Tag Archives: DNA

Microwave Stimulated Nanoparticles To Fight Efficiently Cancer

A physicist at The University of Texas at Arlington (UTA) has proposed a new concept for treating cancer cells. In a recently published paper in the journal Nanomedicine: Nanotechnology, Biology and Medicine, UTA physics Professor Wei Chen and a team of international collaborators advanced the idea of using titanium dioxide (TiO2) nanoparticles stimulated by microwaves to trigger the death of cancer cells without damaging the normal cells around them.

The method is called microwave-induced radical therapy, which the team refers to as microdynamic therapy, or MDT. The use of TiO2 nanoparticles activated by light and ultrasound in cancer treatments has been studied extensively, but this marks the first time researchers have shown that the nanoparticles can be effectively activated by microwaves for cancer cell destruction—potentially opening new doors to treatment for patients fighting the disease. Chen said the new therapy centers on reactive oxygen species, or ROS, which are a natural byproduct of the body’s metabolism of oxygen. ROS help kill toxins in the body, but can also be damaging to cells if they reach a critical level. TiO2 enters cells and produces ROS, which are able to damage plasma membranes, mitochondria and DNA, causing cell death.

Cancer cells are characterized by a higher steady-state saturation of ROS than normal, healthy cells,” Chen said. “This new therapy allows us to exploit that by raising the saturation of ROS in cancer cells to a critical level that triggers cell death without pushing the normal cells to that same threshold.

The pilot study for this new treatment concept builds upon Chen’s expertise in the use of nanoparticles to combat cancer.

Chen’s collaborators hail from the Guangdong Academy of Medical Sciences and Beihang University. The team conducted experiments that demonstrate the nanoparticles can significantly suppress the growth of osteosarcomas under microwave irradiation.

While TiO2 and low-power microwave irradiation alone did not effectively kill cancer cells, the combination of the two proved successful in creating a toxic effect for the tumor cells. Microwave ablation therapy has already proven to be an effective treatment against bone cancer, obtaining better results than MDT. However, MDT has applications for combatting other types of cancer, not just the osteosarcomas used for this pilot case.

Using light to activate ROS—as is seen in photodynamic therapy—can be challenging for the treatment of tumors deeply located within the body; in contrast, microwaves lend the ability to create deeper penetration that propagates through all types of tissues and non-metallic materials.

This new discovery is exciting because it potentially creates new avenues for treating cancer patients without causing debilitating side effects,” Chen said. “This targeted, localized method allows us to keep healthy cells intact so patients are better equipped to battle the disease.

Source: https://www.uta.edu/

Gold Nanoparticles Ship With Efficiency CRISPR Cargo

Forget UPS and FedEx: Tiny golden delivery trucks created at Fred Hutchinson Cancer Research Center can ship CRISPR into human blood stem cells, offering a potential way to treat diseases like HIV and sickle cell anemia. And the researchers behind those trucks have even bigger distribution dreams. Gene therapy — the editing of our DNA to treat disease — is a clinical reality today, but only in a handful of rich countries. Fred Hutch scientists think their new CRISPR courier could help deliver gene therapy to patients around the world.

A new paper published in Nature Materials describes how the scientists loaded CRISPR onto spherical gold nanoparticles. These tiny shuttles then deposited the gene-editing tool into blood stem cells donated by healthy individuals and isolated in test tubes, where CRISPR altered genes related to HIV and certain blood disorders.   It is the first time that nanoparticles have successfully ferried CRISPR into blood stem cells to edit DNA, the researchers said. And it’s a promising step toward addressing CRISPR’s critical delivery problems. The first of these problems has vexed the field since the gene-editing technique was discovered. Scientists need to deliver CRISPR into the right spot in a cell. That is proving tricky enough. DNA represents the body’s crown jewels, and CRISPR must sneak past all sorts of security systems to gain access.

And then CRISPR must go global. Gene editing could benefit millions of people worldwide. But as the treatment process stands right now, the vast majority won’t. That process depends almost entirely on highly engineered viruses made in high-tech, multimillion-dollar facilities.
The researchers think their golden nanoparticles can solve both problems. As efficient couriers, they could reduce the need for engineered viruses and specialized research centers. And that could help make these emerging, high-tech treatments accessible and affordable, said senior scientist Dr. Jennifer Adair of Fred Hutch.

