PRESS-NEWS.org - Press Release Distribution
FREE PRESS RELEASES DISTRIBUTION

New technique reveals switches in RNA

Structural switches could be targets to fight coronavirus

New technique reveals switches in RNA
2021-02-22
(Press-News.org) Scientists at the University of Groningen (The Netherlands), in collaboration with colleagues from the University of Torino (Italy), have developed a method to visualize and quantify alternative structures of RNA molecules. These alternative RNA 'shapes' can have important functional relevance in viruses and bacteria. The researchers used an algorithm to rapidly analyse large quantities of chemically modified RNA molecules and calculate how many differently folded conformations were present. This technique was used to identify a conserved structural switch in the RNA of the SARS-CoV-2 virus. The results of this analysis were published in the journal Nature Methods on 22 February.

RNA molecules carry information in their nucleobase sequence that is needed to produce proteins. However, the molecules' 2D and 3D structures are also important. There are different ways in which the molecules can fold and some of these alternative conformations will affect the way in which the RNA functions. Riboswitches are a clear example: these are regulatory segments that are found in certain bacterial RNA molecules, the folding of which depends on the external environment and either allows or blocks translation of associated genes into proteins.

Mutations Viral RNA also folds and the switch between alternative conformations can be important to the life cycle of a virus. 'Whenever you see a dynamic structure in the RNA, this suggests a regulatory system,' says Danny Incarnato, a molecular geneticist at the University of Groningen. 'So, we devised a method to find in experimental data whether an RNA can form different conformations.'

Single-stranded RNA molecules fold through the pairing of nucleobases. This pairing protects the bases from mutation by chemical modification. Therefore, the mutation technique can indicate which bases are unpaired. Reverse transcriptase is used to convert the modified RNA into DNA, which is then sequenced to detect the modified nucleobases, which will be 'read' as mutations. 'The process is not very efficient and, therefore, not all the unpaired bases will be mutated,' comments Incarnato. This means that analysing the mutations and inferring the conformations that they represent is complex. Adding to this is that the same site can fold in multiple ways. 'However, the number of theoretically possible folds is much higher than we see in reality,' says Incarnato. The trick is to find them.

Visual inspection Several techniques have been proposed to calculate which folds are present in an RNA molecule and at what relative abundance. 'The idea is to see which mutations occur together in a particular region and which do not. This pattern points to alternative conformations.' The first proposed technique depended in part on visual inspection of the experimental data. A more recent system is fully automated, but Incarnato and his colleagues felt that it left room for improvement.

Incarnato: 'We created an algorithm that can rapidly analyse the huge number of reverse-transcribed RNA molecules.' In comparison to previously proposed systems, theirs requires less information to recognize alternative conformations and is less prone to overestimating the number of conformations. 'Our algorithm is more robust and very fast.'

Structurome Finding regions in RNA molecules that can have different conformations, and are therefore potential switches, is important. Incarnato: 'It helps us to understand the "RNA structurome" and the effect it has on viruses and cells.' In a virus, switches would be targets for antiviral drugs. It is also possible that riboswitches turn out to be present in eukaryotic cells, and even in mammalian cells. 'Certain mutations that have so far been overlooked because they do not change the sequence of the encoded proteins can instead change the structure of the RNA molecule. Hence, they can play a major role in cancer.'

In the Nature Methods paper, 22 regions that form alternative conformations were identified in the SARS-CoV-2 genome. 'A cool thing is that in two preprints by other groups, some of these regions are confirmed using a different technique.' Incarnato and his colleagues find one of the potential switches extremely interesting: 'The two conformations involved in this switch are highly conserved among coronaviruses, which means that they are important. That makes them a perfect target for RNA-targeted antiviral drugs.'

