Physical theory improves protein folding prediction

Protein folding models. Four iterations of WSME, from the original to the new, and two specialized versions for more specific circumstances.
Illustration Credit: ©2023 Ooka & Arai CC-BY

Proteins are important molecules that perform a variety of functions essential to life. To function properly, many proteins must fold into specific structures. However, the way proteins fold into specific structures is still largely unknown. Researchers from the University of Tokyo developed a novel physical theory that can accurately predict how proteins fold. Their model can predict things previous models cannot. Improved knowledge of protein folding could offer huge benefits to medical research, as well as to various industrial processes.

You are literally made of proteins. These chainlike molecules, made from tens to thousands of smaller molecules called amino acids, form things like hair, bones, muscles, enzymes for digestion, antibodies to fight diseases, and more. Proteins make these things by folding into various structures that in turn build up these larger tissues and biological components. And by knowing more about this folding process, researchers can better understand more about the processes that constitute life itself. Such knowledge is also essential to medicine, not only for the development of new treatments and industrial processes to produce medicines, but also for knowledge of how certain diseases work, as some are examples of protein folding gone wrong. So, to say proteins are important is putting it mildly. Proteins are the stuff of life.

Biodegradable plastics still damaging to fish

Professor Indrawati Oey, of the Department of Food Science, and Dr Bridie Allan, of the Department of Marine Science, hold the biodegradable plastic used in the study and a photo of the mottled triplefin, the species analyzed.
Photo Credit: University of Otago

Biodegradable plastics may not be the solution to plastic pollution many hoped for, with a University of Otago study showing they are still harmful to fish.

Petroleum-derived microplastics are known to impact marine life, but little is known about the impact of biodegradable alternatives.

The study, published in Science of the Total Environment and funded by a University of Otago Research Grant, is the first to assess the impact petroleum-derived plastic and biodegradable plastic have on wild fish.

Lead author Ashleigh Hawke, who completed a Master of Science in Otago’s Department of Marine Science, says petroleum-derived plastic exposure negatively affected the fish’s escape performance, routine swimming, and aerobic metabolism.

New insights into the genetics of the common octopus: genome at the chromosome level decoded

Octopus vulgaris
Photo Credit: ©Antonio, Valerio Cirillo (BEOM SZN), 2023

Octopuses are fascinating animals – and serve as important model organisms in neuroscience, cognition research and developmental biology. To gain a deeper understanding of their biology and evolutionary history, validated data on the composition of their genome is needed, which has been lacking until now. Scientists from the University of Vienna together with an international research team have now been able to close this gap and, in a study, determined impressive figures: 2.8 billion base pairs - organized in 30 chromosomes. What sounds so simple is the result of complex, computer-assisted genome analyses and comparisons with the genomes of other cephalopod species. This groundbreaking research has just been published in the renowned journal G3: Genes / Genomes / Genetics.

Octopuses, together with squid and cuttlefish, belong to a group of coleoid cephalopods consisting of several hundreds of species that are characterized by highly diversified lifestyles, body structure and adaptations to their environment. The study of these animals looks back on a long tradition, especially since the neuronal plasticity of the octopus brain – meaning the brain's ability to change and adapt as you learn and experience new things – provides evidence for the existence of functionally analogous structures to the brains of mammals. This is making them a comparative model group for neurophysiological studies. Also, their ability to regenerate parts of their bodies as well as the rapid changes of their body patterns, which are important for camouflage and communication, make octopuses a popular research subject for studying how these innovative traits arose – and how they have changed – during evolution.

Climate change could limit bats' lifespans

Greater Horseshoe Bat
Photo Credit: Professor Gareth Jones

The extraordinary lifespans of bats could be under threat from rising global temperatures, according to new research.

A study by researchers from the University of Bristol and University College Dublin has found that the hibernation cycle of a group of wild greater horseshoe bats affected by fluctuations in the weather had altered the molecular mechanism thought to give bat species their long lives.

Telomeres are pieces of DNA that act as a protective structure at the end of chromosomes. Each time a cell divides, they shorten. And it is this shortening that is associated with aging and aging-related diseases.

