Posts belonging to Category DNA

Artificial Intelligence At The Hospital

Diagnosing cancer is a slow and laborious process. Here researchers at University Hospital Zurich painstakingly make up biopsy slides – up to 50 for each patient – for the pathologist to examine for signs of prostate cancer. A pathologist takes around an hour and a half per patient – a task IBMs Watson supercomputer is now doing in fractions of a second.

“If the pathologist becomes faster by using such a system I think it will pay off. Because my time is also worth something. If I sit here one and a half hours looking at slides, screening all these slides, instead of just signing out the two or three positive ones, and taking into account that there may be a .1 error rate, percent error rate. this will pay off, because I can do in one and a half hours at the end five patients,” says Dr. Peter Wild, University Hospital Zürich.

The hospital’s archive of biopsy images is being slowly fed into Watson – a process that will take years. But maybe one day pathologists won’t have to view slides through a microscope at all. Diagnosis is not the only area benefiting from AI. The technology is helping this University of Sheffield team design a new drug that could slow down the progress of motor neurone disease. A system built by British start-up BenevolentAI is identifying new areas for further exploration far faster than a person could ever hope to.

Benevolent basically uses their artificial intelligence system to scan the whole medical and biomedical literature. It’s not really easy for us to stay on top of millions of publications that come out every year. So they can interrogate that information, using artificial intelligence and come up with ideas for new drugs that might be used in a completely different disease, but may be applicable on motor neurone disease. So that’s the real benefit in their system, the kind of novel ideas that they come up with,” explains Dr. Richard Mead, Sitran, University of Sheffield. BenevolentAI has raised one hundred million dollars in investment to develop its AI system, and help revolutionise the pharmaceutical industry.


A Single Drop Of Blood To Test Agressive Prostate Cancer

A new diagnostic developed by Alberta scientists will allow men to bypass painful biopsies to test for aggressive prostate cancer. The test incorporates a unique nanotechnology platform to make the diagnostic using only a single drop of blood, and is significantly more accurate than current screening methods.

The Extracellular Vesicle Fingerprint Predictive Score (EV-FPS) test uses machine learning to combine information from millions of cancer cell nanoparticles in the blood to recognize the unique fingerprint of aggressive cancer. The diagnostic, developed by members of the Alberta Prostate Cancer Research Initiative (APCaRI), was evaluated in a group of 377 Albertan men who were referred to their urologist with suspected prostate cancer. It was found that EV-FPS correctly identified men with aggressive prostate cancer 40 percent more accurately than the most common test—Prostate-Specific Antigen (PSA) blood test—in wide use today.

Higher sensitivity means that our test will miss fewer aggressive cancers,” said John Lewis, the Alberta Cancer Foundation‘s Frank and Carla Sojonky Chair of Prostate Cancer Research at the University of Alberta. “For this kind of test you want the sensitivity to be as high as possible because you don’t want to miss a single cancer that should be treated.”

According to the team, current tests such as the PSA and digital rectal exam (DRE) often lead to unneeded biopsies. Lewis says more than 50 per cent of men who undergo biopsy do not have prostate cancer, yet suffer the pain and side effects of the procedure such as infection or sepsis. Less than 20 per cent of men who receive a are diagnosed with the aggressive form of prostate cancer that could most benefit from treatment.

It’s estimated that successful implementation of the EV-FPS test could eventually eliminate up to 600-thousand unnecessary biopsies, 24-thousand hospitalizations and up to 50 per cent of unnecessary treatments for prostate each year in North America alone. Beyond cost savings to the health care system, the researchers say the diagnostic test will have a dramatic impact on the health care experience and quality of life for men and their families.

Compared to elevated total PSA alone, the EV-FPS test can more accurately predict the result of prostate biopsy in previously unscreened men,” said Adrian Fairey, urologist at the Northern Alberta Urology Centre and member of APCaRI. “This information can be used by clinicians to determine which men should be advised to undergo immediate prostate biopsy and which men should be advised to defer and continue screening.”


