Monday, December 30, 2019

Life Could Have Emerged from Lakes with High Phosphorus



Life as we know it requires phosphorus. It’s one of the six main chemical elements of life, it forms the backbone of DNA and RNA molecules, acts as the main currency for energy in all cells and anchors the lipids that separate cells from their surrounding environment.

But how did a lifeless environment on the early Earth supply this key ingredient?

“For 50 years, what’s called ‘the phosphate problem,’ has plagued studies on the origin of life,” said first author Jonathan Toner, a University of Washington research assistant professor of Earth and space sciences.

The problem is that chemical reactions that make the building blocks of living things need a lot of phosphorus, but phosphorus is scarce. A new UW study, published Dec. 30 in the Proceedings of the National Academy of Sciences, finds an answer to this problem in certain types of lakes.


This 2007 photo shows Lake Magadi in Kenya, a carbonate-rich lake whose bed is made of volcanic rock. The lake’s salty water is rich in microbes and it attracts other life, including these flamingoes and zebras.

Credit: Stig Nygaard/Flickr

The study focuses on carbonate-rich lakes, which form in dry environments within depressions that funnel water draining from the surrounding landscape. Because of high evaporation rates, the lake waters concentrate into salty and alkaline, or high-pH, solutions. Such lakes, also known as alkaline or soda lakes, are found on all seven continents.

The researchers first looked at phosphorus measurements in existing carbonate-rich lakes, including Mono Lake in California, Lake Magadi in Kenya and Lonar Lake in India.

While the exact concentration depends on where the samples were taken and during what season, the researchers found that carbonate-rich lakes have up to 50,000 times phosphorus levels found in seawater, rivers and other types of lakes. Such high concentrations point to the existence of some common, natural mechanism that accumulates phosphorus in these lakes.

Today these carbonate-rich lakes are biologically rich and support life ranging from microbes to Lake Magadi’s famous flocks of flamingoes. These living things affect the lake chemistry. So researchers did lab experiments with bottles of carbonate-rich water at different chemical compositions to understand how the lakes accumulate phosphorus, and how high phosphorus concentrations could get in a lifeless environment.

Eastern California’s Mono Lake has no outflow, allowing salts to build up over time. The high salts in this carbonate-rich lake can grow into pillars.

Credit: Matthew Dillon/Flickr

The reason these waters have high phosphorus is their carbonate content. In most lakes, calcium, which is much more abundant on Earth, binds to phosphorus to make solid calcium phosphate minerals, which life can’t access. But in carbonate-rich waters, the carbonate outcompetes phosphate to bind with calcium, leaving some of the phosphate unattached. Lab tests that combined ingredients at different concentrations show that calcium binds to carbonate and leaves the phosphate freely available in the water.

“It’s a straightforward idea, which is its appeal,” Toner said. “It solves the phosphate problem in an elegant and plausible way.”

Phosphate levels could climb even higher, to a million times levels in seawater, when lake waters evaporate during dry seasons, along shorelines, or in pools separated from the main body of the lake.

“The extremely high phosphate levels in these lakes and ponds would have driven reactions that put phosphorus into the molecular building blocks of RNA, proteins, and fats, all of which were needed to get life going,” said co-author David Catling, a UW professor of Earth & space sciences.

Colored dots show the level of phosphorus measured in different carbonate-rich lakes around the world. Existing carbonate-rich lakes can contain up to 50,000 times the levels of phosphate found in seawater, with the highest levels measured in British Columbia’s Goodenough and Last Chance lake system (yellow dots).


Credit: Toner et al/PNAS

The carbon dioxide-rich air on the early Earth, some four billion years ago, would have been ideal for creating such lakes and allowing them to reach maximum levels of phosphorus. Carbonate-rich lakes tend to form in atmospheres with high carbon dioxide. Plus, carbon dioxide dissolves in water to create acid conditions that efficiently release phosphorus from rocks.

“The early Earth was a volcanically active place, so you would have had lots of fresh volcanic rock reacting with carbon dioxide and supplying carbonate and phosphorus to lakes,” Toner said. “The early Earth could have hosted many carbonate-rich lakes, which would have had high enough phosphorus concentrations to get life started.”

Another recent study by the two authors showed that these types of lakes can also provide abundant cyanide to support the formation of amino acids and nucleotides, the building blocks of proteins, DNA and RNA. Before then researchers had struggled to find a natural environment with enough cyanide to support an origin of life. Cyanide is poisonous to humans, but not to primitive microbes, and is critical for the kind of chemistry that readily makes the building blocks of life.

The research was funded by the Simons Foundation’s Collaboration on the Origins of Life.

Contacts and sources:
James Urton, Hannah Hickey
University of Washington







Study: Children Who Drank Whole Milk Had Lower Risk of Being Overweight or Obese

A review analyzing almost 21,000 children suggests children who drank whole milk were less likely to be overweight or obese

A systematic review and meta-analysis led by St. Michael's Hospital of Unity Health Toronto found children who drank whole milk had 40 per cent lower odds of being overweight or obese compared with children who consumed reduced-fat milk.

File:Whole milk aisle (17132962560).jpg
Credit: 

The research, published in The American Journal of Clinical Nutrition, analyzed 28 studies from seven countries that explored the relationship between children drinking cow's milk and the risk of being overweight or obese. None of the studies - which involved a total almost 21,000 children between the ages of one and 18 years old - showed that kids who drank reduced-fat milk had a lower risk of being overweight or obese. Eighteen of the 28 studies suggested children who drank whole milk were less likely to be overweight or obese.

The findings challenge Canadian and international guidelines that recommend children consume reduced-fat cow milk instead of whole milk starting at age two to reduce the risk of obesity.

"The majority of children in Canada and the United States consume cow's milk on a daily basis and it is a major contributor of dietary fat for many children," said Dr. Jonathon Maguire, lead author of the review and a pediatrician at St. Michael's Hospital.

Dr. Jonathon Maguire
 Credit:  Unity Health Toronto

"In our review, children following the current recommendation of switching to reduced-fat milk at age two were not leaner than those consuming whole milk."

Dr. Maguire, who is also a scientist at the MAP Centre for Urban Health Solutions, next hopes to establish the cause and effect of whole milk and lower risk of obesity in a randomized controlled trial.

"All of the studies we examined were observational studies, meaning that we cannot be sure if whole milk caused the lower risk of overweight or obesity. Whole milk may have been related to other factors which lowered the risk of overweight or obesity," Dr. Maguire said.

"A randomized controlled trial would help to establish cause and effect but none were found in the literature."


Contacts and sources:
Jennifer Stranges
St. Michael's Hospital

Citation: Whole milk compared with reduced-fat milk and childhood overweight: a systematic review and meta-analysis Shelley M Vanderhout, Mary Aglipay, Nazi Torabi, Peter Jüni, Bruno R da Costa, Catherine S Birken, Deborah L O'Connor, Kevin E Thorpe, Jonathon L Maguire The American Journal of Clinical Nutrition, nqz276, https://doi.org/10.1093/ajcn/nqz276 https://academic.oup.com/ajcn/advance-article-abstract/doi/10.1093/ajcn/nqz276/5680464?redirectedFrom=fulltext http://dx.doi.org/10.1093/ajcn/nqz276




The Growing Tibetan Plateau Shaped Modern Biodiversity



Holding particular biological resources, the Tibetan Plateau is a unique geologic-geographic-biotic interactively unite and hence plays an important role in the global biodiversity domain. The Tibetan Plateau has undergone vigorous environmental changes since the Cenozoic, and played roles as switching from "a paradise of tropical animals and plants" to "the cradle of Ice Age mammalian fauna". '

Intercontinental dispersals via Tibet, taking Ailanthus and climbing perches as examples 
Credit: ©Science China Press

Recent significant paleontological discoveries have refined a big picture of the evolutionary history of biodiversity on that plateau against the backdrop of major environmental changes, and paved the way for the assessment of its far-reaching impact upon the biota around the plateau and even in more remote regions. Based on the newly reported fossils from the Tibetan Plateau which include diverse animals and plants, this paper presented general viewpoints of the biodiversity history on the Tibetan Plateau and its influence in a global scale.

This paper defined the Tibetan Plateau as an evolutionary junction of the history of modern biodiversity, whose performance can be categorized in the following three patterns: (1) Local origination of endemism; (2) Local origination and "Out of Tibet"; (3) Intercontinental dispersal via Tibet.

Local origination of endemism of fishes and mammals in the Tibetan Plateau

Credit: ©Science China Press

The first pattern is exemplified by the snow carps (schizothoracine fishes), the major component of the freshwater fish fauna on the plateau, whose temporal distribution pattern of the fossil schizothoracines approximately mirrors the spatial distribution pattern of their living counterparts. Through ascent with modification, their history reflects the biological responses to the stepwise uplift of the Tibetan Plateau.

