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Tag: St Petersburg University

Scientist at St Petersburg University discover the possible reason of mammoth extinction in Siberia

Posted on by Alina Perevizintsova

An international group of scientists from the USA, the UK, Canada, Denmark, Germany, France, Norway, Sweden, China and Russia including researchers from St Petersburg University have found that an abrupt climate change caused the extinction of mammoths in Siberia 12,000 years ago. The findings are published in the scientific journal Nature.

Scientists performed a metagenomics analysis of ancient environmental DNA (eDNA) of plants and animals recovered from sediments at the sites distributed across much of the Arctic covering the past 50,000 years. Multiple remains enabled the scientists not only to learn more about the representatives of the ancient megafauna, but also find the reasons of their extinction.

The woolly mammoth is an extinct species of the ancient ancestors of elephants that appeared about 450 years ago in the territory of modern Siberia and became globally extinct about 4 thousand years ago. The meat of mammals was used as food for early humans, while the skeleton and tusks were utilised in the construction of houses and weapons. For a long time, it was considered that human hunting caused the extinction of mammoths. However, scientists determined that the main reason was an abrupt climate change.

The research showed that the animals became extinct due to the lack of food caused by melting ices of the Arctic. Eske Willerslev, Professor of St. John’s College at the University of Cambridge, Director of University of Copenhagen’s Centre of Excellence GeoGenetics explained that the reason of the mammal extinction was a dramatic climate change. Ice melt in the Arctic caused increased humidity, formation of lakes, rivers and swamps and almost complete extinction of vegetation that served as food to mammoths. Large animals were unable to adapt promptly to the scarce ratio after the prominent landscape change. Moreover, trees and swamp plants occupied the mammoth grazing areas after the warming.

‘The ecosystem changed and the reduced plant biomass could not feed herds of mammoths anymore. We demonstrated that the climate change and, particularly, precipitation directly affects the vegetation, while people had no impact whatsoever,’ explained Yucheng Wang, researcher of the Department of Zoology at the University of Cambridge.

A group of scientists at St Petersburg University works on reconstructing the development of climate and environment based on the study of lakes and lake sediments. The researchers at St Petersburg University presented samples of quaternary sediments obtained during the excavation at Severnaya Zemlya Archipelago and Taimyr Peninsula. These data have contributed to the collection of materials from 535 locations in the Arctic.

The findings based on the international scientific research demonstrated that the woolly mammoth and its ancestors inhabited all continents apart from Australia and South America. Previously, it was considered that the population survived the end of the last ice age in small areas along the coastline of Siberia and Alaska in Wrangel Island and St. Paul Island. However, recent research has shown that they actually lived for longer periods of time in other areas. Notably, the breeds of mammoths in both islands were closely related despite their geographical segregation.

‘Modern methods allow the scientists to determine DNA traces of various animals and plants, for instance, in lake sediments and along the hydrographic water basins previously inhabited by these organisms. This is a powerful tool to reconstruct the habitat of distinct species, the character of vegetation, the composition of fauna in specific regions and, ultimately, the development of climate and the environment as a whole,’ said Grigory Fedorov, Associate Professor at the Department of Geomorphology, St Petersburg University.

A large number of collected DNA samples allowed for the scientists to create a map of the mammal distribution as well as demonstrate the dynamics of the population extinction. The experts managed to prove that after the last glacier period (the Late Pleistocene that completed 12,000 years ago) the mammoth habitat significantly reduced, however, they survived in various regions of the Arctic and lived much longer than previously presumed. Thus, according to the recent data, woolly mammoths lived up to the Holocene – a modern geological epoch of the Quaternary period that followed the Pleistocene about 12,000 years ago.

COVID-19 vaccination before surgery could help avoid 58,000 deaths a year

Posted on by Alina Perevizintsova

Scientists from St Petersburg University have taken part in a large-scale project to study SARSCoV-2 in surgical patients. One of the findings of the study is that vaccinations will help prevent more than 58,000 coronavirus-related deaths a year. 15,025 researchers from 122 countries have taken part in the work to make a new world record for the number of authors of a scientific article.