Startup Promises Immortality Through AI, Nanotechnology, and Cloning

One of the things humans have plotted for centuries is escaping death, with little to show for it, until now. One startup called Humai has a plan to make immortality a reality. The CEO, Josh Bocanegra says when the time comes and all the necessary advancements are in place, we’ll be able to freeze your brain, create a new, artificial body, repair any damage to your brain, and transfer it into your new body. This process could then be repeated in perpetuityHUMAI stands for: Human Resurrection through Artificial Intelligence. The technology to accomplish this isn’t here now, but on the horizon. Bocanegra says they’ll reach this Promethean feat within 30 years. 2045 is currently their target date. So how do they plan to do it?

We’re using artificial intelligence and nanotechnology to store data of conversational styles, behavioral patterns, thought processes and information about how your body functions from the inside-out. This data will be coded into multiple sensor technologies, which will be built into an artificial body with the brain of a deceased human, explains the website.


Inkjet Printers Grow Nerve Stem Cells

Inkjet printers and lasers are parts of a new way to produce cells important to research on nerve regeneration. Researchers at Iowa State University have developed a nanotechnology that uses inkjet printers to print multi-layer graphene circuits….It turns out mesenchymal stem cells adhere and grow well on the treated circuit’s raised, rough, and 3D nanostructures. Add small doses of electricity—100 millivolts for 10 minutes per day over 15 days—and the stem cells become Schwann-like cells, [which secrete substances that promote the health of nerve cells].

nerve cells

This technology could lead to a better way to differentiate stem cells,” says Metin Uz, a postdoctoral research associate in chemical and biological engineering. The researchers report the results could lead to changes in how nerve injuries are treated inside the body. “These results help pave the way for in vivo peripheral nerve regeneration where the flexible graphene electrodes could conform to the injury site and provide intimate electrical stimulation for nerve cell regrowth,” the researchers write in a summary of their findings.


How To Capture Quickly Cancer Markers

A nanoscale product of human cells that was once considered junk is now known to play an important role in intercellular communication and in many disease processes, including cancer metastasis. Researchers at Penn State have developed nanoprobes to rapidly isolate these rare markers, called extracellular vesicles (EVs), for potential development of precision cancer diagnoses and personalized anticancer treatments.

Lipid nanoprobes

Most cells generate and secrete extracellular vesicles,” says Siyang Zheng, associate professor of biomedical engineering and electrical engineering. “But they are difficult for us to study. They are sub-micrometer particles, so we really need an electron microscope to see them. There are many technical challenges in the isolation of nanoscale EVs that we are trying to overcome for point-of-care cancer diagnostics.”

At one time, researchers believed that EVs were little more than garbage bags that were tossed out by cells. More recently, they have come to understand that these tiny fat-enclosed sacks — lipids — contain double-stranded DNA, RNA and proteins that are responsible for communicating between cells and can carry markers for their origin cells, including tumor cells. In the case of cancer, at least one function for EVs is to prepare distant tissue for metastasis.

The team’s initial challenge was to develop a method to isolate and purify EVs in blood samples that contain multiple other components. The use of liquid biopsy, or blood testing, for cancer diagnosis is a recent development that offers benefits over traditional biopsy, which requires removing a tumor or sticking a needle into a tumor to extract cancer cells. For lung cancer or brain cancers, such invasive techniques are difficult, expensive and can be painful.

Noninvasive techniques such as liquid biopsy are preferable for not only detection and discovery, but also for monitoring treatment,” explains Chandra Belani, professor of medicine and deputy director of the Cancer Institute,Penn State College of Medicine, and clinical collaborator on the study.

We invented a system of two micro/nano materials,” adds Zheng. “One is a labeling probe with two lipid tails that spontaneously insert into the lipid surface of the extracellular vesicle. At the other end of the probe we have a biotin molecule that will be recognized by an avidin molecule we have attached to a magnetic bead.”


Artificial Embryo From Stem Cells

Scientists at the University of Cambridge have managed to create a structure resembling a mouse embryo in culture, using two types of stem cells – the body’s ‘master cells’ – and a 3D scaffold on which they can grow. Understanding the very early stages of embryo development is of interest because this knowledge may help explain why a significant number of human pregnancies fail at this time.

