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Tag: Uppsala University

  • Ancient sea monster discovery reveals oldest mega-predator

    Ancient sea monster discovery reveals oldest mega-predator

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    Newswise — The fossils were found 40 years ago in north-eastern France. An international team of palaeontologists from the Naturkunde-Museum Bielefeld in Germany, the Institute of Paleobiology of the Polish Academy of Sciences in Warsaw, Poland, the Natural History Museum in Luxembourg and The Museum of Evolution at Uppsala University in Sweden have now analysed them and identified them as a new pliosaur genus: Lorrainosaurus.

    Pliosaurs were a type of plesiosaur with short necks and massive skulls. They appeared over 200 million years ago, but remained minor components of marine ecosystems until suddenly developing into enormous apex predators. The new study shows that this adaptive shift followed feeding niche differentiation and the global decline of other predatory marine reptiles over 170 million years ago.

    Lorrainosaurus is the oldest large-bodied pliosaur represented by an associated skeleton. It had jaws over 1.3 m long with large conical teeth and a bulky ‘torpedo-shaped’ body propelled by four flipper-like limbs.

    “Lorrainosaurus was one of the first truly huge pliosaurs. It gave rise to a dynasty of marine reptile mega-predators that ruled the oceans for around 80 million years,” explains Sven Sachs, a researcher at the Naturkunde-Museum Bielefeld, who led the study.

    This giant reptile probably reached over 6 m from snout to tail, and lived during the early Middle Jurassic period. Intriguingly, very little is known about plesiosaurs from that time.

    “Our identification of Lorrainosaurus as one of the earliest mega-predatory pliosaurs demonstrates that these creatures emerged immediately after a landmark restructuring of marine predator ecosystems across the Early-to-Middle Jurassic boundary, some 175 to 171 million years ago. This event profoundly affected many marine reptile groups and brought mega-predatory pliosaurids to dominance over ‘fish-like’ ichthyosaurs, ancient marine crocodile relatives, and other large-bodied predatory plesiosaurs”, adds Daniel Madzia from the Institute of Paleobiology of the Polish Academy of Sciences, who co-led the study.

    Pliosaurs were some of the most successful marine predators of their time.

    “Famous examples, such as Pliosaurus and Kronosaurus – some of the world’s largest pliosaurs – were absolutely enormous with body-lengths exceeding 10 m. They were ecological equivalents of today’s Killer whales and would have eaten a range of prey including squid-like cephalopods, large fish and other marine reptiles. These have all been found as preserved gut contents”, said senior co-author Benjamin Kear, Curator of Vertebrate Palaeontology and Researcher in Palaeontology at The Museum of Evolution, Uppsala University.

    The recovered bones and teeth of Lorrainosaurus represent remnants of what was once a complete skeleton that decomposed and was dispersed across the ancient sea floor by currents and scavengers.

    “The remains were unearthed in 1983 from a road cutting near Metz in Lorraine, north-eastern France. Palaeontology enthusiasts from the Association minéralogique et paléontologique d’Hayange et des environs recognised the significance of their discovery and donated the fossils to the Natural History Museum in Luxembourg”, said co-author Ben Thuy, Curator at the Natural History Museum in Luxembourg.

    Other than a brief report published in 1994, the fossils of Lorrainosaurus remained obscure until this new study re-evaluated the finds. Lorrainosaurus indicates that the reign of gigantic mega-predatory pliosaurs must have commenced earlier than previously thought, and was locally responsive to major ecological changes affecting marine environments covering what is now western Europe during the early Middle Jurassic.

    “Lorrainosaurus is thus a critical addition to our knowledge of ancient marine reptiles from a time in the Age of Dinosaurs that has as yet been incompletely understood”, says Benjamin Kear.

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  • Gut bacteria linked to heart artery plaque

    Gut bacteria linked to heart artery plaque

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    Newswise — In a major Swedish study, researchers have discovered a link between the levels of certain bacteria living in the gut and coronary atherosclerotic plaques. Such atherosclerotic plaques, which are formed by the build-up of fatty and cholesterol deposits, constitute a major cause of heart attacks. The study was led by researchers at Uppsala and Lund University and the findings have now been published in the scientific journal Circulation.

    The new study was based on analyses of gut bacteria and cardiac imaging among 8,973 participants aged 50 to 65 from Uppsala and Malmö without previously known heart disease. They were all participants in the Swedish CArdioPulmonary bioImage Study (SCAPIS).