The second pattern is represented by the dispersal history of some mammals since the Pliocene and some plants. The ancestors of some Ice Age mammals, e.g., the wholly rhino, Arctic fox, and argali sheep first originated and evolved in the uplifted and frozen Tibet during the Pliocene, and then migrated toward the Arctic regions or even the North American continent at beginning of the Ice Age; the ancestor of pantherines (big cats) first rose in Tibetan Plateau during the Pliocene, followed by the disperse of its descendants to other parts of Asia, Africa, North and South America to play as top predators of the local ecosystems. The early members of some plants, e.g., Elaeagnaceae appeared in Tibet during the Late Eocene and then dispersed and widely distributed to other regions.

Local origination and "Out of Tibet" of mammals in the Tibetan Plateau
Credit: ©Science China Press

The last pattern is typified by the history of the tree of heaven (Ailanthus) and climbing perch. Ailanthus originated in the Indian subcontinent, then colonized into Tibet after the Indian-Asian plate collision, and dispersed from the Tibetan Plateau to East Asia, Europe and even North America. The climbing perches among freshwater fishes probably rose in Southeast Asia during the Middle Eocene, dispersed to Tibet and then migrated into Africa via the docked India. These cases highlight the role of Tibet, which was involved in the continental collision, in the intercontinental biotic interchanges. The three evolutionary patterns above reflect both the history of biodiversity on the plateau as well as the biological and environmental effects of tectonic uplift.

Since the initiation of the Second Tibetan Plateau Scientific Expedition in 2017, this review is the first comprehensive conclusions on the relationship between the uplift of the Tibetan Plateau and the evolution of biota based on latest numerous fossil records. It provides important scientific evidence for the influence of the uplift of the Tibetan Plateau on the environment and biota.

This paper is entitled "Tibetan Plateau: An evolutionary junction for the history of modern biodiversity", with coauthors Tao Deng and Feixiang Wu from Institute of Vertebrate Paleontology and Paleoanthropology, Zhekun Zhou and Tao Su from Xishuangbanna Tropical Botanical Garden, CAS. It is published in special issue "Cenozoic mammals and plants from Tibetan Plateau and their biogeographical significance" in Science China: Earth Science.

This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant Nos. XDB26000000, XDA20070203, XDA20070301), the Second Comprehensive Scientific Expedition on the Tibetan Plateau (Grant No. QZK0705, 2019), the National Natural Science Foundation of China (Grant Nos. 41430102, 41872006), the Frontier Science Key Research Project (Grant No. QYZDY-SSW-DQC022), the International Partnership Program (Grant No. GJHZ1885), and the Youth Innovation Promotion Association of the Chinese Academy of Sciences (Grant No. 2017103).



Contacts and sources:
Deng Tao
Science China Press
Citation:  Deng T, Wu F, Su T, Zhou Z. 2019. Tibetan Plateau: An evolutionary junction for the history of modern biodiversity. Science China Earth Sciences, https://doi.org/10.1007/s11430-019-9507-5





North Atlantic Current May Cease Temporarily in the Next Century

The North Atlantic Current transports warm water from the Gulf of Mexico towards Europe, providing much of north-western Europe with a relatively mild climate. However, scientists suspect that meltwater from Greenland and excessive rainfall could interfere with this ocean current. 

Simulations by scientists from the University of Groningen and Utrecht University showed that it is unlikely that the current will come to a complete stop, due to small and rapid changes in precipitation over the North Atlantic. However, there is a 15 percent likelihood that there will be a temporary change in the current in the next 100 years. However a total collapse in the next 1,000 years is unlikely. The results were published on 30 December in the journal Scientific Reports.

This image shows the Atlantic Ocean Circulation, which transports relatively warm water from the Gulf of Mexico to north-western Europe. 
Credit:  Sven Baars, University of Groningen

'The oceans store an immense amount of energy and the ocean currents have a strong effect on the Earth's climate,' says University of Groningen Associate Professor in Numerical Mathematics, Fred Wubs. Together with his colleague Henk Dijkstra from Utrecht University, he has studied ocean currents for some 20 years.

Box model

Ocean scientists have found that the Atlantic Ocean currents are sensitive to the amount of fresh water at the surface. Since the run-off of meltwater from Greenland has increased due to climate change, as has rainfall over the ocean, it has been suggested that this may slow down or even reverse the North Atlantic Current, blocking the transport of heat to Europe.

Simulations of the effects of freshwater on the currents have already been performed for some decades. 'Both high-resolution models, based on the equations describing fluid flows, and highly simplified box models have been used,' explains Wubs. 'Our colleagues in Utrecht created a box model that describes present-day large-scale processes in the ocean rather well.'

Total collapse

The idea was to use this box model to estimate the likelihood of small fluctuations in freshwater input causing a temporary slowing down or a total collapse of the North Atlantic Current. The current shows non-linear behaviour, which means that small changes can have large effects. The evolution of the physics described by the box model can only be obtained using simulations. 'As the transitions we were looking for are expected to be rare events, you need a huge number of simulations to estimate the chance of them happening,' says Wubs. However, the Dutch scientists found that a French scientist had devised a method to select the most promising simulations, reducing the number of full simulations required.

Sven Baars, a PhD student of Wubs, implemented this method efficiently and linked it to the Utrecht box model. Daniele Castellana, a PhD student of Dijkstra, performed the simulations. 'These simulations showed that the chances of a total collapse of the North Atlantic Current within the next thousand years are negligible,' says Wubs.

Interruption

A temporary interruption in the delivery of relatively warm water to north-western Europe is more likely: 'In our simulations, the chances of this happening in the next 100 years are 15 percent.' Such temporary transitions may cause cold spells in the North Atlantic, although this needs to be verified in further studies. Therefore, the current study is just a first step in determining the risk. The model does not take into account considerable changes in freshwater in the North Atlantic, which can be caused by the melting of the ice sheets. Wubs: 'Confirming our results through simulation with a high-resolution climate model will be the next challenge.'



Contacts and sources:
Rene Fransen
University of Groningen


Citation: Transition probabilities of noise-induced transitions of the Atlantic Ocean Circulation. D. Castellana, S. Baars, F.W. Wubs and H.A. Dijkstra:  Scientific Reports 30 December 2019





Learning from Bears to Help Humans



Grizzly bears spend many months in hibernation, but their muscles do not suffer from the lack of movement. In the journal "Scientific Reports", a team led by Michael Gotthardt reports on how they manage to do this. The grizzly bears' strategy could help prevent muscle atrophy in humans as well.

A grizzly bear only knows three seasons during the year. Its time of activity starts between March and May. Around September the bear begins to eat large quantities of food. And sometime between November and January, it falls into hibernation. From a physiological point of view, this is the strangest time of all. The bear's metabolism and heart rate drop rapidly. It excretes neither urine nor feces. The amount of nitrogen in the blood increases drastically and the bear becomes resistant to the hormone insulin.

Grizzly bears’ muscles manage to survive hibernation virtually unharmed. Researchers are trying to understand the mechanisms behind this ability in order to help bedridden patients.
Credit: © Gotthardt Lab, MDC

A person could hardly survive this four-month phase in a healthy state. Afterwards, he or she would most likely have to cope with thromboses or psychological changes. Above all, the muscles would suffer from this prolonged period of disuse. Anyone who has ever had an arm or leg in a cast for a few weeks or has had to lie in bed for a long time due to an illness has probably experienced this.

A little sluggish, but otherwise fine

Not so the grizzly bear. In the spring, the bear wakes up from hibernation, perhaps still a bit sluggish at first, but otherwise well. Many scientists have long been interested in the bear's strategies for adapting to its three seasons.

A team led by Professor Michael Gotthardt, head of the Neuromuscular and Cardiovascular Cell Biology group at the Max Delbrueck Center for Molecular Medicine (MDC) in Berlin, has now investigated how the bear's muscles manage to survive hibernation virtually unharmed. The scientists from Berlin, Greifswald and the United States were particularly interested in the question of which genes in the bear's muscle cells are transcribed and converted into proteins, and what effect this has on the cells.

Understanding and copying the tricks of nature

"Muscle atrophy is a real human problem that occurs in many circumstances. We are still not very good at preventing it," says the lead author of the study, Dr. Douaa Mugahid, once a member of Gotthardt's research group and now a postdoctoral researcher in the laboratory of Professor Marc 
Kirschner of the Department of Systems Biology at Harvard Medical School in Boston.

Grizzly bear sow & cub with radio neckband, Yellowstone National Park
Credit: John Good, National Park Service (NPS) / Wikimedia Commons

"For me, the beauty of our work was to learn how nature has perfected a way to maintain muscle functions under the difficult conditions of hibernation," says Mugahid. "If we can better understand these strategies, we will be able to develop novel and non-intuitive methods to better prevent and treat muscle atrophy in patients."

