New Genetic Analysis Tool Tracks Risks Tied to CRISPR Edits

UC San Diego researchers have created a new system that reveals specific categories of potentially risky mutations resulting from CRISPR edits. This high magnification image reveals CRISPR-based DNA transcription of the homothorax gene in fruit fly embryos.
Image Credit: Bier Lab, UC San Diego

Since its breakthrough development more than a decade ago, CRISPR has revolutionized DNA editing across a broad range of fields. Now scientists are applying the technology’s immense potential to human health and disease, targeting new therapies for an array of disorders spanning cancers, blood conditions and diabetes.

In some designed treatments, patients are injected with CRISPR-treated cells or with packaged CRISPR components with a goal of repairing diseased cells with precision gene edits. Yet, while CRISPR has shown immense promise as a next-generation therapeutic tool, the technology’s edits are still imperfect. CRISPR-based gene therapies can cause unintended but harmful “bystander” edits to parts of the genome, at times leading to new cancers or other diseases.

Next-generation solutions are needed to help scientists unravel the complex biological dynamics behind both on- and off-target CRISPR edits. But the landscape for such novel tools is daunting, since intricate bodily tissues feature thousands of different cell types and CRISPR edits can depend on many different biological pathways.

Researchers a step closer to a cure for HIV

HIV, the AIDS virus (yellow), infecting a human cell
Image Credit: National Cancer Institute

A new study involving University of Bristol researchers has shown a virus-like particle (HLP) can effectively 'shock and kill' the latent HIV reservoir.

By 2030, the World Health Organization (WHO), the Global Fund and UNAIDS are hoping to end the human immunodeficiency virus (HIV) and AIDS epidemic. An international team of researchers led by Professor Eric Arts from the Schulich School of Medicine & Dentistry, Canada, and Dr Jamie Mann, Senior Lecturer at the University of Bristol, has brought us another step closer to meeting this goal, by finding an effective and affordable targeted treatment strategy for an HIV cure. 

In a first, the study published in Emerging Microbes and Infections demonstrated the team's patented therapeutic candidate. The HIV-virus-like-particle (HLP), is 100 times more effective than other candidate HIV cure therapeutics for people living with chronic HIV on combined antiretroviral therapy (cART). If successful in clinical trials, HLP could be used by millions of people living around the world to free them of HIV. This study was done using blood samples from people living with chronic HIV. 

HLPs are dead HIV particles hosting a comprehensive set of HIV proteins that increase immune responses without infecting a person. When compared with other potential cure approaches, HLP is an affordable biotherapeutic and can be administered by intramuscular injection – similar to the seasonal flu vaccine. 

Two-Way Cell-based Treatment Repairs Muscle After Rotator Cuff Injury

A combination of mobilizing agent, designed to “push” pro-healing cells into the blood, and SDF-1a, designed to “pull” the cells into the injury site, leads to an increase in muscle regeneration following a rotator cuff tear. Muscle regeneration was characterized based on the number of centrally located nuclei (marked with the white arrows).
Image Credit: Courtesy of the researchers / Georgia Institute of Technology

A team of Georgia Tech researchers has introduced a new therapeutic system to offset the poor clinical outcomes often associated with common rotator cuff surgery.

It’s the kind of surgery that makes headlines whenever a famous athlete is sidelined with a torn rotator cuff. Major League Baseball All-Star pitchers Clayton Kershaw and Justin Verlander, for example, both had rotator cuff surgeries and made successful comebacks.

For those of us who can’t throw baseballs 95 miles an hour, the rotator cuff may tear over time from repeated overhead motions (painters and carpenters, for instance). Or an injury can occur as we age and our body’s tissues naturally degenerate. And although rotator cuff injuries are common, they can be serious, leading to muscle degeneration after surgery.

Now, two professors from the Wallace H. Coulter Department of Biomedical Engineering, a joint department of Georgia Tech and Emory University, have addressed the problem with a novel cell-based dual treatment, which they describe in a study published recently in the journal Tissue Engineering.

Climate change will see Australia’s soil emit CO2 and add to global warming

Australian Outback
Photo Credit: Nathan March

New Curtin University research has shown the warming climate will turn Australia’s soil into a net emitter of carbon dioxide (CO2), unless action is taken.

Soil helps to keep the planet cool by absorbing carbon, however as the climate gets warmer its ability to retain carbon decreases — and in some instances can start to release some carbon back into the air.

A global research team — led by Professor Raphael Viscarra Rossel from Curtin’s School of Molecular and Life Sciences— predicted the changes in the amount of carbon in Australia’s soil between now and the year 2100.

To do so, the team ran simulations using three different paths for society: an eco-focused ‘sustainable’ scenario, a ‘middle-of-the-road’ scenario and another which predicted a continued reliance on ‘fossil-fueled development’.