    “We found that oral bacteria, especially species from the Streptococcus genus, are associated with increased occurrence of atherosclerotic plaques in the small arteries of the heart when present in the gut flora. Species from the Streptococcus genus are common causes of pneumonia and infections of the throat, skin and heart valves. We now need to understand whether these bacteria are contributing to atherosclerosis development,” says Tove Fall, Professor in Molecular Epidemiology at the Department of Medical Sciences and the SciLifeLab, Uppsala University, who coordinated the study together with researchers from Lund University.

    Advancements in technology have enabled large-scale deep characterisation of bacterial communities in biological samples by sequencing the DNA content and comparing it to known bacteria sequences. Additionally, improvements in imaging techniques have enabled the detection and measurement of early changes in the small vessels of the heart. The SCAPIS study represents one of the largest collections in the world of both these kinds of data. In this study, scientists investigated the links between the gut microbiota and the build-up of fatty deposits in the arteries of the heart.

    “The large number of samples with high-quality data from cardiac imaging and gut flora allowed us to identify novel associations. Among our most significant findings, Streptococcus anginosus and S. oralis subsp. oralis were the two strongest ones,” says Sergi Sayols-Baixeras, lead author from Uppsala University.

    The research team also found that some of the species linked to the build-up of fatty deposits in heart arteries were linked to the levels of the same species in the mouth. This was measured using faecal and saliva samples collected from the Malmö Offspring Study and Malmö Offspring Dental Study. Furthermore, these bacteria were associated with inflammation markers in the blood, even after accounting for differences in diet and medication between the participants who carried the bacteria and those who did not.

    “We have just started to understand how the human host and the bacterial community in the different compartments of the body affect each other. Our study shows worse cardiovascular health in carriers of streptococci in their gut. We now need to investigate if these bacteria are important players in atherosclerosis development,” notes Marju Orho-Melander, Professor in Genetic Epidemiology at Lund University and one of the senior authors of the study.

    Publication: Sergi Sayols-Baixeras et al.; Streptococcus species abundance in the gut is linked to subclinical coronary atherosclerosis in 8973 participants from the SCAPIS cohort. Circulation. 2023. DOI: 10.1161/CIRCULATIONAHA.123.063914 [Online ahead-of-print], the link will be: https://doi.org/10.1161/CIRCULATIONAHA.123.063914

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  • Antarctic bacteria and computer calculations used to create new enzyme

    Antarctic bacteria and computer calculations used to create new enzyme

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    Newswise — For the first time, researchers have succeeded in predicting how to change the optimum temperature of an enzyme using large computer calculations. A cold-adapted enzyme from an Antarctic bacterium was used as a basis. The study is to be published in the journal Science Advances and is a collaboration between researchers at Uppsala University and the University of Tromsø.

    The type of cold-adapted enzymes used by the researchers for their study can be found in bacteria and fish that live in icy water, for example. Evolution has shaped them to be able to function even at very low temperatures at which other enzymes are normally stone dead. These enzymes also always have a lower optimum temperature and melting point than enzymes from warm-blooded animals and organisms that live at higher temperatures.

    The researchers wondered whether computer simulations of the catalysed chemical reaction could predict a small number of mutations in the Antarctic enzyme that could result in an increase in its optimum temperature. The results of the calculation showed that this would be possible if 16 mutations were inserted from the corresponding pig enzyme into the bacterial variant.

    The researchers then produced this hybrid enzyme and measured its catalytic activity as a function of temperature, and it was indeed found that the new variant had a 6 °C higher optimum than the original variant and was faster than both the Antarctic and pig enzymes at 50 °C . They also solved the three-dimensional structure of the hybrid enzyme by X-ray crystallography and showed that the necessary structural changes predicted by the computer calculations had indeed taken place.

    Computer-based enzyme design has become a major and hotly pursued research area in recent years. The goal is to create enzymes with new properties and to do so with the help of computer calculations instead of labour-intensive experiments.

    “For example, this may involve creating new enzymes that catalyse chemical reactions not found in nature or changing their properties so that they can better cope with heat, cold, high pressure, increased salinity and so on. This area is therefore the subject of great biotechnological interest,” notes Johan Åqvist, Professor of Theoretical Chemistry at Uppsala University.

    https://www.science.org/doi/10.1126/sciadv.adi0963

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  • X-rays show how nature’s strongest bond breaks

    X-rays show how nature’s strongest bond breaks

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    Newswise — The use of short flashes of X-ray light brings scientists one big step closer toward developing better catalysts to transform the greenhouse gas methane into a less harmful chemical. The result, published in the journal Science, reveals for the first time how carbon-hydrogen bonds of alkanes break and how the catalyst works in this reaction.

