A new method for studying ribosome function

Illustration showing the principle of native chemical ligation approach developed by Syroegin, et al. Addition of the cysteine amino acid (red) to tRNA (blue, top left) allows for the tRNA to fuse to a peptide (yellow, lower left). The resulting ribosome structure (middle) and the captured electron density maps for the peptidyl-tRNA inside the ribosome (right) were obtained by X-ray crystallography in the UIC experiments.
Image Credit: Syroegin, et al.

Inside tiny cellular machines called ribosomes, chains of genetic material called messenger RNAs (mRNAs) are matched with the corresponding transfer RNAs (tRNAs) to create sequences of amino acids that exit the ribosome as proteins. Unfinished proteins are called nascent chainsm and they are left attached to the ribosome.

Scientists know that some of these nascent chains can regulate the activity of the ribosome and that the nascent chains can sometimes interfere with antibiotics — many of which work by targeting bacterial ribosome activity. Scientists do not know why this happens, mainly because it is hard to visualize what the ribosome-peptide-drug interactions look like while the unfinished proteins are still tethered to the ribosome.

Now, scientists at the University of Illinois Chicago are the first to report a method for stable attachment of peptides to tRNAs, which has allowed them to gain new fundamental insights into ribosome function by determining the atomic-level structures of ribosomes and the shapes that these peptides take inside the ribosome.

How much microplastic do whales eat? Up to 10 million pieces per day

Humpback whales lunge feed in Monterey Bay. New research shows whales are ingesting plastic in larger quantities than previously thought, and nearly all comes from their prey, not from the enormous volumes of seawater the whales gulp when feeding.
Photo Credit: shadowfaxone

Analysis of ocean plastic pollution and whale foraging behavior tracked with noninvasive tags shows whales are ingesting tiny specks of plastic in far bigger quantities than previously thought, and nearly all of it comes from the animals they eat – not the water they gulp.

The largest animals ever known to have lived on Earth ingest the tiniest specks of plastic in colossal amounts, Stanford University scientists have found.

Published in Nature Communications, the study focuses on blue, fin, and humpback whales and their consumption of plastic fragments no bigger than a few grains of sand, which are commonly called microplastics. The authors combined measures of microplastic concentrations up and down the water column off the coast of California with detailed logs of where hundreds of whales carrying tracking devices foraged for food between 2010 and 2019.

They found the whales predominantly feed 50 to 250 meters below the surface, a depth that coincides with the highest concentrations of microplastic in the open ocean. The planet’s biggest creature – the blue whale – ingests the most plastic, at an estimated 10 million pieces per day as it feeds almost exclusively on shrimplike animals called krill.

“They’re lower on the food chain than you might expect by their massive size, which puts them closer to where the plastic is in the water. There’s only one link: The krill eats the plastic, and then the whale eats the krill,” said study co-author Matthew Savoca, a postdoctoral scholar at Hopkins Marine Station, Stanford’s marine laboratory on the Monterey Peninsula.

Arctic Hydrothermal Vent Site Could Help in Search for Extraterrestrial Life

The view from over ice-floes in the Arctic Ocean, covering the Aurora hydrothermal Field, Gakkel Ridge from the R/V Polarstern.
Photo Credit Chris German, ©Woods Hole Oceanographic Institution

When scientists discovered a hydrothermal vent site in the Arctic Ocean’s Aurora hydrothermal system in 2014, they did not immediately realize just how exciting their discovery was.

“Although finding any vent in the Arctic Ocean was a first, we figured what we had found was one of the least interesting kinds of vent sites that there are,” said Chris German, senior scientist with the Woods Hole Oceanographic Institution’s Department of Geology and Geophysics. “We came home from the expedition thinking, ‘Okay, we found a site in the Arctic. That’s great, but if you take away the ice-cover, it is just another vent site’.”

However, after further analysis and a follow-on 2019 expedition to the remote site, German and other researchers now think this is a very significant finding. They believe that this vent—and others still to be located within the Arctic Ocean’s Gakkel Ridge rift-valley floor—could change our understanding of ultra-slow spreading mid-ocean ridges, substantially expand the estimates of valuable marine mineral deposits rich in copper and gold and serve as natural laboratories to help inform the search for extraterrestrial life.

“Our findings have implications for ultra-slow ridge cooling, global marine mineral distributions, and the diversity of geologic settings that can host abiotic organic synthesis–pertinent to the search for life beyond Earth,” according to the paper, “Volcanically hosted venting with indications of ultramafic influence at Aurora hydrothermal field on Gakkel Ridge,” published in Nature Communications.

