Saturday, October 28, 2023


Okinawa’s ants change their seasonal rhythms amid land-cover changes


Ant communities in areas with more human development show reduced seasonal behavior.

Peer-Reviewed Publication

OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY (OIST) GRADUATE UNIVERSITY

Ants were collected in special traps at 24 sites across Okinawa over two years. 

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ANTS WERE COLLECTED IN SPECIAL TRAPS AT 24 SITES ACROSS OKINAWA OVER TWO YEARS.

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CREDIT: OKEON, OIST




Insects have an important role in maintaining the health of ecosystems, but our understanding of how human activities affect their populations is limited. This gap in knowledge is worrying because of the decline of insect populations and the severe consequences on ecosystems and agriculture. 

Researchers at the Okinawa Institute of Science and Technology (OIST), working with collaborators in Ireland, have led a project to understand how land-cover changes affect the seasonal behavior of ant communities in Okinawa. 

After collecting and identifying a whopping 1.2 million ants in different environments across Okinawa Island, they found that ant communities in areas with more human development lose their natural seasonal behavior and are more unpredictable when compared to sites with greater forest cover. Their results have been published in the journal Proceedings of the Royal Society B.  

“In forest areas, these natural seasonal cycles are preserved; however, in areas with more human development activities, these patterns become disrupted and degraded,” Prof. Evan Economo, head of OIST’s Biodiversity and Biocomplexity Unit, explained. “This results in a certain unpredictability regarding which species are active and a reduction in the natural cycles observed throughout the year.” 

The seasonal patterns of insect communities are linked to the important roles they play in the ecosystem, including decomposition, nutrient cycling, water purification, and seed dispersal. Ants hold a key position because of their large numbers and the multiple functions they perform.  

For Prof. Jamie Kass, a former OIST researcher who is now at Tohoku University, understanding how insect behavior changes over time is key. “If we only record their activities a few times a year, we risk missing important seasonal changes. Most studies do not consider this aspect, which makes our research unique. We show that human activities may be disrupting the normal seasonal behavior of insect communities, and this is an important but underexplored result of serious environmental changes worldwide.”  

In natural environments, especially those with very distinct seasons, insects in general are more active in spring and summer, and less active in winter. This pattern repeats every year. However, this study shows how changes to land cover by humans can disrupt these patterns, which are linked to important ecosystem services that people depend on.   

Every two weeks, worker ants were collected from traps across 24 sites in the Okinawa Environmental Observation Network (OKEON), managed by the Environmental Science and Informatics Section at OIST. Researchers identified the different ant species and counted how many of each they found. Using these data, they calculated how much ant communities were varying over time, and they modeled relationships with land cover characterized by site using remote sensing imagery. After finding that communities were changing less over time for developed areas than forested ones, they delved deeper and found that the seasonality of these communities in particular was diminished. 


Will machines soon be conscious?


Peer-Reviewed Publication

ESTONIAN RESEARCH COUNCIL

Differences between mammalian brains and large language models 

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LEFT: A SCHEMATIC DEPICTING THE BASIC ARCHITECTURE OF A LARGE LANGUAGE MODEL, WHICH CAN HAVE
TENS OR EVEN MORE THAN A HUNDRED DECODER BLOCKS ARRANGED IN A FEED-FORWARD FASHION.
RIGHT: A HEURISTIC MAP OF THE THALAMOCORTICAL SYSTEM, WHICH GENERATES COMPLEX ACTIVITY PATTERNS THOUGHT TO UNDERLIE CONSCIOUSNESS.

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CREDIT: MAC SHINE, JAAN ARU




The rise of the capabilities of artificial intelligence (AI) systems has led to the view that these systems might soon be conscious. However, we might underestimate the neurobiological mechanisms underlying human consciousness.

Modern AI systems are capable of many amazing behaviors. For instance, when one uses systems like ChatGPT, the responses are (sometimes) quite human-like and intelligent. When we, humans, are interacting with ChatGPT, we consciously perceive the text the language model generates. You are currently consciously perceiving this text here! The question is whether the language model also perceives our text when we prompt it. Or is it just a zombie, working based on clever pattern-matching algorithms? Based on the text it generates, it is easy to be swayed that the system might be conscious. However, in this new research, Jaan Aru, Matthew Larkum and Mac Shine take a neuroscientific angle to answer this question.