Once a mammalian egg has been fertilised by a sperm, it divides multiple times to generate a small, free-floating ball of stem cells. The particular stem cells that will eventually make the future body, the embryonic stem cells (ESCs) cluster together inside the embryo towards one end: this stage of development is known as the blastocyst. The other two types of stem cell in the blastocyst are the extra-embryonic trophoblast stem cells (TSCs), which will form the placenta, and primitive endoderm stem cells that will form the so-called yolk sac, ensuring that the foetus’s organs develop properly and providing essential nutrients.

Using a combination of genetically-modified mouse ESCs and TSCs, together with a 3D scaffold known as an extracellular matrix, Cambridge researchers were able to grow a structure capable of assembling itself and whose development and architecture very closely resembled the natural embryo.  There is a  remarkable degree of communication between the two types of stem cell: in a sense, the cells are telling each other where in the embryo to place themselves.

artificial embryo

We knew that interactions between the different types of stem cell are important for development, but the striking thing that our new work illustrates is that this is a real partnership – these cells truly guide each other,”  says Professor Zernicka-Goetz. “Without this partnership, the correct development of shape and form and the timely activity of key biological mechanisms doesn’t take place properly.”

Comparing their artificial ‘embryo’ to a normally-developing embryo, the team was able to show that its development followed the same pattern of development. The stem cells organise themselves, with ESCs at one end and TSCs at the other.

The study has been published in the journal Science.


How To Eradicate Undetectable HIV Cells

French researchers have identified a marker that makes it possible to differentiate “dormantHIVinfected cells from healthy cells. This discovery will make it possible to isolate and analyze reservoir cells which, by silently hosting the virus, are responsible for its persistence even among patients receiving antiviral treatment, whose viral load is undetectable. It offers new therapeutic strategies for targeting infected cells. This research is part of the ANRS strategic program “Réservoirs du VIH”.

HIV detection

Since 1996, there has been consensus among the scientific community that a cure for HIV will involve targetingreservoir cells” that host the virus in the organisms of patients undergoing triple therapy. HIV can remain hidden in these reservoirs, in latent form, for several decades, eluding the immune system’s response and antiviral treatments, without any viral protein being expressed. But if treatment ceases, the virus massively proliferates and the disease progresses again. Patients must therefore receive treatment for life. To envisage eliminating this dormant virus, a first stage consists in distinguishing the HIV-infected reservoir cells from their healthy counterpart cells, which resemble them to a very large degree. This is what has been achieved by a team of researchers, who have identified a marker of reservoir cells: a protein present only on the surface of infected cells.

Hypothesizing that HIV might leave a mark on the surface of its host cell, researchers from the Institut de génétique humaine (CNRS/Montpellier University) first worked in vitro on an infection model developed in their laboratory. After comparing infected cells and healthy cells, they noticed one particular protein, coded by a gene among the hundred of those expressed in a specific way by infected cells. Present only on the surface of the infected cells, the CD32a protein thus met, in vitro, the criteria of a reservoir cell marker. This was then confirmed by experiments on clinical samples. By studying blood samples from 12 patients living with HIV and receiving treatment, the researchers isolated the cells expressing the marker and observed that almost all were HIV carriers. In vitro, the activation of these cells induced a production of viruses capable of reinfecting healthy cells whereas their elimination entailed a significant delay in viral production.

The findings are the result of a collaboration between the CNRS, Montpellier University, Inserm, the Institut Pasteur, the Henri-Mondor AP-HP hospital in Créteil, the Gui de Chauliac hospital (CHU de Montpellier) and the VRI (Vaccine Research Institute), and is published in the journal Nature on March 15, 2017. A patent owned by the CNRS has been filed for the diagnostic and therapeutic use of the identified marker.


Shape-shifting Molecular Robots

A research group at Tohoku University and Japan Advanced Institute of Science and Technology has developed a molecular robot consisting of biomolecules, such as DNA and protein. The molecular robot was developed by integrating molecular machines into an artificial cell membrane. It can start and stop its shape-changing function in response to a specific DNA signal.

This is the first time that a molecular robotic system has been able to recognize signals and control its shape-changing function. What this means is that molecular robots could, in the near future, function in a way similar to living organisms.