Gene sequencing and mass spectrometry

To understand the bears' tricks, the team led by Mugahid and Gotthardt examined muscle samples from grizzly bears both during and between the times of hibernation, which they had received from Washington State University. "By combining cutting-edge sequencing techniques with mass spectrometry, we wanted to determine which genes and proteins are upregulated or shut down both during and between the times of hibernation," explains Gotthardt.

"This task proved to be tricky - because neither the full genome nor the proteome, i.e., the totality of all proteins of the grizzly bear, were known," says the MDC scientist. In a further step, he and his team compared the findings with observations of humans, mice and nematode worms.

Non-essential amino acids allowed muscle cells to grow

As the researchers reported in the journal "Scientific Reports", they found proteins in their experiments that strongly influence a bear's amino acid metabolism during hibernation. As a result, its muscle cells contain higher amounts of certain non-essential amino acids (NEAAs).

"In experiments with isolated muscle cells of humans and mice that exhibit muscle atrophy, cell growth could also be stimulated by NEAAs," says Gotthardt, adding that "it is known, however, from earlier clinical studies that the administration of amino acids in the form of pills or powders is not enough to prevent muscle atrophy in elderly or bedridden people."

"Obviously, it is important for the muscle to produce these amino acids itself - otherwise the amino acids might not reach the places where they are needed," speculates the MDC scientist. A therapeutic starting point, he says, could be the attempt to induce the human muscle to produce NEAAs itself by activating corresponding metabolic pathways with suitable agents during longer rest periods.

Tissue samples from bedridden patients

In order to find out which signaling pathways need to be activated in the muscle, Gotthardt and his team compared the activity of genes in grizzly bears, humans and mice. The required data came from elderly or bedridden patients and from mice suffering from muscle atrophy - for example, as a result of reduced movement after the application of a plaster cast. "We wanted to find out which genes are regulated differently between animals that hibernate and those that do not," explains Gotthardt.

However, the scientists came across a whole series of such genes. To narrow down the possible candidates that could prove to be a starting point for muscle atrophy therapy, the team subsequently carried out experiments with nematode worms. "In worms, individual genes can be deactivated relatively easily and one can quickly see what effects this has on muscle growth," explains Gotthardt.

A gene for circadian rhythms

With the help of these experiments, his team has now found a handful of genes whose influence they hope to further investigate in future experiments with mice. These include the genes Pdk4 and Serpinf1, which are involved in glucose and amino acid metabolism, and the gene Rora, which contributes to the development of circadian rhythms. "We will now examine the effects of deactivating these genes," says Gotthardt. "After all, they are only suitable as therapeutic targets if there are either limited side effects or none at all."



Contacts and sources:
Jana SchluetterMax Delbrueck Center for Molecular Medicine (MDC)

Citation: "Proteomic and Transcriptomic Changes in Hibernating Grizzly Bears Reveal Metabolic and Signaling Pathways that Protect against Muscle Atrophy," Douaa Mugahid et al. (2019) Scientific Reports, DOI: 10.1038/s41598-019-56007-8 http://dx.doi.org/10.1038/s41598-019-56007-8




Mealworms Can Safely Consume Toxic Additive-Containing Plastic Say Researchers


Mealworms are not only able to eat various forms of plastic, as previous research has shown, they can consume potentially toxic plastic additives in Styrofoam with no ill effects, a new study shows. The worms can then be used as a safe, protein-rich feed supplement.

Tiny mealworms may hold part of the solution to our giant plastics problem. Not only are they able to consume various forms of plastic, as previous Stanford research has shown, they can eat Styrofoam containing a common toxic chemical additive and still be safely used as protein-rich feedstock for other animals, according to a new Stanford study published in Environmental Science & Technology.


Video by Rob Jordan / Stanford Woods Institute for the Environment

A new Stanford study shows mealworms can eat Styrofoam containing a common toxic chemical additive and still be safely used as protein-rich feedstock for other animals.

The study is the first to look at where chemicals in plastic end up after being broken down in a natural system – a yellow mealworm’s gut, in this case. It serves as a proof of concept for deriving value from plastic waste.

Styrofoam waste in a puddle
File:Reflections in puddles. img 022.jpg
Credit: Dmitry Makeev / Wikimedia Commons

“This is definitely not what we expected to see,” said study lead author Anja Malawi Brandon, a PhD candidate in civil and environmental engineering at Stanford. “It’s amazing that mealworms can eat a chemical additive without it building up in their body over time.”

In earlier work, Stanford researchers and collaborators at other institutions revealed that mealworms, which are easy to cultivate and widely used as a food for animals ranging from chickens and snakes to fish and shrimp, can subsist on a diet of various types of plastic. They found that microorganisms in the worms’ guts biodegrade the plastic in the process – a surprising and hopeful finding. However, concern remained about whether it was safe to use the plastic-eating mealworms as feed for other animals given the possibility that harmful chemicals in plastic additives might accumulate in the worms over time.

“This work provides an answer to many people who asked us whether it is safe to feed animals with mealworms that ate Styrofoam”, said Wei-Min Wu, a senior research engineer in Stanford’s Department of Civil and Environmental Engineering who has led or co-authored most of the Stanford studies of plastic-eating mealworms.

Styrofoam solution

Brandon, Wu and their colleagues looked at Styrofoam or polystyrene, a common plastic typically used for packaging and insulation, that is costly to recycle because of its low density and bulkiness. It contained a flame retardant called hexabromocyclododecane, or HBCD, that is commonly added to polystyrene. The additive is one of many used to improve plastics’ manufacturing properties or decrease flammability. In 2015 alone, nearly 25 million metric tons of these chemicals were added to plastics, according to various studies. Some, such as HBCD, can have significant health and environmental impacts, ranging from endocrine disruption to neurotoxicity. Because of this, the European Union plans to ban HBCD, and U.S. Environmental Protection Agency is evaluating its risk.

Coffee in a Styrofoam cup.
File:Flickr - cyclonebill - Kaffe (13).jpg
Credit: cyclonebill / Wikimedia Commons

Mealworms in the experiment excreted about half of the polystyrene they consumed as tiny, partially degraded fragments and the other half as carbon dioxide. With it, they excreted the HBCD – about 90 percent within 24 hours of consumption and essentially all of it after 48 hours. Mealworms fed a steady diet of HBCD-laden polystyrene were as healthy as those eating a normal diet. The same was true of shrimp fed a steady diet of the HBCD-ingesting mealworms and their counterparts on a normal diet. The plastic in the mealworms’ guts likely played an important role in concentrating and removing the HBCD.

The researchers acknowledge that mealworm-excreted HBCD still poses a hazard, and that other common plastic additives may have different fates within plastic-degrading mealworms. While hopeful for mealworm-derived solutions to the world’s plastic waste crisis, they caution that lasting answers will only come in the form of biodegradable plastic replacement materials and reduced reliance on single-use products.

“This is a wake-up call,” said Brandon. “It reminds us that we need to think about what we’re adding to our plastics and how we deal with it.”

Co-authors of the study include Craig Criddle, a professor of civil and environmental engineering in Stanford’s School of Engineering, a senior fellow at the Stanford Woods Institute for the Environment, a member of Bio-X and an affiliate of the Precourt Institute for Energy. Other co-authors of the study include Sahar El Abbadi, a civil and environmental engineering graduate student; Uwakmfon Ibekwe, an undergraduate student in civil and environmental engineering at the time of the research and current graduate student at Carnegie Mellon University; and YeoMyoung Cho, a senior research engineer in civil and environmental engineering.

The research was funded by the Stanford Woods Institute for Environment, the National Science Foundation and the Stanford Interdisciplinary Graduate Fellowship.



Contacts and sources:Rob Jordanm Stanford Woods Institute for the Environment
Anja Malawi-Brandon, Stanford School of Engineering
Wei-Min Wu, Stanford School of Engineering







Sunday, December 29, 2019

Space Weather: Nightside Barrier Gently Brakes ‘Bursty’ Plasma Bubbles



The solar wind that pummels the Earth's dayside magnetosphere causes turbulence, like air over a wing. Physicists at Rice University have developed new methods to characterize how that influences space weather on the nightside.

It's rarely quiet up there. The solar wind streams around the Earth and cruises off into the night, but closer to the planet, parcels of plasma get caught in the turbulence and sink back toward Earth. That turbulence causes big ripples in the plasma.

A magnetohydrodynamic simulation by the Gamera project at the Johns Hopkins Applied Physics Laboratory shows bursty bulk flows (in red and brown) in the plasma sheet approaching Earth on the nightside. Rice University space plasma physicists have developed algorithms to measure the buoyancy waves that appear in thin filaments of magnetic flux on the nightside.

Courtesy of Gamera/JHUAP


With the help of several spacecraft and computational tools developed over the past decade, Rice scientists led by space plasma physicist Frank Toffoletto can now assess the ripples, called buoyancy waves, caused by the turbulence.

These waves, or oscillations, have been observed in the thin layer of magnetic flux along the base of the plasma sheet that tails away from the planet's nightside. The Rice theory is the first to quantify their motion.