Gene therapy has a lot of potential across many diseases, but the process we have right now is just not feasible in every place in the world,” Adair said. “We want to end up delivering gene therapy in a syringe. This gold nanoparticle represents the first possibility we have to do that for blood stem cells.”

Source: https://www.fredhutch.org/

How To Offer Commercially Attractive Carbon-Capturing

Chemical engineers from the Ecole Polytechnique Fédérale de Lausanne  (EPFL ) in Switzerland have designed an easy method to achieve commercially attractive carbon-capturing with metal-organic frameworksMetal-organic frameworks (MOFs) are versatile compounds hosting nano-sized pores in their crystal structure. Because of their nanopores, MOFs are now used in a wide range of applications, including separating petrochemicalsmimicking DNA, and removing heavy metals, fluoride anions, hydrogen, and even gold from waterGas separation in particular is of great interest to a number of industries, such as biogas production, enriching air in metal working, purifying natural gas, and recovering hydrogen from ammonia plants and oil refineries.

The flexible ‘lattice’ structure of metal-organic frameworks soaks up gas molecules that are even larger than its pore window making it difficult to carry out efficient membrane-based separation,” says Kumar Varoon Agrawal, who holds the GAZNAT Chair for Advanced Separations at EPFL Valais Wallis.

Now, scientists from Agrawal’s lab have greatly improved the gas separation by making the MOF lattice structure rigid. They did this by using a novel “post-synthetic rapid heat treatment” method, which basically involved baking a popular MOF called ZIF-8 (zeolitic imidazolate framework 8) at 360°C for a few seconds. The method drastically improved ZIF-8’s gas-separation performance – specifically in ‘carbon capture’, a process that captures carbon dioxide emissions produced from the use of fossil fuels, preventing it from entering the atmosphere. “For the first time, we have achieved commercially attractive dioxide sieving performance a MOF membrane,” says Agrawal.

Source: https://actu.epfl.ch/

DNA Folds Into A Smart Nanocapsule For Drug Delivery

Researchers from University of Jyväskylä and Aalto University in Finland have developed a customized DNA nanostructure that can perform a predefined task in human body-like conditions. To do so, the team built a capsule-like carrier that opens and closes according to the pH level of the surrounding solution. The nanocapsule can be loaded—or packed—with a variety of cargo, closed for delivery and opened again through a subtle pH increase.

DNA folds into a smart nanocapsule for drug delivery
The pH-responsive DNA origami nanocapsule (blue) loaded with an enzyme (yellow color, high pH). 

The function of the DNA nanocapsule is based on pH-responsive DNA residues.To make this happen, the team designed a capsule-like DNA origami structure functionalized with pH-responsive DNA strands. Such dynamic DNA nanodesigns are often controlled by the simple hydrogen-bonding of two complementary DNA sequences. Here, one half of the capsule was equipped with specific double-stranded DNA domains that could further form a DNA triple helix — in other words a helical structure comprised of three, not just two DNA molecules — by attaching to a suitable single-stranded DNA in the other half.

Source: https://www.jyu.fi/

How To Detect Genetic Mutations In Minutes

A team of engineers at the UC Berkeley and the Keck Graduate Institute (KGI) of The Claremont Colleges combined CRISPR with electronic transistors made from graphene to create a new hand-held device that can detect specific genetic mutations in a matter of minutes.

The device, dubbed CRISPR-Chip, could be used to rapidly diagnose genetic diseases or to evaluate the accuracy of gene-editing techniques. The team used the device to identify genetic mutations in DNA samples from Duchenne muscular dystrophy patients.

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We have developed the first transistor that uses CRISPR to search your genome for potential mutations,” said Kiana Aran, an assistant professor at KGI who conceived of the technology while a postdoctoral scholar in UC Berkeley bioengineering professor Irina Conboy’s lab. “You just put your purified DNA sample on the chip, allow CRISPR to do the search and the graphene transistor reports the result of this search in minutes.”

