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Researchers are developing Nanopore-Tal technology that allows cells to communicate with computers.



Researchers are developing Nanopore-Tal technology that allows cells to communicate with computers.


Pipetting NanoporeTERS

Researchers at the University of Washington and Microsoft have unveiled a new class of reporter proteins that can be read directly with a commercially available nanopore detector. Here, UW doctoral student Nicholas Cardoso injects a solution containing NanoporeTER onto a portable MinION device under the supervision of UW associate research assistant Jeff Nival. Credit: Dennis Wise / University of Washington.

Genetically encoded reporter proteins have been the backbone of biotechnology research, allowing scientists to track gene expression, understand intracellular processes, and debug engineered genetic circuits.

But traditional reporting schemes based on fluorescence and other optical approaches have practical limitations that could cast a shadow on future progress in this area. Now researchers from University of Washington and Microsoft created a nanoport of what happens inside these complex biological systems, allowing scientists to look at reporter proteins in a whole new light.

The team presented a new class of reporter proteins that can be read directly with a commercially available nanopore measuring device. The new system, dubbed Reporter Nanopore Protein Labels or NanoporeTERs, can detect multiple levels of protein expression in bacterial and human cell cultures, far beyond the capabilities of existing methods.

The study was published on August 12, 2021 in The Nature of Biotechnology.

Raw nanopore signals

Researchers at the University of Washington and Microsoft have unveiled a new class of reporter proteins that can be read directly with a commercially available nanopore detector. The raw nanopore signals come from the MinION device, which contains an array of hundreds of nanopore sensors. Each color represents data from a single nanopore. The team uses machine learning to interpret these signals as NanoporeTERs barcodes. Credit: Dennis Wise / University of Washington.

“NanoporeTERs offer a new and richer vocabulary for engineering cells to express themselves and shed new light on the factors they are designed to track. They can tell us a lot more immediately about what’s going on in their environment, ”said co-lead author Nicholas Cardoso, a doctoral student at the Institute of Molecular Engineering and Sciences at the University of Washington. “Basically, we are enabling these cells to ‘talk’ to computers about what is happening in their environment at a new level of granularity, scale and efficiency that will allow for deeper analysis than we could before.”

With traditional labeling techniques, researchers can only track a few optical reporter proteins, such as green fluorescent protein, at the same time due to their overlapping spectral properties. For example, it is difficult to distinguish more than three different colors of fluorescent proteins at the same time. In contrast, NanoporeTER have been developed to carry various protein “barcodes” composed of chains amino acids which, when used in combination, provide at least ten times the multiplexing capabilities.

These synthetic proteins are secreted outside the cell into the environment, where researchers can collect and analyze them using a commercially available array of nanopores. Here, the team used an Oxford Nanopore Technologies MinION device.

Nanopore Tal Research Group

Researchers at the University of Washington and Microsoft have unveiled a new class of reporter proteins that can be read directly with a commercially available nanopore detector. Here (from left to right): Karen Zhang, Nicholas Cardoso, Katherine Doroschak and Jeff Nivala. Not pictured: Aerilynn Nguyen, Zocheb Siddiqi, Nicholas Bogard, Karin Strauss and Luis Sese. Note: This photo was taken before the COVID-19 pandemic. Credit: Photo by Tara Brown.

The researchers designed NanoporeTER proteins with charged tails so that they could be drawn into nanopore sensors using an electric field. The team then uses machine learning to classify the electrical signals for each NanoporeTER barcode to determine the yield levels of each protein.

“This is a fundamentally new interface between cells and computers,” said senior author Jeff Nywala, assistant research professor at the Paul Allen School of Computer Science and Engineering. “I like to draw the analogy that fluorescent protein reporters are like beacons and NanoporeTER are like messages in a bottle.

“Lighthouses are really useful for indicating physical location because you can literally see where the signal is coming from, but it’s difficult to fit more information into such a signal. On the other hand, a message in a bottle can hold a lot of information in a very small vessel, and you can send many of them elsewhere to be read. You may lose sight of the exact physical location where the messages were sent, but for many applications this will not be a problem. “

As a proof of concept, the team developed a library of over 20 different NanoporeTERs tags. But the potential is much greater, according to co-lead author Karen Zhang, who is currently pursuing a PhD in bioengineering at the University of California, Berkeley-UCSF.