The theory adds another element to the Rice Convection Model, an established, decades-in-the-making algorithm that helps scientists calculate how the inner and middle magnetosphere will react to events like solar storms that threaten satellites, communications and power grids on Earth.

The new paper in JGR Space Physics by Toffoletto, emeritus professor Richard Wolf and former graduate student Aaron Schutza starts by describing the bubbles -- "bursty bulk flows" predicted by Wolf and Rice alumnus Duane Pontius in 1990 -- that fall back toward Earth through the plasma tail.

An image from a magnetohydrodynamic simulation by the Gamera project at the Johns Hopkins Applied Physics Laboratory shows bursty flows (in red and brown) in the plasma sheet. Rice University space plasma physicists developed algorithms to measure the buoyancy waves that appear in thin filaments of magnetic flux on Earth's nightside.

Credit: K. Sorathia/JHUAPL

Functionally, they're the reverse of buoyant air bubbles that bob up and down in the atmosphere because of gravity, but the plasma bubbles respond to magnetic fields instead. The plasma bubbles lose most of their momentum by the time they touch down at the theoretical, filamentlike boundary between the inner plasma sheet and the protective plasmasphere.

That sets the braking boundary into a gentle oscillation, which lasts mere minutes before stabilizing again. Toffoletto compared the motion to a plucked guitar string that quickly returns to equilibrium.

"The fancy name for this is the eigenmode," he said. "We're trying to figure out the low-frequency eigenmodes of the magnetosphere. They haven't been studied very much, though they appear to be associated with dynamic disruptions to the magnetosphere."

A simulation by Rice University space plasma physicist Frank Toffoletto shows buoyancy wave oscillations in a magnetic field, due to bursty bulk flows drawn toward Earth on the nightside. 
 Courtesy of Frank Toffoletto

Toffoletto said the Rice team has in recent years discovered through simulations that the magnetosphere doesn't always respond in a linear fashion to the steady driving force of the solar wind.

"You get all kinds of wave modes in the system," he said, explaining that bursty bulk flows are one such mode. "Every time one of these things come flying in, when they hit the inner region, they basically reach their equilibrium point and oscillate with a certain frequency. Finding that frequency is what this paper is all about."

As measured by the THEMIS spacecraft, the periods of these waves are a few minutes and the amplitudes are often bigger than the Earth.

"Understanding the natural frequency of the system and how it behaves can tell us a lot about the physical properties of plasma on the nightside, its transport and how it might be related to the aurora," he said. "A lot of these phenomena show up in the ionosphere as auroral structures, and we don't understand where these structures come from."

Toffoletto said the models suggest buoyant waves may play a role in the formation of the ring current that consists of charged particles that flow around Earth as well as magnetospheric substorms, all of which are connected to the aurora.

He said that no more than a decade ago, many magnetosphere simulations "would look very uniform, kind of boring." The Rice group is collaborating with the Applied Physics Laboratory to include the Rice Convection Model in a newly developed global magnetosphere code called "Gamera," named after the fictional Japanese monster.

"Now, with such higher-resolution models and much better numerical methods, these structures are starting to show up in the simulations," Toffoletto said. "This paper is one little piece of the puzzle we're putting together of how the system behaves. All this plays a big role in understanding how space weather works and how that in turn impacts technology, satellites and ground-based systems."

The Rice Convection Model itself was refreshed this month in a paper led by recent Rice alumnus Jian Yang, now an associate professor of Earth and space sciences at the Southern University of Science and Technology, Shenzhen, China.

The new study was supported by a NASA Heliophysics Supporting Research grant.
Video lecture: The Effects of Plasma Sheet Bubbles on the Inner Magnetosphere

Contacts and sources:
Mike Williams
Rice University


Citation:    The Inertialized Rice Convection Model Jian Yang  Richard Wolf  Frank Toffoletto  Stanislav Sazykin  Wenrui Wang  Jun Cui  https://doi.org/10.1029/2019JA026811   https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2019JA026811


Buoyancy Waves in Earth’s Magnetosphere: Calculations for a 2D Wedge Magnetosphere: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2017JA025006

Theory of thin-filament motion in Earth’s magnetotail and its application to bursty bulk flows: https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/1999JA900005

Space Plasma Physics at Rice: https://physics.rice.edu/space-plasma-physics

Grid Agnostic MHD for Extended Research Applications (Gamera): https://civspace.jhuapl.edu/Science/tools.php?tool=gamera

New Clues on Dark Matter from The Darkest Galaxies


They are called low-surface-brightness galaxies and it is thanks to them that important confirmations and new information have been obtained on one of the largest mysteries of the cosmos: dark matter.

"We have found that disc galaxies can be represented by a universal relationship. In particular, in this study we analysed the so-called Low-Surface-Brightness (LSB) galaxies, a particular type of galaxy with a rotating disc called this way because they have a low-density brightness "says Chiara di Paolo, astrophysicist at SISSA and lead author of a study recently published in MNRAS together with Paolo Salucci (astrophysicist at SISSA) and Erkurt Adnan (Istanbul University).

The researchers analysed the speed at which the stars and gases that compose the galaxies subject matter of the study rotate, noting that the LSBs also have a very homogenous behaviour. This result consolidates several clues on the presence and behaviour of dark matter, opening up new scenarios on its interactions with bright matter.

Lights and shadows on matter

It is there but you cannot see it. Dark matter appears to account for approximately 90% of the mass of the Universe; it has effects that can be detected on the other objects present in the cosmos, and yet it cannot be observed directly because it does not emit light (at least for the way in which it has been searched for to date). 

NASA/ESA Hubble Space Telescope image capturing UGC 477, a low surface brightness galaxy located just over 110 million light-years away in the constellation of Pisces (The Fish).

Credit: ESA/Hubble & NASA Acknowledgement: Judy Schmidt

One of the methods for studying it is that of rotation curves of the galaxies, systems that describe the trend of the speed of stars based on their distance from the center of the galaxy. The variations observed are connected to the gravitational interactions due to the presence of stars and to the dark component of matter. Consequently, the rotation curves are a good way to have information on the dark matter based on its effects on what it is possible to observe. In particular, the analysis of the rotation curves can be conducted individually or on groups of galaxies that share similar characteristics according to the universal rotation curve (URC) method.

The novelty of the research lies in having applied the URC method for the first time, already used for other types of galaxies, to a large sample of low-surface-brightness galaxies, obtaining similar results. "We have compared rotation curves of various LSB galaxies finding that there is no discontinuity but gradual and ordered variations starting from the small to the large. Something similar was also observed for spiral galaxies," explains Salucci, the other author of the study: "This method was applied for the first time in 1996, and to date it has shown that all disc, spiral, dwarf and now also the LSB galaxies can be represented by a universal relationship. This means that we are able to express an ordered trend through a formula which, keeping account of very few parameters, describes how dark matter and luminous matter are distributed".

New possible scenarios

As it often happens in scientific research, the study has revealed further surprising and unexpected results. "We have discovered relationships of scale between the properties of the stellar disc and those of the dark matter halo, for example a relationship between the dimensions of the stellar discs and the dimensions of the internal region with a constant density of the dark matter halo" explains Chiara Di Paolo. "Furthermore, by comparing the relationships found in the LSB with those obtained in different types of galaxies, we have found that they are all almost coincidental. And it has been a great surprise to verify that galaxies with a very different morphology and history show the same relationships between the properties of dark matter and those of luminous matter". 

This result, together with some specific features of LSB galaxies, opens up a new series of scenarios including that of the existence of another type of direct interaction, in addition to the gravitational one, between the two types of matter that form galaxies. A fascinating idea to be verified by new observations.


Contacts and sources:
Marina D'Alessandro
Scuola Internazionale Superiore Di Studi Avanzati (SISSA)

Citation: The universal rotation curve of low surface brightness galaxies – IV. The interrelation between dark and luminous matter Chiara Di Paolo, Paolo Salucci, Adnan Erkurt Monthly Notices of the Royal Astronomical Society, Volume 490, Issue 4, December 2019, Pages 5451–5477, https://academic.oup.com/mnras/article/490/4/5451/5574405 http://dx.doi.org/10.1093/mnras/stz2700




Snowmageddon Warnings in North America Come from Tropics More Than Arctic Stratosphere



Winter weather patterns in North America are dictated by changes to the polar vortex winds high in the atmosphere, but the most significant cold snaps are more likely influenced by the tropics, scientists have found.

A team led by the University of Reading conducted the first ever study to identify how the four main winter weather patterns in North America behave depending on the strength of the stratospheric polar vortex. This is a ribbon of wind and low pressure that circles the Arctic at heights of 10-50km, trapping cold air inside.