Aran, who developed this technology and brought it to fruition at KGI, is the senior author of a paper describing the device that appears online March 25 in the journal Nature Biomedical Engineering.

Doctors and geneticists can now sequence DNA to pinpoint genetic mutations underlying a host of traits and conditions, and companies like 23andMe and AncestryDNA even make these tests available to curious consumers.

Source: https://news.berkeley.edu/

Molecular Nanocomputers

Computer scientists at Caltech have designed DNA molecules that can carry out reprogrammable computations, for the first time creating so-called algorithmic self-assembly in which the same “hardware” can be configured to run differentsoftware.”

A team headed by Caltech‘s Erik Winfree (PhD ’98), professor of computer science, computation and neural systems, and bioengineering, showed how the DNA computations could execute six-bit algorithms that perform simple tasks. The system is analogous to a computer, but instead of using transistors and diodes, it uses molecules to represent a six-bit binary number (for example, 011001) as input, during computation, and as output. One such algorithm determines whether the number of 1-bits in the input is odd or even, (the example above would be odd, since it has three 1-bits); while another determines whether the input is a palindrome; and yet another generates random numbers.

Think of them as nano apps,” says Damien Woods, professor of computer science at Maynooth University near Dublin, Ireland, and one of two lead authors of the study. “The ability to run any type of software program without having to change the hardware is what allowed computers to become so useful. We are implementing that idea in molecules, essentially embedding an algorithm within chemistry to control chemical processes.”

The system works by self-assembly: small, specially designed DNA strands stick together to build a logic circuit while simultaneously executing the circuit algorithm. Starting with the original six bits that represent the input, the system adds row after row of molecules—progressively running the algorithm. Modern digital electronic computers use electricity flowing through circuits to manipulate information; here, the rows of DNA strands sticking together perform the computation. The end result is a test tube filled with billions of completed algorithms, each one resembling a knitted scarf of DNA, representing a readout of the computation. The pattern on each “scarf” gives you the solution to the algorithm that you were running. The system can be reprogrammed to run a different algorithm by simply selecting a different subset of strands from the roughly 700 that constitute the system.

We were surprised by the versatility of programs we were able to design, despite being limited to six-bit inputs,” says David Doty, fellow lead author and assistant professor of computer science at the University of California, Davis. “When we began experiments, we had only designed three programs. But once we started using the system, we realized just how much potential it has. It was the same excitement we felt the first time we programmed a computer, and we became intensely curious about what else these strands could do. By the end, we had designed and run a total of 21 circuits.”

The findings have been reported in the journal Nature.

Source: https://www.caltech.edu/

‘Epigenetic’ Gene Tweaks Could Trigger Cancer

You could be forgiven for thinking of cancer as a genetic disease. Sure, we know it can be triggered by things you do – smoking being the classic example – but most of us probably assume that we get cancer because of a genetic mutation – a glitch in our DNA. It turns out that this is not quite the end of the story.

We now have the first direct evidence that switching off certain genes – something that can be caused by our lifestyle or the environment we live in – can trigger tumours, without mutating the DNA itself. The good news is that these changes are, in theory, reversible.

All cells contain the same DNA, but individual genes in any cell can be switched on or off by the addition or subtraction of a methyl group – a process known as epigenetic methylation.

For years, researchers have known that mutations to our DNA – either those passed on at birth or those acquired as a result of exposure to radiation, for example – can cause cancer. But epigenetic changes have also been implicated in cancer because abnormal patterns of gene methylation are seen in virtually all types of human tumours.

For example, a gene called MLH1 produces a protein that repairs DNA damage. It is often mutated in colon cancer tumours, but in some tumour samples the gene is healthy, but appears to have been silenced by methylationThe problem is that it has been difficult to test whether abnormal methylation occurs as a result of a tumour or is a cause of its growth.

In genetics you can easily delete a gene and see what the consequence is, but it’s much harder to direct methylation to specific regions of the genome,” says Lanlan Shen of Baylor College of Medicine in Houston, Texas.