“We are currently working to increase the number of NanoporeTERs to hundreds, thousands, maybe even millions,” said Zhang, who graduated from UW this year with a bachelor’s degree in biochemistry and microbiology. “The more we have, the more things we can track.

“We’re particularly excited about the potential of unicellular proteomics, but it could also be a game changer in terms of our ability to conduct a multiplex biosensor to diagnose disease and even target therapeutic agents to specific areas within the body. And debugging complex designs of genetic circuits would become much easier and take much less time if we could measure the performance of all components in parallel, and not through trial and error. “

These researchers previously used the MinION device in new ways when they developed a molecular labeling system to replace traditional inventory management methods. This system was based on barcodes composed of synthetic filaments. DNA which could be decoded on demand using a handheld reader.

This time the team went even further.

“This is the first article to show how a commercial nanopore sensor device can be repurposed for applications other than DNA and RNA the sequencing for which they were originally designed, ”said co-author Katherine Doroschak, a computational biologist at Adaptive Biotechnologies, who completed this work as a doctoral student at Allen School. “This is great because nanopore technology will become more accessible and ubiquitous in the future. You can already connect the nanopore device to your mobile phone. I could imagine that someday I would have a choice of “molecular applications” that would be relatively inexpensive and widely available outside of traditional genomics. “

Reference: “Multiplex Direct Detection of Protein Reporters with Barcodes on an Array of Nanopores” by Nicolas Cardoso, Karen Zhang, Katherine Doroschak, Erilynn Nguyen, Zocheb Siddiqi, Nicholas Bogard, Karin Strauss, Luis Sese and Jeff Nivala, 12 August 2021, The Nature of Biotechnology
DOI: 10.1038 / s41587-021-01002-6

Additional contributors to the article are Erilynn Nguyen of Northeastern University and Zoheb Siddiqi of Amazon, both former undergraduate students at Washington State University; Nicholas Bogard of Patch Biosciences, a former postdoctoral fellow at the University of Washington; Luis Sese, professor at the Allen School; and Karin Strauss, an affiliate professor at the Allen School and senior general manager of research at Microsoft. This study was funded by the National Science Foundation, National Institutes of Health, and a sponsored research agreement with Oxford Nanopore Technologies.


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Researchers reconfigure material topology at microscale





Encrypted Harvard Shield

The researchers encoded the patterns and designs in the material, making tiny, invisible changes to the geometry of the triangular lattice. Credit: Image courtesy of Shukong Lee / Bolei Deng / Harvard SEAS.

Reconfigurable materials can do amazing things. Flat sheets turn to faceExtruded cube transforms into dozens of different shapes… But there is one thing that a reconfigurable material cannot change yet: its underlying topology. A 100 cell reconfigurable material will always have 100 cells, even if those cells are stretched or compressed.

Now researchers at the Harvard School of Engineering and Applied Sciences. John A. Paulson (SEAS) developed a method for altering the fundamental topology of cellular material at the microscale. Research published in Nature

“The creation of cellular structures that can dynamically change their topology will open up new possibilities in the development of active materials with information encryption, selective particle capture, and customizable mechanical, chemical and acoustic properties,” said Joanna Eisenberg, professor of materials science Amy Smith Berilson. at SEAS, professor of chemistry and chemical biology and senior article author.

Triangle material topology

Hexagon material topology

Researchers have developed a method for altering the fundamental topology of a cellular material at the microscale, paving the way for active materials with tunable mechanical, chemical and acoustic properties. Credit: Images courtesy of Shukong Lee / Bolei Deng / Harvard SEAS.

The researchers used the same physics that binds our hair when it gets wet – capillary force. Capillary force works well on soft, pliable material like our hair, but it fights tough cellular structures that require bending, stretching, or folding, especially around strong, connected knots. Capillary force is also temporary as materials tend to return to their original configuration after drying.