Using sophisticated biomolecules such as DNA and proteins, living organisms perform important functions. For example, white blood cells can chase bacteria by sensing chemical signals and migrating toward the target. In the field of chemistry and synthetic biology, elemental technologies for making various molecular machines, such as sensors, processors and actuators, are created using biomolecules. A molecular robot is an artificial molecular system that is built by integrating molecular machines. The researchers believe that realization of such a system could lead to a significant breakthrough – a bio-inspired robot designed on a molecular basis.

molecular robot

The molecular robot developed by the research group is extremely small – about one millionth of a meter – similar in size to human cells. It consists of a molecular actuator, composed of protein, and a molecular clutch, composed of DNA. The shape of the robot’s body (artificial cell membrane) can be changed by the actuator, while the transmission of the force generated by the actuator can be controlled by the molecular clutch. The research group demonstrated through experiments that the molecular robot could start and stop the shape-changing behavior in response to a specific DNA signal.

The findings were published in Science Robotics.


Car Pollution: Nanoparticles Travel Directly From The Nose To The Brain

The closer a person lives to a source of pollution, like a traffic dense highway, the more likely they are to develop Alzheimer’s or dementia, according to a study by the University of Southern California (USC) that has linked a close connection to pollution and the diseases. In a mobile lab, located just off of one of Los Angeles’ busiest freeways, USC scientists used a state-of-the-art pollution particle collector capable of gathering nano-sized particulate matter.

car pollution


We have shown that, as you would expect, the closer you get to the sources of these particles in our case the freeways, the higher the concentrations. So there is an exponential decay with distance. That means basically that, the concentration of where we are right now and if we were, let’s just say 20 or 10 or 50 yards from the freeway, those levels would be probably 10 times higher than where we are right now,” says Costas Sioutas, USC Professor of Environmental Engineering.

That means proximity to high concentrations of fossil fuel pollution, like a congested freeway, could be hazardous. Particulate matter roughly 30 times thinner than the width of a human hair, called PM2.5, is inhaled and can travel directly through the nose into the brain. Once there, the particles cause inflammatory responses and can result in the buildup of a type of plaque, which is thought to further the progression of Alzheimer’s. “Our study brought in this new evidence and I would say probably so far the most convincing evidence that the particle may increase the risk of dementia. This is really a public health problem. And I think the policy makers need to be aware of that, the public health risk associated with high level of PM2.5,” explains Jiu-Chiuan Chen, Associate Professor of Preventive Medicine.

USC researchers analyzed the data of more than 3,500 women who had the APOE4 gene, the major known risk-factor gene for Alzheimer’s disease. It showed that, over the course of a decade, the women who lived in a location with high levels of the PM2.5 pollution were 92 percent more likely to develop dementia.


Killing Cancer Cells From Inside

Researchers have witnessed – for the first time – cancer cells being targeted and destroyed from the inside, by an organo-metal compound discovered by the University of Warwick (UK). Professor Peter J. Sadler, and his group in the Department of Chemistry, have demonstrated that Organo-Osmium FY26 – which was first discovered at Warwick – kills cancer cells by locating and attacking their weakest part.

osmium compound fy26 in cancer cell
This is the first time that an Osmium-based compound – which is fifty times more active than the current cancer drug cisplatin – has been seen to target the disease. Using the European Synchrotron Radiation Facility (ESRF), researchers analysed the effects of Organo-Osmium FY26 in ovarian cancer cells – detecting emissions of X-ray fluorescent light to track the activity of the compound inside the cells

Looking at sections of cancer cells under nano-focus, it was possible to see an unprecedented level of minute detail. Organelles like mitochondria, which are the ‘powerhouses’ of cells and generate their energy, were detectable. In cancer cells, there are errors and mutations in the DNA of mitochondria, making them very weak and susceptible to attack.

FY26 was found to have positioned itself in the mitochondriaattacking and destroying the vital functions of cancer cells from within, at their weakest point. Researchers were also able to see natural metals which are produced by the body – such as zinc and calcium – moving around the cells. Calcium in particular is known to affect the function of cells, and it is thought that this naturally-produced metal helps FY26 to achieve an optimal position for attacking cancer.


How To Track Stem Cells In The Body

Rice University researchers have synthesized a new and greatly improved generation of contrast agents for tagging and real-time tracking of stem cells in the body. The agent combines ultrashort carbon nanotubes and bismuth clusters that show up on X-rays taken with computed tomography (CT) scanners. The stable compound performs more than eight times better than the first-generation material introduced in 2013, according to the researchers.

