the amount of collagen and rigidity. “Our experiments show that these changes are enough to put the balance of forces out of order, causing cells to spread around,” says Xavier Trepat.
These findings show the importance of physical forces in metastasis, opening the window to the development of therapies to alter the mechanics of tumors as a potential treatment.
“How a sleeping cancer awakens and metastasizes”
Scientists at Cold Spring Harbor Laboratory (CSHL) have determined one of the ways in which cancers in remission can spring back into action. This knowledge has inspired a new treatment idea designed to prevent cancer recurrence and metastasis.
Even after successful cancer treatment, dormant, non-dividing cancer cells that previously detached from the original tumor may still exist elsewhere in the body. If awakened, these cells can proliferate and grow into metastatic tumors. A CSHL team studying metastasis to the lungs has now identified signals accompanying inflammation that can awaken dormant cancer cells.
Whether inflammation can directly cause cancer recurrence, and if so how, has not been clear. In their new research, the team demonstrates that sustained lung inflammation, including that caused by tobacco smoke exposure, can cause dormant breast and prostate cancer cells that have traveled to the lungs to awaken and begin to divide. These cells can now form a metastasis in the lungs. Metastasis accounts for the bulk of lethality from most common cancers.
Importantly, the team, led by CSHL Associate Professor Mikala Egeblad,and including researchers from the Dana Farber Cancer Institute and UC Davis, also demonstrates a way of blocking the signaling that awakened the dormant cancer cells, a concept that could prevent cancer recurrence or lessen its frequency.
Egeblad’s team showed that sustained lung inflammation, caused either by exposing mice to tobacco smoke or to a component of bacteria known as endotoxin, induced common white blood cells called neutrophils to awaken nearby dormant cancer cells in an extraordinary way.
Neutrophils, which we normally rely upon to kill invaders like bacteria and yeast, have several ways of vanquishing their prey. One is to expel their DNA into the space beyond the cell membrane. Laced with toxic enzymes, this expelled DNA forms a gauzy, net-like trap (called neutrophil extracellular traps, or NETs) that can kill a pathogen.
The new research shows that sustained lung inflammation causes the formation of NETs in the area around dormant cancer cells. Two enzymes in the NETs, called NE (neutrophil elastase) and MMP9 (matrix metalloproteinase 9), interact with a protein in tissue called laminin. In sequence, first NE then MMP9 make cuts in laminin proteins. This changes the protein’s shape, exposing a new surface, called an epitope.
This epitope, when recognized by dormant cancer cells nearby, spurs signaling that awakens the cancer cells. “The dormant cancer cells recognize that new shape of the laminin and they say, ‘we should start growing again,'” Egeblad says.
The team created an antibody to block the epitope exposed on the laminin proteins. In mice, this prevented the reawakening of dormant cancer cells nearby. Work has begun to optimize the antibody and compare it with other approaches to interfere with NETs, with the hope of eventually conducting trials in people.
Albrengues J et al, “Neutrophil extracellular traps produced during inflammation awaken dormant cancer cells in mice” appears online in Science, September 28, 2018.
“Tiny vortices driven by magnetic fields might be able to move microscopic particles”
scientists at the Department of Energy’s (DOE) Argonne National Laboratory think that, on a much smaller scale, tiny vortices could one day be used to move microscopic particles.
The vortices could one day be used in lab-on-a-chip designs to move particles, like blood cells, from one place to another, or to build materials with self-healing properties.
Before they can harness the tiny vortices, though, scientists need to understand how their components, or colloidal particles, form and function. By exposing groups of microscopic metal magnetic rollers to various magnetic fields, Argonne physicist Alexey Snezhko and postdoc Gasper Kokot are creating their own vortices to accelerate that understanding.
“Transporting objects is a far reaching goal, but we’re working on the first steps, which is to understand the basic principles,” Snezhko said. “We are doing this as a search for a new kind of active material. Materials existing out-of-equilibrium.”
The pair published recent findings in the June 14 issue of Nature Communications.
In their first series of tests, researchers put about 100 miniscule magnetic nickel rollers, or spheres, in a water matrix exposed to a single axis magnetic field, followed by an alternating magnetic field.
“Each particle is like a small compass,” Snezhko explained. “And we use a magnetic field to transfer energy.”
Within the single magnetic field, the rollers lined up as if they were indeed part of a compass needle, but when exposed to a magnetic field that changed orientation 60 times a second, the rollers instead flocked together and formed vortices.
In the experiments, the vortices were allowed to move freely in the water matrix, where researchers studied their natural behavior. When exposed to the flipping magnetic field, the particles flipped as well and started to roll.