To develop a durable but reversible method for transforming the topology of rigid cellular microstructures, the researchers developed a two-tier dynamic strategy. They started with a rigid polymer honeycomb microstructure with a triangular lattice topology and exposed it to droplets of a volatile solvent chosen to swell and soften the polymer at the molecular level. This made the material temporarily more flexible, and in this flexible state, the capillary forces created by the evaporating liquid brought the edges of the triangles closer together, changing their bonds with each other and turning them into hexagons. Then, as the solvent quickly evaporated, the material dried out and was trapped in its new configuration, regaining its stiffness. The whole process took a matter of seconds.

“When you think about applications, it is very important not to lose the mechanical properties of the material after the transformation process,” said Shukong Lee, a graduate student at Eisenberg’s lab and co-author of the paper. “Here we have shown that we can start with a hard material and end with a hard material while temporarily softening it during the reconfiguration phase.”

Assembly of microstructures

Microstructure assembly video. A liquid acts on the triangular lattice, which swells and softens the polymer. In this flexible state, the capillary forces created by the evaporating liquid brought the edges of the triangles closer together, changing their bonds with each other and turning them into hexagons. Credit: Video courtesy of Shukong Lee / Bolei Deng / Harvard SEAS

The new material topology is so strong that it can withstand heat or immersion in some fluids for days without disassembly. Its reliability actually posed a problem for researchers who hoped to make the conversion reversible.

To go back to the original topology, the researchers developed a method for combining two fluids. The former temporarily enlarges the lattice, which causes the adhering walls of the hexagons to flake off and allows the lattice to return to its original triangular structure. The second, less volatile liquid delays the emergence of capillary forces until the first liquid evaporates and the material regains its rigidity. Thus, structures can be repeatedly assembled and disassembled and held in any intermediate configuration.

Disassembly of microstructures

Video of disassembly of microstructures. The first one temporarily swells the lattice, which peels off the adhered walls. The second, less volatile liquid delays the emergence of capillary forces until the first liquid evaporates and the material regains its rigidity. Credit: Video courtesy of Shukong Lee / Bolei Deng / Harvard SEAS

“To expand our approach to arbitrary lattices, it was important to develop a generalized theoretical model that links cell geometry, material stiffness, and capillary forces,” said Bolei Deng, paper co-author and graduate student at Katya Bertholdi’s laboratory, William and Ami Kuan Danoff Professor of Applied Mechanics. in SEAS.

Guided by this model, the researchers demonstrated programmed reversible topological transformations of various lattice geometries and reacting materials, including the transformation of a lattice of circles into squares.

Researchers have studied various applications for research. For example, the team encoded the patterns and designs in the material, making tiny invisible changes to the geometry of the triangular lattice.

“You can imagine that this will be used to encrypt information in the future, because you cannot see the pattern in the material when it is disassembled,” Lee said.

The researchers also demonstrated very local transformation, assembly and disassembly of sections of the lattice using a tiny liquid droplet. This method can be used to adjust the friction and wetting properties of a material, change its acoustic properties and mechanical elasticity, and even trap gas particles and bubbles.

“Our strategy can be applied to a variety of applications,” said Bertholdi, who is also a co-author of the article. “We can apply this method to a variety of materials, including sensitive materials, with different geometries and different scales, even at the nanoscale, where topology plays a key role in the development of tunable photonic metasurfaces. The design space for that is huge. “

Reference: “Fluid-Induced Topological Transformations of Cellular Microstructures” by Shukong Lee, Bolei Deng, Alison Grintal, Alisha Schneider-Yamamura, Jinliang Kang, Reese S. Martens, Katie T. Zhang, Jiang Li, Xicin Yu, Katya Bertholdi, and Joanna. Eisenberg, April 14, 2021, Nature
DOI: 10.1038 / s41586-021-03404-7

This study was co-authored by Alison Grintal, Alissha Schneider-Yamamura, Jinliang Kang, Reese S. Martens, Katie T. Zhang, Jian Li, and Xiqing Yu.