The article is published in the British Journal of Surgery.

The researchers’ goal was to determine how COVID affects the results of surgical interventions and how to minimise the risk of infection during elective surgery. The first COVID-19 wave caused about 70% of the world’s operations (28 million) to be postponed or cancelled. It was found that COVID-19 before or after surgery increases the probability of postoperative mortality.

The international team of surgeons and scientists from CovidSurg analysed 140,000 patients’ data from 116 countries. Their aim was to develop clinical guidelines for the surgical treatment of patients with coronavirus and for reducing the risk of infection in the postoperative period.

The study participants were clinicians, residents and students of St Petersburg University. Six research groups worked in the clinical departments of cardiovascular surgery, urology, traumatology, gynaecology, endocrine surgery and general surgery at the Pirogov Clinic of High Medical Technologies at the University.

The goal was to collect clinical data – anamneses, medical histories, COVID status, operation characteristics – of all patients hospitalised for elective surgery within one week. After 30 days, the immediate results of treatment were assessed. The data were recorded in an online individual registration card available to the organisers of the study.

“We have learned more about how covid-19 affects prognosis and overall surgical outcomes. This will enable both our specialists and doctors around the world to better plan surgical interventions and increase the safety of treatment,” said Sergei Efremov, head of the research department, Anaesthesiologist-resuscitator at the Pirogov Clinic of High Medical Technologies, St Petersburg University

One of the main conclusions that scientists have come to is that patients preparing for surgery should be vaccinated as a priority. Among the most vulnerable patients are elderly people above 70 years old. They should be vaccinated first. According to the researchers, priority preoperative vaccination of routine surgical patients will help avoid more than 58,000 COVID-associated deaths a year.

New fluorescent nanoparticles to contribute to medical diagnostic testing with contrast

Posted on by Alina Perevizintsova

Scientists at St Petersburg University, LAT University (Finland) and Sirius University have synthesised new fluorescent nanoparticles based on the fluorides of rare earth elements – yttrium and europium with the addition of gadolinium ions. Potentially, they can be used in laser microscopy and in diagnostics of various diseases with the use of contrast. The article describing the synthesised phosphor was published in The New Journal of Chemistry published by the Royal Society of Chemistry. The research results appeared on the journal cover.

Phosphors are substances that can radiate light when exposed to UV rays, electromagnetic field or different disturbing action. Today, these materials are used in lamps and LEDs (for example, in electric appliances of everyday use), evacuation and fire alarm systems. They are also used to produce paints and pigments, secure value documents, and conduct medical research. Thus, the synthesised substance will allow for magnetic resonance tomography and fluorescence microscopy to be performed simultaneously, which will speed up the diagnostics.

Recently, among various fluorescent materials, researchers have paid particular attention to nanocrystalline non-organic phosphors based on the composites of rare earth elements. For this purpose, the NaYF4 composites are mostly used, since the material itself only slightly reduces the luminescence of the dopded ions.

St Petersburg University scientists replaced the ions of yttrium (Y) with the ions of europium (Eu) and gadolinium (Gd) and studied the way it affects the size of nanoparticles as well as the substance emission properties. Based on the experimental results, the optimum europium doping concentration in the composite is 30%, since exactly this amount of substance provides for the maximal emission intensity. However, luminescence intensity can still be increased. To do so, additionally a small number of yttrium ions should be replaced by gadolinium, while keeping the concentration of europium unchanged. Despite the fact that gadolinium ions show almost no luminescence, they significantly increase the brightness of the substance luminosity.

To achieve this result, scientists synthesise the particles with the ions of yttrium, europium and gadolinium in an autoclave – a chemical reactor that elevates the temperature of substances under pressure above atmospheric. Chemists gradually add citric acid, sodium hydroxide and a mixture of ammonium fluoride and sodium hydroxide to water solutions of yttrium, europium and gadolinium chlorides. Then, the resulted solution is held in an autoclave for 24 hours at a temperature of 180°C. This method allows getting the final substance with improved luminescence properties.