All three being neuroscientists, these authors argue that although the responses of systems like ChatGPT seem conscious, they are most likely not. First, the inputs to language models lack the embodied, embedded information content characteristic of our sensory contact with the world around us. Secondly, the architectures of present-day AI algorithms are missing key features of the thalamocortical system that have been linked to conscious awareness in mammals. Finally, the evolutionary and developmental trajectories that led to the emergence of living conscious organisms arguably have no parallels in artificial systems as envisioned today. The existence of living organisms depends on their actions and their survival is intricately linked to multi-level cellular, inter-cellular, and organismal processes culminating in agency and consciousness.

Thus, while it is tempting to assume that ChatGPT and similar systems might be conscious, this would severely underestimate the complexity of the neural mechanisms that generate consciousness in our brains. Researchers do not have a consensus on how consciousness rises in our brains. What we know, and what this new paper points out, is that the mechanisms are likely way more complex than the mechanisms underlying current language models. For instance, as pointed out in this work, real neurons are not akin neurons in artificial neural networks. Biological neurons are real physical entities, which can grow and change shape, whereas neurons in large language models are just meaningless pieces of code. We still have a long way to understand consciousness and, hence, a long way to conscious machines.

Overview of an EU project’s wild pollinator conservation efforts: Safeguard’s open-access collection


The EU Horizon 2020 project Safeguard has opened an outcomes collection in the Research Ideas and Outcomes (RIO) journal.


Reports and Proceedings

PENSOFT PUBLISHERS

Safeguard open-access collection in RIO journal 

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SAFEGUARD OPEN-ACCESS COLLECTION IN RIO JOURNAL

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CREDIT: PROJECT SAFEGUARD




For the past decade, the European Union has been actively investing in innovative projects, addressing major social concerns, such as climate change, renewable energy, and biodiversity loss. Although these projects give valuable results, some of the outcomes remain unseen and undiscovered by many. To avoid this knowledge oblivion, Safeguard has recently released an open-access collection in the Research Ideas and Outcomes (RIO) journal.

Safeguarding European wild pollinators (Safeguard) is a four-year EU Horizon 2020 funded project (2021-2025) that brings together world-leading researchers, NGOs, and industry and policy experts to substantially contribute to Europe’s capacity to reverse the losses of wild pollinators. Safeguard aims to significantly expand current assessments of the status and trends of European wild pollinators including bees, butterflies, flies, and other pollinating insects.

The open-access collection of the project in the RIO journal will not only increase the discoverability, visibility, and recognition of the research outcomes, but also set a comfortable digital environment for knowledge exchange, collaboration, sharing, and re-use of research. The collection in RIO will ensure that Safeguard outputs remain findable, accessible, interoperable, and reusable beyond the project’s lifetime. 

Currently, the collection hosts 14 project papers, published in different journals and linked through their metadata. The collection will further expand to a one-stop knowledge hub, hosting a range of outputs, reports, protocols, methodologies, and research papers.

Access the Safeguard RIO collection here.


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This project receives funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 101003476.

Views and opinions expressed are those of the author(s) only and do not necessarily reflect those of the European Union or the European Commission. Neither the EU nor the EC can be held responsible for them.

 

FOREVER CHEMICALS

Tracking down environmental toxins


Detection of per- and polyfluoroalkyl substances (PFAS) by interrupted energy transfer

Peer-Reviewed Publication

WILEY




PFAS, a family of highly fluorinated substances, represent a danger for humans and the environment. Particularly problematic members of this family, such as perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) appear to cause organ damage and cancer, as well as disrupting the endocrine system. In the journal Angewandte Chemie, researchers have now introduced a new method for an economical, easy-to-use fluorescence sensor for sensitive on-site testing for PFAS in water samples.

The term per- and polyfluoroalkyl substances (PFAS) refers to a group of organic compounds in which most or all the hydrogen atoms bound to the carbon atoms have been replaced with fluorine atoms. They are used to provide water-, oil-, and dirt-resistance to a variety of products, such as nonstick pans, outdoor clothing, and packaging. They may also be found in fire-suppressing foam, paint, and car polish. These compounds are highly useful—and highly dangerous when they find their way into the environment: they do not break down and thus become concentrated in plants, animals, and people.

