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Diving into devonian seas: Ancient marine faunas unlock secrets of warming oceans

Credit: Syracuse University Members of Syracuse University’s College of Arts and Sciences are shining new light on an enduring mystery–one

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Members of Syracuse University’s College of Arts and Sciences are shining new light on an enduring mystery–one that is millions of years in the making.

A team of paleontologists led by Professor Cathryn Newton has increased scientists’ understanding of whether Devonian marine faunas, whose fossils are lodged in a unit of bedrock in Central New York known as the Hamilton Group, were stable for millions of years before succumbing to waves of extinctions.

Drawing on 15 years of quantitative analysis with fellow professor Jim Brower (who died in 2018), Newton has continued to probe the structure of these ancient fossil communities, among the most renowned on Earth.

The group’s findings, reported by the Geological Society of America (GSA), provide critical new evidence for the unusual, long-term stability of these Devonian period communities.

Such persistence, Newton says, is a longstanding scientific enigma. She and her colleagues tested the hypothesis that these ancient communities displayed coordinated stasis–a theory that attempts to explain the emergence and disappearance of species across geologic time.

Newton and Brower, along with their student Willis Newman G’93, found that Devonian marine communities vary more in species composition than the theory predicts. Newton points out that they sought not to disprove coordinated stasis but rather to gain a more sophisticated understanding of when it is applicable. “Discovering more about the dynamics of these apparently stable Devonian communities is critical,” she says. “Such knowledge has immediate significance for marine community changes in our rapidly warming seas.”

Since geologist James Hall Jr. first published a series of volumes on the region’s Devonian fossils and strata in the 1840s, the Hamilton Group has become a magnet for research scientists and amateur collectors alike. Today, Central New York is frequently used to test new ideas about large-scale changes in Earth’s organisms and environments.

During Middle Devonian time (approximately 380-390 million years ago), the faunal composition of the region changed little over 4-6 million years. “It’s a significant amount for marine invertebrate communities to remain stable, or ‘locked,’” explains Newton, a professor in the Department of Earth and Environmental Sciences.

She, Brower and student researchers spent years examining eight communities of animals that once dwelled in a warm, shallow sea on the northern rim of the Appalachian Basin (which, eons ago, lay south of the equator). When the organisms died, sediment from the seafloor began covering their shells and exoskeletons. Minerals from the sediment gradually seeped into their remains, causing them to fossilize. The process also preserved many of them in living position, conserving original shell materials at some sites.

These fossils currently populate exposed bedrock throughout Central New York, ranging from soft, dark, deep-water shale to hard, species-rich, shelf siltstone. “Communities near the top of the bedrock exhibit more taxonomic and ecological diversity than those at the bottom,” Newton says. “We can compare the community types and composition through time. They are remarkable sites.”

Coordinated stasis has been a source of contention since 1995, when it was introduced. At the center of the dispute are two model-based explanations: environmental tracking and ecological locking.

Environmental tracking suggests that faunas follow their environment. “Here, periods of relative stasis are flanked by coordinated extinctions or regional disappearances. When the environment changes, so do marine faunas,” says Newton, also Professor of Interdisciplinary Sciences and Dean Emerita of Arts and Sciences.

Ecological locking, in contrast, views marine faunas as tightly structured communities, resistant to large-scale taxonomic change. Traditionally, this model has been used to describe the stability of lower Hamilton faunas.

Newton and her colleagues analyzed more than 80 sample sites, each containing some 300 specimens. Special emphasis was placed on the Cardiff and Pecksport Members, two rock formations in the Finger Lakes region that are part of the ancient Marcellus subgroup, famed for its natural gas reserves.

“We found that lower Hamilton faunas, with two exceptions, do not have clear counterparts among upper ones. Therefore, our quantitative tests do not support the ecological locking model as an explanation for community stability in these faunas,” she continues.

Newton considers this project a final tribute to Newman, a professor of biology at the State University of New York at Cortland, who died in 2014, and Brower, who fell seriously ill while the manuscript was being finalized. “Jim knew that he likely would not live to see its publication,” says Newton, adding that Brower died as the paper was submitted to GSA.

She says this new work extends and, in some ways, completes the team’s earlier research by further analyzing community structures in the Marcellus subgroup. “It has the potential to change how scientists view long-term stability in ecological communities.”