“This is the only known system where we’ve seen this type of rolling and self-organization with this flocking behavior,” Kokot said. “The group moves as one, just like a flock of birds.”
As the particles flock together, the system spontaneously forms a vortex, but the vortex also has some strange properties, like inexplicably switching directions. In their study, the vortex switched rotational direction on average once every 160 minutes.
Personal Note: This was posted/published after I had written my own theory of such events taking place in my notebook. Another personal note: You have to be an idiot to talk about waiting to start talking about utility. What is going on with these guys? Are they going to consider it to only be usable if it involves data protection like 99% of all other scientific discoveries lately? — A group of scientists also found out light could be sped up, and they say it isn’t applicable because it wouldn’t work with fiber optics. Use it for better telescopes through feedback systems, and slowing light back down with crystals and speeding it back up. That will give you a nice clear picture if you can perfect it, and cause all wavelengths to hit at the same time.
“We would like to know why it switches, what controls the rate of switching,” expressed Kokot. “Because if we can control it, we can start talking about utility.”
The researchers suspect the magnetic particles can actually talk to each other in a manner similar to birds to avoid each other in flight. And the hope is scientists can eventually use the knowledge to self-assemble and transport structures in the microscopic world.
There’s a lot more to study before scientists will fully understand or be able to control the vortices, but Snezhko said he thinks that, eventually, they could be used like tweezers, moving non-metallic particles in and out of a liquid matrix.
“This vortex interacts with particles through liquid,” he said. “It can capture a particle inside and move it.”
But it’s not a one-size fits all solution, Kokot said. Particles being transported have to be the right size. If they’re too small, they get incorporated into the body of the vortex and slow it down. And if they’re too large, they destroy the vortex. Only the right size particle will be captured in the eye of the vortex core and transported. It might also be possible to use a particle to pin a vortex in place, where it could hold or capture particles flowing past, Snezhko said.
“Eventually, as you develop better control of these vortices, you can use them to capture cargo and move it across a surface,” Snezhko said. “Right now, we can capture a particle, but we can’t steer it. So doing that in a more controlled way is something to look at.”
For now, the researchers continue to experiment with an array of magnetic field types to see how the rollers respond in different environments and elicit new and perhaps more complex responses and controls.
“Study finds ‘sweet spot’ where tissue stiffness drives cancer’s spread”
In order for cancer to spread, malignant cells must break away from a tumor and through the tough netting of extracellular matrix, or ECM, that surrounds it. To fit through the holes in this net, those cancerous cells must elongate into a torpedo-like shape.
Researchers from the University of Pennsylvania and The Wistar Institute have now found that physical forces exerted between these cells and the ECM are enough to drive this shape change. Those forces converge on an optimal stiffness that allows cancer cells to spread.
The findings, published in the Proceedings of the National Academy of Sciences, suggest that drugs that target the stiffness of the ECM could potentially be used to prevent metastasis.
he study was led by Vivek Shenoy, professor in the Department of Materials Science and Engineering in Penn’s School of Engineering and Applied Science, and Hossein Ahmadzadeh, a graduate student in his lab, with contributions from Ashani Weeraratna, the Ira Brind Associate Professor and program leader of the Tumor Microenvironment and Metastasis Program at Wistar.
Research on the physical-feedback mechanisms between cancer cells and their environment is part of Penn Engineering’s larger efforts to understand such dynamics, housed at the Physical Sciences Oncology Center and the new Center for Engineering Mechanobiology, which is co-directed by Shenoy.
Shenoy and colleagues published findings that detailed the feedback mechanism exhibited by cancer cells and the ECM surrounding them. There, they showed how this mechanism stiffens and aligns the collagen fibers found in ECM. The new work looks at the cell side of the equation and how cells must switch from rounded to elongated in order to leave the tumor squeeze through the ECM.
“What we’re showing is that the mechanical factors alone can lead to the change in phenotype in cancer cells,” Shenoy said. “This is the first quantitative analysis of the shapes of cancer cells as they invade from the tumor.”
The Penn researchers postulated that the key factor of this interplay is finding a “sweet spot” in the stiffness of the ECM.
“The cells in a tumor are sticky,” Shenoy said. “Without the collagen fibers of the ECM pulling on those cells, you can’t break that cell-cell adhesion. But, if the ECM is too stiff, the pores in the matrix become too narrow and the cells can’t escape.”
After the Penn team modeled these interactions in computer simulations, the Weeraratna lab at Wistar conducted matching experiments to see if the results held up.