To get round this problem, Shen and her colleagues used a naturally occurring sequence of DNA, which draws in methyl groups to methylate nearby genes. They call it their “methylation magnet”.

The team inserted this sequence next to the tumour suppressor gene, p16, in mouse embryonic stem cells. These embryos then developed into mice that carry the “methylation magnet” in all of their cells. The team focused on methylating p16 because it is abnormally methylated in numerous cancers.

They monitored the rodents for 18 months – until they reached the mouse equivalent of middle age. Over this time, 30 per cent of the mice developed tumours around their body, including in their liver, colon, lungs and spleen. None of a control group of genetically identical mice developed tumours.

Some tissues showed faster methylation than others, for example in the liver, colon and spleen, and that’s exactly where we saw the tumours grow,” says Shen. “It seems like methylation predisposed the tissue to tumour development.” She reckons that methylation silences p16, which lifts the break that it normally places on any abnormal cell division.

Source: https://www.newscientist.com/

Have China’s CRISPR Twins Enhanced Brains?

New research suggests that a controversial gene-editing experiment to make children resistant to HIV may also have enhanced their ability to learn and form memories. The twins, called Lulu and Nana, reportedly had their genes modified before birth by a Chinese scientific team using the new editing tool CRISPR. The goal was to make the girls immune to infection by HIV, the virus that causes AIDS. Now, new research shows that the same alteration introduced into the girls’ DNA, deletion of a gene called CCR5, not only makes mice smarter but also improves human brain recovery after stroke, and could be linked to greater success in school.

The answer is likely yes, it did affect their brains,” says Alcino J. Silva, a neurobiologist at the University of California, Los Angeles, whose lab uncovered a major new role for the CCR5 gene in memory and the brain’s ability to form new connections.

“The simplest interpretation is that those mutations will probably have an impact on cognitive function in the twins,” says Silva. He says the exact effect on the girls’ cognition is impossible to predict, and “that is why it should not be done.”

The Chinese team, led by He Jiankui of the Southern University of Science and Technology in Shenzhen, claimed it used CRISPR to delete CCR5 from human embryos, some of which were later used to create pregnanciesHIV requires the CCR5 gene to enter human blood cells.

The experiment has been widely condemned as irresponsible, and He is under investigation in China. News of the first gene-edited babies also inflamed speculation about whether CRISPR technology could one day be used to create super-intelligent humans, perhaps as part of a biotechnology race between the US and China.

There is no evidence that He actually set out to modify the twins’ intelligence. MIT Technology Review contacted scientists studying the effects of CCR5 on cognition, and they say the Chinese scientist never reached out to them, as he did to others from whom he hoped to get scientific advice or support.
As far as I know, we never heard from him,” says Miou Zhou, a professor at the Western University of Health Sciences in California.

Although He never consulted the brain researchers, the Chinese scientist was certainly aware of the link between CCR5 and cognition.  It was first shown in 2016 by Zhou and Silva, who found that removing the gene from mice significantly improved their memory. The team had looked at more than 140 different genetic alterations to find which made mice smarter.

Source: https://www.technologyreview.com/

Sharpen Molecular Scissors And Expand The Gene Editing Toolbox

Wake Forest Institute for Regenerative Medicine (WFIRM) scientists have figured out a better way to deliver a DNA editing tool to shorten the presence of the editor proteins in the cells in what they describe as a “hit and run” approach.

CRISPR (clustered regularly interspaced short palindromic repeats) technology is used to alter DNA sequences and modify gene function. CRISPR/Cas9 is an enzyme that is used like a pair of scissors to cut two strands of DNA at a specific location to add, remove or repair bits of DNA. But CRISPR/Cas9 is not 100 percent accurate and could potentially cut unexpected locations, causing unwanted results.

One of the major challenges of CRISPR/Cas9 mRNA technologies is the possibility of off-targets which may cause tumors or mutations,” said Baisong Lu, Ph.D, assistant professor of regenerative medicine at WFIRM and one of the lead authors of the paper. Although other types of lentivirus-like bionanoparticles (LVLPs) have been described for delivering proteins or mRNAs, Lu said, “the LVLP we developed has unique features which will make it a useful tool in the expanding genome editing toolbox.