Limits of 100 ng/l for individual specific PFAS substances and 500 ng/l for the total of all PFAS were set for drinking water in the EU. In Germany, water providers must begin testing drinking water for PFAS in 2026. The US Environmental Protection Agency has set stricter limits: for the most widespread PFAS (PFOS and PFOA), the upper limit is set at 4nm/l for each substance.

The usual method used to detect such trace amounts involves chromatography and mass spectrometry, is time-consuming and expensive, and requires complex equipment and experienced personnel. Timothy M. Swager and Alberto Concellón at the Massachusetts Institute of Technology (MIT) in Cambridge, USA, have now introduced a technique for making a portable, inexpensive test that uses fluorescence measurements to easily and selectively detect PFAS in water samples.

The test is based on a polymer—in the form of a thin film or nanoparticles—with fluorinated sidechains that have fluorinated dye molecules (squaraine derivatives) embedded in them. The special polymer backbone (poly-phenylene ethynylene) absorbs violet light and transfers the light energy to the dye by an electron exchange (Dexter mechanism). The dye then fluoresces red. If PFAS are present in the sample, they enter the polymer and displace the dye molecules by a fraction of a nanometer. This is enough to stop the electron exchange and thus the energy transfer. The dye’s red fluorescence is “switched off”, while the blue fluorescence of the polymer is “switched on”. The degree of fluorescence change is proportional to the concentration of PFAS.

This new technique, which has a detection limit in the µg/l range for PFOA and PFOS is suitable for on-site detection in highly contaminated regions. Detection of trace amounts of these contaminants in drinking water can be achieved with sufficient precision after pre-concentration of the samples by solid-phase extraction.

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About the Author

Dr. Timothy M. Swager is a Professor of Chemistry at the Massachusetts Institute of Technology. His research is at the chemistry/materials interface and he has pioneered the use of novel materials in the creation of chemical sensors with ultra-trace detection capabilities. Dr. Alberto Concellón was a postdoctoral researcher at MIT, and is presently at Ramón y Cajal Researcher at the University of Zaragoza, Spain working on functional self-assembled materials.

 

New discovery concerning receptors used by coronaviruses to enter human cells


Peer-Reviewed Publication

INSTITUT PASTEUR

Different routes of entry into human cells for SARS-CoV-2 and HKU1 

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SARS-COV-2 BINDS TO ACE2 PROTEIN. THE PROTEASE TMPRSS2 THEN CLEAVES THE SPIKE TO ENABLE VIRAL FUSION AND ENTRY INTO THE TARGET CELL. HKU1 BINDS DIRECTLY TO TMPRSS2 IN ORDER TO ENTER THE CELL WITHOUT USING ACE2.

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CREDIT: © INSTITUT PASTEUR




The SARS-CoV-2 virus responsible for COVID-19 can cause severe acute respiratory syndrome, contrasting with other coronaviruses that were known to cause mild seasonal colds prior to its emergence in 2019. This raises the question of why one coronavirus affects humans more severely than another. Scientists at the Institut Pasteur, Université Paris Cité and the VRI have now provided part of the answer by identifying a gateway used by the seasonal coronavirus HKU1 to enter human cells. HKU1 binds to a different receptor than SARS-CoV-2, which may partly explain the difference in severity between these two coronaviruses. Receptors provide a useful means of elucidating coronavirus transmissibility and pathology as part of surveillance work on viral evolution. These results are published in the October 25, 2023 issue of Nature.

Seven coronaviruses are known for their ability to infect humans. Four of these are generally mild: HKU1, 229E, NL63 and OC43, while the other three are more pathogenic: SARS-CoV-1, Mers-CoV and SARS-CoV-2.

The HKU1 virus was first identified in an elderly patient with severe pneumonia in Hong Kong in 2005. Like SARS-CoV-2, HKU1 mainly infects upper respiratory tract cells. However, it rarely affects the bronchi and alveoli in the lungs. The HKU1 virus causes colds and other mild respiratory symptoms. Complications may also occur, including severe respiratory tract infections, particularly in young children, the elderly and immunocompromised individuals. It is estimated that 70% of children are infected before the age of 6. In total, 75 to 95% of the global population has been exposed to HKU1, which is comparable to other seasonal human coronaviruses.