“We used melanoma spheroids embedded in a collagen matrix as a 3-D model to mimic in vitro what happens in the body when tumor cells leave the primary tumor to invade other tissues,” said Weeraratna. “Our observations perfectly matched and complemented the computer model. This study reaffirms, from a mechanobiology standpoint, the crucial role of the tumor microenvironment in orchestrating the fate of cancer cells and dictating prognosis and response to therapy.”
Insights from cancer mechanobiology could inform future diagnostics and potentially even treatments.
“The takeaway is that, if you look at what’s going on outside the tumor, you could make a prognosis of whether it will spread,” Shenoy said.
“Why is a remote Colombian town a hot spot of an inherited intellectual disability?”
RICAURTE, COLOMBIA—It’s late afternoon in this tiny town tucked into the Colombian Andes, when Mercedes Triviño, 82, lights the wood stove to start to prepare dinner. Smoke fills the two-bedroom home she shares with six of her adult children.
Francia, 38, one of the youngest, is the family’s primary breadwinner. She brings home 28,000 Colombian pesos (roughly $10) a day harvesting papayas in the fields just outside town. “Really, what I earn is just enough for eating and nothing else,” she says. Four of her siblings have fragile X syndrome, a genetic condition that causes intellectual disability, physical abnormalities, and often autism. Jair, 57, works alongside Francia when he can. Hector, 45, is also somewhat able to care for himself. Victor, 55, and Joanna, 35—who has both fragile X and Down syndrome—are less independent.
As Mercedes serves coffee on this July afternoon, sweetening it with a hefty dose of sugar and offering her best cups to her guests, she talks about the condition that dominates the lives of her family and many others here. Her niece, Patricia, 48, who lives a few blocks away, cares for two adult sons and a nephew with fragile X. More distant kin in town, the Quinteros, also have grown children with the condition. Other neighbors are adults with fragile X who have no caretaker and look after one another.
In Colombia, this town has long been known as the home of los bobos, “the foolish ones”—thanks in part to a 1980s novel and a later TV series that depicted families like the Triviños. More recently, scientists have caught on that it is home to the world’s largest known cluster of people with fragile X. One researcher, medical geneticist Wilmar Saldarriaga-Gil of the University of Valle (Univalle) in Cali, Colombia, has made Ricaurte the focal point of his scientific inquiry. Saldarriaga-Gil, who vacationed nearby as a child, says he has visited about a hundred times since the mid-1990s to trace how fragile X affected the town and its inhabitants—and to try to understand details of the syndrome’s biology. “This is a history of scientific research, a history of my community, a history of my life,” he says.
The payoff from research in this town could have global impacts. Caused by mutations in a gene called FMR1 on the X chromosome, fragile X syndrome is the leading cause of inherited intellectual disability worldwide; it affects as many as one in 2000 men and one in 4000 women. And as a single-gene cause of autism—a recalcitrantly complex condition—fragile X has been the focus of efforts to develop drugs for autism. The proteins disrupted in people with the syndrome are also key players in brain development.
In March, Saldarriaga-Gil and his colleagues reported that at least 5% of residents here carry either the full-blown fragile X mutation or less severe “premutations” that can trigger the condition in future generations. Premutation carriers usually escape cognitive problems, but some develop physical symptoms, including tremors and fertility problems. The research here might explain such variability, which could reflect how the protein FMR1 encodes, FMRP, interacts with other proteins and pathways.
The scale of Saldarriaga-Gil’s investigations is small—Ricaurte only has 58 full mutation and premutation carriers, by his count—but the research benefits because the town’s residents share the same environment and a similar genetic background, offering a natural control for some variables. “What you have [here] is something that certainly warrants a lot more intensive investigation,” says Jim Grigsby, a clinical health psychologist at the University of Colorado in Denver.
Saldarriaga-Gil’s obsession with this town began in 1980. As a boy, he spent summers at a family home in Huasano, 10 kilometers away. When he attended church here, he couldn’t help noticing the lanky men and women with large, flat ears who spoke very little or not at all. “Everyone who knows Ricaurte had curiosity,” Saldarriaga-Gil says. “Why is it happening here?”
Growing up, he heard many stories. According to one, nearby magnesium mines had poisoned Ricaurte’s groundwater, damaging the minds of people who drank it. Protestant missionaries to the region warned residents that God had sent “the foolishness” to punish them for worshiping “El Divino,” an image of Jesus in Ricaurte’s white A-frame church that draws Catholic pilgrims. “The other hypothesis was sorcery of some sort,” Saldarriaga-Gil says. In that version, women in the town prepared a love potion that sometimes went wrong, producing intellectual disability instead of undying devotion. Saldarriaga-Gil’s father warned him never to drink anything offered by a woman from Ricaurte.