    Methane, one of the most potent greenhouse gases, is being released into the atmosphere at an increasing rate by livestock farming as well as the continuing unfreezing of permafrost. Transforming methane and longer-chain alkanes into less harmful and in fact useful chemicals would remove the associated threats, and in turn make a huge feedstock for the chemical industry available. However, transforming methane necessitates as a first step the breaking of a C-H bond, one of the strongest chemical linkages in nature.

    Forty years ago, molecular metal catalysts were discovered that can easily split C-H bonds. The only thing found to be necessary was a short flash of visible light to “switch on” the catalyst and, as by magic, the strong C-H bonds of alkanes passing nearby are easily broken almost without using any energy. Despite the importance of this so-called C-H activation reaction, it remained unknown over the decades how that catalyst performs this function.

    The research was led by scientists from Uppsala University in collaboration with the Paul Scherrer Institute in Switzerland, Stockholm University, Hamburg University and the European XFEL in Germany. For the first time, the scientists were able to directly watch the catalyst at work and reveal how it breaks those C-H bonds.

    In two experiments conducted at the Paul Scherrer Institute in Switzerland, the researchers were able to follow the delicate exchange of electrons between a rhodium catalyst and an octane C-H group as it gets broken. Using two of the most powerful sources of X-ray flashes in the world, the X-ray laser SwissFEL and the X-ray synchrotron Swiss Light Source, the reaction could be followed all the way from the beginning to the end. The measurements revealed the initial light-induced activation of the catalyst within 400 femtoseconds (0.0000000000004 seconds) to the final C-H bond breaking after 14 nanoseconds (0.000000014 seconds).

    “The time-resolved X-ray absorption experiments we performed are only possible at large-scale facilities like SwissFEL and the Swiss Light Source, which provide extremely bright and short X-ray pulses. The catalyst is immersed in a dense octane solution, but by taking the perspective of the metal, we could specifically pick the one C-H bond out of hundreds of thousands which is made to break,” explains Raphael Jay, Researcher at Uppsala University and lead experimentalist of the study.

    To interpret the complex experimental data, theoreticians from Uppsala University and Stockholm University teamed up and performed advanced quantum-chemical calculations.

    “Our calculations allow us to clearly identify how electronic charge flows between the metal catalyst and the C-H group in just the right proportion. We can see how charge flowing from the metal onto the C-H bond glues the two chemical groups together. Charge flowing in the opposite direction instead acts as a scissor that eventually breaks the C and the H atom apart,” explains Ambar Banerjee, Postdoctoral researcher at Uppsala University and lead theoretician of the study.

    The study solves a forty-year-old mystery about how an activated catalyst can actually break strong C-H bonds by carefully exchanging fractions of electrons and without the need for huge temperatures or pressures. With their new tool to hand, the researchers next want to learn how to direct the flow of electrons to help develop better catalysts for the chemical industry in order to make something useful out of methane and other alkanes.

    Facts

    The study builds on the pioneering work of grandfather, father and son Manne, Kai, and Per Siegbahn.

    Manne Siegbahn (Uppsala University), who received the Nobel Prize in Physics in 1924, pioneered how different elements can be distinguished by X-rays.

    Kai Siegbahn (Uppsala University), who received the Nobel Prize in Physics in 1981, pioneered how different chemical environments of the same element can be distinguished by X-rays.

    Per Siegbahn (Stockholm University) theoretically predicted the concerted exchange of electronic charge required for breaking a C-H bond.

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  • 240 Mammal Genomes Reveal Human Disease Risks

    240 Mammal Genomes Reveal Human Disease Risks

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    Newswise — Why is it that certain mammals have an exceptional sense of smell, some hibernate, and yet others, including humans, are predisposed to disease? A major international research project, jointly led by Uppsala University, Sweden and the Broad Institute, USA, has surveyed and analysed the genomes of 240 different mammals. The results, now published in 11 articles in the journal Science, show how the genomes of humans and other mammals have developed over the course of evolution. The research shows which regions have important functions in mammals, which genetic changes have led to specific characteristics in different species and which mutations can cause disease.

    “In combination, the 11 articles we are now publishing in Science provide an enormous amount of information about the function and development of mammalian genomes,” says Kerstin Lindblad-Toh, Professor of Comparative Genomics at Uppsala University and one of two leaders of the international consortium of researchers. “Moreover, we have produced data that can be used for studies of evolution and medical research for many years to come.”