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The group’s findings, reported by the Geological Society of America (GSA), provide critical new evidence for the unusual, long-term stability of these Devonian period communities.

Source: https://bioengineer.org/diving-into-devonian-seas-ancient-marine-faunas-unlock-secrets-of-warming-oceans/

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Reduced microbial stability linked to soil carbon loss in active layer under alpine permafrost degra

Credit: NIEER Chinese researchers have recently discovered links between reduction in microbial stability and soil carbon loss in the active

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Chinese researchers have recently discovered links between reduction in microbial stability and soil carbon loss in the active layer of degraded alpine permafrost on the Qinghai-Tibet Plateau (QTP).

The researchers, headed by Prof. CHEN Shengyun from the Northwest Institute of Eco-Environment and Resources (NIEER) of the Chinese Academy of Sciences (CAS), and XUE Kai from University of Chinese Academy of Sciences, conducted a combined in-depth analysis of soil microbial communities and their co-occurrence networks in the active permafrost layer along an extensive gradient of permafrost degradation.

The QTP encompasses the largest extent of high-altitude mountain permafrost in the world. This permafrost is different than high-latitude permafrost and stores massive soil carbon. An often ignored characteristic of permafrost is that the carbon pool in the active layer soil is more active and directly affected by climate change, compared to deeper layers.

Triggered by climate warming, permafrost degradation may decrease soil carbon stability and induce massive carbon loss, thus leading to positive carbon-climate feedback. However, microbial-mediated mechanisms for carbon loss from the active layer soil in degraded permafrost still remain unclear.

In this study, the researchers found that alpine permafrost degradation reduced the stability of active layer microbial communities as evidenced by increased sensitivity of microbial composition to environmental change, promoted destabilizing network properties and reduced resistance to node or edge attacking of the microbial network.

They discovered that soil organic carbon loss in severely degraded permafrost is associated with increased microbial dissimilarity, thereby potentially contributing to a positive carbon feedback in alpine permafrost on the QTP.

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The results were published in PNAS in an article entitled “Reduced microbial stability in the active layer is associated with carbon loss under alpine permafrost degradation”.

This research was financially supported by the National Natural Science Foundation of China, the Strategic Priority Research Program (A) of CAS and the Second Tibetan Plateau Scientific Expedition and Research Program.

Triggered by climate warming, permafrost degradation may decrease soil carbon stability and induce massive carbon loss, thus leading to positive carbon-climate feedback. However, microbial-mediated mechanisms for carbon loss from the active layer soil in degraded permafrost still remain unclear.

Source: https://bioengineer.org/reduced-microbial-stability-linked-to-soil-carbon-loss-in-active-layer-under-alpine-permafrost-degra/

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SNMMI Image of the Year: PET imaging measures cognitive impairment in COVID-19 patients

Credit: G Blazhenets et al., Department of Nuclear Medicine, Medical Center – University of Freiburg, Faculty of Medicine, University of

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Credit: G Blazhenets et al., Department of Nuclear Medicine, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg.

Reston, VA–The effects of COVID-19 on the brain can be accurately measured with positron emission tomography (PET), according to research presented at the Society of Nuclear Medicine and Molecular Imaging (SNMMI) 2021 Annual Meeting. In the study, newly diagnosed COVID-19 patients, who required inpatient treatment and underwent PET brain scans, were found to have deficits in neuronal function and accompanying cognitive impairment, and in some, this impairment continued six months after their diagnosis. The detailed depiction of areas of cognitive impairment, neurological symptoms and comparison of impairment over a six-month time frame has been selected as SNMMI’s 2021 Image of the Year.

Each year, SNMMI chooses an image that best exemplifies the most promising advances in the field of nuclear medicine and molecular imaging. The state-of-the-art technologies captured in these images demonstrate the capacity to improve patient care by detecting disease, aiding diagnosis, improving clinical confidence, and providing a means of selecting appropriate treatments. This year, the SNMMI Henry N. Wagner, Jr., Image of the Year was chosen from more than 1,280 abstracts submitted to the meeting and voted on by reviewers and the society leadership.

“As the SARS-CoV-2 pandemic proceeds, it has become increasingly clear that neurocognitive long-term consequences occur not only in severe COVID-19 cases, but in mild and moderate cases as well. Neurocognitive deficits like impaired memory, disturbed concentration and cognitive problems may persist well beyond the acute phase of the disease,” said Ganna Blazhenets, PhD, a post-doctoral researcher in Medical Imaging at the University Medical Center Freiburg, in Freiburg, Germany.

