Why synonymous mutations are not always silent

New modeling shows how synonymous mutations that change the DNA sequence of a gene, but not the sequence of the encoded protein can impact protein production and function by changing the rate of protein synthesis. Top: illustration of a new class of protein misfolding called a non-covalent lasso entanglement that can result from changes to the rate of protein synthesis caused by synonymous mutations. Bottom: structure of a protein showing its native state and misfolded state with non-covalent lasso entanglement.
Illustration Credit: Yang Jiang | Pennsylvania State University

New modeling shows how synonymous mutations — those that change the DNA sequence of a gene but not the sequence of the encoded protein — can still impact protein production and function. A team of researchers led by Penn State chemists modeled how genetic changes that alter the speed of protein synthesis, but not the sequence of amino acids that comprise the protein, can lead to misfolding that changes the protein’s activity level, and then corroborated their models experimentally. The results demonstrate the importance of kinetics — the rate of protein synthesis — in addition to sequence for determining protein structure and function and could have implications in fields such as biopharmaceutics for fine tuning the activity of synthesized proteins.

Proteins are composed of long strings of amino acids that then fold up into three-dimensional functional structures. Each amino acid is encoded by a triplet of letters in the DNA alphabet of A, T, C and G called a codon, but there is redundancy built in to the system such that more than one codon can correspond to the same amino acid. Therefore, a mutation that changes the DNA sequence of a gene won’t necessarily change the sequence of the encoded protein if the mutation results in a "synonymous codon." To make a protein, DNA in the nucleus of a cell is first transcribed into a messenger RNA (mRNA). The mRNA is then transported out of the nucleus where it is translated into a nascent protein by a cellular organelle called a ribosome. After translation the protein is folded into its final functional form.

Forest Resilience Linked with Higher Mortality Risk in Western U.S.

A new study assesses decades of U.S. forest health data, revealing a twist in Western U.S. forest fate amid climate change — higher ecosystem resilience is linked with higher mortality risk
Photo Credit: Sarah Ardin

A forest’s resilience, or ability to absorb environmental disturbances, has long been thought to be a boost for its odds of survival against the looming threat of climate change.

But a new study suggests that for some Western U.S. forests, it’s quite the opposite.

In the journal Global Change Biology, researchers have published one of the first large-scale studies of U.S. forest land exploring the link between forest resilience and mortality.

The study is based on more than three decades of satellite image data used for assessing forest resilience, and more than two decades of ground observations of forest tree death across the continental United States.

The results show that while high ecosystem resilience correlates with low mortality in eastern forests, it is linked to high mortality in western regions.

“It’s a surprising finding. … It was widely assumed that greater forest resilience indicates lower mortality risk, but this relationship hadn’t been rigorously evaluated at such a large scale until now,” said Xiaonan Tai, assistant professor of biology at New Jersey Institute of Technology and the corresponding author.

FAU study finds low salinity can work to culture Florida pompano fish

Florida Pompano larvae (juvenile fish) pictured under a microscope.
Photo Credit: Victoria Uribe, FAU Harbor Branch

The Florida pompano, Trachinotus carolinus, a fish species that can live in waters of a wide range of salinity, is a prime candidate for aquaculture commercial fish production in the United States. Identified by its compressed silvery body with yellow dorsal and ventral surfaces, this species is found in warm water habitats along the eastern Atlantic Ocean. Florida pompano also is a popular target for recreational anglers along the U.S. Atlantic Coast from Massachusetts to Florida.

There are less than 10 aquaculture farms across the U.S. that have been successful in commercially raising and distributing Florida pompano. Many farms import their broodstock from countries such as Mexico, the Dominican Republic and Brazil. When attempting to rear Florida pompano from hatch to market, farms face a variety of challenges including access to seawater. On inland farms, seawater must be mixed on-site using artificial sea salt products, which can contribute to high production costs and lower profit returns.

