Category Archives: Uncategorized
COVID-19 Thirty Seconds Test Has Successful Results
Rapid detection of the SARS-CoV-2 virus, in about 30 seconds following the test, has had successful preliminary results in Mano Misra’s lab at the University of Nevada, Reno. The test uses a nanotube-based electrochemical biosensor, a similar technology that Misra has used in the past for detecting tuberculosis and colorectal cancer as well as detection of biomarkers for food safety.
Professor Misra, in the University’s College of Engineering Chemical and Materials Department, has been working on nano-sensors for 10 years. He has expertise in detecting a specific biomarker in tuberculosis patients’ breath using a metal functionalized nano sensor.
Testing a nanotube-based electrochemical biosensor
“I thought that similar technology can be used to detect the SARS-CoV-2 virus, which is a folded protein,” Misra said. “
This is Point of Care testing to assess the exposure to COVID-19. We do not need a laboratory setting or trained health care workers to administer the test. Electrochemical biosensors are advantageous for sensing purposes as they are sensitive, accurate and simple.”
The test does not require a blood sample, it is run using a nasal swab or even exhaled breath, which has biomarkers of COVID-19. Misra and his team have successfully demonstrated a simple, inexpensive, rapid and non-invasive diagnostic platform that has the potential to effectively detect the SARS-CoV-2 virus.
The team includes Associate Professor Subhash Verma, virologist, and Research Scientist Timsy Uppal at the University’s School of Medicine, and Misra’s post-doctoral researcher Bhaskar Vadlamani.
“Our role on this project is to provide viral material to be used for detection by the nanomaterial sensor developed by Mano,” Verma said. “Mano contacted me back in April or May and asked whether we can collaborate to develop a test to detect SARS-CoV-2 infection by analyzing patients’ breath. That’s where we came in, to provide biological material and started with providing the surface protein of the virus, which can be used for detecting the presence of the virus.”
Source: https://www.unr.edu
How To Protect Cells From Premature Aging
Molecules that accumulate at the tip of chromosomes are known to play a key role in preventing damage to our DNA. Now, researchers at EPFL (Ecole Polytechnique Fédérale de Lausanne in Switzerland) have unraveled how these molecules home in on specific sections of chromosomes—a finding that could help to better understand the processes that regulate cell survival in aging and cancer.
Much like an aglet of a shoelace prevents the end of the lace from fraying, stretches of DNA called telomeres form protective caps at the ends of chromosomes. But as cells divide, telomeres become shorter, making the protective cap less effective. Once telomeres get too short, the cell stops dividing. Telomere shortening and malfunction have been linked to cell aging and age-related diseases, including cancer.
A new study by EPFL researchers shows how RNA species called TERRA muster at the tip of chromosomes, where they help to prevent telomere shortening and premature cell aging
Scientists have known that RNA species called TERRA help to regulate the length and function of telomeres. Discovered in 2007 by postdoc Claus Azzalin in the team of EPFL Professor Joachim Lingner, TERRA belongs to a class of molecules called noncoding RNAs, which are not translated into proteins but function as structural components of chromosomes. TERRA accumulates at chromosome ends, signaling that telomeres should be elongated or repaired.
However, it was unclear how TERRA got to the tip of chromosomes and remained there. “The telomere makes up only a tiny bit of the total chromosomal DNA, so the question is ‘how does this RNA find its home?’”, Lingner says. To address this question, postdoc Marianna Feretzaki and others in the teams of Joachim Lingner at EPFL and Lumir Krejci at Masaryk University set out to analyze the mechanism through which TERRA accumulates at telomeres, as well as the proteins involved in this process. The findings are published in Nature.
By visualizing TERRA molecules under a microscope, the researchers found that a short stretch of the RNA is crucial to bring it to telomeres. Further experiments showed that once TERRA reaches the tip of chromosomes, several proteins regulate its association with telomeres. Among these proteins, one called RAD51 plays a particularly important role, Lingner says.
RAD51 is a well-known enzyme that is involved in the repair of broken DNA molecules. The protein also seems to help TERRA stick to telomeric DNA to form a so-called “RNA-DNA hybrid molecule”. Scientists thought this type of reaction, which leads to the formation of a three-stranded nucleic acid structure, mainly happened during DNA repair. The new study shows that it can also happen at chromosome ends when TERRA binds to telomeres. “This is paradigm-shifting,” Lingner says.