Saldarriaga-Gil eventually set out to discover the truth as a medical student in the late 1990s. His adviser suggested the people here might have Down syndrome. But when Saldarriaga-Gil paged through a 1000-page medical textbook, he saw photographs of people who looked eerily similar to a boy he knew in Ricaurte—Patricia Triviño’s nephew Ronald. The people in the textbook had fragile X syndrome.
To confirm that the resemblance was more than coincidence, in 1997 Saldarriaga-Gil took blood samples from 28 people in town who he suspected were affected, Ronald included. He analyzed each person’s karyotype—the number and appearance of their chromosomes—by inspecting their blood cells under a microscope.
In most people, FMR1 contains anywhere from six to 54 repeats of a specific set of three DNA “letters,” or bases: CGG. In people with fragile X syndrome, however, the gene has more than 200 repeats. The extra DNA disrupts the X chromosome; under the microscope, tiny islands appear to break away from the chromosome, making it look fragile. Of the 28 people whose karyotypes Saldarriaga-Gil analyzed, 19 showed those telltale islands.
Premutation carriers, however, have between 55 and 200 CGG repeats—too few to be obvious under a microscope. In 2012, Saldarriaga-Gil decided to try to identify those carriers by building a pedigree chart to trace the condition’s inheritance through Ricaurte’s families. Premutation carriers often have affected children or grandchildren because in fragile X—as in other “triplet repeat” conditions such as Huntington disease—the number of repeats typically increases with successive generations. Working backward from affected individuals, Saldarriaga-Gil tried to guess at who had passed the mutation on. That approach took him only so far, however, because he had no definitive test for premutations.
The next year, his karyotype research caught the attention of experts in fragile X, including Randi Hagerman, medical director of the Medical Investigation of Neurodevelopmental Disorders Institute at the University of California, Davis. She and her colleagues offered to help spot the premutation carriers by using a polymerase chain reaction (PCR) test—which Saldarriaga-Gil wasn’t equipped to do in his own lab. PCR would make it possible to amplify and sequence the residents’ DNA.
Hagerman recalls being struck by Ricaurte’s promise for studying fragile X: “When I first visited this town, I was surrounded by individuals with fragile X syndrome, and I said, ‘Oh, my God, this is like ground zero for fragile X.’”
The two lane road to Ricaurte from Cali traverses sugarcane fields between the cloud-shrouded Andes that enclose the town. Saldarriaga-Gil estimates he has driven the route dozens of times in the past 5 years. Before 2010, Colombia’s drug trade made the trip dangerous. The region is safer now, he says, but the mountains still teem with farmers secretly growing coca, the raw material of cocaine.
Saldarriaga-Gil checks in on residents with fragile X every 2 months or so, offering routine checkups and monitoring them for complications. Over multiple visits between 2015 and 2016, he and his students also collected blood samples from 926 people, about 80% of the population. Genetic analysis of the samples led to his recent finding that about 5% of Ricaurte’s residents have either the full mutation or a premutation. He supplemented the genetic work by recording oral histories and digging up centuries-old land, marriage, and birth records with help from a local historian. Ultimately, Saldarriaga-Gil reconstructed much of the town’s history of the syndrome.
An unwieldy pedigree chart now dominates one of his office walls, spanning nine generations and 420 names. Two big families—the Triviños and Gordillos—form its trunk. Saldarriaga-Gil slashes lines through the deceased and scrawls notes in looping handwriting where he is still guessing at kinship.
One name is circled, with sunlike rays extending out in every direction: Manuel Triviño, who may be Mercedes’s greatgrandfather. Saldarriaga-Gil says he suspects Manuel was one of the town’s original settlers in the early 1880s and carried the premutation to Ricaurte. Everyone here with fragile X could be his direct descendant (although how the mutation spread to the Gordillos is still unclear). To confirm that “founder effect,” Saldarriaga-Gil’s team is conducting a haplotype analysis: The scientists are looking for other genetic variants shared by people with the condition, which would imply that they all share a common forebear.
Saldarriaga-Gil and colleagues from Univalle are also sequencing the exomes—the protein-coding portions of the genome—of the people from whom they took blood samples in 2015 and 2016. They hope to learn how genetic variability outside the FMR1 gene influences how fragile X mutations manifest themselves—and why people with the same FMR1 mutations can have such different outcomes.
