Targeted method for probing the function of 3D chromosomal structure

A new method—chemically induced chromosomal interaction (CICI)—can induce interactions between any two regions of the genome to test relationships between genome structure and function. The illustration (top) shows the scheme of the method. Researchers insert long arrays of binding sites into two genomic locations. These arrays are associated with a large amount of two transcription factor proteins, LacI and TetR. LacI and TetR then fuse with two additional proteins, FKBP12 and FRB, that bind in the presence of the compound rapamycin. Thus, researchers can induce the two genomic loci to strongly associate with each other by adding rapamycin to the cells and compare cellular function before and after the induced interaction. Typical data are shown below. The two loci (labeled by the red and green fluorescent dots) are spatially separated prior to the addition of rapamycin, but become co-localized after adding rapamycin.
Credit: Bai Laboratory, Pennsylvania State University

A new method that can induce interactions between specifically chosen locations on the genome allows researchers to begin to identify the causal relationship between three-dimensional chromosome structure and genome function. A paper by researchers at Penn State describing the method, called “chemically induced chromosomal interaction (CICI),” and two functional tests of the method appears in the journal Nature Communications.

The genomes of eukaryotes — organisms ranging from yeast to humans whose cells have a distinct nucleus — are made up of chromosomes. Inside the nucleus, the chromosomes, which are long, linear strands of DNA packaged with numerous proteins that carry genetic information, are arranged in a three-dimensional conformation that, depending on the cell type, can bring genomic regions that are linearly distant from one another into close enough contact to functionally interact. These interactions are thought to be important for things like gene regulation, which controls when and where certain genes are used by the cell.

Chemists discover a range of environmental contaminants in fracking wastewater

As companies that drill for oil and natural gas using hydraulic fracturing consider recycling and reusing wastewater that surfaces from wells during the fracking process, chemists at The University of Toledo discovered that the new and unexplored waste contains many environmental contaminants including organic chemicals and metallic elements.

Research scientists at UToledo’s Dr. Nina McClelland Laboratory for Water Chemistry and Environmental Analysis in collaboration with the University of Texas Arlington achieved a comprehensive characterization of the chemical composition of produced water samples extracted in Texas, indicating the presence of toxic and carcinogenic contaminants in untreated samples, which can pose a threat to wildlife and human health.

Unraveling the complex composition of produced water by specialized extraction methodologies, the results published in Environmental Science and Technology provide critical information that can help regulatory agencies fine-tune proposed guidelines related to the safe treatment and disposal of fracking wastewater to protect drinking water sources.

“The discovery of these chemicals in produced water suggests that greater monitoring and remediation efforts are needed since many of them are listed to be dangerous for human health by the World Health Organization,” said Dr. Emanuela Gionfriddo, assistant professor of analytical chemistry in the UToledo Department of Chemistry and Biochemistry, and the School of Green Chemistry and Engineering. “Our comprehensive characterization sheds insight into the processes taking place during hydraulic fracturing and the nature of the geologic formation of each well site.”

Bacteria in the nose may increase risk of Alzheimer’s disease

Associate Professor Jenny Ekberg, Clem Jones Centre for Neurobiology and Stem Cell Research

New research from Griffith University has shown that a bacterium commonly present in the nose can sneak into the brain and set off a cascade of events that may lead to Alzheimer’s disease.

Associate Professor Jenny Ekberg and colleagues from the Clem Jones Centre for Neurobiology and Stem Cell Research at Menzies Health Institute Queensland and Griffith Institute for Drug Discovery, in collaboration with Queensland University of Technology, have discovered that the bacterium Chlamydia pneumoniae can invade the brain via the nerves of the nasal cavity.

While this bacterium often causes respiratory tract infections, it has also been found in the brain which has raised the question of whether it causes damage to the central nervous system.

The research team has performed extensive research in animal models to show not only how the bacteria gets into the brain, but also how it leads to Alzheimer disease pathologies.