It was supported by the National Science Foundation under the Material Design for Revolution and Design for Our Future (DMREF) Program # DMR-1922321, Harvard University Materials Research and Engineering Center (MRSEC), award # DMR-18 2011754 and the Department of Energy USA (DOE), Office of Science, Basic Energy Sciences (BES) under number DE-SC0005247.


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Help clean up space junk with the first of its kind Mission Optimizer



Help clean up space junk with the first of its kind Mission Optimizer


ClearSpace-1 takes over Vespa

Illustration ClearSpace-1, a planned mission for active garbage collection. Credit: ClearSpace SA.

Less than a year after the UK Space Agency pledged £ 1 million to combat space debris, Fujitsu UK has successfully combined quantum computing and artificial intelligence to support the transformation of its debris removal system.

Fujitsu Prototype – Created in collaboration with Glasgow University, Amazon Web Services and Astroscale UK will improve mission planning so that a single spacecraft can efficiently choose which pieces of space debris to remove in a single mission, much faster than is currently possible.

Removing space debris is key to sustainability in space, reducing or even preventing the risk of legacy spacecraft colliding with new and existing satellites.

What’s more, supporting debris removal missions with Fujitsu technology will help reduce the risk of catastrophic collisions in orbit, which could lead to thousands of other new debris that pose a real threat to operational satellites in orbit.

By carefully deciding what debris and when to collect, Digital Annealer’s quantum proposal optimizes a mission plan to determine the minimum fuel and minimum time needed to safely return a failed spacecraft or satellites to disposal orbit. Finding the optimal route for collecting space debris will significantly save time and money during the mission planning phase, as well as, as a result, increase commercial profitability.

Space debris objects in low Earth orbit

The debris objects shown in the images are artist’s impression based on actual density data. However, debris objects are shown zoomed in to make them visible at the specified scale. Credit: ESA.

With 2350 inoperative satellites Currently in orbit and more than 28,000 debris tracked by space surveillance networks, this technology will help the UK increase its market share in the space sector. It will also further support the UK government’s commitment to a more sustainable future overall.

Dr. Matteo Ceriotti, professor of space engineering, and graduate student Julia Viavattene, who led the project for the University of Glasgow, said: “The University of Glasgow was involved in this project from the very beginning – developing the trajectory. the models needed to efficiently remove space debris as well as to estimate the cost of travel.

“The University has a long history of experience in the design and optimization of space trajectories, which is why we have strived to be at the forefront of any government initiative to enhance the UK’s image in the space sector. With the help of Fujitsu, AWS and Astroscale UK, we have helped overcome the challenges of removing space debris to make future projects easier. ”

Ellen Devereux, digital firing consultant for Fujitsu UK and Ireland, said: “All space debris presents a potential risk of collision with operating systems that many of us take for granted, from weather forecasts to telecommunications.

“With the support of the UK Space Agency, Astroscale UK, AWS and the University of Glasgow, we have developed a solution to optimize the planning of a maintenance ship’s mission before it goes into space. This means that organizations like Astroscale UK can choose to collect more trash faster than ever before.

“This not only makes the process much more cost-effective for organizations that need to move and dispose of garbage, but it also leverages artificial intelligence and quantum computing.

“Over the past six months, we have learned that this technology has tremendous value for optimization in space; not only for garbage collection, but also for in-orbit maintenance and more. We now understand its potential better, and we can’t wait to see how the technology will be applied during the future mission. ”

Jacob Gere, head of space surveillance and tracking at the UK space agency, said: “Monitoring dangerous space objects is vital to protect the services we all rely on, from communications devices to satellite navigation. This project is one of the first examples of the use of quantum computing and artificial intelligence to solve space debris problems, but it is unlikely to be the last.

“The UK is committed to making space sustainable, and Fujitsu, working with Astroscale UK, the University of Glasgow and AWS, has demonstrated the real value of keeping space uncluttered by making it accessible to future generations.”