The four US weather regimes (clockwise from top left): Pacific Trough, Arctic High, Alaskan Ridge, Arctic Low. Red indicates warmer conditions and blue colder conditions

Credit: Simon Lee

It is already well established that the vortex wind strength influences weather in Europe and Asia, and the study revealed it also has a strong effect on three out of the four main winter weather patterns in North America, giving forecasters an additional tool to understand potentially high-impact weather during winter.

The study, published in Geophysical Research Letters, also revealed that, unlike in Europe, the most extreme cold snaps affecting the whole of North America are not most likely to occur after a weak vortex. Instead, the shape of the vortex and conditions in the tropics were identified as stronger influences of these conditions.

Simon Lee, atmospheric scientist at the University of Reading and lead author of the study, said: "Despite the most extreme cold snaps experienced in North America often being described as 'polar vortex outbreaks', our study suggests vortex strength should not be considered as a cause.

"We know that a weakened polar vortex allows cold air to flood out from the Arctic over Europe and Asia, but we found this is surprisingly not the case the other side of the Atlantic.

"In fact, our work suggests we should actually look south to conditions around the equator, rather than north to the Arctic, for the causes of these widespread freezing conditions in North America.

"Our results did reveal that the polar vortex strength provides useful information on the likelihood of most weather patterns over the US and Canada further in advance, including some potentially disruptive temperature changes or heavy rain. The more accurate information populations have about upcoming changes in weather, the better they can prepare."

Conditions seen during the Alaskan Ridge regime -- which is associated with the most extreme, widespread cold in North America.

Credit: Simon Lee

One of the clearest suggested effects of a strong vortex was a 10-15% likelihood of extremely cold conditions in western parts of North America, including Alaska, but milder conditions in central and eastern parts of the US.

Another weather pattern found to most often follow neutral or strong vortex wind speeds brings temperatures 5°C above normal and wetter weather in the eastern US.

The exception in the results was that the weather pattern associated with the highest chance of the most widespread extreme cold in North America, in which average temperatures in the central US are more than 5°C below normal, was not found to have a strong dependence on a weaker vortex, as it does in Europe.

They found widespread extreme cold is more common when an area of high pressure extends up to Alaska, and the polar vortex stretches down towards North America - pushing cold Arctic air southward in the lower atmosphere.

The scientists say the influence of the stratosphere on weather patterns, as well as how this interacts with long-term weather patterns in the tropics like El Niño, should be studied further and incorporated into forecasts to improve their accuracy.



Contacts and sources:
Pete BryantUniversity of Reading


Citation: Wintertime North American Weather Regimes and the Arctic Stratospheric Polar Vortex S. H. Lee J. C. Furtado A. J. Charlton‐Perez Geophysical Research Letters https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019GL085592 http://dx.doi.org/10.1029/2019GL085592





The Coolest LEGO ® in the Universe


For the first time, LEGO ® has been cooled to the lowest temperature possible in an experiment which reveals a new use for the popular toy.

Its special properties mean it could be useful in the development of quantum computing.

A world leading team of ultra-low temperature physicists at Lancaster University decided to place a LEGO ® figure and four LEGO ® blocks inside their record-breaking dilution refrigerator.

The LEGO ® figure and block used in the experiment
the Lego
Credit: Lancaster University

This machine - specially made at the University - is the most effective refrigerator in the world, capable of reaching 1.6 millidegrees above absolute zero (minus 273.15 Centigrade), which is about 200,000 times colder than room temperature and 2,000 times colder than deep space.

The results - published in the prestigious journal Scientific Reports - were surprising.

Dr Dmitry Zmeev, who led the research team, said:  “Our results are significant because we found that the clamping arrangement between the LEGO ® blocks causes the LEGO ® structures to behave as an extremely good thermal insulator at cryogenic temperatures."

“This is very desirable for construction materials used for the design of future scientific equipment like dilution refrigerators.” 

Credit: Hamster Productions / https://youtu.be/zaIFZsBOeZc

Invented 50 years ago, the dilution refrigerator is at the center of a global multi-billion dollar industry and is crucial to the work of modern experimental physics and engineering, including the development of quantum computers.

The use of ABS plastic structures, such as LEGO ®, instead of the solid materials currently in use, means that any future thermal insulator could be produced at a significantly reduced cost.

Researchers say the next step is to design and 3D print a new thermal insulator for the next generation of dilution refrigerators.



Contacts and sources:
Lancaster University


Citation: LEGO® Block Structures as a Sub-Kelvin Thermal Insulator. J. M. A. Chawner, A. T. Jones, M. T. Noble, G. R. Pickett, V. Tsepelin, D. E. Zmeev. Scientific Reports, 2019; 9 (1) DOI: 10.1038/s41598-019-55616-7







Thursday, December 26, 2019

A New Gene Therapy Strategy, Courtesy of Mother Nature, Could Reverse Disease Progress

Scientists have developed a new gene-therapy technique by transforming human cells into mass producers of tiny nano-sized particles full of genetic material that has the potential to reverse disease processes.  The scientists turned a natural cellular process into a drug-delivery system

3D illustration of cells releasing exosomes 
3D illustration of cells releasing exosomes
Credit:  Ohio State University

Though the research was intended as a proof of concept, the experimental therapy slowed tumor growth and prolonged survival in mice with gliomas, which constitute about 80 percent of malignant brain tumors in humans.

The technique takes advantage of exosomes, fluid-filled sacs that cells release as a way to communicate with other cells.

While exosomes are gaining ground as biologically friendly carriers of therapeutic materials – because there are a lot of them and they don’t prompt an immune response – the trick with gene therapy is finding a way to fit those comparatively large genetic instructions inside their tiny bodies on a scale that will have a therapeutic effect.

This new method relies on patented technology that prompts donated human cells such as adult stem cells to spit out millions of exosomes that, after being collected and purified, function as nanocarriers containing a drug. When they are injected into the bloodstream, they know exactly where in the body to find their target – even if it’s in the brain.

“Think of them like Christmas gifts: The gift is inside a wrapped container that is postage paid and ready to go,” said senior study author L. James Lee, professor emeritus of chemical and biomolecular engineering at The Ohio State University.

L. James Lee

Credit:  Ohio State University


And they are gifts that keep on giving, Lee noted: “This is a Mother Nature-induced therapeutic nanoparticle.”

The study is published today (Dec. 16) in the journal Nature Biomedical Engineering.

In 2017, Lee and colleagues made waves with news of a regenerative medicine discovery called tissue nanotransfection (TNT). The technique uses a nanotechnology-based chip to deliver biological cargo directly into skin, an action that converts adult cells into any cell type of interest for treatment within a patient’s own body.

By looking further into the mechanism behind TNT’s success, scientists in Lee’s lab discovered that exosomes were the secret to delivering regenerative goods to tissue far below the skin’s surface.

The technology was adapted in this study into a technique first author Zhaogang Yang, a former Ohio State postdoctoral researcher now at the University of Texas Southwestern Medical Center, termed cellular nanoporation.

The scientists placed about 1 million donated cells (such as mesenchymal cells collected from human fat) on a nano-engineered silicon wafer and used an electrical stimulus to inject synthetic DNA into the donor cells. As a result of this DNA force-feeding, as Lee described it, the cells need to eject unwanted material as part of DNA transcribed messenger RNA and repair holes that have been poked in their membranes.

“They kill two birds with one stone: They fix the leakage to the cell membrane and dump the garbage out,” Lee said. “The garbage bag they throw out is the exosome. What’s expelled from the cell is our drug.”

The electrical stimulation had a bonus effect of a thousand-fold increase of therapeutic genes in a large number of exosomes released by the cells, a sign that the technology is scalable to produce enough nanoparticles for use in humans.

Essential to any gene therapy, of course, is knowing what genes need to be delivered to fix a medical problem. For this work, the researchers chose to test the results on glioma brain tumors by delivering a gene called PTEN, a cancer-suppressor gene. Mutations of PTEN that turn off that suppression role can allow cancer cells to grow unchecked.

For Lee, founder of Ohio State’s Center for Affordable Nanoengineering of Polymeric Biomedical Devices, producing the gene is the easy part. The synthetic DNA force-fed to donor cells is copied into a new molecule consisting of messenger RNA, which contains the instructions needed to produce a specific protein. Each exosome bubble containing messenger RNA is transformed into a nanoparticle ready for transport, with no blood-brain barrier to worry about.

“The advantage of this is there is no toxicity, nothing to provoke an immune response,” said Lee, also a member of Ohio State’s Comprehensive Cancer Center. “Exosomes go almost everywhere in the body, including passing the blood-brain barrier. Most drugs can’t go to the brain.

“We don’t want the exosomes to go to the wrong place. They’re programmed not only to kill cancer cells, but to know where to go to find the cancer cells. You don’t want to kill the good guys.”

The testing in mice showed the labeled exosomes were far more likely to travel to the brain tumors and slow their growth compared to substances used as controls.

Because of exosomes’ safe access to the brain, Lee said, this drug-delivery system has promise for future applications in neurological diseases such as Alzheimer’s and Parkinson’s disease.