To study cognitive impairment associated with COVID-19, researchers carried out a prospective study on recently diagnosed COVID-19 patients who required inpatient treatment for non-neurological complaints. A cognitive assessment was performed, followed by imaging with 18F-FDG PET if at least two new neurological symptoms were present. By comparing COVID-19 patients to controls, the Freiburg group established a COVID-19-related covariance pattern of brain metabolism with most prominent decreases in cortical regions. Across patients, the expression of this pattern showed a very high correlation with the patients’ cognitive performance.

Follow-up PET imaging was performed six months after the initial COVID-19 diagnosis. Imaging results showed a significant improvement in the neurocognitive deficits in most patients, accompanied by an almost complete normalization of the brain metabolism.

“We can clearly state that a significant recovery of regional neuronal function and cognition occurs for most COVID-19 patients based on the results of this study. However, it is important to recognize the evidence of longer-lasting deficits in neuronal function and accompanying cognitive deficits is still measurable in some patients six months after manifestation of disease,” noted Blazhenets. “As a result, post-COVID-19 patients with persistent cognitive complaints should be presented to a neurologist and possibly allocated to cognitive rehabilitation programs.”

“18F-FDG PET is an established biomarker of neuronal function and neuronal injury,” stated SNMMI’s Scientific Program Committee chair, Umar Mahmood, MD, PhD. “As shown the Image of the Year, it can be applied to unravel neuronal correlates of the cognitive decline in patients after COVID-19. Since 18F-FDG PET is widely available, it may therefore aid in the diagnostic work-up and follow-up in patients with persistent cognitive impairment after COVID-19.”

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Abstract 41. “Altered regional cerebral function and its association with cognitive impairment in COVID 19: A prospective FDG PET study.” Ganna Blazhenets, Johannes Thurow, Lars Frings and Philipp Meyer, Department of Nuclear Medicine, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Nils Schroeter, Tobias Bormann, Cornelius Weiller, Andrea Dressing and Jonas Hosp; Department of Neurology and Clinical Neuroscience, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; and Dirk Wagner, Department of Internal Medicine, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.

All 2021 SNMMI Annual Meeting abstracts can be found online at https://jnm.snmjournals.org/content/62/supplement_1.

About the Society of Nuclear Medicine and Molecular Imaging

The Society of Nuclear Medicine and Molecular Imaging (SNMMI) is an international scientific and medical organization dedicated to advancing nuclear medicine and molecular imaging, vital elements of precision medicine that allow diagnosis and treatment to be tailored to individual patients in order to achieve the best possible outcomes.

SNMMI’s members set the standard for molecular imaging and nuclear medicine practice by creating guidelines, sharing information through journals and meetings and leading advocacy on key issues that affect molecular imaging and therapy research and practice. For more information, visit http://www.snmmi.org.

“As the SARS-CoV-2 pandemic proceeds, it has become increasingly clear that neurocognitive long-term consequences occur not only in severe COVID-19 cases, but in mild and moderate cases as well. Neurocognitive deficits like impaired memory, disturbed concentration and cognitive problems may persist well beyond the acute phase of the disease,” said Ganna Blazhenets, PhD, a post-doctoral researcher in Medical Imaging at the University Medical Center Freiburg, in Freiburg, Germany.

Source: https://bioengineer.org/snmmi-image-of-the-year-pet-imaging-measures-cognitive-impairment-in-covid-19-patients/

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Scientists demonstrate promising new approach for treating cystic fibrosis

Scientists led by UNC School of Medicine researchers Silvia Kreda, Ph.D., and Rudolph Juliano, Ph.D., created an improved oligonucleotide therapy

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Scientists led by UNC School of Medicine researchers Silvia Kreda, Ph.D., and Rudolph Juliano, Ph.D., created an improved oligonucleotide therapy strategy with the potential for treating other pulmonary diseases, such as COPD and asthma

CHAPEL HILL, NC – UNC School of Medicine scientists led a collaboration of researchers to demonstrate a potentially powerful new strategy for treating cystic fibrosis (CF) and potentially a wide range of other diseases. It involves small, nucleic acid molecules called oligonucleotides that can correct some of the gene defects that underlie CF but are not addressed by existing modulator therapies. The researchers used a new delivery method that overcomes traditional obstacles of getting oligonucleotides into lung cells.