At cellular level, coronavirus spike proteins are cleaved, or split in two, after binding to their receptors. This cleavage phenomenon is vital for viral fusion, entry and multiplication. Some coronaviruses (SARS-CoV-2 and NL63) use the ACE2 receptor as a gateway for entering cells. Until now, HKU1 and OC43 were the only coronaviruses with unknown receptors.

Through collaboration between scientists at eight Institut Pasteur units, it was possible to identify the TMPRSS2 enzyme as the receptor to which HKU1 binds to enter cells. Once binding has occurred, TMPRSS2 triggers fusion of HKU1 with the cell, leading to viral infection. Through a combination of techniques performed in vitro and in cell culture, the scientists demonstrated that the TMPRSS2 receptor has high affinity with the HKU1 spike, which is not the case for SARS-CoV-2.

"Once a receptor has been identified for a virus, it is possible to characterize target cells more accurately, while also gaining insights on viral entry and multiplication mechanisms and infection pathophysiology," comments, Olivier Schwartz, co-last author of the study and Head of the Institut Pasteur's Virus and Immunity unit.

"Our findings also shed light on the various evolution strategies employed by coronaviruses, which use TMPRSS2 either to bind to target cells or trigger fusion and viral entry," adds Julian Buchrieser, co-last author of the study and scientist in the Institut Pasteur's Virus and Immunity unit.

These human-pathogenic viruses' use of different receptors probably affects their degree of severity. Receptor levels vary among respiratory tract cells, thus influencing the sensitivity of cells to infection and viral spread. Once the route of viral entry into cells is known, it should also be possible to fight infection more effectively by developing targeted therapies and assess the risk of virulence posed by any future emerging coronaviruses.

In parallel with this work, Institut Pasteur teams led by Pierre Lafaye and Felix Rey have developed and characterized nano-antibodies (very small antibodies) that inhibit HKU1 infection by binding to the TMPRSS2 receptor. These reagents have been patented for potential therapeutic activities.

This work was funded by the above-mentioned research bodies with additional support from the French Foundation for Medical Research (FRM), ANRS-Emerging Infectious Diseases, Vaccine Research Institute, the European HERA DURABLE project, the Labex IBEID and the ANR/FRM Flash Covid project.

  

Human respiratory tissue with ciliated cells stained green (anti-TMPRSS2 antibodies), nuclei in dark blue and cell membranes in light blue.

CREDIT

© Vincent Michel, Institut Pasteur

 

The race of water droplets

A team of researchers has delved into the mechanisms governing the speed at which a water droplet slides along one or several fibers.

Peer-Reviewed Publication

UNIVERSITY OF LIÈGE

The race of water droplets 

VIDEO: 

HOW FAST DOES A DROPLET FLOW ALONG A FIBRE? IT DEPENDS ON THE DIAMETER OF THE FIBRE... AND ALSO ON ITS SUBSTRUCTURE! THESE ARE THE FINDINGS OF A STUDY CONDUCTED BY RESEARCHERS FROM THE GRASP MABPRATORY OF THE UNIVERSITY OF LIÈGE WHO ARE INTERESTED IN MICROFLUIDICS, ESPECIALLY WATER HARVESTING IN ARID/SEMI-ARID REGIONS OF OUR PLANET.

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CREDIT: @UNIVERSITY OF LIÈGE / GRASP / M.LEONARD

How fast does a droplet flow along a fiber? It depends on the diameter of the fiber... and also on its substructure! These are the findings of a study conducted by researchers from the University of Liège who are interested in microfluidics, especially water harvesting in arid/semi-arid regions of our planet. These results are the subject of a publication highlighted by the editors in the journal Physical Review Fluids.

Similar to moisture farms imagined in science-fiction worlds like that of "Star Wars," many plant species from arid or semi-arid regions of Earth have developed ingenious strategies to capture water from the air, ensuring their survival. Recently, researchers have focused on understanding the fundamental mechanisms of water transport, intending to reproduce and improve them, especially for facilitating the collection of atmospheric moisture in deserts. A recent study led by the GRASP at the University of Liège (ULiège) has sought to better grasp the factors influencing these precious droplets' movement. To do this, scientists have tracked in real-time the characteristics and dynamics of these droplets as they slid along individual fibres or bundles of fibres.