“Hopefully, one day this can be used for medical needs,” Lee said. “We’ve provided the method. If somebody knows what kind of gene combination can cure a certain disease but they need a therapy, here it is.”

This work was supported by the National Science Foundation; the National Natural Science Foundation of China; the National Heart, Lung, and Blood Institute; the National Institute of Neurological Disorders and Stroke; the Cancer Prevention and Research Institute of Texas; the American Brain Tumor Association; and the National Cancer Institute.

Ohio State co-authors Junfeng Shi, Jingyao Sun, Xinmei Wang, Yifan Ma, Veysi Malkoc, Chiling Chiang, Kwang Kwak, Yamin Fan, Paul Bertani, Jose Otero and Wu Lu also worked on the research.



Contacts and sources:
Emily Caldwell
Ohio State University


Citation: Large-scale generation of functional mRNA-encapsulating exosomes via cellular nanoporation.
Zhaogang Yang, Junfeng Shi, Jing Xie, Yifan Wang, Jingyao Sun, Tongzheng Liu, Yarong Zhao, Xiuting Zhao, Xinmei Wang, Yifan Ma, Veysi Malkoc, Chiling Chiang, Weiye Deng, Yuanxin Chen, Yuan Fu, Kwang J. Kwak, Yamin Fan, Chen Kang, Changcheng Yin, June Rhee, Paul Bertani, Jose Otero, Wu Lu, Kyuson Yun, Andrew S. Lee, Wen Jiang, Lesheng Teng, Betty Y. S. Kim, L. James Lee. Nature Biomedical Engineering, 2019; DOI: 10.1038/s41551-019-0485-1




Role of Atmospheric Dust on Marine Ecosystems 300 Million Years Ago Documented by OU Geoscientists

Dust plays a crucial role in the life and health of our planet. In our modern world, dust-borne nutrients traveling in great dust storms from the Saharan Desert fertilize the soil in the Amazon Rainforest and feed photosynthetic organisms like algae in the Atlantic Ocean. In turn, it is those organisms that breathe in carbon dioxide and expel oxygen.

Mehrdad Sardar Abadi, a researcher in the Mewbourne College of Earth and Energy School of Geosciences and School director Lynn Soreghan, led a study with researchers from Florida State University, the Massachusetts Institute of Technology, Hampton University and the College of Charleston, to understand the role of dust on the Earth’s atmosphere in deep time – 300 million years ago.

This specimen of rock consists almost entirely of fossilized cyanobacteria that once lived in an ancient shallow sea. Their proliferation decreased the amount of carbon dioxide in the atmosphere but also outcompeted other life in ancient oceans.
Credit: University of Oklahoma

To do this research, the team needed to find ancient atmospheric dust, which led them to the remnants of a shallow marine ecosystem in modern-day Iran.

Similar to areas of our modern world like the Bahamas, these shallow marine ecosystems cannot survive unless they are in pristine water away from river runoff, Sardar Abadi explained. By targeting the systems, Sardar Abadi and Soreghan knew that silicate particles they found would have been deposited through the air and not from a river.

Sardar Abadi and Soreghan identified and sampled dust trapped in carbonate rocks from two intervals of limestone now preserved in outcroppings in the mountains of northern and central Iran.

Rocks were then subjected to a series of chemical treatments to extract the ancient dust. What was left were silicate minerals like clay and quartz that entered the environment as air-borne particles – 300-million-year-old dust.

Ancient dust in hand, Sardar Abadi could determine how much dust was in the Late Paleozoic atmosphere. Their results suggested that Earth’s atmosphere was much dustier during this ancient time. Working with collaborators at Florida State University, he performed geochemical tests to analyze the iron in the samples. Those tests revealed that the ancient dust also contained remarkable proportions of highly reactive iron — a particularly rich source of this key micronutrient.

University of Oklahoma post-doctoral researcher Merhdad Sardar Abadi works in Dr. Lynn Soreghan's lab where they use a variety of chemicals to isolate silicate particles and uncover 300-million-year-old dust.
Credit: University of Oklahoma

While iron is not the only micronutrient potentially carried in dust, it is estimated that this ancient dust contained twice the bioavailable iron as the modern dust that fertilizes the Amazon Rainforest.

This potent dust fertilization led to a massive surge in marine photosynthesizers. Fueled by iron-rich dust, algae and cyanobacteria took in carbon dioxide and expelled oxygen. Researchers speculate that this action, operating over millions of years, changed the planet’s atmosphere.

“Higher abundances in primary producers like plants and algae could lead to higher carbon capture, helping to explain declines in atmospheric carbon dioxide around 300 million years ago,” said Sardar Abadi.

“If what we are seeing from our samples was happening on a global scale, it means that the dust fertilization effect brought down atmospheric carbon dioxide and was a fairly significant part of the carbon cycle during this time in the Earth’s history,” said Soreghan.

One carbon sequestration method scientists have proposed is adding bioavailable iron to isolated parts of the ocean that are so remote and far from dust-containing continents, they are essentially deserts. Scientists who have attempted this on a small scale have documented resultant phytoplankton blooms.

But, Soreghan warned, no one knows the unintended consequences of doing this on a large scale. This is why Sardar Abadi and the team of researchers delved into deep time for answers.

“The Earth’s geologic record is like a laboratory book. It has run an infinite number of experiments. We can open Earth’s lab book, reconstruct what happened in the past and see how the Earth responded to these sometimes very extreme states,” said Soreghan.

The data and syntheses help constrain and refine computer climate models. The further back into deep time a modeler goes, the more unconstrained variables there are. By providing data, models can be more accurate.

“By delving back in time, we can uncover the most extreme states the Earth and atmosphere have experienced,” said Soreghan. “That information can potentially help us solve problems today.”

Glaciers on the left-hand side represent the continental ice sheets on Gondwana. The Persian microcontinents 300 million years ago resembled the present-day islands of the Bahamas. The red cloud depicts iron-rich dust sourced from the mainland that fertilized the shallow marine communities. Two types of ecological communities are shown: on the bottom left we show the cyanobacteria-dominated ecosystem present in iron-rich conditions, while on the bottom center-right we show the diverse ecological community (including green algae, red algae, phylloid algae, crinoids, bryozoan, brachiopods, foraminifera, etc.) that was present in relatively iron-poor conditions.

Persian Microcontinents During the late Paleozoic Icehouse by Ellen Welti

The team’s research was recently published in the Geological Survey of America’s journal, Geology. The article is available here. The research was funded by the National Science Foundation and the University of Oklahoma.


Contacts and sources:
Sarah Warren
University of Oklahoma

Citation:  Atmospheric dust stimulated marine primary productivity during Earth’s penultimate icehouse Mehrdad Sardar Abadi ; Jeremy D. Owens ; Xiaolei Liu ; Theodore R. Them, II ; Xingqian Cui ; Nicholas G. Heavens ; Gerilyn S. Soreghan Geology (2019) https://doi.org/10.1130/G46977.1  https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G46977.1/579747/Atmospheric-dust-stimulated-marine-primary?redirectedFrom=fulltext





Report Links Recommended Physical Activity Levels to Lower Risk of Seven Cancers

More physical activities have been linked to a lower risk for seven different types of cancer. 

A pooled analysis of nine prospective studies involving more than 750,000 adults finds that recommended amounts of leisure-time physical activity were linked to a lower risk for seven cancers, with several cancer types having a 'dose/response' relationship. The study was led by investigators at the National Cancer Institute, the American Cancer Society, and the Harvard T.H. Chan School of Public Health and appears in the Journal of Clinical Oncology.

While it's long been known that physical activity is associated with a lower risk of several cancers, less clear has been the shape of the relationship and whether recommended amounts of physical activity are associated with lower risk. Updated guidelines for activity now state that people should aim for 2.5 to 5 hours/week of moderate-intensity activity or 1.25 to 2.5 hours/week of vigorous activity. Moderate-intensity activities are those that get you moving fast enough or strenuously enough to burn off three to six times as much energy per minute as sitting quietly (3 to 6 METs). Vigorous-intensity activities burn more than 6 METs.

For the current analysis, investigators pooled data from nine prospective cohorts with self-reported leisure-time physical activity and follow-up for cancer incidence, looking at the relationship between physical activity with incidence of 15 types of cancer.

File:Physical Training Session at Fleet Activities Yokosuka DVIDS363815.jpg
Credit: Seaman Charles Oki, U.S. Navy / Wikimedia Commons

They found engaging in recommended amounts of activity (7.5 to 15 MET hours/week) was associated with a statistically significant lower risk of seven of the 15 cancer types studied, with the reduction increasing with more MET hours. Physical activity was associated with a lower risk of colon cancer in men (8% for 7.5 MET hours/week; 14% for 15 MET hours/week), female breast cancer (6%-10%), endometrial cancer (10%-18%), kidney cancer (11%-17%), myeloma (14%-19%), liver cancer (18%-27%), and non-Hodgkin lymphoma (11%-18% in women). The dose response was linear in shape for half of the associations and nonlinear for the others.