A New Protocol for Live Imaging Emerges from MBL Embryology Course

A stylized image of a nematode worm (C. elegans) adult encircled by embryos.
Credit: Yicong Wu

The beauty of live-imaging studies is that the specimen is alive, allowing dynamics such as cell division and embryonic development to be recorded over time.

Yet the frustration of live-imaging studies is the specimen is alive – wriggling, twisting, escaping the field of view. Plus, it’s delicate, susceptible to heat damage or death from the imaging equipment itself.

A technical solution to this quandary recently emerged from the MBL Embryology course, in “a classic example of the collaborative effort here at MBL,” says MBL Imaging Research Specialist Carsten Wolff.

“During the 2021 Embryology course, we started to develop a technique that enables us to image adult C. elegans worms for longer periods of time, and at high resolution, using light sheet microscopy,” says Wolff. A group of course faculty and staff, collaborating with MBL imagers, fine-tuned the protocol during the 2022 course and wrote up the paper, which is published this month in Frontiers in Cell and Developmental Biology.

The nematode C. elegans is a popular organism in biological and biomedical research. Light-sheet fluorescence microscopy (LSFM) has been very successful in capturing embryonic processes in C. elegans, as well as in mice and zebrafish. But once the organisms hatch out, LSFM presents limitations.

As dense as it gets: New Model for Matter in Neutron Star Collisions

Illustration of the new method: the researchers use five-dimensional black holes (right) to calculate the phase diagram of strongly coupled matter (middle), enabling simulations of neutron star mergers and the produced gravitational waves (left).
Source/Credit: Goethe University

With the exception of black holes, neutron stars are the densest objects in our universe. As their name suggests, neutron stars are mainly made of neutrons. However, our knowledge about the matter produced during the collision of two neutron stars is still limited. Scientists from Goethe University Frankfurt and the Asia Pacific Center for Theoretical Physics in Pohang have now developed a new model that gives insights about matter under such extreme conditions.

After a massive star has burned its fuel and explodes as a supernova, an extremely compact object, called a neutron star, can be formed. Neutron stars are extraordinarily dense: To reach the density inside them, one would need to squeeze a massive body like our sun down to the size of a city like Frankfurt. In 2017, gravitational waves, the small ripples in spacetime that are produced during a collision of two neutron stars, could be directly measured here on earth for the first time. However, the composition of the resulting hot and dense merger product is not known precisely. It is still an open question, for instance, whether quarks, which are otherwise trapped in neutrons, can appear in free form after the collision. Dr. Christian Ecker from the Institute for Theoretical Physics of Goethe University Frankfurt, Germany, and Dr. Matti Järvinen and Dr. Tuna Demircik from the Asia Pacific Center for Theoretical Physics in Pohang, South Korea, have now developed a new model that allows them to get one step closer to answering this question.

Learning to Better Understand the Language of Algae

A view through the microscope onto the diverse microalgal community of a freshwater lake, including diatoms, green algae and dinoflagellates/chryosphytes.
Photo: Maria Stockenreiter /LMU München

Communication is everything - and that applies for algae, too. However, their chemical language and its significance in aquatic ecosystems remain largely unknown. A research duo from the Helmholtz Centre for Environmental research (UFZ) and the Plymouth Marine Laboratory (PML) have published a corresponding review in Biological Reviews. This summarizes the current state of knowledge and identifies new approaches for future research in the language of algae and their ecological relationships.

Can algae talk? "Well, although they don't have any mouth or ears, algae still communicate with their own kind and with other organisms in their surroundings. They do this with volatile organic substances they release into the water," says Dr. Patrick Fink, a water ecologist at the UFZ's Magdeburg site. These chemical signals are known as BVOCs (biogenic volatile organic compounds) and are the equivalent of odors in the air with which flowering plants communicate and attract their pollinators. When under attack by parasites, some plant species release odors that attract the parasites' natural enemies to them. "Algae also employ such interactions and protective mechanisms," says Fink. "After all, they are among the oldest organisms on Earth, and chemical communication is the most original form of exchanging information in evolutionary history. However, our knowledge in this area still remains very fragmentary."

New Technique Helps ID Genes Related to Aging

The head of a C. elegans showing fluorescently labeled protein aggregates.
Source: North Carolina State University

Researchers from North Carolina State University have developed a new method for determining which genes are relevant to the aging process. The work was done in an animal species widely used as a model for genetic and biological research, but the finding has broader applications for research into the genetics of aging.

“There are a lot of genes out there that we still don’t know what they do, particularly in regard to aging,” says Adriana San Miguel, corresponding author of a paper on the work and an assistant professor of chemical and biomolecular engineering at NC State. “That’s because this field faces a very specific technical challenge: by the time you know whether an organism is going to live for a long time, it’s old and no longer able to reproduce. But the techniques we use to study genes require us to work with animals that are capable of reproducing, so we can study the role of specific genes in subsequent generations.