Among women, “mosaicism”—in which a person’s cells aren’t all genetically identical—explains part of it. Because women have two X chromosomes, each cell turns off one of them at random. If most of a woman’s cells turn off the mutated copy, she might show few outward signs of the mutation; if the normal copy is shut down more often, she might be more severely affected. Mosaicism emerges differently in men, who have a single X chromosome: Some of their cells may have the full FMR1 mutation—200-plus CGG repeats—whereas others end up with the shorter premutation or with a complete deletion of FMR1.
The array of symptoms resulting from a mutation might also depend on how FMRP interacts with other proteins. FMRP is missing in people with the full mutation, which silences FMR1. Because FMRP controls the activity of nearly 1000 other proteins, many of which are crucial to the interactions between neurons, its loss can have far-reaching effects—particularly during brain development. But in people with the premutation, the impact of the reduced protein might be more or less severe depending on other genetic variations.
Saldarriaga-Gil and his colleagues predict that genetic analyses will reveal that people whose fragile X symptoms are similar have overlapping patterns of gene expression and protein interaction. “This type of population is ideal for this study because these people have a similar genetic background,” says Univalle geneticist Julián Andrés Ramírez Cheyne, who leads the exome study.
The ultimate goal for fragile X researchers is to develop treatments. Because of its connection to intellectual disability and autism, fragile X has been the focus of an extensive—and so far, unsuccessful—drug development program. Several candidates that showed promise in early clinical trials fizzled out in larger trials. Researchers are seeking new proteins or pathways to target—and some of those may emerge from the work done here. “Most geneticists would say there are genetic modifiers in some of these families,” says Eric Klann, director of the Center for Neural Science at New York University in New York City—clues, he says, to possible treatments.
Understanding the molecular underpinnings of fragile X might also explain why general anesthesia and some seizure medications are more toxic to premutation carriers than to typical people. Hagerman says she was struck by the number of premutation carriers here whose symptoms are unusually severe. Patricia Triviño’s sister Rosaura, 60, for example, is deaf and mute; her sister Julieta, 58, has seizures and uses a wheelchair. Hagerman says pesticides, sprayed heavily in the nearby fields, might be to blame. “Looking at the environmental contaminants could tell us a lot about vulnerability” in people with the mutations, she says.
No one here is waiting for radical new treatments. Even if the residents can help researchers develop drugs, they know they are likely to be among the last to receive them.
Mercedes Triviño’s son Jair is one of the oldest workers in the papaya fields, but he has no complaints. Even though his work is arduous, living among others with similar symptoms has given him a degree of freedom he’d be hard-pressed to find anywhere else. At the end of his shift on a hot July day, Jair fills the back of a pickup truck with fruit. He swings the heavy crates one by one, his wiry arms flexing until he has stacked nearly 100. He stops to wipe sweat from his brow and secures the truck’s door with an iron bolt. The driver starts the engine as Jair hops in the back. Jair says he looks forward to being back the next day “if it’s God’s wish.”
Back in town, Patricia, who is Jair’s cousin, says all she wants is a good drug to control the seizures of her sister Julieta. For years, Julieta has taken phenobarbital to control her convulsions, but the drug is risky for premutation carriers like her, who may be particularly vulnerable to its neurotoxic effects. Scans that Saldarriaga-Gil took show that portions of Julieta’s brain have shrunk, and in the past few weeks, she has started to complain of headaches. Another of Patricia’s sisters, Esperanza, 60, who also was a premutation carrier and relied on phenobarbital for years, died in 2015 after several massive seizures. Julieta could take safer medications, such as valproate, but getting a prescription hasn’t been easy.
In July, a new doctor who serves Ricaurte and three other towns arrives to make her rounds. Rubbing Julieta’s temples below her cropped black hair, the doctor explains that she doesn’t have the correct paperwork to prescribe valporate. She suggests Patricia take Julieta to a doctor in Bolívar, about 7 kilometers away. Patricia doesn’t own a car, and walking there would take her about an hour and a half.
For months, Patricia has pleaded with a local health minister, Viviana Alvarez, to secure basic sanitary supplies and protein supplements for Julieta—but to no avail. Although the family is entitled to free care through the government, Alvarez says her hands are tied: “Health insurance takes its time; the problem is on the national level.” The Hospital Santa Ana in Bolívar can’t help much, either. With just eight doctors, it fielded 15,000 appointments and 5000 emergency room visits in 2017. The hospital director has hired a physical therapist to visit about 15 people here with fragile X every weekday but he says Ricaurte will probably never have its own physician.