‘We have found out that by adding only 1% of gadolinium, we can enhance the luminescence intensity by 2.5 times.  A decrease in symmetry leads to an increase in luminescence properties of lanthanides that include the three utilised rare earth elements. Probably, the replacement of yttrium ions with larger gadolinium ions causes structural defects that reduce the symmetry and, consequently, enhance luminescence making the substance emission brighter,’ says Andrey Mereshchenko, a co-author of the research, Associate Professor in the Department of Laser Chemistry at St Petersburg University.

During the research, the University chemists also found out that the replacement of yttrium ions by gadolinium and europium ions causes the size reduction of synthesised particles. This simplifies further use of the substance for medical purposes. The images below demonstrate the dependence of the size on the content of europium. These images were obtained by an electronic microscope at Interdisciplinary Resource Centre for Nanotechnology at the St Petersburg University Research Park.

‘We assume that a decrease in the size of particles is related to the crystal-growth rate. Gadolinium and europium ions have a larger radius than yttrium ions. Thus, the surface positive charge density of the particles containing europium and gadolinium is lower.   For this reason, the charged fluoride ions are less attracted to such particles, and they grow slower,’ clarified Andrey Mereshchenko.

In photobiology and biomedicine, bioparticles based on NaYF4 in combination with other rare earth ions are widely used due to low toxicity of the material and ability to penetrate into the tissues because of its small size (unites and tens of nanometres). Thus, gadolinium with its magnetic properties is currently used to design contrast agents for magnetic resonance therapy. Fluorescent nanoparticles with europium ions are used as markers of different diseases to examine biological tissues with the help of fluorescence microscopy. A new phosphor designed by the University scientists enables specialists to perform two types of diagnostics simultaneously – with the help of light and magnetic field, which significantly increases the efficiency of the search.

‘We have to modify our particles by making them more sensitive to certain viruses and cells. Then, we can perform diagnostics, for example, by looking for cancer cells in the human body. We can take samples of cells or tissues and examine them by means of fluorescent microscope. Europium will light up those areas where the particles ‘preconfigured’ to look for cancerous tumour have arrived. The use of magnetic resonance therapy in a living organism will allow to detect a tumour, since the nanoparticles with magnetic gadolinium ions will concentrate there.    Thus, by introducing one functional element we can perform two independent tests at the same time. This is the practical application of our substance,’ explains Andrey Mereshchenko.

In further research, ions in the composite can be partially replaced with radioactive ions and be used in the treatment of cancer. Apart from medicine, these materials can be applied in developing fluorescent paints to safeguard documents, money and securities, where especially bright luminescence is required.

St Petersburg University students become first recipients of an award for young mathematicians in Russia

Posted on by Alina Perevizintsova

Students from St Petersburg University have won the award for young mathematicians and have taken the entire podium in the Student category. The award ceremony took place at the Conference of World-class International Mathematical Centres held at the Sirius University of Science and Technology.

The winners in the student category were three master’s students from St Petersburg University- Yaroslav Alekseev, author of ‘A Lower Bound for Polynomial Calculus with Extension Rule’; Ivan Bochkov (‘On zeros and poles of Helson zeta functions’); and Aleksei Kulikov (‘Fourier interpolation and time-frequency localisation’). Aleksei Kulikov was awarded the Medal of the Russian Academy of Sciences in Mathematics this year for his research in harmonic analysis.

The prize for young mathematicians was established by the Sirius Educational Centre and is awarded for a cycle of scientific work in mathematics in three categories: Young Scientists (up to and including 35 years old), Postgraduate Students and Students.

A total of 58 young mathematicians from all over Russia – 19 students, 17 postgraduates and 22 scientists – were nominated for it.

Also, among the finalists were: Danila Cherkashin, a research associate at the Chebyshev Laboratory at St Petersburg University; and Viacheslav Borovitskiy, a postgraduate student at St Petersburg University.

Candidates for the prize were nominated by members of the mathematical community. these candidates provided short descriptions of their work and were backed by recommendations by well-known scientists.  Then an international jury headed by Fields medallist Andrei Okounkov selected the country’s strongest mathematicians.