    In a large international project jointly led by Uppsala University and the Broad Institute, more than 30 research teams have together surveyed and analysed the genomes of 240 mammal species. The results, now published in 11 articles in the journal Science, show how the genomes of humans and other mammals have developed in the course of evolution.

    The human genome contains approximately 20,000 genes that constitute the code for manufacturing all the proteins in the body. The genome also contains instructions that direct where, when and how much of the proteins are produced. These parts of the genome, which are called regulatory elements, are much more difficult to identify than the parts that give rise to proteins. However, studying a great many mammals’ genomes makes it possible to figure out which parts of the genome are functionally important.

    The hypothesis shared by the researchers behind the publications in Science has been that if a position in the genome has been preserved throughout 100 million years of evolution, it likely serves a function in all mammals. For the first time, they have been able to test this hypothesis on a large scale. By making a detailed survey and systematic comparison of the genomes of 240 mammals, the researchers have identified regions of the human genome with previously uncharacterised function. These regions are likely regulatory elements and are significant for the correct functioning of the genome. Mutations in these can play an important role in the origin of diseases or in the distinctive features of mammal species.

    The researchers identified more than three million important regulatory elements in the human genome, about half of which were previously unknown. They were also able to ascertain that at least 10 per cent of the genome is functional, ten times as much as the approximately one per cent that codes for proteins.

    The 240 different mammals in the study vary widely in their characteristics, such as the acuteness of their sense of smell or the size of their brain. The researchers were able to find regions in the genomes that lead to some species having a superior sense of smell or to certain species hibernating.

    “It’s exciting to now have a picture of which mutations have steered the development of specific traits in these widely divergent mammals,” says Matthew Christmas, researcher and co-first author of one of the articles focusing on the function of the genome and how it affects distinctive features in different species.

    One of the studies shows that mammals had begun to change and diverge ven before the Earth was hit by the asteroid that killed the dinosaurs, approximately 65 million years ago.

    “Our results can also provide important information about whether mammals are at risk of extinction, depending on how much variation they have in their genome. This is information that can lay the foundation for understanding how to manage a species to help it survive,” says Professor Lindblad-Toh.

    The new knowledge also helps researchers understand how diseases arise, by linking the positions in the genome conserved by evolution to known conditions. This can be done for all species and will also be usable with reference to human diseases.

    “Our analyses of 240 mammals give us a better insight into the regulatory signals in the genome. We calibrated our results on positions that are known to contribute to disease, and then could use these to suggest additional positions which could be prioritised for neurological traits, such as schizophrenia or immune conditions including asthma or eczema,” says Jennifer Meadows, researcher and co-first author of the second article, which focuses on how the project’s data can contribute to knowledge about diseases.

    The genome of healthy and sick people is compared to understand which mutations lead to disease. This produces a picture of the region in the genome that may be important, but does not yield an exact knowledge of which mutation causes the disease.

    “A large proportion of the mutations that lead to common diseases, like diabetes or obsessive-compulsive disorder, lie outside the genes and have to do with gene regulation. Our studies make it easier to identify the mutations that lead to disease and to understand what goes wrong,” says Lindblad-Toh.

    The researchers also studied the cancer medulloblastoma, which is the most common type of malignant brain tumour in children. Although modern treatments have improved the prognosis, not all children can be cured. Moreover, those that survive often experience lifelong side-effects from the aggressive treatment.

    “In patients with medulloblastoma, we found many new mutations in evolutionarily conserved positions. We hope that analysis of these mutations will lay the ground for new diagnostics and therapies,” says Karin Forsberg-Nilsson, Professor of Stem Cell Research at Uppsala University, who led the cancer part of the study.

    This work was supported in part by the National Institutes of Health (US), the Swedish Research Council (SWE), the Knut and Alice Wallenberg Foundation (SWE), and the National Science Foundation (US).

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  • Widespread metabolic dysregulation in different organs in type 2 diabetes

    Widespread metabolic dysregulation in different organs in type 2 diabetes

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    Newswise — The most typical alterations in people with type 2 diabetes are insufficient secretion of insulin and reduced sensitivity to insulin in different organs. To examine what happens in these organs when type 2 diabetes develops, the researchers in the current study have looked at proteins both in the cell islets in the pancreas where insulin is produced, and in the main tissues that insulin acts on, namely the liver, skeletal muscle, fat and blood.