The researchers also found that short telomeres recruit TERRA much more efficiently than long telomeres. Although the mechanism behind this phenomenon is unclear, the researchers hypothesize that when telomeres get too short, either due to DNA damage or because the cell has divided too many times, they recruit TERRA molecules. This recruitment is mediated by RAD51, which also promotes the elongation and repair of telomeres. “TERRA and RAD51 help to prevent accidental loss or shortening of telomeres,” Lingner says. “That’s an important function.”
Source: https://actu.epfl.ch/
Algorithms Boost Cell Therapy
Cellular therapy is a powerful strategy to produce patient-specific, personalised cells to treat many diseases, including heart disease and neurological disorders. But a major challenge for cell therapy applications is keeping cells alive and well in the lab.
That may soon change as researchers at Duke-NUS Medical School, Singapore, and Monash University, Australia, have devised an algorithm that can predict what molecules are needed to keep cells healthy in laboratory cultures. They developed a computational approach called EpiMogrify, that can predict the molecules needed to signal stem cells to change into specific tissue cells, which can help accelerate treatments that require growing patient cells in the lab.
“Computational biology is rapidly becoming a key enabler in cell therapy, providing a way to short-circuit otherwise expensive and time-consuming discovery approaches with cleverly designed algorithms,” said Assistant Professor Owen Rackham, a computational biologist at Duke-NUS, and a senior and corresponding author of the study, published today in the journal Cell Systems.
In the laboratory, cells are often grown and maintained in cell cultures, formed of a substance, called a medium, which contains nutrients and other molecules. It has been an ongoing challenge to identify the necessary molecules to maintain high-quality cells in culture, as well as finding molecules that can induce stem cells to convert to other cell types.
The research team developed a computer model called EpiMogrify that successfully identified molecules to add to cell culture media to maintain healthy nerve cells, called astrocytes, and heart cells, called cardiomyocytes. They also used their model to successfully predict molecules that trigger stem cells to turn into astrocytes and cardiomyocytes. “Research at Duke-NUS is paving the road for cell therapies and regenerative medicine to enter the clinic in Singapore and worldwide; this study leverages our expertise in computational and systems biology to facilitate the good manufacturing practice (GMP) production of high-quality cells for these much needed therapeutic applications,” said Associate Professor Enrico Petretto, who leads the Systems Genetics group at Duke-NUS, and is a senior and corresponding author of the study.
Source: https://www.duke-nus.edu.sg/
Machine Learning Predicts Heart Failure
Every year, roughly one out of eight U.S. deaths is caused at least in part by heart failure. One of acute heart failure’s most common warning signs is excess fluid in the lungs, a condition known as “pulmonary edema.” A patient’s exact level of excess fluid often dictates the doctor’s course of action, but making such determinations is difficult and requires clinicians to rely on subtle features in X-rays that sometimes lead to inconsistent diagnoses and treatment plans.
To better handle that kind of nuance, a group led by researchers at MIT’s Computer Science and Artificial Intelligence Lab (CSAIL) has developed a machine learning model that can look at an X-ray to quantify how severe the edema is, on a four-level scale ranging from 0 (healthy) to 3 (very, very bad). The system determined the right level more than half of the time, and correctly diagnosed level 3 cases 90 percent of the time.
Working with Beth Israel Deaconess Medical Center (BIDMC) and Philips, the team plans to integrate the model into BIDMC’s emergency-room workflow this fall.
“This project is meant to augment doctors’ workflow by providing additional information that can be used to inform their diagnoses as well as enable retrospective analyses,” says PhD student Ruizhi Liao, who was the co-lead author of a related paper with fellow PhD student Geeticka Chauhan and MIT professors Polina Golland and Peter Szolovits.
The team says that better edema diagnosis would help doctors manage not only acute heart issues, but other conditions like sepsis and kidney failure that are strongly associated with edema.
As part of a separate journal article, Liao and colleagues also took an existing public dataset of X-ray images and developed new annotations of severity labels that were agreed upon by a team of four radiologists. Liao’s hope is that these consensus labels can serve as a universal standard to benchmark future machine learning development.