The International Congress of Mathematicians is the most important meeting in basic and applied mathematics and one of the oldest scientific congresses. The aim of the congress is to present as wide a spectrum of advanced mathematics as possible, including all scientific fields and mathematical schools from different geographical regions, and thus determine the future direction of the development of mathematics. The guest speakers are mathematicians of the highest calibre, capable of presenting current research trends to a wide audience.

“The fact that all three students of the University have become laureates of the new prize for young mathematicians is a quite natural result’, said Yurii Belov, Professor at St Petersburg University.

“These are graduates of the bachelor’s programme in Mathematics, established in 2015. Talented applicants have come to us and continued their studies in the master’s programme ‘Advanced Mathematics’. After six years we can see that their training has been successful. I should point out that St Petersburg University has always had a strong mathematical scientific school.”

All finalists were invited to give a presentation at the Conference of World-class International Mathematical Centres and also received a grant to attend the International Congress of Mathematicians to be held in St Petersburg in 2022.

Researchers discover that Fritillary butterflies sporadically interbreed with their very distant relatives

Posted on by Alina Perevizintsova

Researchers from St Petersburg University and the Zoological Institute of the Russian Academy of Sciences have found that genealogically distant butterfly species Melitaea didyma and M. acentria sometimes interbreed. These species separated at least five million years ago (almost the same period separates humans and chimpanzees).

For small-numbered M. acentria this sporadic introgressive hybridisation results in higher genetic diversity, increasing their survival chances.  The research that makes us take a fresh look at the evolution of living organisms is supported by a grant from the Russian Science Foundation. The research findings are published in the journal Molecular Ecology.

The formation of hybrids – organisms obtained after crossing genetically different forms – is more widespread in nature previously thought. Usually, only closely related species can hybridize. For example, hybrids occur in some populations of Daphnia – crustaceans from plankton.

They significantly complicate the definition of the boundaries between different species. However, some cases are known when hybridisation occurred between very distant relatives: for example, between Homo sapiens and Neanderthals, whose common ancestor lived about 800,000 years ago.

The researchers from St Petersburg University and the Zoological Institute of the Russian Academy of Sciences have managed to detect the hybridisation of even more distant species: fritillary butterflies M. didyma and M. acentria, living on the slopes of the popular Mount Hermon ski resort in northern Israel.

Their common ancestor existed at least five million years ago – modern humans and chimpanzees are about as far apart on the phylogenetic tree (six million years). To obtain this result the scientists performed whole-genome sequencing and analysed 27 genomes of three species of fritillary butterflies.

It turned out that some specimens of small-numbered M. acentria sporadically interbreed with more common M. didyma, resulting in gene flow from M. didyma to M. acentria. In general, one of the reasons for species extinction is precisely the loss of genetic diversity. The fact that acentria butterflies are ‘fed’ with genetic material through hybridisation with a distant congener could therefore be a factor of survival and further evolution for the acentria.

Moreover, as the researchers note, introgressive hybridisation is not total in this case. Only some specimens interbreed with another species. However, this is sufficient for the emergence of a stable gene flow. The researchers even managed to catch one butterfly that turned out to be an interspecific hybrid.

“When we examined the morphology of M. acentria, we noticed that it resembled M. didyma. This was unexpected for us because these two species are distant relatives. Such “coincidences” are mostly the result of adaptation to similar environmental conditions. However, sometimes they occur as a result of introgressive hybridisation. We have analysed whole genomes, which showed a unidirectional gene flow from didyma to acentria,” said Elena Pazhenkova, the first author of the article, a doctoral student at St Petersburg University.

Elena Pazhenkova, a doctoral student at St Petersburg University (left) and Vladimir Lukhtanov, Principal Researcher at the Zoological Institute of the Russian Academy of Sciences and Professor at St Petersburg University (right), during their expedition to Mongolia in 2019. Photo by Vladimir Lukhtanov

Vladimir Lukhtanov is a Principal Researcher at the Zoological Institute of the Russian Academy of Sciences and a Professor at St Petersburg University. He says that hybridization usually leads to the fusion of two species or to the appearance of infertile offspring, that is, to the dead-end of evolution. That is the dead-end of evolution.