Data from the new study showed that bats who more frequently arose from hibernating due to warmer conditions during the 2019/2020 hibernation period had significantly shorter telomeres compared to those recorded in previous, colder, winters.

“We were surprised and then worried at this finding, given that the predicted rise in global temperatures could limit the beneficial effects of hibernation in our wild bats.” said UCD Professor Emma Teeling.

Superdeep diamonds provide a window on supercontinent growth

Deep diamonds from Collier-4 from the Juina area, Brazil. 
Photo Credit: Sarah Milne, University of Alberta.

Diamonds contain evidence of the mantle rocks that helped buoy and grow the ancient supercontinent Gondwana from below, according to new research from a team of scientists led by Suzette Timmerman—formerly of the University of Alberta and now at the University of Bern—and including Carnegie’s Steven Shirey, Michael Walter, and Andrew Steele. Their findings, published in Nature, demonstrate that superdeep diamonds can provide a window through space and time into the supercontinent growth and formation process.

For billions of years, Earth’s landmasses have been ripped apart and smashed back together by plate tectonics, periodically forming giant supercontinents. This formation process results from large-scale convection of the planet’s mantle.  But the records of these events are poorly preserved, because the oceanic crust is young and continually sinks beneath the planet’s surface by a process called subduction, while the continental crust only provides a limited view of Earth’s deep workings.

Surprisingly, the research team was able to show that superdeep diamonds that formed between 300 and 700 kilometers below Earth’s surface can reveal how material was added to the base of a once-mighty supercontinent.

“These diamonds allow us to see how deep plate tectonic processes relate to the supercontinent cycle,” Shirey said.

How the Greenland ice sheet can be saved

Greenland binds enormous amounts of water with its ice sheet. If it melts, sea levels will rise worldwide.
Photo Credit: rawpixel

Climate researchers around the world are sounding the alarm about exceeding critical temperature values on the Earth. If temperatures pass what are called tipping points, the results could be catastrophic. An international team of researchers, including members from the Technical University of Munich (TUM), has now demonstrated in simulations that the temperature tipping point for the Greenland ice sheet can be exceeded in certain cases for a short time, as long as extreme countermeasures are taken afterwards. If the ice mass melted entirely, the result would be a massive rise in the sea level.

Greenland is the second largest permanently ice-covered surface on the Earth; only Antarctica is larger. The Greenland ice sheet is drastically impacted by the effects of climate change. If the ice sheet melts completely, it would cause a sea level rise of more than seven meters – a catastrophe for coastal regions worldwide and for the people who live there. The critical threshold for the worst-case scenario is between 1.7 and 2.3 degrees Celsius of global warming above the preindustrial level on an annual average. Until now climate research has assumed that if this point is exceeded, the Greenland ice sheet would be lost forever. However, the international research team has now been able to show in a large set of simulations that there would be a way back after passing the tipping point.

California Supervolcano is Cooling Off but May Still Cause Quakes

View is toward the east across the northern part of Long Valley Caldera, California, United States. The caldera rim extends east from the Glass Creek flow (lower left) to Bald Mountain and Glass Mountain in the far distance. Lookout Mountain is behind the tree
Photo Credit: United States Geological Survey

Since the 1980s, researchers have observed significant periods of unrest in a region of California's Eastern Sierra Nevada mountains characterized by swarms of earthquakes as well as the ground inflating and rising by almost half an inch per year during these periods. The activity is concerning because the area, called the Long Valley Caldera, sits atop a massive dormant supervolcano. Seven hundred and sixty thousand years ago, the Long Valley Caldera was formed in a violent eruption that sent 650 cubic kilometers of ash into the air—a volume that could cover the entire Los Angeles area in a layer of sediment 1 kilometer thick.

What is behind the increased activity in the last few decades? Could it be that the area is preparing to erupt again? Or could the uptick in activity actually be a sign that the risk of a massive eruption is decreasing?

To answer these questions, Caltech researchers have created the most detailed underground images to date of the Long Valley Caldera, reaching depths up to 10 kilometers within the Earth's crust. These high-resolution images reveal the structure of the earth beneath the caldera and show that the recent seismic activity is a result of fluids and gases being released as the area cools off and settles down.