An important aspect of the system is that it was trained not just on more than 300,000 X-ray images, but also on the corresponding text of reports about the X-rays that were written by radiologists. “By learning the association between images and their corresponding reports, the method has the potential for a new way of automatic report generation from the detection of image-driven findings,” says Tanveer Syeda-Mahmood, a researcher not involved in the project who serves as chief scientist for IBM’s Medical Sieve Radiology Grand Challenge. “Of course, further experiments would have to be done for this to be broadly applicable to other findings and their fine-grained descriptors.”
Chauhan, Golland, Liao and Szolovits co-wrote the paper with MIT Assistant Professor Jacob Andreas, Professor William Wells of Brigham and Women’s Hospital, Xin Wang of Philips, and Seth Berkowitz and Steven Horng of BIDMC.
Source: https://news.mit.edu/
Coronavirus Vaccine: Moderna and Pfizer Final Test Results Imminent
Moderna should have enough data from its late-stage trial to know whether its coronavirus vaccine works in November, CEO Stephane Bancel said Thursday. The company could have enough data by October, but that’s unlikely, Bancel said during an interview on CNBC’s “Squawk Box.”
“If the infection rate in the country were to slow down in the next weeks, it could potentially be pushed out in a worst-case scenario in December,” he added.
Moderna is one of three drugmakers backed by the U.S. in late-stage testing for a potential vaccine. The other two are companies Pfizer and AstraZeneca.
Moderna‘s experimental vaccine contains genetic material called messenger RNA, or mRNA, which scientists hope provokes the immune system to fight the virus. In July, the company released early-stage data that showed its potential vaccine generated a promising immune response in a small group of patients.
Bancel’s comment came four days after the CEO of Pfizer said its vaccine could be distributed to Americans before the end of the year. CEO Albert Bourla told CBS’ “Face the Nation” that the company should have key data from its late-stage trial for the Food and Drug Administration by the end of October. If the FDA approves the vaccine, the company is prepared to distribute “hundreds of thousands of doses,” he said.
Source: https://www.cnbc.com/
Nobel Chemistry Prize Awarded For CRISPR ‘NanoScissors’
A humbling lesson of science is that, even when it comes to many of humanity’s most brilliant inventions, nature got there first. The 2020 selection for the Nobel Prize in Chemistry goes to two scientists who share credit for identifying and developing a revolutionary method of genome editing — one that has allowed researchers to modify and investigate the genomes of microbial, plant and animal cells with an ease, precision and effectiveness that would have been unfathomable even a decade ago. Yet the technology that came out of their work, revolutionary as it is, springs from an innovation that first evolved in bacteria, probably more than a billion years ago, and went unnoticed until recently.
Emmanuelle Charpentier of the Max Planck Unit for the Science of Pathogens Institute for Infection Biology and Jennifer Doudna of the University of California, Berkeley have been recognized for their work on CRISPR/Cas9 genome editing — a technique routinely called CRISPR for short and often referred to as “genetic scissors.” This award marks the first time that two women have been award a Nobel Prize for science.
In a seminal 2012 paper, Charpentier and Doudna showed that key components of the ancient immune system found in bacteria and archaea could be retooled to edit DNA, to essentially “rewrite the code of life,” as the Nobel committee put it this morning.
In the eight years since, the discovery has transformed the life sciences, making genome editing commonplace in laboratories around the world. It has enabled researchers to probe the functions of genes at will, pushing the field of molecular biology ahead by leaps and bounds; to innovate new methods of plant breeding; and to develop promising new gene therapies, some now in clinical trials, for conditions such as sickle cell disease.
The Nobel committee’s selection will undoubtedly be greeted as controversial because of well-publicized disputes about the intellectual property associated with CRISPR. Virginijus Šikšnys of Vilnius University in Lithuania independently developed the idea of using these genetic features of bacteria as a genome-editing tool at about the same time as Charpentier and Doudna, and he has sometimes been honored alongside them. Two other scientists, Feng Zhang of the Massachusetts Institute of Technology and George Church of Harvard University, are also often credited as early co-discoverers and developers of CRISPR technology, and their exclusion will fuel arguments. However, no one in the scientific community would dispute that Charpentier and Doudna’s work laid the foundation for CRISPR’s prolific and game-changing use today.