Until recently, it was therefore believed that such a scenario of ‘enrichment’ of a species with new genetic material was in principle impossible. However, in recent years, more and more works have appeared that encourage scientists to take a different view on the processes of evolution of living beings.

“It seems that we are at the stage of changing the scientific paradigm. Biologists have long been convinced that the evolution of living beings can be represented as a branching tree. This metaphor  (Tree of Life) might not be entirely correct and might soon be discarded,” said Vladimir Lukhtanov.

“Introgressive hybridisation suggests that it might be more correct to represent evolution as Web of Life, in which the emerging new branches are horizontally linked to each other due to the gene exchange.”

“Additionally, the fact that we have identified an understudied natural mechanism that makes it possible to maintain genetic diversity may be important for the development of a general strategy for the conservation of a wide variety of living organisms,” said Vladimir Lukhtanov.

A unique surgery by surgical oncologists and endoscopists at the Pirogov Clinic of SPbU

Posted on by Alina Perevizintsova

For the first time, surgical oncologists and endoscopists at the Pirogov Clinic of High Medical Technologies at St Petersburg University (SPbU) have performed surgery to remove a malignant tumour of the oesophagus and conduct a biopsy of the lymph node.

This approach enabled doctors to perform radical surgery of the tumour endoscopically, without needing to perform surgical intervention. The procedure was similar to the well-known and common fibrogastroduodenoscopy (FGDS) and was performed under general anaesthesia.

“The doctors also had to perform additional diagnostics in order to find whether cancer cells break away from where they first formed and to prevent future relapses. For that reason, we performed a sentinel lymph node biopsy,” said Rostislav Pavlov, an oncologist and Deputy Director for Medicine (Oncology) at the St Petersburg University’s Pirogov Clinic.

The doctors at the St Petersburg University’s Pirogov Clinic examined the sentinel lymph node. The sentinel lymph node is the organ that can evidence first that cancer cells from the tumour have begun to travel through the body. Medical technologies we have today enable us to find easily this lymph node.

During the endoscopic stage of the surgery, the doctors injected a fluorescent substance into the tumour. Through the lymphatic vessels, it entered the nearest lymph nodes creating a green glow. This highlighted signalling node had to be removed and checked for cancer cells.

Laparoscopy was used to take biopsy samples. It is a minimally invasive approach to modern surgery on internal organs through small openings, avoiding large incisions and noticeable sutures. This results in reducing to a minimum what has to be done during the surgery and lessens patient’s pain in the postoperative period. Additionally, this can reduce the recovery phase that usually takes long after abdominal surgery.

“The surgery was successful. We removed the tumour and performed a full diagnostics minimising the risk of recurrence. We discharged the patient on the third day after the intervention,” said Rostislav Pavlov.

St Petersburg University researchers describe for the first time all structures in the braincase of present-day crocodylians

Posted on by Alina Perevizintsova

Paleontologists from St Petersburg University have been the first in the world to describe all the structures in the braincase of present-day crocodylians and to assign a single individual name to each of its components. Additionally, during the work, the researchers managed to find new evolutionary traits in the animal’s braincase and figure out through what developmental mechanisms it acquired its current structure. The research findings are published in Journal of Anatomy.

The braincase of crocodylians has a distinctive structure. Unlike evolutionary relatives (birds and squamates), in crocodylians, all braincase bones are rigidly fixed together and form an akinetic structure. In the process of evolution, this made it possible for animals to develop powerful jaws and stronger bite forces, thanks to which crocodylians could gnaw through the hard shell of crayfish and turtles and hunt fish and land animals, including dinosaurs. As a result, they have managed to fill the niche of predators and survive to the present day.

At present, in comparison with other parts of the crocodylian skull, the structure of their braincase has been understudied.  This is because, until recently, scientists did not have the opportunity to investigate the complicated akinetic structure so that in the end the valuable collection specimen remained intact. At the same time, there is confusion in the already known data in terms and names. This complicates the work of many researchers studying the evolution of crocodylians.