Stephen Vox, CTO at Astroscale UK, said: “Finding the optimal mission plan manually is time consuming and difficult. Astroscale UK is leading the next pioneering move under the End-of-Life Services by Astroscale (ELSA) program to remove not only one piece of debris, but multiple objects of debris with a single serving satellite known as ELSA-M, which is essentially a more economical way to remove debris from orbit. By teaming up with Fujitsu, AWS and the University of Glasgow, we hope to further optimize this for future missions. ”

The study was carried out under a grant from the UK Space Agency “Expanding Space Surveillance and Tracking Research”. The project, which was developed over six months in accordance with government digital services guidelines, uses fast technologies based on an artificial neural network (ANN). Trajectory design algorithms developed by the University of Glasgow, together with Fujitsu Digital Annealer and Quantum Inspired Optimization Services, to address some of the major optimization problems associated with Active Debris Removal (ADR) mission planning.

Amazon Web Services provided Cloud and AI and ML tools and services to support the project. The Amazon Sagemaker toolbox has been used to rapidly develop ANNs that accurately predict the cost of orbital movements in a fraction of the time required to fully calculate them. Astroscale UK, the world’s first commercial company to embark on a debris removal demonstration mission from lower Earth orbit, offers an end-use case as a typical user of multi-mission optimization.

Fujitsu, which spearheaded the project, is one of seven UK companies to receive more than £ 1 million in space debris tracking from the UK Space Agency. The UK Space Agency and the Department of Defense have announced the next step in their joint initiative to raise UK awareness of events in space.


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Scientists use human protein to deliver RNA molecular drugs to cells



SEND Technology Restoring Health


Fully assembled SEND packages

The fully assembled SEND bags are released from the collection cage for gene therapy. Credit: McGovern Institute

A programmable system built from human body components is a step towards safer and more targeted delivery of gene editing and other molecular therapeutics.

Researchers from Massachusetts Institute of TechnologyThe McGovern Institute for Brain Research at MIT, Howard Hughes Medical Institute and the Broad Institute at MIT and Harvard have developed a new way to deliver molecular therapy to cells. A system called SEND can be programmed to encapsulate and deliver various RNA cargo. SEND uses natural proteins in the body that form virus-like particles and bind RNA, and may elicit a smaller immune response than other delivery approaches.

The new delivery platform works effectively in cell models and, with further development, could open up a new class of delivery methods for a wide range of molecular drugs, including gene editing and gene replacement. Existing delivery vehicles for these therapeutic agents may be ineffective and randomly integrate into the genome of cells, and some may stimulate unwanted immune responses. SEND promises to overcome these limitations, which could open up new avenues for the introduction of molecular medicine.

Researchers at MIT, MIT’s McGovern Brain Research Institute, Howard Hughes Medical Institute, and MIT’s Broad Institute and Harvard have developed a new way to deliver molecular therapy to cells. Credit: Created by the McGovern Institute and Opus Design in collaboration with Feng Zhang, Rhiannon Macrae, and the Broad Institute.

“The biomedical community is developing powerful molecular therapeutics, but getting them to cells in an accurate and efficient manner is not an easy task,” said CRISPR pioneer Feng Zhang, senior study author, member of the Broad Institute core institute, researcher at McGovern. Institute, and Professor of Neuroscience James and Patricia Poitras at MIT. “SEND can solve these problems.” Zhang is also a researcher at Howard Hughes Medical Institute and a professor in the Department of Brain, Cognitive Sciences, and Biological Engineering at MIT.

I report The science, the command describes how to SEND (Selective Eendogenous eNcapsidization for cell Delivery) uses molecules produced by human cells. At the center of SEND is a protein called PEG10, which usually binds to its own mRNA and forms a spherical protective capsule around it. In their research, the team developed PEG10 to selectively package and deliver other RNAs. The scientists used SEND to deliver the CRISPR-Cas9 gene editing system to mouse and human cells to edit target genes.