Source: https://www.quantamagazine.org/
Diabetics die 3 times more of Covid-19
From the outset of the pandemic, data coming out of early coronavirus hot spots like China, Italy, and New York City foretold that certain groups of people would be more vulnerable to Covid-19. The disease hit older people and people with underlying medical conditions the hardest. As early as February, diabetes had emerged as one of the conditions associated with the highest risk. In one large study out of China, people with diabetes were more than three times as likely to die of Covid-19 than the overall population.
But that’s not what brought four diabetes experts from Australia and the United Kingdom onto a Zoom call back in April. They were supposed to just be catching up—a virtual tea among friends. But talk soon turned to something strange that they’d been seeing in their own hospitals and hearing about through the grapevine. The weird thing was that people were showing up in Covid-19 wards, after having tested positive for the virus, with lots of sugar in their blood. These were people with no known history of diabetes. But you wouldn’t know it from their lab results.
After that call, the experts reached out to colleagues in other countries to see if they’d seen or heard of similar cases. They had. Acute viral infections of all sorts can stress the body, causing blood sugar levels to rise. So that in itself wasn’t unusual, says Francesco Rubino, a bariatric surgeon and diabetes researcher at King’s College in London, who was on that first Zoom call. “What we were seeing and hearing was a little bit different.”
Doctors around the world had described to him strange situations in which Covid-19 patients were showing symptoms of diabetes that didn’t fit the typical two-flavor manifestation of the disease. In most people with type 1 diabetes, their immune cells suddenly turn traitorous, destroying the cells in the pancreas that produce insulin—the hormone that allows glucose to exit the bloodstream and enter cells. People with type 2 diabetes have a different problem; their body slowly becomes resistant to the insulin it does produce. Rubino and his colleagues were seeing blended features of both types showing up spontaneously in people who’d recently been diagnosed with Covid-19.
“That was the first clinical puzzle,” he says. For clues to an explanation, Rubino and his colleagues looked to ACE2, the protein receptor that SARS-CoV-2 uses to invade human cells. It appears in the airways, yes, but also in other organs involved in controlling blood sugar, including the gut. Doctors in China discovered copies of the coronavirus in the poop of their Covid-19 patients. And a meta-analysis found that gastrointestinal symptoms plague one out of 10 Covid-19 sufferers.
In the last few decades, scientists have discovered that the gut is not the passive digestive organ once thought. It actually is a major endocrine player—responsible for producing hormone signals that talk to the pancreas, telling it to make more insulin, and to the brain, ordering it to make its owner stop eating. If the coronavirus is messing with these signals, that could provide a biological basis for why Covid-19 would be associated with different forms of diabetes, including hybrid and previously unknown manifestations of the disease. Rubino is one of a growing number of researchers who think that the relationship between the coronavirus and diabetes is actually a two-way street. Having diabetes doesn’t just tip the odds toward contracting a worse case of Covid-19. In some people, the virus might actually trigger the onset of diabetes, and the potential for a lifetime of having to manage it.
Source: https://www.wired.com/
How To Recycle Plastic Infinitely And Reduce Plastic Pollution
The scientists who re-engineered the plastic-eating enzyme PETase have now created an enzyme ‘cocktail’ which can digest plastic up to six times faster. A second enzyme, found in the same rubbish dwelling bacterium that lives on a diet of plastic bottles, has been combined with PETase to speed up the breakdown of plastic. PETase breaks down polyethylene terephthalate (PET) back into its building blocks, creating an opportunity to recycle plastic infinitely and reduce plastic pollution and the greenhouse gases driving climate change. PET is the most common thermoplastic, used to make single-use drinks bottles, clothing and carpets and it takes hundreds of years to break down in the environment, but PETase can shorten this time to days.