“To expedite research in this field, we wanted to find a way of identifying genes that may be relevant to aging while the organisms are still young enough to work with.”

For this work, the researchers focused on a species of roundworm called C. elegans, which is one of the most important model species for research into genetics and aging. Specifically, the researchers focused on protein aggregation in cells, which is well established as being related to aging.

Pancreatic cancer could be diagnosed up to three years earlier

The desmoplastic reaction is a prominent pathological characteristic of pancreatic cancer. 
Credit: National Cancer Institute

Pancreatic cancer could be identified in patients up to three years earlier than current diagnoses, new research suggests. Weight loss and increasing blood glucose levels are early indicators of pancreatic cancer and could lead to a timelier diagnosis, helping to improve survival rates.

In the largest study of its kind, researchers from the University of Oxford, in partnership with Pancreatic Cancer Action and the University of Surrey, investigated signs of pancreatic cancer, including weight loss, hyperglycemia and diabetes and demonstrated the timelines for when they develop in relation to cancer. The pancreas is a vital organ with two key functions, to produce insulin and digestive enzymes. Cancer can affect one or both of these functions leading to the above symptoms. Currently, almost 90 per cent of people with pancreatic cancer are diagnosed too late for curative treatment.

Lead author Dr Agnieszka Lemanska, Lecturer in Data Science at the University of Surrey, said: 'Due to the difficulty in detecting pancreatic cancer, survival rates are extremely poor compared to other cancers, with less than 10 per cent of people surviving five years or more after diagnosis.

'Weight loss and increased blood glucose are recognized symptoms of pancreatic cancer. However, the extent of these symptoms and when they manifest have been unknown. Knowing when they develop will help clinicians to diagnose this deadly cancer, meaning treatment can begin earlier.'

Physicists Proposed Theory of Solidification of Nickel and Iron Alloys

Nickel-iron alloy is used when high dimensional stability of finished parts is required.
Photo: unsplash.com / Laura Ockel

Physicists at Ural Federal University have created a theory for the solidification of a nickel-iron alloy (invar). They determined that an important role in the technology of creating products from invar, namely in the solidification process, is played by the oncoming flow: when the alloy cools, the liquid layer flows on top of the solidified layer. If you regulate this process, you can control the characteristics of the alloys, obtain a more homogeneous structure, thereby improving the properties of the final product.

The work of scientists is extremely important because nickel and iron alloys are used in creating high-precision devices: clocks, seismic sensors, substrates for chips, valves and engines in aircraft structures, and instruments for telescopes. The calculations will help to create an alloy with the desired structure, which will affect the quality of the finished products. Description of the model and behavior of melts, as well as analytical calculations, scientists have published in the journal Scientific Reports. The research was supported by the Russian Science Foundation (Project No. 21-79-10012).

"Let me explain the work with an analogy. When water freezes, it pushes out all the dirt. So, you can put a piece of ice in your mouth, it will be clean. This is roughly what happens to melts when they cool. The only difference is that they do not push out all the impurities, but some of them. Some of the impurities leak out, and some of the impurities stay in the melt. What remains in the melt fills the gaps between the crystals, which solidify, and the voids, which remain. As a result, the alloys are heterogeneous: one tiny piece is enriched and the neighboring piece is not. This affects the properties of the finished product," says Dmitry Aleksandrov, Head of the Ural Federal University's Laboratory of Multi-Scale Mathematical Modeling.

Habitat mapping data can fill gaps in knowledge on biodiversity

Dry sand heaths are also among the biotopes found in Hamburg.
Photo Credit: Christiane Buchwald

Data gathered by habitat mapping programs can make important contributions to biodiversity research. They provide insight into changes of the local flora since the 1980s – a period that is covered by hardly any other sources of information. A team from the Martin Luther University Halle-Wittenberg and the Hamburg Authorities for the Environment, Climate, Energy and Agriculture has now shown how research can benefit from this historic habitat mapping data using habitat maps of the city and federal state of Hamburg as an example. Their results, which have been published in "Ecosphere", also show a clear decline of species-rich habitats due to urbanization over the last decades.

In Germany, habitat mapping programs (Biotopkartierungen) have been carried out in almost every federal state since the 1980s. Similar sources exist in many other European countries. "The mapping programs are carried out by the authorities to obtain an overview of natural and semi-natural habitats for landscape planning and nature conservation," says Lina Lüttgert from the Institute of Biology of MLU. These datasets contain comprehensive data on all habitats of the local flora and fauna. Often, they also include information on the plant species found in these areas. This makes the data interesting for research: "They can provide insight into the changes over the last decades. Also, we do not have any other systematic surveys on local diversity from that period," says Lüttgert.