It found Australian soil will be a net emitter and could account for 8.3 per cent of Australia’s total current emissions under the ‘sustainable’ scenario and more than 14 per cent by 2045 under the ‘middle-of-the-road’ and ‘fossil-fueled’ scenarios.

Study explores severe hurricanes and coral reef sponge recolonization

For the study, scuba divers collected small samples of the thin purple morphotype sponges 14 and 22 months after the two Category 5 hurricanes in St. Thomas.
Photo Credit: Karli Hollister

Named for its ropy-looking long branches, Aplysina cauliformis, a coral reef sponge, provides a critical 3D habitat for marine organisms and helps to stabilize the foundation of coral reefs. However, these upright branching sponges are highly susceptible to breaking during storms, which increases sponge fragmentation and contributes to population clonality and inbreeding.

Many sponges can survive severe damage and undergo frequent fragmentation, which is considered a mechanism for asexual reproduction. While fragmentation is a commonly utilized reproductive strategy in rope sponges, they also can reproduce sexually by producing larvae. How and whether they recolonize following extreme weather events is critical for the restoration and resilience of coral reef ecosystems.

Hurricanes Irma and Maria – both in 2017 – were two rapid succession storms that provided researchers from Florida Atlantic University’s Harriet L. Wilkes Honors College and Harbor Branch Oceanographic Institute, and collaborators from the University of the Virgin Islands, the University of Mississippi and the University of Alabama, with a unique opportunity to address a priority concern – the resilience of coral reef sponge populations after severe hurricanes. 

Gut microbiota and antibiotics: Missing puzzle piece discovered

3D model of the small ribonucleic acid MasB.
Image Credit: Alexander Westermann/HIRI

HIRI scientists have identified a small RNA that influences the sensitivity of the intestinal commensal Bacteroides thetaiotaomicron to certain antibiotics.

The intricacies of how intestinal bacteria adapt to their environment have yet to be fully explored. Researchers from the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg and the University of California, Berkeley, USA, have now successfully closed a gap in this knowledge: They have identified a small ribonucleic acid (sRNA) that affects the susceptibility of the gut commensal Bacteroides thetaiotaomicron to specific antibiotics. The findings, published today in the journal Nature Microbiology, could serve as the foundation for novel therapies addressing intestinal diseases and combating antibiotic resistance. 

The gut, a complex ecosystem of numerous microorganisms, plays a pivotal role in human well-being. Factors like dietary changes, medications, or bile salts can influence the microbiota, impacting health. Among the prevalent intestinal bacteria in humans are Bacteroides thetaiotaomicron. These gut microbes play a role in breaking down polysaccharides during digestion, contributing to human health. Yet they can also promote infections when the ecosystem is disbalanced, such as after antibiotic treatment. However, the molecular mechanisms enabling these gut microbes to adapt to their environment remain largely unknown.

New Study Reveals Who Was More Vulnerable to Post-COVID Syndrome in Early Phases of the Pandemic

Fatigue, malaise and difficulty breathing were associated with post-COVID syndrome, according to the new Nordic study.
Photo Credit: Kinga Howard

People with post-COVID syndrome (PCS) following the COVID-19 infection often suffer from intense fatigue and dyspnea. This is what emerges from a new Nordic study led by Umeå University and recently published in the BMJ Public Health journal. High blood pressure also appears to be a risk factor for PCS diagnosis, according to the study’s findings.

"These scientific results are an important step in better understanding PCS. By identifying key factors, we can improve diagnosis, adapt care and pave the way for research into more effective treatments," says Anne-Marie Fors Connolly, MD PhD, Assoc Prof, clinical researcher at Umeå University and the study's senior author.

The study analyzed data from over one million people in Sweden who tested positive for COVID-19 during the period from February 2020 to May 2021. Of these, 1.5 percent, just over 16,000 people, were diagnosed with PCS after the main COVID-19 infection. They were diagnosed in both outpatient and inpatient care, which provided large datasets for the researchers to examine the clinical footprint of PCS. The researchers conducted an in-depth study of PCS symptoms in individuals who required ongoing healthcare three months after the COVID-19 infection.

Behavior of ant queens is shaped by their social environment

A black garden ant queen caring for her brood
Photo Credit: © Romain Libbrecht)

The queens in colonies of social insects, such as ants, bees, and wasps, are considered the veritable embodiment of specialization in the animal kingdom. The common perception is that the queen's only task is to lay eggs – and that this attribute is an inherent trait, not influenced by external factors. In contrast, recent research undertaken at Johannes Gutenberg University Mainz (JGU) has demonstrated that in certain ant colonies the social environment can play a crucial role in shaping the behavioral specialization of the queens. "With regard to the ant species we studied, it is social factors that control whether queens become specialized or not. Our findings challenge the widely accepted notion of social insect queens as inherently specialized egg-laying machines," stated Dr. Romain Libbrecht.