While several studies have investigated using juvenile Florida pompano in low salinity, no low salinity experiments have been conducted on Florida pompano larvae (early stages of a fish). To address the knowledge gaps of the impact of low salinity on Florida pompano larval health, researchers from Florida Atlantic University’s Harbor Branch Oceanographic Institute, in collaboration with two local fish farms, Live Advantage Baits and Proaquatix, conducted a novel experiment that serves as a model study for future on-farm collaborations and helps build a bridge between scientists and farmers in aquaculture.

Seaweed molecules used to improve outcomes for bypass surgery

Researchers use material made from seaweed to modify synthetic blood vessels
Photo Credit: Oleksandr Sushko

Researchers are using a natural material derived from seaweed to promote vascular cell growth, prevent blood clots and improve the performance of synthetic vascular grafts used in heart bypass surgery.

The new approach, developed and tested at the University of Waterloo, is especially important in cases involving small artificial blood vessels - those less than six millimeters in diameter - which are prone to clots that can develop into full blockages.

“There is a crucial need to develop synthetic vascular graft materials that will increase the rate of long-term functions,” said Dr. Evelyn Yim, a chemical engineering professor and University Research Chair who leads the project.

Researchers added a material called fucoidan, which is made from seaweed, to modify synthetic blood vessels. Fucoidan has a structure similar to heparin, a drug used as an anticoagulant.

Masks can put cognitive performance in check

The study found that while masks had a negative impact, the effect subsided over time. 
Photo Credit: Alena Beliaeva

Wearing a face mask can temporarily disrupt decision-making in some situations according to University of Queensland research.

Dr David Smerdon from UQ’s School of Economics analyzed almost three million chess moves played by more than eight thousand people in 18 countries before and during the COVID-19 pandemic and found wearing a mask substantially reduced the average quality of player decisions.

“The decrease in performance was due to the annoyance caused by the masks rather than a physiological mechanism, but people adapted to the distraction over time,” Dr Smerdon said.

“The data showed masks were more likely to decrease performance in situations where there was a demanding mental task with a high working memory load.

“This is something to keep in mind for occupations in the STEM fields of science, technology, engineering and mathematics as well as other professions that demand a high level of working memory such as language interpreters, performers, waiters and teachers.”

Detecting dark matter with quantum computers

Akash Dixit works on a team that uses quantum computers to look for dark matter. Here, Dixit holds a microwave cavity containing a superconducting qubit. The cavity has holes in its side in the same way the screen on a microwave oven door has holes; the holes are simply too small for microwaves to escape.
Photo Credit: Ryan Postel, Fermilab

Dark matter makes up about 27% of the matter and energy budget in the universe, but scientists do not know much about it. They do know that it is cold, meaning that the particles that make up dark matter are slow-moving. It is also difficult to detect dark matter directly because it does not interact with light. However, scientists at the U.S. Department of Energy’s Fermi National Accelerator Laboratory have found a way to look for dark matter using quantum computers.

Aaron Chou, a senior scientist at Fermilab, works on detecting dark matter through quantum science. As part of DOE’s Office of High Energy Physics QuantISED program, he has developed a way to use qubits, the main component of quantum computing systems, to detect single photons produced by dark matter in the presence of a strong magnetic field.

How to Edit the Genes of Nature’s Master Manipulators

Scientists are using CRISPR to engineer the viruses that evolved to engineer bacteria
Illustration Credit: Davian Ho

CRISPR, the Nobel Prize-winning gene editing technology, is poised to have a profound impact on the fields of microbiology and medicine yet again.

A team led by CRISPR pioneer Jennifer Doudna and her longtime collaborator Jill Banfield has developed a clever tool to edit the genomes of bacteria-infecting viruses called bacteriophages using a rare form of CRISPR. The ability to easily engineer custom-designed phages – which has long eluded the research community – could help researchers control microbiomes without antibiotics or harsh chemicals, and treat dangerous drug-resistant infections. A paper describing the work was recently published in Nature Microbiology.