To address the inaccuracy issue, WFIRM researchers asked the question: Is there a way to efficiently deliver Cas9 activity but achieve transient expression of genome editing proteins? They tested various strategies and then took the best properties of two widely used delivery vehicles – lentivirus vector and nanoparticles – and combined them, creating a system that efficiently packages Cas9 mRNA into LVLPs, enabling transient expression and highly efficient editing.

Lentiviral vector is a widely used gene delivery vehicle in research labs and is already widely used for delivering the CRISPR/Cas9 mRNA technology for efficient genome editing. Nanoparticles are also being used but they are not as efficient in delivery of CRISPR/Cas9.

By combining the transient expression feature of nanoparticle-delivery strategies while retaining the transduction efficiency of lentiviral vectors, we have created a system that may be used for packaging various editor protein mRNA for genome editing in a ‘hit and run’ manner,” said Anthony Atala, M.D., director of WFIRM and co-lead author of the paper. “This system will not only improve safety but also avoid possible immune response to the editor proteins, which could improve in vivo gene editing efficiency which will be useful in research and clinical applications.

The WFIRM team published its findings in a paper published recently in the journal  Nucleic Acids Research.

Source: https://school.wakehealth.edu/

 

How To Use The Body’s Inbuilt Healing System

Imperial researchers have developed a new bioinspired material that interacts with surrounding tissues to promote healing. Materials are widely used to help heal wounds: Collagen sponges help treat burns and pressure sores, and scaffold-like implants are used to repair broken bones. However, the process of tissue repair changes over time, so scientists are looking to biomaterials that interact with tissues as healing takes place.

Now, Dr Ben Almquist and his team at Imperial College London have created a new molecule that could change the way traditional materials work with the body. Known as traction force-activated payloads (TrAPs), their method lets materials talk to the body’s natural repair systems to drive healing.

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The researchers say incorporating TrAPs into existing medical materials could revolutionise the way injuries are treated.

Our technology could help launch a new generation of materials that actively work with tissues to drive healing,” said Dr Almquist, from mperial’s Department of Bioengineering.
After an injury, cells ‘crawl’ through the collagen ‘scaffolds’ found in wounds, like spiders navigating webs. As they move, they pull on the scaffold, which activates hidden healing proteins that begin to repair injured tissue. The researchers in the study designed TrAPs as a way to recreate this natural healing method. They folded the DNA segments into three-dimensional shapes known as aptamers that cling tightly to proteins. Then, they attached a customisable ‘handle’ that cells can grab onto on one end, before attaching the opposite end to a scaffold such as collagen.
During laboratory testing of their technique, they found that cells pulled on the TrAPs as they crawled through the collagen scaffolds. The researchers tailor TrAPs to release specific therapeutic proteins based on which cells are present at a given point in time.

This is the first time scientists have activated healing proteins using differing cell types in man-made materials. The technique mimics healing methods found in nature. “Creatures from sea sponges to humans use cell movement to activate healing. Our approach mimics this by using the different cell varieties in wounds to drive healing,” explains Dr Almquist.”

This approach is adaptable to different cell types, so could be used in a variety of injuries such as fractured bones, scar tissue after heart attacks, and damaged nerves. New techniques are also desperately needed for patients whose wounds won’t heal despite current interventions, like diabetic foot ulcers, which are the leading cause of non-traumatic lower leg amputationsTrAPs are relatively straightforward to create and are fully man-made, meaning they are easily recreated in different labs and can be scaled up to industrial quantities.

TrAPs could harness the body’s natural healing powers to repair bone

TrAPs provide a flexible method of actively communicating with wounds, as well as key instructions when and where they are needed. This intelligent healing is useful during every phase of the healing process, has the potential to increase the body’s chance to recover, and has far-reaching uses on many different types of wounds. This technology could serve as a conductor of wound repair, orchestrating different cells over time to work together to heal damaged tissues,” said Dr Almquist.

The findings are published in Advanced Materials.

Source: https://www.imperial.ac.uk/