The research was conducted by the Reproduction, Nutrition, and Behavior in Insect Societies group at JGU under the supervision of Dr. Romain Libbrecht, an evolutionary biologist. The corresponding paper has recently been published in Functional Ecology. Dr. Romain Libbrecht currently works at the Centre National de la Recherche Scientifique (CNRS) in the Insect Biology Research Institute of the University of Tours.

Seeing a Path to Nerve Regeneration

The image on the left (A) shows four optic nerves that have been crushed. Live nerve tissue glows green in this image, while damaged nerve tissue is dark. The top nerve was not treated with any regenerative factors, and there is no regrowth of the nerve (shown by the uniformly dark area on the right.) The second and third nerves were treated with previously identified regeneration factors, and show some live nerve tissue beyond the crushed area. The bottom nerve was treated with Nfe3, and also shows live nerve tissue beyond the crushed region. (B) shows close-ups of the left, middle, and far right sections of the crushed nerves. The nerve treated with Nfe3 (bottom) shows regeneration as good or better than the nerves treated with the other factors (middle two rows).
Image Credit: Courtesy of researcher Et al Experimental Neurology and University of Connecticut

This opens a whole new novel realm of research. It could help glaucoma and other types of nerve damage

Damage to the optic nerve can lead to irreversible blindness. A newly investigated regeneration factor could change that, UConn researchers report in the May 2024 issue of Experimental Neurology.

Blindness and vision impairment due to optic nerve damage affect more than 3 million people in the US alone, according to the Centers for Disease Control (CDC). The most common reason for that damage is glaucoma, a family of eye diseases that affect the flow of liquid in the eye, eventually damaging the long bundle of cells that connect the retina to the brain. That bundle of cells is the optic nerve. They don’t grow back after being damaged, leading to permanent vision loss.

Now, a team of researchers in the lab of UConn School of Medicine neuroscientist Ephraim Trakhtenberg have shown that a protein previously thought unimportant can stimulate regrowth of nerve cells. The protein is called nuclear factor erythroid 3 (Nfe3), and it is unique to nerves originating in the retina. Normally it is not produced by adult neurons.

Protect habitat to prevent pandemics

Photo Credit: Vlad Kutepov

An international research team has proposed using ecological perspectives to prevent the occurrence of disease outbreaks.

Pandemics begin when disease-harboring animals, such as bats, come in close proximity with people, livestock or other animals and pass on new pathogens. Viruses such as SARS-CoV-2, SARS-CoV-1, Nipah, Hendra and possibly Ebola have all fatally spilled over from bats to humans, sometimes through an intermediate host.

Led by Cornell University expert, Professor Raina Plowright, the international team has proposed a roadmap for how to prevent the next pandemic by conserving natural areas and promoting biodiversity, thereby providing animals with enough food, safe havens and distance to limit contact and transfer of pathogens to humans.

Professor Plowright said: “The world is focused on how can we detect and then contain a novel pathogen once it is circulating in humans, rather than how can we prevent that pathogen from entering the human population in the first place.”

The roadmap uses insights from recently published case studies to explain the mechanisms linking environmental change and spillover of pathogens from animals to humans and identifies ecological interventions to disrupt these links and policy frameworks to implement them.

Blood analysis predicts sepsis and organ failure in children

Photo Credit: Edward Jenner

University of Queensland researchers have developed a method to predict if a child is likely to develop sepsis and go into organ failure.

Associate Professor Lachlan Coin from UQ’s Institute for Molecular Bioscience said sepsis was a life-threatening condition where a severe immune response to infection causes organ damage.

“Our research involved more than 900 critically ill children in the emergency departments and intensive care units of four Queensland hospitals,” Dr Coin said.

“Blood samples were taken from these patients at the acute stage of their infection, and we analyzed which genes were activated or deactivated.

“We were able to identify patterns of gene expression which could predict whether the child would develop organ failure within the next 24 hours, as well as whether the child had a bacterial or viral infection or a non-infectious inflammatory syndrome.”

Professor Luregn Schlapbach from UQ’s Child Health Research Centre said sepsis is best treated when recognized early, so the finding could help clinicians in the future.

Astronomers discover 49 new galaxies in under three hours

The MeerKAT radio telescope, located in South Africa, enabled this discovery of 49 brand new galaxies.
Photo Credit: South African Radio Astronomy Observatory (SARAO)

An international team of astronomers has discovered 49 new gas-rich galaxies using the MeerKAT radio telescope in South Africa.