“I always want them to do more,” Saldarriaga-Gil says, although he understands the financial constraints. He tries to fill in the gaps during his visits and has enlisted a Colombian nonprofit to donate clothes and mattresses to many of the families.
Given the harsh realities of life here with fragile X, some residents have made difficult decisions about the future of their families. Rosario Quintero’s daughter, Sara, has the full mutation but shows no signs of the syndrome. Before Sara learned that she carried the mutation, she had a son, who also seems unaffected. But afterward, she had her fallopian tubes cut so that she cannot have any more children. Another carrier, who chose to remain anonymous, also decided not to have children.
Over the past decade here, only three children with fragile X have been born, and many with the condition are older than 50. Trapped in this valley by economic hardship and unyielding geography, the population with fragile X could slowly die out, Saldarriaga-Gil says. He is racing to understand the syndrome’s secrets before that happens.
This story was produced in collaboration with Spectrum, where Hannah Furfaro is a staff reporter.
“Focus: MRI of Electrons”
Physicists have developed nuclear magnetic resonance (NMR) as a tool to study physics and chemistry by probing nuclear spins. Today physicians use it for magnetic resonance imaging (MRI). In the 27 March PRL a team shows how the technology has now come back to physics: They used the principles of MRI to map the locations and mobilities of conduction electrons in crystals. They found a wide range of environments for the electrons, with some parts of the crystals restricting electronic motion much more than others. The technique allows the team to study electronic properties on a more microscopic scale than traditional “bulk” measures, which average properties over an entire crystal.
MRI using electron spin resonance (ESR) is similar to conventional NMR imaging, except that it probes the responses of electron spins to magnetic fields, rather than the responses of nuclear spins. With current technology, MRI is not possible with conduction electrons in metals because the so-called spin echo response to electromagnetic pulses normally decays in nanoseconds–too quick to measure. But Noam Kaplan of the Hebrew University in Jerusalem and his colleagues studied a type of organic crystal whose ESR signal lasts for microseconds, apparently related to its unusual anisotropic conductivity.
In these crystals–the radical cation salts–electrons flow essentially in one dimension, along molecular chains that span the length of the crystal (about 1 mm). In the past Kaplan and his colleagues measured electron density and mobility in the crystals using ESR, but these previous experiments produced data that were averaged over an entire crystal, despite clear indications that the crystals were not homogeneous. Inspired by his experience consulting for an Israeli medical imaging company, Kaplan suggested his students use the crystals as MRI “patients.”
The key to magnetic resonance imaging is to apply a magnetic field gradient–a field that varies with position. Since the frequency with which the nuclear or electron spins rotate depends on the strength of the local field, the location of an individual spin can be identified by the frequency of radiation it emits. Kaplan and his colleagues used field gradients in the two nonconducting directions of the crystal to get images with 30 µm resolution. In the high conductivity direction they turned on a gradient for two brief periods separated by about 10 µs–equivalent to two position measurements–as a way of determining electron mobility in that direction.
The technique gave two-dimensional maps of both electron density and mobility, with averages along the high conductivity direction in the crystals. The team found some correlations between low density and low mobility regions, possibly due to macroscopic “vacancies.” Although previous measurements showed that microscopic defects limited the electrons’ average range of motion to tens of micrometers, the new results revealed some regions where the electrons could traverse the entire crystal’s length unimpeded.
The work is “important because it [gives] a localized picture” of the electrons, rather than an averaged view, says Guenter Maresch of the National High Magnetic Field Laboratory in Tallahassee, FL. He says researchers would like a detailed understanding of the interaction of the electrons with crystal defects, in part as a model for one-dimensional conduction in nanoscale wires for molecular computers. Alex Smirnov of the University of Illinois in Urbana says ESR imaging has been applied to many areas of biology and chemistry, but the Israeli team has gotten a rare glimpse of conduction electrons by looking at these eccentric crystals. “They’ve brought ESR imaging into today’s physics.”
“Focus: Electron Speedometer”
“Like traffic cops with radar guns, physicists can now gauge the speed of electrons in a current. In the 27 January PRL, researchers describe a speed-measuring system that uses magnetic resonance and demonstrate a test in which they verified Ohm’s Law by directly observing electrons. The technique could eventually create the first images of the flow of electrons through materials at the micron scale.
The electric current in a material is not the same as the electron velocity but more like the number of cars that pass a specific highway exit per hour. A high car current could mean one lane of fast cars or many lanes of slow traffic. So Elmar Dormann of the University of Karlsruhe in Germany and his colleagues developed a technique to measure electron velocity, separate from current.