The team was co-led by the scientists who engineered PETase, Professor John McGeehan, Director of the Centre for Enzyme Innovation (CEI) at the University of Portsmouth in UK, and Dr Gregg Beckham, Senior Research Fellow at the National Renewable Energy Laboratory (NREL) in the US. “Gregg and I were chatting about how PETase attacks the surface of the plastics and MHETase chops things up further, so it seemed natural to see if we could use them together, mimicking what happens in nature,” said Professor McGeehan
“Our first experiments showed that they did indeed work better together, so we decided to try to physically link them, like two Pac-men joined by a piece of string. “It took a great deal of work on both sides of the Atlantic, but it was worth the effort – we were delighted to see that our new chimeric enzyme is up to three times faster than the naturally evolved separate enzymes, opening new avenues for further improvements.”
The initial discovery set up the prospect of a revolution in plastic recycling, creating a potential low-energy solution to tackle plastic waste. The team engineered the natural PETase enzyme in the laboratory to be around 20 percent faster at breaking down PET. Now, the same trans-Atlantic team have combined PETase and its ‘partner’, a second enzyme called MHETase, to generate much bigger improvements: simply mixing PETase with MHETase doubled the speed of PET breakdown, and engineering a connection between the two enzymes to create a ‘super-enzyme’, increased this activity by a further three times.
The study is published in the journal Proceedings of the National Academy of Sciences of the United States of America.
Hundreds of Thousands Of People In China Should Have Been Vaccinated At Present
China in recent months has been injecting hundreds of thousands of people with three preliminary coronavirus vaccines that are being tested for safety and efficacy. While the world awaits a proven drug to fight the pandemic, at least three vaccine candidates have been given to front-line medical professionals, staff of state-owned companies, and government officials since July under an emergency use program approved by Beijing.
China National Biotec Group (CNBG), a subsidiary of state-owned Sinopharm, has administered two experimental vaccine candidates to around 350,000 people outside its clinical trials, CNBG chairman Yang Xiaoming said recently. The company also donated 200,000 doses of one of the candidate vaccines that is still undergoing clinical trials in Wuhan, where the pandemic was first reported.
Another drugmaker, Sinovac Biotech, has injected 90% of its employees and their family members, or about 3,000 people, Yin Weidong, the company’s CEO, said this month.
“At present, tens of thousands of people in Beijing should have been vaccinated with Sinovac’s vaccine,” Yin told Chinese state media. Separately, Beijing also gave approval in June for members of the armed forces to receive an experimental vaccine developed by CanSino Biologics, a biopharmaceutical company that is backed by the military.
Under China’s law, vaccines developed for major public health emergencies can be deployed for urgent use if the National Medical Products Administration considers that the benefits of the treatment outweigh the risks.
Source: https://www.voanews.com/
What Is Regeneron, The Antibody Cocktail Used To Cure Trump?
A descriptive analysis of Regeneron Pharmaceuticals‘ Phase I/II/III clinical trial has found that its antibody cocktail REGN-COV2 lowered viral load and the time to symptoms improvement in non-hospitalised Covid-19 patients. The therapy also demonstrated positive trends in decreasing medical visits. During the ongoing, randomised, double-blind trial, the combination of REGN-COV2 and usual standard-of-care is being compared to placebo plus standard-of-care.
Regeneron noted that trial participants were given a one-time infusion of 8g or 2.4g of REGN-COV2 or placebo. Data from the descriptive analysis is based on the findings from the initial 275 patients. The analysis evaluated anti-viral activity with the therapy and is intended to detect patients who are most likely to benefit from treatment. Safety analysis revealed that both doses of the therapy were well-tolerated, with infusion reactions found in four patients.
“The greatest treatment benefit was in patients who had not mounted their own effective immune response, suggesting that REGN-COV2 could provide a therapeutic substitute for the naturally-occurring immune response, ” said Regeneron Pharmaceuticals president and chief scientific officer George Yancopoulos. “We are highly encouraged by the robust and consistent nature of these initial data, as well as the emerging well-tolerated safety profile, and we have begun discussing our findings with regulatory authorities while continuing our ongoing trials.”
This trial is part of a clinical programme, which includes studies of REGN-COV2 to treat hospitalised patients and to prevent infection in people exposed to Covid-19 patients. More than 2,000 subjects have been recruited across the overall REGN-COV2 development programme. At least 1,300 participants will be part of the Phase II/III portion of the outpatient trial overall. In July, Regeneron launched Phase III trials of REGN-COV2 for the treatment and prevention of Covid-19.