Ivan Kuzmin, a doctoral student at St Petersburg University, decided to readdress this situation together with his colleagues from St Petersburg University, the Borissiak Paleontological Institute of the Russian Academy of Sciences, the Research and Practical Clinical Centre for Diagnostics and Telemedicine of the Moscow Department of Health, and the Smithsonian Institution (USA). To achieve this, they used computed tomography and a special 3D visualisation programme to create and study 3D models of 75 braincases of present-day crocodylians. This made it possible, without damaging the collection samples, to literally disassemble them by the bones and study every detail. Additionally, the researchers analysed academic papers describing the structure of the braincase from the beginning of the 19th century. The earliest work studied was an article dated 1821.

As a result, the scientists compiled a summary table in which they assigned a name to each structure in the crocodylian braincase. ‘Our paper is the first one in which this part of the skull is described in detail and a complete ordered list of all its details is provided. We have introduced some terms, for example, the names of bone processes in the auditory area. In some cases, because the structures were named incorrectly before us, in others, because we have discovered new elements,’ notes Ivan Kuzmin, the main author of the study, Master of Science from St Petersburg University.

While studying 3D models of braincases, the researchers found previously unknown evolutionary features. According to the scientists, recent data can help to better understand the structure of the crocodylian skeleton and resolve the contradictions around the genealogical tree of reptiles. The fact is that for almost 30 years, molecular biologists and palaeontologists have been unable to agree on the sequence in which crocodylian species should be located on the evolutionary tree.

For example, based on gene studies, molecular biologists assume that alligators are the most basal ones, while palaeontologists, studying fossil remains, come to the conclusion that the most primitive ones are gharials. ‘In the future, we plan to conduct a phylogenetic analysis and, based on its results, resolve this conflict,’ says Ivan Kuzmin. ‘The initial assumptions show that molecular biologists might be right.’

During the research, the authors also found out through what developmental mechanisms the crocodylian braincase acquired an akinetic structure. The researchers compared the evolution of the braincase in fossil relatives of crocodylians (crocodylomorphs) with the development of the braincase in the embryos of present-day animals. They have found out that in the crocodylian braincase area, in contrast to lizards and birds, complimentary structures appear at the initial stages of ontogenesis.

“Bones in an embryo are formed in two ways: endochondral and dermal. In the former case, cartilage first appears; then it ossifies. In the latter case, bones are formed as bones initially,” explains Ivan Kuzmin.

“Most of the braincase of all animals is formed by the endochondral process. However, it has turned out that everything happens differently in crocodylians.”

“In addition to structures that are formed through endochondral ossification, they have new elements that are formed embryonically in the form of dermal ossifications. That is, new bone blocks that are missing in other animals are attached to the cartilaginous structures, as in the LEGO construction set. With further development of the embryo, cartilages are transformed into bones, and everything merges into a single structure. The same embryonic processes likely happened during the early stages of crocodylomorph evolution,” Ivan says.

Scientists from St Petersburg University discover at the Dead Sea a mineral previously only known in meteorites

Posted on by Alina Perevizintsova

Scientists from St Petersburg University, in cooperation with researchers from Germany, USA and Italy, have discovered terrestrial allabogdanite, (Fe,Ni)2P. It is a mineral that, until now, has been found only in the extraterrestrial substance of meteorites. The discovery was made in the vicinity of the Dead Sea, in the historical region of the South Levant in the Middle East. The research was supported by the Russian Science Foundation and published in American Mineralogist.

The general view of the rock with allabogdanite-barringerite association. © Mineralogical Society of America.

Allabogdanite was first reported in the early 2000s from the Onello – a small iron meteorite recovered from the gold placer at the Bolshoi Dolguchan River in Eastern Yakutia. Chemically, the mineral belongs to phosphides – the compounds containing phosphorus in a negative oxidation state. It was named in honour of the crystallographer Alla Bogdanova. Since that, allabogdanite was identified in several iron meteorites.

The recent discovery at the Dead Sea is the first confirmation of the mineral on Earth. Allabogdanite was detected in the course of a systematic study of terrestrial phosphides from the Dead Sea region.