    The researchers compared proteins in samples from people with type 2 diabetes, prediabetes, i.e. a stage before fully developed type 2 diabetes, and without any diabetes. The results showed far more disturbances in metabolic pathways than previously known. There was also a correlation between the alterations and the different stages of the disease.

    “We detected many protein levels that were either higher or lower than normal in tissues from people at different stages of disease. People with prediabetes displayed major alterations that are associated with inflammation, coagulation and the immune system in the pancreatic islets. In fully developed type 2 diabetes there were more widespread abnormalities, for example in lipid and glucose metabolism and in energy production in the liver, muscle and fat,” says Professor Claes Wadelius, who coordinated the study.

    The study builds on tissue samples collected from donors at different stages of disease and healthy individuals. The samples have been collected in the strategic initiative EXODIAB, which is led in Uppsala by Professor Olle Korsgren.

    Using novel techniques, the researchers could quantify thousands of proteins from each organ and therefore obtain a view of the metabolism that has not been possible before.

    “The techniques for measuring proteins have evolved rapidly in recent years and our colleagues at Copenhagen University who participated in the study are world leaders in the field,” says Dr Klev Diamanti, who performed the analyses in Uppsala together with Associate Professor Marco Cavalli and Professor Jan Eriksson.

    In summary, the findings show a highly disturbed metabolism in different pathways in examined organs and at different stages of disease. The data points to new potentially causal mechanisms of the disease, which can be further investigated in the search for new ways of preventing or treating type 2 diabetes.

    “Our results may also support the development of simple tests that can identify people at high risk of diabetes and its complications, and also guide which type of intervention is best for the individual,” says clinical diabetologist Jan Eriksson.

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  • Oldest Teeth Ever Found In China Fish Fossil Catch

    Oldest Teeth Ever Found In China Fish Fossil Catch

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    NEW YORK (AP) — A big catch of fish fossils in southern China includes the oldest teeth ever found — and may help scientists learn how our aquatic ancestors got their bite.

    The finds offer new clues about a key period of evolution that’s been hard to flesh out because until now scientists haven’t found many fossils from that era. In a series of four studies, published Wednesday in the journal Nature, researchers detail some of their finds, from ancient teeth to never-before-seen species.

    The fossils date back to the Silurian period, an important era for life on earth from 443 million years ago to 419 million years ago. Scientists believe our backboned ancestors, who were still swimming around on a watery planet, may have started evolving teeth and jaws around this time.

    This let the fish hunt for prey instead of “grubbing around” as bottom feeders, filtering out food from the muck. It also sparked a series of other changes in their anatomy, including different kinds of fins, said Philip Donoghue, a University of Bristol paleontologist and an author on one of the studies.

    “It’s just at this interface between the Old World and the New World,” Donoghue said.

    But in the past, scientists haven’t found many fossils to show this shift, said Matt Friedman, a University of Michigan paleontologist who was not involved in the research. They’ve been relying on fragments from the time — a chunk of spine here, a bit of scale there.

    The fossils from China are expected to fill in some of those gaps as researchers around the world pore over them.

    A field team discovered the fossil trove in 2019, Min Zhu, a paleontologist at the Chinese Academy of Sciences who led the research, said in an email. On a rainy day, after a frustrating trip that hadn’t revealed any fossils, researchers explored a pile of rocks near a roadside cliff. When they split one rock open, they found fossilized fish heads looking back at them.

    After hauling more rocks back to the lab for examination, the research team wound up with a huge range of fossils that were in great condition for their age.

    The most common species in the bunch is a little boomerang-shaped fish that likely used its jaws to scoop up worms, said Per Erik Ahlberg of Sweden’s Uppsala University, an author on one of the studies.

    Another fossil shows a sharklike creature with bony armor on its front — an unusual combination. A well-preserved jawless fish offers clues to how ancient fins evolved into arms and legs. While fossil heads for these fish are commonly found, this fossil included the whole body, Donoghue said.

    And then there are the teeth. The researchers found bones called tooth whorls with multiple teeth growing on them. The fossils are 14 million years older than any other teeth found from any species — and provide the earliest solid evidence of jaws to date, Zhu said.

    Alice Clement, an evolutionary biologist at Australia’s Flinders University who was not involved with the research, said the fossil find is “remarkable” and could rewrite our understanding of this period.

    The wide range of fossils suggests there were plenty of toothy creatures swimming around at this time, Clement said in an email, even though it’s the next evolutionary era that is considered the “Age of Fishes.”

    The Associated Press Health and Science Department receives support from the Howard Hughes Medical Institute’s Department of Science Education. The AP is solely responsible for all content.

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