Dr Marcin Glowacki, from the Curtin University node of the International Centre for Radio Astronomy Research (ICRAR) in Western Australia, led the research, which aimed to study the star-forming gas in a single radio galaxy.  Although the team didn’t find any star-forming gas in the galaxy they were studying, Dr Glowacki instead discovered other galaxies while inspecting the data.

In total, the gas of 49 galaxies were detected. Dr Glowacki said this was a great example of how fantastic an instrument like MeerKAT is for finding the star-forming gas in galaxies.

The observations, which lasted less than three hours and were facilitated by IDIA (Inter-University Institute for Data Intensive Astronomy), made this discovery possible.

“I did not expect to find almost fifty new galaxies in such a short time,” Dr Glowacki said. “By implementing different techniques for finding galaxies, which are used for other MeerKAT surveys, we were able to detect all of these galaxies and reveal their gas content.”

The new galaxies have been informally nicknamed the 49ers, a reference to the 1849 California gold rush miners. Dr Glowacki views the 49 new galaxies as valuable as gold nuggets in our night sky. Many galaxies are near each other, forming galaxy groups, with several identified in one observation.

Human brains are getting larger. That may be good news for dementia risk

Image Credit: Dmitriy Gutarev

A new study by researchers at UC Davis Health found human brains are getting larger. Study participants born in the 1970s had 6.6% larger brain volumes and almost 15% larger brain surface area than those born in the 1930s.

The researchers hypothesize the increased brain size may lead to an increased brain reserve, potentially reducing the overall risk of age-related dementias.

The findings were published in JAMA Neurology.

“The decade someone is born appears to impact brain size and potentially long-term brain health,” said Charles DeCarli, first author of the study. DeCarli is a distinguished professor of neurology and director of the UC Davis Alzheimer’s Disease Research Center. “Genetics plays a major role in determining brain size, but our findings indicate external influences — such as health, social, cultural and educational factors — may also play a role.”

Electrochemistry helps clean up electronic waste recycling, precious metal mining

A new study from the University of Illinois Urbana-Champaign shows how electrochemistry can be used to extract precious metals from discarded electronics in an efficient and environmentally friendly manner. 
Photo Credit: Fred Zwicky

A new method safely extracts valuable metals locked up in discarded electronics and low-grade ore using dramatically less energy and fewer chemical materials than current methods, report University of Illinois Urbana-Champaign researchers in the journal Nature Chemical Engineering. 

Gold and platinum group metals such as palladium, platinum and iridium are in high demand for use in electronics. However, sourcing these metals from mining and current electronics recycling techniques is not sustainable and comes with a high carbon footprint. Gold used in electronics accounts for 8% of the metal’s overall demand, and 90% of the gold used in electronics ends up in U.S. landfills yearly, the study reports. 

The study, led by chemical and biomolecular engineering professor Xiao Su, describes the first precious metal extraction and separation process fully powered by the inherent energy of electrochemical liquid-liquid extraction, or e-LLE. The method uses a reduction-oxidation reaction to selectively extract gold and platinum group metal ions from a liquid containing dissolved electronic waste. 

Elusive 3D printed nanoparticles could lead to new shapeshifting materials

Optical images of truncated tetrahedrons forming two large hexagonal grains at an anti-phase boundary (left), and transforming into a quasi-diamond phase that initiated at the anti-phase boundary (right). Scale bars are 25 um.
Image Credit: David Doan & John Kulikowski

Stanford materials engineers have 3D printed tens of thousands of hard-to-manufacture nanoparticles long predicted to yield promising new materials that change form in an instant.

In nanomaterials, shape is destiny. That is, the geometry of the particle in the material defines the physical characteristics of the resulting material.

“A crystal made of nano-ball bearings will arrange themselves differently than a crystal made of nano-dice and these arrangements will produce very different physical properties,” said Wendy Gu, an assistant professor of mechanical engineering at Stanford University, introducing her latest paper which appears in the journal Nature Communications. “We’ve used a 3D nanoprinting technique to produce one of the most promising shapes known – Archimedean truncated tetrahedrons. They are micron-scale tetrahedrons with the tips lopped off.”

In the paper, Gu and her co-authors describe how they nanoprinted tens of thousands of these challenging nanoparticles, stirred them into a solution, and then watched as they self-assembled into various promising crystal structures. More critically, these materials can shift between states in minutes simply by rearranging the particles into new geometric patterns.

This ability to change “phases,” as materials engineers refer to the shapeshifting quality, is similar to the atomic rearrangement that turns iron into tempered steel, or in materials that allow computers to store terabytes of valuable data in digital form.

“If we can learn to control these phase shifts in materials made of these Archimedean truncated tetrahedrons it could lead in many promising engineering directions,” she said.