First author Michael Segel, a postdoctoral fellow at Zhang’s lab, and Blake Lash, a second author and graduate student at the lab, said PEG10 is not unique in its ability to carry RNA. “That’s what is so exciting,” Segel said. “This study shows that there are probably other RNA transfer systems in the human body that can also be used for therapeutic purposes. It also raises some really interesting questions about what the natural roles of these proteins might be. “

Inspiration from within

The PEG10 protein exists naturally in the human body and comes from the “retrotransposon” – a virus-like genetic element that was integrated into the genome of human ancestors millions of years ago. Over time, PEG10 was metabolized by the body to become part of the repertoire of proteins essential for life.

Four years ago, researchers showed that another protein derived from the retrotransposon, ARC, forms virus-like structures and is involved in the transfer of RNA between cells. Although these studies have shown that it is possible to create retrotransposon proteins as a delivery platform, scientists have not been able to successfully use these proteins to package and deliver specific RNA shipments into mammalian cells.

SEND Health Recovery Technologies

SEND packages are injected into diseased cells to deliver therapeutic mRNA and restore health. Credit: McGovern Institute

Knowing that some proteins derived from the retrotransposon are capable of binding and packaging molecular loads, Zhang’s team turned to these proteins as possible delivery vehicles. They systematically searched for these proteins in the human genome, looking for those that could form protective capsules. In their initial analysis, the team found 48 human genes encoding proteins that could have this ability. Of these, 19 candidate proteins were present in both mice and humans. In the cell line that the team studied, PEG10 stood out as an efficient shuttle; the cells released significantly more PEG10 particles than any other protein tested. PEG10 particles also predominantly contain their own mRNA, suggesting that PEG10 may be able to package certain RNA molecules.

Development of a modular system

To develop the SEND technology, the team identified molecular sequences or “signals” in PEG10 mRNA that PEG10 recognizes and uses to package its mRNA. The researchers then used these signals to construct both PEG10 and other RNA cargoes so that PEG10 could selectively package those RNAs. The team then adorned the PEG10 capsules with additional proteins called “fusogens” that sit on the surface of cells and help them fuse together.

By creating fusogens on PEG10 capsules, researchers must be able to target the capsule to a specific type of cell, tissue, or organ. As a first step towards this goal, the team used two different fusogens, including one found in the human body, to ensure the delivery of the SEND cargo.

“By mixing and matching the various components in the SEND system, we believe it will provide a modular platform for the development of therapeutic agents for a variety of diseases,” Zhang said.

Progressive gene therapy

SEND is made up of proteins that are naturally produced in the body, which means it cannot trigger an immune response. If demonstrated in further research, the researchers say SEND could open the door to multiple uses of gene therapy with minimal side effects. “SEND technology will augment viral delivery vectors and lipid nanoparticles to further expand the toolbox for gene delivery and therapies into cells,” Lash said.

The team will then test SEND on animals and further develop a system to deliver the cargo to various tissues and cells. They will also continue to explore the natural diversity of these systems in the human body to identify other components that can be added to the SEND platform.

“We are delighted to continue to advance this approach,” Zhang said. “The realization that we can use PEG10 and most likely other proteins to engineer a delivery pathway in the human body to package and deliver new RNA and other potential therapies is a really powerful concept.”

Reference: “The mammalian retrovirus-like protein PEG10 packs its own mRNA and can be pseudotyped to deliver mRNA” Michael Segel, Blake Lash, Jingwei Song, Alim Ladha, Catherine S. Liu, Xin Jin, Sergey L. Mehedov, Rhiannon K. Macrae , Evgeny Kunin and Feng Zhang, August 20, 2021, The science
DOI: 10.1126 / science.abg6155

This work was made possible with the support of the Simons Center for the Social Brain at MIT; Internal Research Program of the National Institutes of Health; National Institutes of Health Grants 1R01-HG009761 and 1DP1-HL141201; Howard Hughes Medical Institute; Open charity; G. Harold and Leila Y. Mathers Charitable Foundation; Edward Mullinkrodt Jr. Foundation; The Poitras Center for Mental Disorders Research at the Massachusetts Institute of Technology; Hock E. Tan and C. Lisa Young, Center for Autism Research, MIT; The Yang Tang Center for Molecular Therapy at the Massachusetts Institute of Technology; Lisa Yang; The Phillips family; R. Metcalfe; and J. and P. Poitras.


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