“Bacteriophages are some of the most abundant and diverse biological entities on Earth. Unlike prior approaches, this editing strategy works against the tremendous genetic diversity of bacteriophages,” said first author Benjamin Adler, a postdoctoral fellow in Doudna’s lab. “There are so many exciting directions here – discovery is literally at our fingertips!”

Bacteriophages, also simply called phages, insert their genetic material into bacterial cells using a syringe-like apparatus, then hijack the protein-building machinery of their hosts in order to reproduce themselves – usually killing the bacteria in the process. (They’re harmless to other organisms, including us humans, even though electron microscopy images have revealed that they look like sinister alien spaceships.)

New Quantum Light Source Paves the Way to a Quantum Internet

A molybdenum ditelluride material (blue and yellow lattice) just atoms thick connects telecom-wavelength quantum emitters to optical fibers with minimal loss. The devices generate single photons (red) when triggered by optical signals (green).
Image Credit: Courtesy of Huan Zhao, Center for Integrated Nanotechnologies, Los Alamos National Laboratory

Conventional light sources for fiber-optic telecommunications emit many photons at the same time. Photons are particles of light that move as waves. In today’s telecommunication networks, information is transmitted by modulating the properties of light waves traveling in optical fibers, similar to how radio waves are modulated in AM and FM channels. In quantum communication, however, information is encoded in the phase of a single photon—the photon’s position in the wave in which it travels. This makes it possible to connect quantum sensors in a network spanning great distances and to connect quantum computers together. Researchers recently produced single-photon sources with operating wavelengths compatible with existing fiber communication networks. They did so by placing molybdenum ditelluride semiconductor layers just atoms thick on top of an array of nano-size pillars. This is the first time that researchers have demonstrated this type of tunable light sources suited to use in telecommunications systems.

Scientists invent pioneering technique to construct rare molecules

Bahamaolide A is a polyketide natural product with potent antifungal activity, which was isolated from bacteria cultured from a sediment sample collected at North Cat Cay in the Bahamas and has now been synthesized in the chemical laboratory for the first time.
Image Credit: University of Bristol and Wikimedia Commons

Scientists have created a much faster way to make certain complex molecules, which are widely used by pharmaceuticals for antibiotics and anti-fungal medicines.

The first-of-its-kind discovery by chemists at the University of Bristol has the potential to speed up the production of such drugs, making them cheaper and more accessible.

The breakthrough, published in Nature Chemistry, marks the culmination of a five-year research project which has finally cracked how to reconstruct in a laboratory a particularly complex molecule, from the family of molecules known as polyketides.

Lead author Sheenagh Aiken, a PhD student at the university’s School of Chemistry when the work was completed, said: “It’s an exciting discovery, which could bring important benefits for the pharmaceutical industry and public health.

Measuring times in billionths of a billionth of a second

Explanation by Prof Igor Litvinyuk and Prof Robert Sang. 

Video Credit: Griffith University

How fast do electrons inside a molecule move? Well, it is so fast that it takes them just a few attoseconds (1 as = 10-18 s or one billionth of billionth of a second) to jump from one atom to another. Blink and you missed it – millions of billions of times. So, measuring such ultrafast processes is a daunting task.

Scientists at the Australian Attosecond Science Facility and the Centre for Quantum Dynamics of Griffith University in Brisbane Australia, led by Professor Robert Sang and Professor Igor Litvinyuk have developed a novel interferometric technique capable of measuring time delays with zeptosecond (a trillionth of a billionth of a second) resolution.

They have used this technique to measure the time delay between extreme ultraviolet light pulses emitted by two different isotopes of hydrogen molecules – H2 and D2 – interacting with intense infrared laser pulses.

This delay was found to be less than three attoseconds (one quintillionth of a second long) and is caused by slightly different motions of the lighter and heavier nuclei.

This study has been published in Ultrafast Science, a new Science Partner Journal.