The analysis had some limitations: Even with 750,000 participants, patient numbers were limited for some cancers; participants were primarily white; there was a limited number of cohorts with detailed physical activity measures; and the authors relied on self-reported physical activity.

The authors conclude: "These findings provide direct quantitative support for the levels of activity recommended for cancer prevention and provide actionable evidence for ongoing and future cancer prevention efforts."

"Physical activity guidelines have largely been based on their impact on chronic diseases like cardiovascular disease and diabetes," said Alpa Patel, Ph.D., senior scientific director of epidemiology research at the American Cancer Society. "These data provide strong support that these recommended levels are important to cancer prevention, as well."


Contacts and sources:
David Sampson
American Cancer Society

Citation:Amount and Intensity of Leisure-Time Physical Activity and Lower Cancer Risk, Matthews et al. J Clin Oncol 2019; http://dx.doi.org/10.1200/JCO.19.02407





Intermittent Fasting: Live ‘Fast,’ Live longer?

For many people, the New Year is a time to adopt new habits as a renewed commitment to personal health. Newly enthusiastic fitness buffs pack into gyms and grocery stores are filled with shoppers eager to try out new diets.

But, does scientific evidence support the claims made for these diets? In a review article published in the Dec. 26 issue of The New England Journal of Medicine, Johns Hopkins Medicine neuroscientist Mark Mattson, Ph.D., concludes that intermittent fasting does.''


Credit: Johns Hopkins Medicine

Mattson, who has studied the health impact of intermittent fasting for 25 years, and adopted it himself about 20 years ago, writes that "intermittent fasting could be part of a healthy lifestyle." A professor of neuroscience at the Johns Hopkins University School of Medicine, Mattson says his new article is intended to help clarify the science and clinical applications of intermittent fasting in ways that may help physicians guide patients who want to try it.

Intermittent fasting diets, he says, fall generally into two categories: daily time-restricted feeding, which narrows eating times to 6-8 hours per day, and so-called 5:2 intermittent fasting, in which people limit themselves to one moderate-sized meal two days each week.

An array of animal and some human studies have shown that alternating between times of fasting and eating supports cellular health, probably by triggering an age-old adaptation to periods of food scarcity called metabolic switching. Such a switch occurs when cells use up their stores of rapidly accessible, sugar-based fuel, and begin converting fat into energy in a slower metabolic process.

Mattson says studies have shown that this switch improves blood sugar regulation, increases resistance to stress and suppresses inflammation. Because most Americans eat three meals plus snacks each day, they do not experience the switch, or the suggested benefits.

In the article, Mattson notes that four studies in both animals and people found intermittent fasting also decreased blood pressure, blood lipid levels and resting heart rates.

Evidence is also mounting that intermittent fasting can modify risk factors associated with obesity and diabetes, says Mattson. Two studies at the University Hospital of South Manchester NHS Foundation Trust of 100 overweight women showed that those on the 5:2 intermittent fasting diet lost the same amount of weight as women who restricted calories, but did better on measures of insulin sensitivity and reduced belly fat than those in the calorie-reduction group.

More recently, Mattson says, preliminary studies suggest that intermittent fasting could benefit brain health too. A multicenter clinical trial at the University of Toronto in April found that 220 healthy, nonobese adults who maintained a calorie restricted diet for two years showed signs of improved memory in a battery of cognitive tests. While far more research needs to be done to prove any effects of intermittent fasting on learning and memory, Mattson says if that proof is found, the fasting -- or a pharmaceutical equivalent that mimics it -- may offer interventions that can stave off neurodegeneration and dementia.

"We are at a transition point where we could soon consider adding information about intermittent fasting to medical school curricula alongside standard advice about healthy diets and exercise," he says.

Mattson acknowledges that researchers do "not fully understand the specific mechanisms of metabolic switching and that "some people are unable or unwilling to adhere" to the fasting regimens. But he argues that with guidance and some patience, most people can incorporate them into their lives. It takes some time for the body to adjust to intermittent fasting, and to get beyond initial hunger pangs and irritability that accompany it. "Patients should be advised that feeling hungry and irritable is common initially and usually passes after two weeks to a month as the body and brain become accustomed to the new habit," Mattson says.

To manage this hurdle, Mattson suggests that physicians advise patients to gradually increase the duration and frequency of the fasting periods over the course of several months, instead of "going cold turkey." As with all lifestyle changes, says Mattson, it's important for physicians to know the science so they can communicate potential benefits, harms and challenges, and offer support.

Rafael de Cabo, Ph.D., of the Translational Gerontology Branch of the National Institute on Aging Intramural Research Program, is a co-author of the published review.

This work was supported by the Intramural Research Program of the National Institute on Aging, National Institutes of Health.

Disclosure forms provided by the authors are available with the full text of this article at NEJM.org.




Contacts and sources:
Rachel Butch
Johns Hopkins Medicine







Caffeine May Offset Some Health Risks of Diets High in Fat, Sugar



A new study in rats suggests that caffeine may offset some of the negative effects of an obesogenic diet by reducing the storage of lipids in fat cells and limiting weight gain and the production of triglycerides.

Rats that consumed the caffeine extracted from mate tea gained 16% less weight and accumulated 22% less body fat than rats that consumed decaffeinated mate tea, scientists at the University of Illinois found in a new study.

The effects were similar with synthetic caffeine and that extracted from coffee.


In a study of rats, University of Illinois scientists found that caffeine limited weight gain and cholesterol production, despite a diet that was high in fat and sugar. Co-authors of the study included, from left, nutritional sciences professor Manabu T. Nakamura; Elvira Gonzalez de Mejia, director of the Division of Nutritional Sciences; and animal sciences professor Jan E. Novakofski.
Photo of, from left, nutritional sciences professor Manabu T. Nakamura; Elvira Gonzalez de Mejia, director of the Division of Nutritional Sciences; and animal sciences professor Jan E. Novakofski.
Photo by Fred Zwicky


Mate tea is an herbal beverage rich in phytochemicals, flavonoids and amino acids that’s consumed as a stimulant by people in southeastern Latin American countries. The amount of caffeine per serving in mate tea ranges from 65-130 milligrams, compared with 30-300 milligrams of caffeine in a cup of brewed coffee, according to the study.

For four weeks, the rats in the study ate a diet that contained 40% fat, 45% carbohydrate and 15% protein. They also ingested one of the forms of caffeine in an amount equivalent to that of a human who drinks four cups of coffee daily.

At the end of the four-week period, the percentage of lean body mass in the various groups of rats differed significantly. The rats that ingested caffeine from mate tea, coffee or synthetic sources accumulated less body fat than rats in the other groups.

The study, published recently in the Journal of Functional Foods, adds to a growing body of research that suggests mate tea may help fight obesity in addition to providing other beneficial health effects associated with the phenolic compounds, vitamins and flavonoids it contains.

“Considering the findings, mate tea and caffeine can be considered anti-obesity agents,” said Elvira Gonzalez de Mejia, a co-author of the study and director of the division of nutritional sciences at the U. of I. “The results of this research could be scaled to humans to understand the roles of mate tea and caffeine as potential strategies to prevent overweight and obesity, as well as the subsequent metabolic disorders associated with these conditions.”

In the rats, the accumulation of lipids in the adipocytes was significantly associated with greater body weight gain and increased body fat, according to the study.

To determine the mechanism of action, the scientists performed cell culture studies in which they exposed adipose cells from mice to synthetic caffeine or the coffee or mate caffeine extracts. They found that regardless of its source, caffeine decreased the accumulation of lipids in adipose cells by 20%-41%.

The scientists also tracked the expression of several genes associated with obesity and lipid metabolism. These included the fatty acid synthase gene (Fasn), an enzyme compound involved in the synthesis of fatty acids from glucose; and the lipoprotein lipase gene (Lpl), which codes for an enzyme that breaks down triglycerides.

All of the caffeine treatments, regardless of origin, significantly downregulated the expression of both Fasn and Lpl. In the cell cultures, Fasn expression diminished by 31%-39%, while Lpl expression decreased by 51%-69% among cells treated with synthetic caffeine or the caffeine from mate tea or coffee, they found.

In the rats that consumed the mate tea caffeine, expression of Fasn decreased by 39% in their fat tissue and by 37% in their livers, the researchers found.

The decreased expression of Fasn and two other genes in the liver evoked lower production of low-density lipoprotein cholesterol and triglycerides in the liver as well, according to the study.

“The consumption of caffeine from mate or from other sources alleviated the negative impact of a high-fat, high-sucrose diet on body composition due to the modulation of certain lipogenic enzymes in both adipose tissue and the liver,” de Mejia said. “The decreased expression of Fasn and Lpl brought about lower synthesis and accumulation of triglycerides in the adipose tissue.”