Ultraprecise atomic clock poised for new physics discoveries

One of the first steps in creating the optical atomic clocks used in this study is to cool strontium atoms to near absolute zero in a vacuum chamber, which makes them appear as a glowing blue ball floating in the chamber.
Credit: Shimon Kolkowitz

University of Wisconsin–Madison physicists have made one of the highest performance atomic clocks ever, they announced Feb. 16 in the journal Nature.

Their instrument, known as an optical lattice atomic clock, can measure differences in time to a precision equivalent to losing just one second every 300 billion years and is the first example of a “multiplexed” optical clock, where six separate clocks can exist in the same environment. Its design allows the team to test ways to search for gravitational waves, attempt to detect dark matter, and discover new physics with clocks.

Stanford scientists combine AI and atomic-scale images in pursuit of better batteries

From left, Will Chueh, associate professor; Tanya Jomaa, high school summer intern; and Haitao “Dean” Deng, PhD ’21. Jomaa, now an undergraduate at Yale University, worked with Deng researching lithium titanate batteries.
Image credit: Norman Jin

Using artificial intelligence to analyze vast amounts of data in atomic-scale images, Stanford researchers answered long-standing questions about an emerging type of rechargeable battery posing competition to lithium-ion chemistry.

Today’s rechargeable batteries are a wonder, but far from perfect. Eventually, they all wear out, begetting expensive replacements and recycling.

“But what if batteries were indestructible?” asks William Chueh, an associate professor of materials science and engineering at Stanford University and senior author of a new paper detailing a first-of-its-kind analytical approach to building better batteries that could help speed that day. The study appears in the journal Nature Materials.

Butterfly eyespots reuse gene regulatory network that patterns antennae, legs and wings

A silky owl (Taenaris catopsv) butterfly with distinctive eyespots on its wings.
Photo credit: Kristof Zyskowski and Yulia Bereshpolova

Findings highlight those novel complex traits, such as eyespots, evolve from gene networks that already pattern pre-existent complex traits in the body

Eyespots, the circular markings of contrasting colors found on the wings of many butterfly species, are used by these fluttering creatures to intimidate or distract predators. A team of scientists led by Professor Antónia Monteiro from the National University of Singapore (NUS) conducted a research study to better understand the evolutionary origins of these eyespots, and they discovered that eyespots appear to have derived from the recruitment of a complex network of genes that was already operating in the body of the butterflies to build antennae, legs, and even wings.

“This new study addresses how novel complex traits might originate. These complex traits require the input of many interacting genes for their development, and are often illustrated by the vertebrate eye, or the bacteria flagellum. In our study, we looked at how butterfly eyespots – an example of a complex trait - came about and concluded that a network recruitment approach is adopted by butterflies for the creation of eyespots. We have also identified the specific network of genes that was likely recruited,” said Prof Monteiro, who is from the NUS Department of Biological Sciences.

The findings were first published in the journal Proceedings of the National Academy of Sciences.

Can a planet have a mind of its own?

In a self-described "thought experiment," University of Rochester astrophysicist Adam Frank and colleagues David Grinspoon at the Planetary Science Institute and Sara Walker at Arizona State University use scientific theory and broader questions about how life alters a planet, to posit four stages to describe Earth's past and possible future.
University of Rochester illustration / Michael Osadciw

Rochester astrophysicist Adam Frank discusses why cognitive activity operating on a planetary scale is necessary to tackle global issues such as climate change.

The collective activity of life—all of the microbes, plants, and animals—have changed planet Earth.

Take, for example, plants: plants ‘invented’ a way of undergoing photosynthesis to enhance their own survival, but in so doing, released oxygen that changed the entire function of our planet. This is just one example of individual lifeforms performing their own tasks, but collectively having an impact on a planetary scale.

If the collective activity of life—known as the biosphere—can change the world, could the collective activity of cognition, and action based on this cognition, also change a planet? Once the biosphere evolved, Earth took on a life of its own. If a planet with life has a life of its own, can it also have a mind of its own?