Finding Order in the Disorder: New Insights into Seemingly Structureless Regions of Proteins

Protein condensates (shown here in a microscope image) are critical to the process of gene expression in cells, and condensate formation depends on proteins’ intrinsically disordered regions.
Image Credit: Amy Strom, Princeton University

Howard Hughes Medical Institute Investigators Cigall Kadoch and Clifford Brangwynne teamed up to challenge long-held beliefs in the scientific community about how – or even if – structureless, unorganized regions of proteins play specific roles in causing or preventing disease pathogenesis. Their work was published earlier this month in the journal Cell.

To understand the significance of the duo’s findings, it helps to first dive deep into the ways in which cells alter genomic structure through a process known as chromatin remodeling. About two meters – or six and a half feet – of DNA are packed inside each cell’s nucleus, which measures no larger than a pinhead. To fit in that space, DNA winds around proteins, forming a compact structure called chromatin. At the Dana-Farber Cancer Institute, Kadoch and her lab have spent years studying chromatin remodeling complexes – molecular machines made up of multiple proteins that change the physical structure of chromatin and, thus, suppress or enable the activity of genes in a programmatic manner.

In recent years, her lab’s focus has centered on a family of complexes known as mammalian SWI/SNF chromatin remodeling complexes – commonly referred to as BAF complexes – which have garnered significant attention due to their disruption and involvement in human disease. BAF complexes are one of the most frequently mutated cellular entities in human cancer, second only to TP53, a well-studied tumor suppressor gene. Studies have shown that approximately 20 percent of human cancers bear BAF complex mutations and that such disruptions are also among the most common in neurodevelopmental disorders (NDDs) such as autism and intellectual disability.

The encounter between Neanderthals and Sapiens as told by their genomes

analysed the distribution of the portion of DNA inherited from Neanderthals in the genomes of humans (Homo sapiens) over the last 40,000 years.
Full Size Image
Image Credit: © Claudio Quilodrán

About 40,000 years ago, Neanderthals, who had lived for hundreds of thousands of years in the western part of the Eurasian continent, gave way to Homo sapiens, who had arrived from Africa. This replacement was not sudden, and the two species coexisted for a few millennia, resulting in the integration of Neanderthal DNA into the genome of Sapiens. Researchers at the University of Geneva (UNIGE) have analyzed the distribution of the portion of DNA inherited from Neanderthals in the genomes of humans (Homo sapiens) over the last 40,000 years. These statistical analyses revealed subtle variations in time and geographical space. This work, published in the journal Science Advances, helps us to understand the common history of these two species. 

Thanks to genome sequencing and comparative analysis, it is established that Neanderthals and Sapiens interbred and that these encounters were sometimes fruitful, leading to the presence of about 2% of DNA of Neanderthal origin in present-day Eurasians. However, this percentage varies slightly between regions of Eurasia, since DNA from Neanderthals is somewhat more abundant in the genomes of Asian populations than in those of European populations. 

Study Elucidates Evolution of Mosquitoes and Their Hosts

Researchers scoured academic literature and used new genomic techniques to create the mosquito family tree.
Photo Credit: Matt Bertone, NC State University.

Researchers at North Carolina State University and global collaborators have mapped the mosquito’s tree of life, a major step toward understanding important traits, such as how the insects choose their hosts, feed on blood and spread disease. The findings will help researchers make better predictions to model disease transmission and understand what makes some mosquitoes better disease carriers than others.

The research suggests that mosquito evolution over the past 200 million years mirrors the Earth’s history of shifting land masses and changing host organisms, says Dr. Brian Wiegmann, William Neal Reynolds Professor of Entomology at NC State and corresponding author of a paper describing the mosquito family tree, published in Nature Communications.

“This ongoing project builds a big-data resource that mines the academic literature with published observations of the sources of blood mosquitoes drink, from animals as diverse as fish to humans,” Wiegmann said. “It focuses explicitly on data collection to infer aspects of mosquito biology in a contextualized way. That means linking up the family, or phylogenetic, tree with the narrative of life on Earth: geologic history, climate history and organism history.”