“Our research included the experiments on phase transitions of terrestrial allabogdanite at high pressure and high temperature at the DESY synchrotron light source in Germany,” said Sergey Britvin, the main author of the article, Professor in the Department of Crystallography at St Petersburg University.

“It has been found that terrestrial allabogdanite could be formed at pressures exceeding 25 gigapascals that corresponds to ca. 250 kbar. Such high pressures on Earth can be attained during catastrophic collisions with large meteorite impactors, or at the Earth’s mantle conditions, at a depth of more than 500 kilometres. However, the discovery of terrestrial allabogdanite is associated with the surface rocks of the Hatrurim Formation (also known as the Mottled Zone) in the Negev Desert in Israel. This is the area where natural cyclophosphates have been recently discovered, ” added Professor Sergey.

The Mottled Zone, or the Hatrurim Formation. (a) Areas of outcrops of the Mottled Zone (brown spots) in the South Levant. The largest territories are the Hatrurim basin (Israel) and the Daba-Siwaqa complex (Jordan). (b) The Hatrurim Basin in the Negev Desert, Israel, and the Halamish bed – the location of associations containing allabogdanite. © Mineralogical Society of America

Professor Sergey Britvin added that the discovery of allabogdanite in the historical region of the South Levant in the Middle East raises many questions related to the formation conditions of surficial rocks in this region.

Despite the fact that allabogdanite was discovered in meteorite almost 20 years ago, it was only in 2008 that it was shown that the mineral belongs to the indicators of high pressure. The results of current research evidence that terrestrial allabogdanite is a metastable high pressure phase. It was formed as a result of transformation from another mineral – barringerite, and was preserved under normal conditions as a result of quenching – an abrupt release of temperature and pressure.

East view of the Hatrurim Basin, Israel. © Mineralogical Society of America

‘This way excludes the possibility of allabogdanite formation as an intermediate phase from the elements under atmospheric pressure. This, in turn, raises a number of key questions regarding the origin of rocks in the Mottled Zone. Until now, no evidence for the large meteorite collisions or the rocks having Earth’s mantle origin has been found in the South Levant. However, such evidence might have been ‘erased’ from the Earth’s surface as a result of later processes of geological erosion. The discovery of allabogdanite justifies the necessity of further research in this direction,’ said Professor Sergey Britvin.

The research is supported by the grant from the Russian Science Foundation (project No 18-17-00079).

New study by St Petersburg University can help better understand the mechanism of neurodegenerative diseases

Posted on by Alina Perevizintsova

Researchers from St Petersburg University have created a new theory of diffusion NMR experiments to study amyloid fibrils. Fibrils are one of the key factors behind various forms of dementia, including Alzheimer’s disease. Based on this theory, the researchers showed that using a diffusion filter it is possible to separate the spectral signals of fibrils and other components of the amyloidogenic sample and obtain their individual spectra, which has been considered impossible for a long time. An article with their research findings was published in one of the most prestigious peer-reviewed chemistry journals Angewandte Chemie.

Application of the diffusion filter in a sample containing Sup35NM amyloid fibrils and proteolytic fragments. Data obtained in the Resource Centre ‘Magnetic Resonance Research Centre’ of the St Petersburg University Research Park

Alzheimer’s disease is the most common neurodegenerative disorder in which neurons gradually die off, leading to dementia. The exact mechanism and causes of this disorder have not yet been identified. However, it is known that amyloid plaques form in the brains of patients. Plaques consist of amyloid fibrils, which are special filamentous assemblies formed by amyloid proteins.

‘The number of patients with neurodegenerative disorders will continue to grow in the future. Thanks to the success of humanity in the treatment of cancer and cardiovascular diseases, more and more people are living into their 80s. At this age, the risk of developing neurodegenerative disorders, including Alzheimer’s disease, becomes very high. Unfortunately, no cures for these diseases have yet been found’ says Nikolai Skrynnikov, a co-author of the research, Ph.D., Professor, Head of the Biomolecular NMR Laboratory at St Petersburg University.

