Institute for Collaborative Biotechnologies

Santa Barbara, CA, United States

Institute for Collaborative Biotechnologies

Santa Barbara, CA, United States
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News Article | April 17, 2017
Site: news.mit.edu

A single cell can contain a wealth of information about the health of an individual. Now, a new method developed at MIT and National Chiao Tung University could make it possible to capture and analyze individual cells from a small sample of blood, potentially leading to very low-cost diagnostic systems that could be used almost anywhere. The new system, based on specially treated sheets of graphene oxide, could ultimately lead to a variety of simple devices that could be produced for as little as $5 apiece and perform a variety of sensitive diagnostic tests even in places far from typical medical facilities. The material used in this research is an oxidized version of the two-dimensional form of pure carbon known as graphene, which has been the subject of widespread research for over a decade because of its unique mechanical and electrical characteristics. The key to the new process is heating the graphene oxide at relatively mild temperatures. This low-temperature annealing, as it is known, makes it possible to bond particular compounds to the material’s surface. These compounds in turn select and bond with specific molecules of interest, including DNA and proteins, or even whole cells. Once captured, those molecules or cells can then be subjected to a variety of tests. The findings are reported in the journal ACS Nano, in a paper co-authored by Neelkanth Bardhan, an MIT postdoc, and Priyank Kumar PhD ’15, now a postdoc at ETH Zurich; Angela Belcher, the James Mason Crafts Professor in biological engineering and materials science and engineering at MIT and a member of the Koch Institute for Integrative Cancer Research; Jeffrey Grossman, the Morton and Claire Goulder and Family Professor in Environmental Systems at MIT; Hidde L. Ploegh, a professor of biology and member of the Whitehead Institute for Biomedical Research; Guan-Yu Chen, an assistant professor in biomedical engineering at National Chiao Tung University in Taiwan; and Zeyang Li, a doctoral student at the Whitehead Institute. Other researchers have been trying to develop diagnostic systems using a graphene oxide substrate to capture specific cells or molecules, but these approaches used just the raw, untreated material. Despite a decade of research, other attempts to improve such devices’ efficiency have relied on external modifications, such as surface patterning through lithographic fabrication techniques, or adding microfluidic channels, which add to the cost and complexity. The new finding offers a mass-producible, low-cost approach to achieving such improvements in efficiency. The heating process changes the material’s surface properties, causing oxygen atoms to cluster together, leaving spaces of bare graphene between them. This makes it relatively easy to attach other chemicals to the surface, which can interact with specific molecules of interest. The new research demonstrates how that basic process could potentially enable a suite of low-cost diagnostic systems, for example for cancer screening or treatment follow-up. For this proof-of-concept test, the team used molecules that can quickly and efficiently capture specific immune cells that are markers for certain cancers. They were able to demonstrate that their treated graphene oxide surfaces were almost twice as effective at capturing such cells from whole blood, compared to devices fabricated using ordinary, untreated graphene oxide, says Bardhan, the paper’s lead author. The system has other advantages as well, Bardhan says. It allows for rapid capture and assessment of cells or biomolecules under ambient conditions within about 10 minutes and without the need for refrigeration of samples or incubators for precise temperature control. And the whole system is compatible with existing large-scale manufacturing methods, making it possible to produce diagnostic devices for less than $5 apiece, the team estimates. Such devices could be used in point-of-care testing or resource-constrained settings. Existing methods for treating graphene oxide to allow functionalization of the surface require high temperature treatments or the use of harsh chemicals, but the new system, which the group has patented, requires no chemical pretreatment and an annealing temperature of just 50 to 80 degrees Celsius (122 to 176 F). While the team’s basic processing method could make possible a wide variety of applications, including solar cells and light-emitting devices, for this work the researchers focused on improving the efficiency of capturing cells and biomolecules that can then be subjected to a suite of tests. They did this by enzymatically coating the treated graphene oxide surface with peptides called nanobodies — subunits of antibodies, which can be cheaply and easily produced in large quantities in bioreactors and are highly selective for particular biomolecules. The researchers found that increasing the annealing time steadily increased the efficiency of cell capture: After nine days of annealing, the efficiency of capturing cells from whole blood went from 54 percent, for untreated graphene oxide, to 92 percent for the treated material. The team then performed molecular dynamics simulations to understand the fundamental changes in the reactivity of the graphene oxide base material. The simulation results, which the team also verified experimentally, suggested that upon annealing, the relative fraction of one type of oxygen (carbonyl) increases at the expense of the other types of oxygen functional groups (epoxy and hydroxyl) as a result of the oxygen clustering. This change makes the material more reactive, which explains the higher density of cell capture agents and increased efficiency of cell capture. “Efficiency is especially important if you’re trying to detect a rare event,” Belcher says. “The goal of this was to show a high efficiency of capture.” The next step after this basic proof of concept, she says, is to try to make a working detector for a specific disease model. In principle, Bardhan says, many different tests could be incorporated on a single device, all of which could be placed on a small glass slide like those used for microscopy. “I think the most interesting aspect of this work is the claimed clustering of oxygen species on graphene sheets and its enhanced performance in surface functionalization and cell capture,” says Younan Xia, a professor of chemistry and biochemistry at Georgia Institute of Technology who was not involved in this work. “It is an interesting idea.” The work was supported by the Army Research Office Institute for Collaborative Biotechnologies and MIT’s Tata Center and Solar Frontiers Center.