Their technique uses magnetic resonance imaging (MRI) technology but is not yet capable of making images. Like all MRI systems, it detects particles by monitoring their spin. In a magnetic field, the spin axis of each electron rotates, or precesses, around the field, just as a tilted, spinning gyroscope or top precesses around the vertical gravitational field. The precession generates radio waves whose frequency depends on the magnetic field strength. Now suppose that field strength varies from place to place inside a sample of material–say, strongest at one end and weakest at the other end, as in all MRI machines. The electrons’ radio wave frequencies will vary with their positions just as the field does.
To measure electron velocity, the team first ran the experiment with no current flowing through a crystal. They applied a short pulse of microwaves to start all the electrons precessing. Although they started out in synch, electrons in different places soon got out of step because of their different local magnetic fields. But before long, a second pulse forced all the spins to jump ahead in their cycles by different amounts, reversing their order, with the slowest-precessing spin in the lead and the fastest behind. After the same period of time, this re-ordering caused the spins to line up again, just where they started, and generate a radio “echo”. It was as though runners on a racetrack suddenly stopped five seconds into the race and then ran backwards for five seconds, putting them all at the start simultaneously. When the team performed the same experiment with a current flowing, many electrons were on the move, exploring a whole range of magnetic field strengths and precession speeds as they moved through the sample. So the second pulse did not re-synchronize all of the spins, and analysis of the radio echo showed how fast they moved.
The spins of protons are relatively easy to detect with MRI, but electron spins randomize more quickly following a pulse. So Dormann and his colleagues used a so-called radical cation salt crystal, a material where it takes microseconds for the electron spins to randomize, rather than nanoseconds, as in ordinary metals. Another major technical problem was that the electron current made its own magnetic field. The team managed to cancel it out by subtracting echoes from two runs with different field arrangements.
As a demonstration, the team showed that electron velocity depends on current in just the way classic theory predicts. But ultimately they hope to image the motion of electrons in a variety of materials. “The work is lovely because the theory just fits so well, and there, at the end of it all, is Ohm’s Law!” says Paul Callaghan of Victoria University in Wellington, New Zealand. Callaghan cautions, however, that the technique may be very difficult to replicate in other materials.
Kim Krieger is a freelance science writer in Norwalk, Connecticut.”
“Ultrafast manipulation of mirror domain walls in a charge density wave”
“Domain walls (DWs) are singularities in an ordered medium that often host exotic phenomena such as charge ordering, insulator-metal transition, or superconductivity. The ability to locally write and erase DWs is highly desirable, as it allows one to design material functionality by patterning DWs in specific configurations. We demonstrate such capability at room temperature in a charge density wave (CDW), a macroscopic condensate of electrons and phonons, in ultrathin 1T-TaS2. A single femtosecond light pulse is shown to locally inject or remove mirror DWs in the CDW condensate, with probabilities tunable by pulse energy and temperature. Using time-resolved electron diffraction, we are able to simultaneously track anti-synchronized CDW amplitude oscillations from both the lattice and the condensate, where photoinjected DWs lead to a red-shifted frequency. Our demonstration of reversible DW manipulation may pave new ways for engineering correlated material systems with light.”
Applying the same laser pulse to the α/β state (Fig. 2C) erased the β domains in the ROI, returning it to the original state (Fig. 2A and fig. S5E). Such reversible switching between α only and α/β states was repeated by more than 1000 pulses on four different samples. The result was also robust with different combinations of pulse wavelength and duration (fig. S2). As we discuss below, the switch is nondeterministic and its probability can be tuned by temperature and pulse fluence. Once switched, the sample remained in the α/β state upon cooling from the NC to the C phase (Fig. 2D). The transition temperature TNC-C is the same in both α and α/β states, again suggesting no pulse-inflicted sample degradation. A single pulse, up to the highest fluence attempted (11 mJ/cm2), was unable to create or annihilate α/β DWs in the C phase.
The diffraction patterns in Fig. 2 (C and D) do not discriminate between interlayer and intralayer DWs because of the large electron beam spot [90 μm × 90 μm, full width at half maximum (FWHM)]. To distinguish between the two possibilities, we performed selected area diffraction (SAD) on the same ROI of Fig. 2 (A to D) using a 1.1-μm-diameter beam of a transmission electron microscope (TEM). We observed intralayer DWs (Fig. 2E), with separate α (red circle) and β (blue circle) domains, divided by α/β DWs (yellow circle). Overlaid color masks denote the approximate domain locations. The yellow region suggests the presence of submicrometer domains, and we cannot rule out the possibility of interlayer DWs in this area. The unmasked corner (Fig. 2E, top right) shows the bright-field electron micrograph in grayscale, featuring bend contours due to underlying strain (25). We note the absence of correlation between locations of bend contours and α/β DWs, even under high magnification (fig. S3). This suggests that pulse-induced α/β DWs are unrelated to any macroscopic lattice deformation.