According to Nikolai Skrynnikov, scientists have deciphered the structural features of amyloid deposits relatively recently. However, a more detailed study of amyloidogenesis is faced with a number of difficulties. In particular, this is because in brain tissues amyloid fibrils coexist with other structural forms of amyloidogenic protein. These are monomers, proteolytic fragments, and various oligomers, some of which serve as ‘seeds’ for building new fibrils. Analysing such a mixture is a major challenge. For example, when studying amyloidogenic samples by means of nuclear magnetic resonance (NMR) spectroscopy, one obtains a multitude of signals that originate not only from fibrils that are of interest to scientists, but also from other protein species. Experts are therefore looking for ways to separate the spectral signals of fibrils and other concomitant structural forms.

The most obvious and straightforward method to achieve this goal is the so-called ‘diffusion filter’. This is a special NMR experiment that makes it possible to separate signals from heavy fibrils and other more mobile components of the sample. However, about ten years ago scientists from Cambridge University published two articles in which the feasibility of such a filter for samples of amyloid fibrils has been put into question. After that, the research in this field has come to a halt.

‘The motion of a fibril can be likened to random motion of a log on the surface of a lake, while the motion of a monomer is like that of a pine needle. The researchers from Cambridge argued that the rotation of the log might be faster — while turning, the linear speed at the ends of the log proves to be sufficiently high. For this reason, according to the authors, it becomes impossible to distinguish between a rapidly turning log and a nimble needle,’ explains Nikolai Skrynnikov. ‘But this is far from the truth’.

The scientists from St Petersburg University put the assertion of their Cambridge colleagues to a rigorous test, and not only disproved it, but also created a new theory of the diffusion NMR experiment. Moreover, the researchers described the essence of the effect by three methods: the analytical method, i.e. by deriving a compact formula that reflects the outcome of the experiment; the numerical method, i.e. by solving certain differential equation by means of a suitable numerical algorithm; and the Monte Carlo method, i.e. by using computer simulation to capture random fibril movements in solution. All three methods showed virtually identical results, thereby validating the new theory.

For the experimental verification of the new theory, the researchers have turned to yeast protein Sup35, which is known to have amyloidogenic properties. Scientists from St Petersburg University played a prominent role in the early studies of this protein. Professor Sergey Inge-Vechtomov, his students and followers were among the first investigators of Sup35. The research team from the Biomolecular NMR Laboratory at St Petersburg University together with the scientists from the University’s Department of Genetics and Biotechnology used Sup35 as a model system to demonstrate that the use of a diffusion filter in samples containing amyloid fibrils is indeed possible. The researchers successfully obtained a spectrum of fibrils, ‘cleared’ from other spectral signals.

Electron micrograph of Sup35NM fibrils. Data obtained in the Resource Centre ‘The Centre for Molecular and Cell Technologies’ of the St Petersburg University Research Park

‘Twenty to thirty years ago, scientists had little understanding of what happens in the human brain with the onset of dementia. Gradually, knowledge has been accumulated and new research methods have been developed. Thanks to these methods, we now know about the existence of amyloid deposits and have a fairly detailed idea of their structure,’ notes Nikolai Skrynnikov. ‘Our theory and its proof is a contribution to the body of fundamental knowledge that medicinal chemists rely on in their search for new drugs. In the future, our proposed diffusion filter for NMR experiments in amyloidogenic systems may help in this search.’

The university’s research team comprised of Boris Kharkov, Postdoc, Research Associate, the Biomolecular NMR Laboratory, Ivan Podkorytov, Deputy Head of the Biomolecular NMR Laboratory, Stanislav Bondarev, Research Associate, the Department of Genetics and Biotechnology, Mikhail Belousov, Junior Research Associate, the Department of Genetics and Biotechnology, Vladislav Salikov, a doctoral student, the Department of Nuclear Physics Research Methods at St Petersburg University, Galina Zhouravleva, Professor, the Department of Genetics and Biotechnology, and Nikolai Skrynnikov, Professor, Head of the Biomolecular NMR Laboratory.