"Following a droplet as it descends along a vertical fibre under the influence of gravity presents a complex experimental challenge: how to track a droplet over several meters of thread? Explains Matteo Léonard, a researcher at GRASP and the study's lead author. To address this problem, researchers devised a clever device in their laboratory. "Instead of following the fall of a droplet, we set the fibre in motion so that its speed is exactly equal and opposite to that of the droplet. This way, the droplet remains 'stationary' in front of the camera." With this challenge overcome, they first used fibres of different diameters. They observed that droplets had a lower speed at a given volume when the fibres were thicker, as predicted by theory. Subsequently, researchers created bundles of fibres by tying the ends of two or more fibres together and applying slight torsion to ensure contact between all the fibres. "This configuration created a bundle of fibres with grooves, similar to the braiding of strands in a rope, which resulted in grooves appearing on the cord," explains Matteo Leonard. In this configuration, researchers observed the same behaviours as with single fibres: as the number of fibres in the bundle increased, the overall diameter of the bundle increased, resulting in lower speed at a given volume. This predictable behaviour, however, concealed a more complex phenomenon...

Indeed, what about the behaviour of the droplet in the case where both configurations (single and bundle) have the same diameter (i.e., a fibre with a diameter of 0.28mm versus two fibres with a diameter of 0.14mm)? Since the hindrance of the phenomenon is dissipation (i.e., friction within the liquid and between the liquid and the fibre), one might expect that both cases would yield identical results because the contact surface between the liquid and the fibre is the same. "Not at all. We observed that over the same distance travelled, the droplet on the bundle of fibres was faster. It also lost the most volume." Researchers believe that in this configuration, the droplet loses volume because it tends to "fill" the grooves with its own volume, thereby creating a liquid rail on which it slides more efficiently and thus faster.

The results of this study make a significant contribution to the field of designing structures for atmospheric water collection. Notably, it can potentially improve the efficiency of cloud nets, which consist of a network of fibres, at a low cost. Furthermore, this research highlights the growing importance of substructures regularly observed on organisms living in desert environments. These substructures, such as micro-grooves or micro-hairs, demonstrate nature's ingenuity in capturing and transporting water, inspiring future technological innovations.

How fast does a TIONdroplet flow along a fibre? It depends on the diameter of the fibre... and also on its substructure!

CREDIT

@University of Liège/GRASP/M.Leonard

*A moisture farm is an area of land devoted to the production of water by extracting moisture from dry air.

 

Protein root discovery seals future of climate proof plants


Peer-Reviewed Publication

UNIVERSITY OF NOTTINGHAM




Researchers have discovered a protein that seals plant roots to regulate the uptake of nutrients and water from the soil, the discovery could help develop climate proof crops that requirless water and chemical fertilizers.

Researchers from the University of Nottingham identified new components of the lignin barrier in plant roots and the specific function of dirigent proteins (DPs), located in the root endodermis that control water and nutrient uptake. Their findings have been published today in Science Direct.

Plant roots function by absorbing mineral nutrients and water from the soil and also controlling their proper balance in the plant. This control is exerted by a specialised layer of root tissue called the endodermis. 

The endodermis contains a barrier to the movement of solutes and water that is made of lignin, the same material present in wood. This impermeable barrier blocks the uncontrolled movement of material into the root, by forming a tight seal between cells. This seal ensures the only pathway for nutrients and water to be taken up by roots is through the cells of the endodermis. This allows full cellular control over what enters and leaves the plant via the roots. 

This research has identified new components of the lignin deposition machinery that focus on the function of dirigent proteins (DPs), located in the root endodermis. These proteins act in coordination with other described root regulatory components to direct and organize the correct deposition of lignin in the endodermis allowing the plant to ensure it receives the optimum balance of nutrients from the soil.

Dr Gabriel Castrillo from the University of Nottingham’s School of Biosciences one of the leaders of the research, said: “With record temperatures being reached in parts of the world this year and erratic rainfall it is ever more important to understand the mechanisms of plants so we can future proof them to secure future food supplies. This research shows how plant roots regulate their uptake of water and nutrients through the deposition of lignin, which is regulated by DPs. Without these proteins, proper root sealing is not completed and the nutrient balance in the plant is compromised. We can use this knowledge to engineer plants to be able to grow with less water and chemical fertilizers.”