As the scientists reported in the journal Nucleic Acids Research, they demonstrated the striking effectiveness of their approach in cells derived from a CF patient and in mice.

“With our oligonucleotide delivery platform, we were able to restore the activity of the protein that does not work normally in CF, and we saw a prolonged effect with just one modest dose, so we’re really excited about the potential of this strategy,” said study senior author Silvia Kreda, PhD, an associate professor in the UNC Department of Medicine and the UNC Department Biochemistry & Biophysics, and a member of the Marsico Lung Institute at the UNC School of Medicine.

Kreda and her lab collaborated on the study with a team headed by Rudolph Juliano, PhD, Boshamer Distinguished Professor Emeritus in the UNC Department of Pharmacology, and co-founder and Chief Scientific Officer of the biotech startup Initos Pharmaceuticals.

About 30,000 people in the United States have CF, an inherited disorder in which gene mutations cause the functional absence of an important protein called CFTR. Absent CFTR, the mucus lining the lungs and upper airways becomes dehydrated and highly susceptible to bacterial infections, which occur frequently and lead to progressive lung damage.

Treatments for CF now include CFTR modulator drugs, which effectively restore partial CFTR function in many cases. However, CFTR modulators cannot help roughly ten percent of CF patients, often because the underlying gene defect is of the type known as a splicing defect.

CF and splicing defects

Splicing is a process that occurs when genes are copied out – or transcribed – into temporary strands of RNA. A complex of enzymes and other molecules then chops up the RNA strand and re-assembles them, typically after deleting certain unwanted segments. Splicing occurs for most human genes, and cells can re-assemble the RNA segments in different ways so different versions of a protein can be made from a single gene. However, defects in splicing can lead to many diseases – including CF when CFTR’s gene transcript is mis-spliced.

In principle, properly designed oligonucleotides can correct some kinds of splicing defects. In recent years the U.S. Food and Drug Administration has approved two “splice switching oligonucleotide” therapies for inherited muscular diseases.

In practice, though, getting oligonucleotides into cells, and to the locations within cells where they can correct RNA splicing defects, has been extremely challenging for some organs.

“It has been especially difficult to get significant concentrations of oligonucleotides into the lungs to target pulmonary diseases,” Kreda said.

Therapeutic oligonucleotides, when injected into the blood, have to run a long gauntlet of biological systems that are designed to keep the body safe from viruses and other unwanted molecules. Even when oligonucleotides get into cells, the most usually are trapped within vesicles called endosomes, and are sent back outside the cell or degraded by enzymes before they can ever do their work.

A new delivery strategy

The strategy developed by Kreda, Juliano, and their colleagues overcomes these obstacles by adding two new features to splice switching oligonucleotides: Firstly, the oligonucleotides are connected to short, protein-like molecules called peptides that are designed to help them to distribute in the body and get into cells. Secondly, there is a separate treatment with small molecules called OECs, developed by Juliano and Initos, which help the therapeutic oligonucleotides escape their entrapment within endosomes.

The researchers demonstrated this combined approach in cultured airway cells from a human CF patient with a common splicing-defect mutation.

“Adding it just once to these cells, at a relatively low concentration, essentially corrected CFTR to a normal level of functioning, with no evidence of toxicity to the cells,” Kreda said.

The results were much better with than without OECs, and improved with OEC dose.

There is no mouse model for splicing-defect CF, but the researchers successfully tested their general approach using a different oligonucleotide in a mouse model of a splicing defect affecting a reporter gene. In these experiments, the researchers observed that the correction of the splicing defect in the mouse lungs lasted for at least three weeks after a single treatment – hinting that patients taking such therapies might need only sporadic dosing.

The researchers now plan further preclinical studies of their potential CF treatment in preparation for possible clinical trials.

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Yan Dang, Catharina van Heusden, Veronica Nickerson, Felicity Chung, Yang Wang, Nancy Quinney, Martina Gentzsch, and Scott Randell were other contributors to this study from the Marsico Lung Institute; Ryszard Kole a co-author from the UNC Department of Pharmacology.

The Cystic Fibrosis Foundation and the National Institutes of Health supported this work.

Scientists Demonstrate Promising New Approach for Treating Cystic Fibrosis

Source: https://bioengineer.org/scientists-demonstrate-promising-new-approach-for-treating-cystic-fibrosis/

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