DW-dependent CDW amplitude oscillation
To investigate how these DWs modify the underlying CDW order, we characterized its amplitude mode (AM) frequency in the α/β state. This mode arises from a broken translational symmetry during the CDW formation (26). It manifests as a breathing mode of the CDW hexagrams (Fig. 3C, inset). In a time-resolved diffraction experiment, the AM causes an oscillatory transfer of intensities between the central Bragg peaks and superlattice peaks of both domains (see the Supplementary Materials for additional details) (27), as confirmed in our measurement performed at 40 K (Fig. 3, A and B, and fig. S4). The intensity sum rule is obeyed through the exact π phase shift between the Bragg and superlattice peaks. We obtained the mode frequency after Fourier transforming the oscillatory parts (Fig. 3, C and D), which is consistent with the AM frequency measured separately in the single-domain state under the same conditions (Fig. 3D, vertical line). In this case, α/β DWs did not modify the spectroscopic signature of the CDW.”
“Unstable cosmic domain walls may decay and produce observable radiation”
A domain wall is a type of topological soliton that occurs whenever a discrete symmetry is spontaneously broken. Domain walls also sometimes called kinks in analogy with closely related kink solution of the sine-Gordon model or models with polynomial potentials. Unstable domain walls can also appear if spontaneously broken discrete symmetry is approximate and there is a false vacuum.
A domain (hyper volume) is extended in three spatial dimensions and one time dimension. A domain wall is the boundary between two neighboring domains. Thus a domain wall is extended in two spatial dimensions and one time dimension.
Important examples are:
- Domain wall (magnetism), an interface separating magnetic domains
- Domain wall (optics), for domain walls in optics
- Domain wall (string theory), a theoretical 2-dimensional singularity
Besides these important cases similar solitons appear in wide spectrum of the models. Here are other examples:
- Early in the universe, spontaneous breaking of discrete symmetries produced domain walls. The resulting network of domain walls influenced the late stages of cosmological inflation and the cosmic microwave background radiation. Observations constrain the existence of stable domain walls. Models beyond the Standard Model can account for those constraints. Unstable cosmic domain walls may decay and produce observable radiation.
- There exist a class of the braneworld models where the brane is assumed to be a domain wall formed by interacting extra-dimensional fields. The matter is localized due to the interaction with this configuration and can leave it at sufficiently high energies. The jargon term for this domain wall is “thick brane” in contrast to the “thin brane” of the models where it is described as delta-potential or simply as some ideal surface with matter fields on it.
“Understanding mNP Hyperthermia for cancer treatment at the cellular scale”
The use of magnetic nanoparticles (mNP’s) to induce local hyperthermia has been emerging in recent years as a promising cancer therapy, in both a stand-alone and combination treatment setting. Studies have shown that cancer cells associate with, internalize, and aggregate mNP’s more preferentially than normal cells. Once the mNP’s are delivered inside the cells, a low frequency (30 kHz–300 kHz) alternating electromagnetic field is used to activate the mNP’s. The nanoparticles absorb the applied field and provide localized heat generation at nano-micron scales. It has been shown experimentally that mNP’s exhibit collective behavior when in close proximity. Although most prevailing mNP heating models assume there is no magnetic interaction between particles, our data suggests that magnetic interaction effects due to mNP aggregation are often significant; In the case of multi-crystal core particles, interaction is guaranteed. To understand the physical phenomena responsible for this effect, we modeled electromagnetic coupling between mNP’s in detail. The computational results are validated using data from the literature as well as measurements obtained in our lab. The computational model presented here is based on a method of moments technique and is used to calculate magnetic field distributions on the nanometer scale, both inside and outside the mNP.
Clinical hyperthermia has proven to be an effective cancer treatment, especially in an adjuvant setting along with radiation and chemotherapy, but has not yet become a standard of care3–8. It has been shown that most cancers have similar thermal tolerance as compared to surrounding normal tissues9. This inherent similarity necessitates the localized application of the heat source to the target tumor region, to prevent heating of normal tissue. Magnetic nanoparticles (mNP’s) provide a promising solution to the problem of providing highly localized heat deposition. Particles which are designed to have higher delivery and uptake in tumor tissues, as compared to surrounding normal tissues, provide a cellular level mechanism of specificity of heat source localization10–12.