Sunlight can help dissolve oil into seawater

A slick of sunlight-altered oil floating on the Gulf of Mexico after the 2010 Deepwater Horizon disaster. A team of Woods Hole Oceanographic Institution researchers found that nearly 10 percent of the oil floating on the Gulf after the spill dissolved into the water by sunlight – a process called photo-dissolution.
Photo by Cabell Davis III © Woods Hole Oceanographic Institution

The 2010 Deepwater Horizon oil spill was the largest marine oil spill in United States history. The disaster was caused by an explosion on the Deepwater Horizon oil rig, taking 11 lives and releasing nearly 210 million gallons of crude oil into the Gulf of Mexico. Twelve years and hundreds of millions of dollars later, scientists are still working to understand where all this oil ended up, a concept known as environmental fate.

The most commonly discussed fates of oil spilled at sea are biodegradation (microorganisms consuming and breaking down the oil), evaporation (liquid oil becoming a gas), and oil stranding on shorelines.

A team of Woods Hole Oceanographic Institution (WHOI) researchers discovered that nearly 10 percent of the oil floating on the Gulf after the Deepwater Horizon disaster was dissolved into seawater by sunlight - a process called “photo-dissolution”. The findings were published today in the paper “Sunlight-driven dissolution is a major fate of oil at sea” in Science Advances.

Engineer develops tool to predict oxygen in water, finds streams along southeastern U.S. in poorer quality

The muddy water in the Monongahela River in Morgantown. WVU engineer Omar Abdul-Aziz has developed a model that can be utilized on any body of water to predict levels of dissolved oxygen, which contributes to water quality.
Photo Provided/Omar Abdul-Aziz

Plants and animals on land aren’t the only organisms that need oxygen to survive. Underwater aquatic life requires dissolved oxygen to live and prosper.

But a variety of factors, such as pollution, water temperature and bacteria, can deplete the amount of dissolved oxygen within a water ecosystem, setting off a chain reaction that kills off aquatic life and potentially spreads disease to humans.

In a new study, one West Virginia University engineer developed a simpler, more effective model that predicts dissolved oxygen in streams across the U.S. Atlantic Coast. Omar Abdul-Aziz, associate professor of civil and environmental engineering, said the model can be applied to water bodies anywhere in the world.

Abdul-Aziz’s research also found that streams in the southern U.S. (Florida and Georgia, for instance) have a higher metabolism, meaning that they contain less dissolved oxygen due to warmer temperatures and the heavy presence of nitrogen and phosphorus.

Study finds older Americans are largely unaware of new Alzheimer‘s drug

There’s a new drug to treat Alzheimer’s disease, but those who might benefit from it know almost nothing about it, a new study shows.

In spring 2021, for the first time in decades, the U.S. Food and Drug Administration approved a drug to treat Alzheimer’s disease. Enthusiasm for the drug, aducanumab, was swiftly eclipsed by concerns about efficacy, prohibitive cost and serious side effects.

Now, USC researchers have found older Americans most at risk for Alzheimer’s know little about aducanumab (brand name Aduhelm™), despite the fact that an overwhelming majority of survey respondents said they were worried about Alzheimer’s disease. The study appears this week in JAMA Network Open.

“The contrast between older Americans who were very concerned about developing Alzheimer’s disease and those that actually knew anything about the drug was surprising,” said Julie Zissimopoulos, the lead study author, associate professor at the USC Price School of Public Policy and a senior fellow at the USC Schaeffer Center for Health Policy & Economics.

Study looks at older Americans’ knowledge about new Alzheimer’s drug

Shortly after the FDA’s decision, the study authors sought to understand older Americans’ knowledge of and opinions about aducanumab and its potential outcomes.

The researchers analyzed more than 1,000 responses to an online survey of people 55 and older who are part of the USC Center for Economic and Social Research large online survey panel, Understanding America Study. The responses, collected just a few weeks after the June 2021 approval, revealed that although more than 8 in 10 respondents were concerned about Alzheimer’s disease, only about 1 in 4 had some knowledge of the drug.