News Article | November 28, 2016
Site: www.eurekalert.org

Studies of brain activity typically draw their findings from measurement averages across entire groups of subjects. But new research out of UC Santa Barbara that highlights a novel method of characterizing and comparing the brain dynamics in individuals may signal a shift in that approach. While UCSB scientists have demonstrated that the groups of regions of the brain that synchronize their activity during memory-related tasks get smaller and more numerous with age, the number of connections is as individual as the study participants. The research findings appear in the journal PLOS Computational Biology. "We found that the way our brain organizes its communications changes as we age," said co-author Kimberly Schlesinger, a Ph.D. student at UCSB. "Even though we saw different patterns of brain activity in older people, we didn't see any changes in memory performance. This suggests that while older people have less synchronized communication across their entire brains, they may be compensating for this by using different strategies to successfully remember things." The scientists used functional magnetic resonance imaging (fMRI) to record healthy people's brain activity during memory tasks, attention tasks and periods of rest. For each person, fMRI data was recast as a network composed of brain regions and the connections among them. The investigators then measured how closely different groups of connections changed together over time. They found that regardless of whether a person is using memory, directing attention or resting, the number of synchronous groups of connections within one brain is consistent for that person. However, among multiple people, these numbers vary dramatically. Specifically during memory, variations among people are closely linked to age. Younger participants had only a few large synchronous groups that link nearly the entire brain in coordinated activity, while older participants showed progressively more and smaller groups of connections, indicating loss of cohesive brain activity -- even in the absence of memory impairment. "This method elegantly captures important differences between individual brains, which are often complex and difficult to describe," said Elizabeth Davison, who initiated the work as an undergraduate at UCSB, where Schlesinger served as her mentor. Davison is now a graduate student at Princeton University. "The resulting tools show promise for understanding how different brain characteristics are related to behavior, health and disease." The research originated from the Worster Summer Research Fellowship in UCSB's Department of Physics. Other UCSB members of the project team included physics professor Jean Carlson, neuroscientist Scott Grafton and then-postdoctoral scholar Danielle Bassett, now an assistant professor at the University of Pennsylvania. Future work will investigate how to use individual brain signatures to differentiate between brains that are healthily aging and those with age-related impairments. This study was supported by the David and Lucile Packard Foundation and the Institute for Collaborative Biotechnologies through a grant from the U.S. Army Research Office. Schlesinger was supported by the National Science Foundation Graduate Research Fellowship Program and by the Worster Summer Research Fellowship.