An improved compound of bismuth and carbon nanotubes called Bi4C@US-tubes, developed at Rice University could enhance the ability to track stem cells as they move through the body and target diseases

The primary application will be to track them in stem-cell therapies to see if the cells are attracted to the site of disease — for example, cancer — and in what concentration,” said Rice chemist Lon Wilson of the compound the researchers call Bi4C@US-tubes.

Magnetic resonance imaging is currently used for that purpose and it works quite well, but X-ray technology in the clinic is much more available,” he said. “It’s faster and cheaper, and it could facilitate preclinical studies to track stem cells in vivo.”

Bismuth is used in cosmetics, pigments and pharmaceuticals, notably as the active ingredient in pink bismuth (aka Pepto-Bismol), an antacid. For this application, bismuth nanoclusters developed by the lab of Rice chemist Kenton Whitmire, a co-author of the paper, are combined with carbon nanotubes chemically treated to shorten them to between 20 and 80 nanometers and add defects to their side walls. The nanoclusters, which make up about 20 percent of the compound, appear to strongly attach to the nanotubes via these defects.

When introduced into stem cells, the treated nanotubes become easy to spot, Wilson said. “It’s very interesting to see a cell culture that is opaque to X-rays. They’re not as dark as bone (which X-rays cannot penetrate), but they’re really dark when they’re loaded with these agents.”

The process developed by Wilson’s team and colleagues at CHI St. Luke’s Health-Baylor St. Luke’s Medical Center and Baylor College of Medicine is detailed this month in the American Chemical Society journal ACS Applied Materials and Interfaces.


‘Protective’ DNA strands are shorter in adults who had more infections as infants

New research indicates that people who had more infections as babies harbor a key marker of cellular aging as young adults: the protective stretches of DNA which “cap” the ends of their chromosomes are shorter than in adults who were healthier as infants.

TELOMERESThe 46 chromosomes of the human genome, with telomeres highlighted in white

These are important and surprising findings because — generally speaking — shorter chromosome ‘caps’ are associated with a higher burden of disease later in life,” said lead author Dan Eisenberg, an assistant professor of anthropology at the University of Washington.

The ‘caps’ Eisenberg and his co-authors measured are called telomeres. These are long stretches of DNA at the ends of our chromosomes, which protect our genes from damage or improper regulation. One Nobel Prize-winning scientist who studies telomeres has compared them to aglets — the plastic or metal sheath covering ends of shoelaces. When aglets wear down, the shoelace is exposed to fraying and degradation from environmental forces.

Like aglets, telomeres don’t last forever. In most of our cells, telomeres get shorter each time that cell divides. And when they get too short, the cell either quits dividing or dies.

That makes telomere length particularly important for the cells of our immune system, especially the white blood cells circulating in our bloodstream. When activated against a pathogen, white blood cells undergo rapid rounds of cell division to raise a defensive force against the infectious invader. But if telomeres in white blood cells are already too short, the body may struggle to mount an effective immune response.

Many studies — in laboratory animals and humans — have associated shorter telomeres with poor health outcomes, especially in adults,” said Eisenberg. But few studies have addressed whether or not events early in a person’s life might affect telomere length. To get at this question, Eisenberg turned to the Cebu Longitudinal Health and Nutrition Survey, which has tracked the health of over 3,000 infants born in 1983-1984 in Cebu City in the Philippines. Researchers collected detailed data every two months from mothers on the health and feeding habits of their babies up through age two. Mothers reported how often their babies had diarrhea — a sign of infection — as well as how often they breastfed their babies. As these babies grew up, scientists collected additional health data during follow-up surveys over the next 20 years. In 2005, 1,776 of these offspring donated a blood sample. By then, they were 21- or 22-year-old young adults.

Eisenberg measured telomere length in cells from those blood samples. He then combined the data on adult telomere length with information about their health and feeding habits as babies. He found that babies with higher reported cases of diarrhea at 6 to 12 months also had the shortest telomeres as adults.

The findings have been published in the American Journal of Human Biology.