INFORMATION:

Reference: Edoardo Morandi, Ilaria Manfredonia, Lisa M. Simon, Francesca Anselmi, Martijn J. van Hemert, Salvatore Oliviero and Danny Incarnato: Genome-scale deconvolution of RNA structure ensembles Nature Methods 22 February 2021


[Attachments] See images for this press release:
New technique reveals switches in RNA

ELSE PRESS RELEASES FROM THIS DATE:

Patient page: Teen vaping

2021-02-22
What The Article Says: How parents can identify whether their teens are vaping, how to help prevent it, and what to do if their teen is addicted are discussed in this JAMA Pediatrics Patient Page. To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/ (doi:10.1001/jamapediatrics.2020.6689) Editor's Note: Please see the article for additional information, including other authors, author contributions and affiliations, conflict of interest and financial disclosures, and funding and support. INFORMATION: Media advisory: The full article is linked to this news release. Embed this link to provide your readers free access to the full-text article This link will be live at the embargo time https://jamanetwork.com/journals/jamapediatrics/fullarticle/10.1001/jamapediatrics.2020.6689?guestAccessKey=8fe3a04c-4e0a-40f3-a883-916eaadb05bb&utm_source=For_The_Media&utm_medium=referral&utm_campaign=ftm_links&utm_content=tfl&utm_term=022221 ...

State legislation related to abortion services

2021-02-22
What The Study Did: This survey study looked at changes in abortion policies among states by examining legislation enacted between January 2017 and November 2020. Authors: Phillip M. Singer, Ph.D., of the University of Utah in Salt Lake City, is the corresponding author. To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/ (doi:10.1001/jamainternmed.2020.8781) Editor's Note: Please see the article for additional information, including other authors, author contributions and affiliations, conflict of interest and financial disclosures, and funding ...

Genomic insights into the origin of pre-historic populations in East Asia

Genomic insights into the origin of pre-historic populations in East Asia
2021-02-22
Diverse East Asians derive ancestry from a coastal expansion tens of thousands of years ago Researchers have long debated whether the peopling of East Asia by modern humans occurred mainly via a coastal or interior route. The answer is probably both. "Indigenous Andaman islanders of the Bay of Bengal, Indigenous Tibetans, ancient Taiwanese, and ancient and modern Japanese all derive ancestry from a deep shared lineage that split from other East Asian lineages more than 40,000 years ago," says David Reich, co-senior author of the study, who is a Professor of Genetics ...

New therapeutic approach may help treat age-related macular degeneration effectively

New therapeutic approach may help treat age-related macular degeneration effectively
2021-02-22
Philadelphia, February 22, 2021 - Runt-related transcription factor 1 (RUNX1) has been linked to retinal neovascularization and the development of abnormal blood vessels, which result in vision loss in diabetic retinopathy. Now, scientists have found that RUNX1 inhibition presents a new therapeutic approach in the treatment of age-related macular degeneration (AMD), which is the leading cause of blindness in the elderly worldwide. Their END ...

New "metalens" shifts focus without tilting or moving

New metalens shifts focus without tilting or moving
2021-02-22
Polished glass has been at the center of imaging systems for centuries. Their precise curvature enables lenses to focus light and produce sharp images, whether the object in view is a single cell, the page of a book, or a far-off galaxy. Changing focus to see clearly at all these scales typically requires physically moving a lens, by tilting, sliding, or otherwise shifting the lens, usually with the help of mechanical parts that add to the bulk of microscopes and telescopes. Now MIT engineers have fabricated a tunable "metalens" that can focus on objects at multiple depths, without changes to its physical position or shape. The lens is made not of solid glass but of a ...

Air pollution puts children at higher risk of disease in adulthood

2021-02-22
Children exposed to air pollution, such as wildfire smoke and car exhaust, for as little as one day may be doomed to higher rates of heart disease and other ailments in adulthood, according to a new Stanford-led study. The analysis, published in Nature Scientific Reports, is the first of its kind to investigate air pollution's effects at the single cell level and to simultaneously focus on both the cardiovascular and immune systems in children. It confirms previous research that bad air can alter gene regulation in a way that may impact long-term health - a finding that could change the way medical experts and parents think about the air children ...

NYUAD researchers develop high throughput paper-based arrays of 3D tumor models

NYUAD researchers develop high throughput paper-based arrays of 3D tumor models
2021-02-22
Abu Dhabi, UAE, February 22: By engineering common filter papers, similar to coffee filters, a team of NYU Abu Dhabi researchers have created high throughput arrays of miniaturized 3D tumor models to replicate key aspects of tumor physiology, which are absent in traditional drug testing platforms. With the new paper-based technology, the formed tumor models can be safely cryopreserved and stored for prolonged periods for on-demand drug testing use. These cryopreservable tumor models could provide the pharmaceutical industry with an easy and low cost method for investigating the outcomes of drug efficacy, potentially bolstering personalized ...