News Article | November 23, 2016
Site: www.eurekalert.org

Groups of brain regions with coordinated activity are consistent for individuals, but shrink with age Groups of brain regions that synchronize their activity during memory tasks become smaller and more numerous as people age, according to a study published in PLOS Computational Biology. Typically, research on brain activity relies on average brain measurements across entire groups of people. In a new study, Elizabeth Davison of Princeton University, New Jersey, and colleagues describe a novel method to characterize and compare the brain dynamics of individual people. The researchers used functional magnetic resonance imaging (fMRI) to record healthy people's brain activity during memory tasks, attention tasks, and at rest. For each person, fMRI data was recast as a network composed of brain regions and the connections between them. The scientists then use this network to measure how closely different groups of connections changed together over time. They found that, regardless of whether a person is using memory, directing attention, or resting, the number of synchronous groups of connections within one brain is consistent for that person. However, between people, these numbers vary dramatically. During memory specifically, variations between people are closely linked to age. Younger participants have only a few large synchronous groups that link nearly the entire brain in coordinated activity, while older participants show progressively more and smaller groups of connections, indicating loss of cohesive brain activity--even in the absence of memory impairment. "This method elegantly captures important differences between individual brains, which are often complex and difficult to describe," Davison says. "The resulting tools show promise for understanding how different brain characteristics are related to behavior, health, and disease." Future work will investigate how to use individual brain signatures to differentiate between healthily aging brains and brains with age-related impairments. In your coverage please use this URL to provide access to the freely available article in PLOS Computational Biology: http://journals. Citation: Davison EN, Turner BO, Schlesinger KJ, Miller MB, Grafton ST, Bassett DS, et al. (2016) Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan. PLoS Comput Biol 12(11): e1005178. doi:10.1371/journal.pcbi.1005178 Funding: This work was supported by the David and Lucile Packard Foundation and the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 from the U.S. Army Research Office. KJS was supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-1144085. END was supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-1656466 and the Francis Robbins Upton Fellowship in Engineering. END and KJS were additionally supported by the Worster Fellowship. DSB acknowledges support from the John D. and Catherine T. MacArthur Foundation, the Army Research Laboratory and the Army Research Office through contract numbers W911NF-10-2-0022 and W911NF-14-1-0679, the National Institute of Mental Health (2-R01-DC- 009209-11), the National Institute of Child Health and Human Development (1R01HD086888-01), the Office of Naval Research, and the National Science Foundation (#BCS-1441502, #BCS-1430087, and #PHY-1554488). The content of the information does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist.


News Article | October 23, 2015
Site: news.mit.edu

MIT chemical engineers have designed tiny particles that can “steer” themselves along preprogrammed trajectories and align themselves to flow through the center of a microchannel, making it possible to control the particles’ flow through microfluidic devices without applying any external forces. Such particles could make it more feasible to design lab-on-a-chip devices, which hold potential as portable diagnostic devices for cancer and other diseases. These devices consist of microfluidic channels engraved on tiny chips, but current versions usually require a great deal of extra instrumentation attached to the chip, limiting their portability. Much of that extra instrumentation is needed to keep the particles flowing single file through the center of the channel, where they can be analyzed. This can be done by applying a magnetic or electric field, or by flowing two streams of liquid along the outer edges of the channel, forcing the particles to stay in the center. The new MIT approach, described in Nature Communications, requires no external forces and takes advantage of hydrodynamic principles that can be exploited simply by altering the shapes of the particles. Lead authors of the paper are Burak Eral, an MIT postdoc, and William Uspal, who recently received a PhD in physics from MIT. Patrick Doyle, the Singapore Research Professor of Chemical Engineering at MIT, is the senior author of the paper. The work builds on previous research showing that when a particle is confined in a narrow channel, it has strong hydrodynamic interactions with both the confining walls and any neighboring particles. These interactions, which originate from how particles perturb the surrounding fluid, are powerful enough that they can be used to control the particles’ trajectory as they flow through the channel. The MIT researchers realized that they could manipulate these interactions by altering the particles’ symmetry. Each of their particles is shaped like a dumbbell, but with a different-size disc at each end. When these asymmetrical particles flow through a narrow channel, the larger disc encounters more resistance, or drag, forcing the particle to rotate until the larger disc is lagging behind. The asymmetrical particles stay in this slanted orientation as they flow. Because of this slanted orientation, the particles not only move forward, in the direction of the flow, they also drift toward one side of the channel. As a particle approaches the wall, the perturbation it creates in the fluid is reflected back by the wall, just as waves in a pool reflect from its wall. This reflection forces the particle to flip its orientation and move toward the center of the channel. Slightly asymmetrical particles will overshoot the center and move toward the other wall, then come back toward the center again until they gradually achieve a straight path. Very asymmetrical particles will approach the center without crossing it, but very slowly. But with just the right amount of asymmetry, a particle will move directly to the centerline in the shortest possible time. “Now that we understand how the asymmetry plays a role, we can tune it to what we want. If you want to focus particles in a given position, you can achieve that by a fundamental understanding of these hydrodynamic interactions,” Eral says. “The paper convincingly shown that shape matters, and swarms can be redirected provided that shapes are well designed,” says Patrick Tabeling, a professor at the École Supérieure de Physique et de Chimie Industrielles in Paris, who was not part of the research team. “The new and quite sophisticated mechanism … may open new routes for manipulating particles and cells in an elegant manner.” In 2006, Doyle’s lab developed a way to create huge batches of identical particles made of hydrogel, a spongy polymer. To create these particles, each thinner than a human hair, the researchers shine ultraviolet light through a mask onto a stream of flowing building blocks, or oligomers. Wherever the light strikes, solid polymeric particles are formed in the shape of the mask, in a process called photopolymerization. During this process, the researchers can also load a fluorescent probe such as an antibody at one end of the dumbbell. The other end is stamped with a barcode — a pattern of dots that reveals the particle’s target molecule. This type of particle can be useful for diagnosing cancer and other diseases, following customization to detect proteins or DNA sequences in blood samples that can be signs of disease. Using a cytometer, scientists can read the fluorescent signal as the particles flow by in single file. “Self-steering particles could lead to simplified flow scanners for point-of-care devices, and also provide a new toolkit from which one can develop other novel bioassays,” Doyle says. The research was funded by the National Science Foundation, Novartis, and the Institute for Collaborative Biotechnologies through the U.S. Army Research Office.


