How do worms develop their gut?

a juvenile C. angaria larva, about 150 microns long.
Photo Credit: Maduro lab/UCR

Were it not for the COVID-19 pandemic, an important discovery about the development of nematodes — elongated cylindrical worms — might not have been made.

With most classes and meetings at universities and schools having moved online in 2020-2021, a husband-and-wife research team at the University of California, Riverside, finally found some time to explore a question they had been mulling over for a long time: How do nematodes distantly related to the best-studied one, Caenorhabditis elegans, make their gut, given that the genes responsible for specifying the gut in C. elegans are absent in other nematodes?

“The pandemic freed up some time for us to think about what research we would like to move forward with when the pandemic eased,” said Morris Maduro, a professor of molecular, cell and systems biology and the corresponding author of the study published in Development, a journal. “Fortunately, an experiment we conducted generated a surprising result. It turns out a simpler gene network seems to be involved in specifying the gut in nematodes related to C. elegans. An ancestral species of C. elegans appears to have duplicated and expanded this simpler gene network to make one that is more complicated, and that complicated network is the one we have been studying all this time in C. elegans.”

Harvesting Light to Grow Food and Clean Energy Together

Solar panels emit a red light over tomato plants growing in a research field at UC Davis in 2022. The work further tests the findings of a UC Davis study showing plants in agrivoltaic systems respond best to the red spectrum of light while blue light is better used for energy production.
Photo Credit: Andre Daccache/UC Davis

People are increasingly trying to grow both food and clean energy on the same land to help meet the challenges of climate change, drought and a growing global population that just topped 8 billion. This effort includes agrivoltaics, in which crops are grown under the shade of solar panels, ideally with less water.

Now scientists from the University of California, Davis, are investigating how to better harvest the sun — and its optimal light spectrum — to make agrivoltaic systems more efficient in arid agricultural regions like California.

Their study, published in Earth’s Future, a journal of the American Geophysical Union, found that the red part of the light spectrum is more efficient for growing plants, while the blue part of the spectrum is better used for solar production.

Researchers propose new structures to harvest untapped source of freshwater

“Eventually, we will need to find a way to increase the supply of fresh water as conservation and recycled water from existing sources, albeit essential, will not be sufficient to meet human needs. We think our newly proposed method can do that at large scales,” said Illinois professor Praveen Kumar. The illustration shows Kumar and his co-authors’ proposed approach for capturing moisture above ocean surfaces and transporting it to land for condensation. 
Illustration Credit: Courtesy Praveen Kumar and Nature Scientific Reports

Researchers said that an almost limitless supply of fresh water exists in the form of water vapor above Earth’s oceans, yet remains untapped. A new study from the University of Illinois Urbana-Champaign is the first to suggest an investment in new infrastructure capable of harvesting oceanic water vapor as a solution to limited supplies of fresh water in various locations around the world.

The study, led by civil and environmental engineering professor and Prairie Research Institute executive director Praveen Kumar, evaluated 14 water-stressed locations across the globe for the feasibility of a hypothetical structure capable of capturing water vapor from above the ocean and condensing it into fresh water – and do so in a manner that will remain feasible in the face of continued climate change.

Kumar, graduate student Afeefa Rahman and atmospheric sciences professor Francina Dominguez published their findings in the journal Nature Scientific Reports.

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.)