Friday, October 27, 2023

 

Mystery of volcanic tsunami solved after 373 years


GEOMAR researchers reconstruct historic volcanic eruption using 3D seismics


Peer-Reviewed Publication

HELMHOLTZ CENTRE FOR OCEAN RESEARCH KIEL (GEOMAR)




From the Greek island of Santorini, the eruption had been visible for several weeks. In the late summer of 1650, people reported that the colour of the water had changed and the water was boiling. About seven kilometres north-east of Santorini, an underwater volcano had risen from the sea and began ejecting glowing rocks. Fire and lightning could be seen, and plumes of smoke darkened the sky. Then the water suddenly receded, only to surge towards the coastline moments later, battering it with waves up to 20 metres high. A huge bang was heard more than 100 kilometres away, pumice and ash fell on the surrounding islands, and a deadly cloud of poisonous gas claimed several lives.

"We know these details of the historic eruption of Kolumbo because there are contemporary reports that were compiled and published by a French volcanologist in the 19th century," says Dr Jens Karstens, marine geophysicist at GEOMAR Helmholtz Centre for Ocean Research Kiel. But how did these devastating events come about? To find out, he and his German and Greek colleagues went to the Greek Aegean Sea in 2019 to study the volcanic crater with special technology. Karstens: "We wanted to understand how the tsunami came about at that time and why the volcano exploded so violently."

On board the now decommissioned research vessel POSEIDON, the team used 3D seismic methods to create a three-dimensional image of the crater, which is now 18 metres below the water's surface. Dr Gareth Crutchley, co-author of the study: "This allows us to look inside the volcano." Not only did the 3D imaging show that the crater was 2.5 kilometres in diameter and 500 metres deep, suggesting a truly massive explosion, the seismic profiles also revealed that one flank of the cone had been severely deformed. Crutchley: "This part of the volcano has certainly slipped." The researchers then took a detective’s approach, comparing the various mechanisms that could have caused the tsunami with the historical eyewitness accounts. They concluded that only a combination of a landslide followed by a volcanic explosion could explain the tsunami. Their findings are published today in the journal Nature Communications.

By combining 3D seismics with computer simulations, the researchers were able to reconstruct how high the waves would have been if they had been generated by the explosion alone. Karstens: "According to this, waves of six metres would have been expected at one particular location, but we know from the reports of eyewitnesses that they were 20 metres high there". Furthermore, the sea is said to have first receded at another point, but in the computer simulation a wave crest reaches the coast first. Thus, the explosion alone cannot explain the tsunami event. However, when the landslide was included in the simulations, the data agreed with historical observations.

Jens Karstens explains: "Kolumbo consists partly of pumice with very steep slopes. It is not very stable. During the eruption, which had been going on for several weeks, lava was continuously ejected. Underneath, in the magma chamber, which contained a lot of gas, there was enormous pressure. When one of the volcano's flanks slipped, the effect was like uncorking a bottle of champagne: the sudden release of pressure allowed the gas in the magma system to expand, resulting in a huge explosion". Something similar could have happened during the 2022 eruption of the Hunga Tonga undersea volcano, whose volcanic crater has a similar shape to Kolumbo's.

The study thus provides valuable information for the development of monitoring programmes for active submarine volcanic activity, such as SANTORY, which is led by co-author Prof. Dr Paraskevi Nomikou of the National and Kapodistrian University of Athens (NKUA). "We hope to be able to use our results to develop new approaches to monitor volcanic unrest," says Jens Karstens, "maybe even an early warning system, collecting data in real time. That would be my dream”.

 

About 3D Marine Reflection Seismics

3D seismics is a geophysical technique that exploits the fact that sound waves are partially reflected at the boundaries of layers. This makes it possible to create cross-sectional profiles of geological structures beneath the seabed. Unlike 2D reflection seismics, marine 3D reflection seismics uses multiple measuring cables (housing receivers) towed in parallel behind the research vessel. The result is a three-dimensional image, known as a seismic volume, which allows us to look beneath the seafloor and analyse the geology in detail.