Xiao Y.,Institute for Polymers and Organic Solids | Xiao Y.,Institute for Collaborative Biotechnologies | Dane K.Y.,Institute for Collaborative Biotechnologies | Uzawa T.,Institute for Collaborative Biotechnologies | And 8 more authors.
Journal of the American Chemical Society | Year: 2010

Although the telomeric repeat amplification protocol (TRAP) has served as a powerful assay for detecting telomerase activity, its use has been significantly limited when performed directly in complex, interferant-laced samples. In this work, we report a modification of the TRAP assay that allows the detection of high-fidelity amplification of telomerase products directly from concentrated cell lysates. Briefly, we covalently attached 12 nm gold nanoparticles (AuNPs) to the telomere strand (TS) primer, which is used as a substrate for telomerase elongation. These TS-modified AuNPs significantly reduce polymerase chain reaction (PCR) artifacts (such as primer dimers) and improve the yield of amplified telomerase products relative to the traditional TRAP assay when amplification is performed in concentrated cell lysates. Specifically, because the TS-modified AuNPs eliminate most of the primer-dimer artifacts normally visible at the same position as the shortest amplified telomerase PCR product apparent on agarose gels, the AuNP-modified TRAP assay exhibits excellent sensitivity. Consequently, we observed a 10-fold increase in sensitivity for cancer cells diluted 1000-fold with somatic cells. It thus appears that the use of AuNP-modified primers significantly improves the sensitivity and specificity of the traditional TRAP assay and may be an effective method by which PCR can be performed directly in concentrated cell lysates. © 2010 American Chemical Society.


PubMed | Institute for Collaborative Biotechnologies
Type: | Journal: BMJ case reports | Year: 2011

Understanding the actions performed by other people is a key aspect of social interaction, including in clinical settings where patients are learning from therapists and caregivers. While lesions of the left cerebral hemisphere induce praxic disorders, the hemispheric specialisation of intention understanding remains unclear. Do patients with a right hemispheric lesion understand the intentions of other people properly? The present study investigates how a split-brain patient understands the means (what) and intentions (why) of the actions of other people. Results show a significant left hemispheric dominance for understanding what is done, and a significant right hemispheric dominance for understanding why an action is carried out. This discovery might have important clinical implications in neurological patients, especially when those with right hemisphere lesions are faced with important decisions related to the interpretation of others intentions.

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