Parents of children with cancer have additional worries during COVID

2021-02-22
DURHAM, N.C. - The COVID-19 pandemic has heaped additional financial strains, childcare complications and other problems on already-burdened caregivers of children diagnosed with cancer, according to a study from researchers at Duke Health and other institutions. Surveying 360 parents and caregivers of children currently in treatment or still being monitored for cancer, the researchers found that half had to cancel or delay appointments, 77% reported increased feelings of anxiety and of those who had lost jobs or wages, 11% struggled to pay for basic needs. The survey findings appear online this month in the journal Pediatric Blood & Cancer. "Parents and caregivers ...

Study could explain tuberculosis bacteria paradox

Study could explain tuberculosis bacteria paradox
2021-02-22
HOUSTON - (Feb. 22, 2021) -Tuberculosis bacteria have evolved to remember stressful encounters and react quickly to future stress, according to a study by computational bioengineers at Rice University and infectious disease experts at Rutgers New Jersey Medical School (NJMS). Published online in the open-access journal mSystems, the research identifies a genetic mechanism that allows the TB-causing bacterium, Mycobacterium tuberculosis, to respond to stress rapidly and in manner that is "history-dependent," said corresponding author Oleg Igoshin, a professor of bioengineering at Rice. Researchers have long suspected that the ability of TB bacteria to remain dormant, sometimes for decades, ...

Tricking the novel coronavirus with a fake "handshake"

2021-02-22
COLUMBUS, Ohio - Fool the novel coronavirus once and it can't cause infection of cells, new research suggests. Scientists have developed protein fragments - called peptides - that fit snugly into a groove on the SARS-CoV-2 Spike protein that it would normally use to access a host cell. These peptides effectively trick the virus into "shaking hands" with a replica rather than with the actual protein on a cell's surface that lets the virus in. Previous research has determined that the novel coronavirus binds to a receptor protein on a target cell's surface called ACE2. This receptor is located on certain types of human cells in the lung and nasal cavity, providing SARS-CoV-2 many access points to infect the body. For this work, Ohio State University scientists designed and tested peptides ...

LAST 30 PRESS RELEASES:

When foams collapse (and when they don't)

Predicts the onset of Alzheimer's Disease (AD) using deep learning-based Splice-AI

Oahu marine protected areas offer limited protection of coral reef herbivorous fishes

'Explicit instruction' provides dramatic benefits in learning to read

Deep brain stimulation and exercise restore movement in ataxia

Atherosclerosis can accelerate the development of clonal hematopoiesis, study finds

Picture books can boost physical activity for youth with autism

Cancer: a new killer lymphocyte enters the ring

When using pyrite to understand Earth's ocean and atmosphere: Think local, not global

New insights into an ancient protein complex

Meteorites remember conditions of stellar explosions

Cerium sidelines silver to make drug precursor

Researchers identify characteristics of highest utilizers for mental health hospital services

Research reveals how bacteria defeat drugs that fight cystic fibrosis

Sensing robot healthcare helpers being developed at SFU

Agents of food-borne zoonoses confirmed to parasitise newly-recorded in Thailand snails

New tools find COVID patients at highest risk of mechanical ventilation and death

Exposure to diverse career paths can help fill labor market 'skills gap'

Engineering the boundary between 2D and 3D materials

Republican and Democratic voters agree on one thing--the need for generous COVID-19 relief

New study highlights importance of context to physical theories

Quantum quirk yields giant magnetic effect, where none should exist

Considering disorder and cooperative effects in photon escape rates from atomic gases

Blood tests offer early indicator of severe COVID-19, study says

New research finds exercise may help slow memory loss for people living with Alzheimer's dementia

Using neutron scattering to better understand milk composition

Unburdening China of cancer: Trend analysis to assist prevention measures

Measuring the tRNA world

Household transmission of SARS-CoV-2

When young people start smoking

[Press-News.org] New technique reveals switches in RNA
Structural switches could be targets to fight coronavirus