Then-graduate student Fatima J. Zapata was the lead author of the study, which was co-written by graduate student Miguel Rebollo-Hernanz, animal sciences professor Jan E. Novakofski and nutritional sciences professor Manabu T. Nakamura.

The work was funded by the U. of I. Division of Nutritional Sciences.




Contacts and sources:
Elvira Gonzalez de Mejia
University of Illinois at Urbana-Champaign



Citation:Caffeine, but not other phytochemicals, in mate tea (Ilex paraguariensis St. Hilaire) attenuates high-fat-high-sucrose-diet-driven lipogenesis and body fat accumulation. Fatima J. Zapata, Miguel Rebollo-Hernanz, Jan E. Novakofski, Manabu T. Nakamura, Elvira Gonzalez de Mejia. Journal of Functional Foods, 2019; 103646 DOI: 10.1016/j.jff.2019.103646





Forgetfulness Might Depend On Time Of Day Says Study



Can’t remember something? Try waiting until later in the day. Researchers have identified a gene in mice that seems to influence memory recall at different times of day and tracked how it causes mice to be more forgetful just before they normally wake up. A recent mouse study connects body clock and memory recall.

“We may have identified the first gene in mice specific to memory retrieval,” said Professor Satoshi Kida from the University of Tokyo Department of Applied Biological Chemistry.


Researchers tested mice's memory of the same object at different times of day to distinguish between them not having learned to recognize the object (memory formation problem) and them not remembering (memory recall problem).

Credit:  Original illustration by Hidemi Takeshita, all rights reserved.

Every time you forget something, it could be because you didn’t truly learn it — like the name of the person you were just introduced to a minute ago; or it could be because you are not able to recall the information from where it is stored in your brain — like the lyrics of your favorite song slipping your mind.

Many memory researchers study how new memories are made. The biology of forgetting is more complicated to study because of the difficulties of distinguishing between not knowing and not recalling.

“We designed a memory test that can differentiate between not learning versus knowing but not being able to remember,” said Kida.

Researchers tested the memories of young adult male and female mice. In the “learning,” or training, phase of the memory tests, researchers allowed mice to explore a new object for a few minutes.

Later, in the “recall” phase of the test, researchers observed how long the mice touched the object when it was reintroduced. Mice spend less time touching objects that they remember seeing previously. Researchers tested the mice’s recall by reintroducing the same object at different times of day.

They did the same experiments with healthy mice and mice without BMAL1, a protein that regulates the expression of many other genes. BMAL1 normally fluctuates between low levels just before waking up and high levels before going to sleep.

Mice trained just before they normally woke up and tested just after they normally went to sleep did recognize the object.

Mice trained at the same time — just before they normally woke up — but tested 24 hours later did not recognize the object.

Healthy mice and mice without BMAL1 had the same pattern of results, but the mice without BMAL1 were even more forgetful just before they normally woke up. Researchers saw the same results when they tested mice on recognizing an object or recognizing another mouse.

Something about the time of day just before they normally wake up, when BMAL1 levels are normally low, causes mice to not recall something they definitely learned and know.

According to Kida, the memory research community has previously suspected that the body’s internal, or circadian, clock that is responsible for regulating sleep-wake cycles also affects learning and memory formation.

“Now we have evidence that the circadian clocks are regulating memory recall,” said Kida.

Researchers have traced the role of BMAL1 in memory retrieval to a specific area of the brain called the hippocampus. Additionally, researchers connected normal BMAL1 to activation of dopamine receptors and modification of other small signaling molecules in the brain.

“If we can identify ways to boost memory retrieval through this BMAL1 pathway, then we can think about applications to human diseases of memory deficit, like dementia and Alzheimer’s disease,” said Kida.

However, the purpose of having memory recall abilities that naturally fluctuate depending on the time of day remains a mystery.

“We really want to know what is the evolutionary benefit of having naturally impaired memory recall at certain times of day,” said Kida.

About the research

Mice are naturally nocturnal. When measured in units of time using zeitgeber, the environmental cue of light turning on, mice are usually asleep from Zeitgeber Time 1 to 12 and awake from Zeitgeber Time 12 to 24. The term “just before normally waking up” refers to Zeitgeber Time 10, while the term “just after normally going to sleep” refers to Zeitgeber Time 4.

Collaborators at the Tokyo University of Agriculture and the University of Toronto also contributed to this research.


Contacts and sources:
University of Tokyo

Citation: Hippocampal clock regulates memory retrieval via Dopamine and PKA-induced GluA1 phosphorylation. Shunsuke Hasegawa, Hotaka Fukushima, Hiroshi Hosoda, Tatsurou Serita, Rie Ishikawa, Tomohiro Rokukawa, Ryouka Kawahara-Miki, Yue Zhang, Miho Ohta, Shintaro Okada, Toshiyuki Tanimizu, Sheena A. Josselyn, Paul W. Frankland, Satoshi Kida. Nature Communications, 2019; 10 (1) DOI: 10.1038/s41467-019-13554-y




New Theory Explaining The “Dark Energy” Phenomenon


Does the Universe have borders?

The International Journal of Modern Physics has published an article by the IKBFU Physics and Mathematics Institute Artyom Astashenok and the Institute’s MA student Alexander Teplyakov. The article refers to the issue of the “Dark Energy” and an assumption is made that the Universe has borders.

Artyom Astashenok said, “The fact that our Universe is expanding was discovered almost a hundred years ago, but how exactly this happens, scientists realized only in the 90s of the last century, when powerful telescopes (including orbital ones) appeared and the era of exact cosmology began. In the course of observations and analysis of the data obtained, it turned out that the Universe is not just expanding, but expanding with acceleration, which began three to four billion years after the birth of the Universe”.

Credit: Immanuel Kant Baltic Federal University

For a long time, it was believed that space is filled with ordinary matter - stars, planets, asteroids, comets and highly rarefied intergalactic gas. But, if this is so, then accelerated expansion is contrary to the law of gravity, which says that bodies are attracted to each other. Gravitational forces tend to slow down the expansion of the Universe but cannot accelerate it.


Artyom Astashenok says: “And then the idea was born that the Universe is filled for the most part not with ordinary matter, but with some "dark energy", which has special properties. No one knows what is it and how it works, so it named “Dark Energy” as something unknown. And 70% of the Universe consists of this Energy”.

There are many theories of what the “Dark Energy” is, and the IKBFU scientists presented their own theory.


“The so-called Casimir effect (named after the Dutch physicist Hendrik Casimir), which consists in the fact that two metal plates placed in a vacuum are attracted to each other, has long been known. It would seem that this cannot be, because there is nothing in the vacuum. But in fact, according to quantum theory, particles constantly appear and disappear there, and as a result of their interaction with plates, which indicate certain boundaries of space (which is extremely important), a very small attraction occurs. And there is an idea according to this, approximately the same thing happens in space. Only this leads, on the contrary, to additional repulsion, which accelerates the expansion of the Universe. That is, there is essentially no “Dark Energy”, but there is a manifestation of the boundaries of the Universe. This of course does not mean that it ends somewhere, but some kind of complex topology can take place. You can draw an analogy with the Earth. After all, it also has no boundaries, but it is finite. The difference between the Earth and the Universe is that in the first case we are dealing with two-dimensional space, and in the second - with three-dimensional”.

The published article, which, as explained by Artem Astashenok, develops the ideas presented in the thesis of Alexander Teplyakov, presents a mathematically sound model of the universe in which additional repulsion occurs, and where there is no contradiction between the fact that the expansion of the Universe accelerates and the law of universal gravitation.



Contacts and sources:
Sergey Bulanov
Immanuel Kant Baltic Federal University

Citation:   Some models of holographic dark energy on the Randall–Sundrum brane and observational data A. V. Astashenok and A. S. Tepliakov International Journal of Modern Physics D   https://doi.org/10.1142/S0218271819501761  https://www.worldscientific.com/doi/abs/10.1142/S0218271819501761





Cultural Evolution Caused Broad-Scale Historical Declines Of Large Mammals Across China

Local extinction of 5 megafauna taxa from much of China over the past 2 millennia were found to be closely linked to filtering effects driven by cultural evolution rather than climate change.

Cultural evolution has been the dominant driver of range contractions in megafauna taxa across China since the beginning of Common Era, with little or no direct importance of climate. A research team led by Aarhus University along with collaborators from Nanjing University analyzed maps of megafauna distribution dynamics and societal development based on Chinese archival records alongside data on climate across China from 2 to 1953 CE.

Human activities are now playing a dominant role in driving changes in Earth's biodiversity and are responsible for the incipient sixth mass extinction, but the historical processes leading to this situation are poorly understood, often without emphasis on cultural evolution as a potential key process underlying anthropogenic impacts. A team of researchers from Aarhus University and Nanjing University has now shown that cultural evolution overshadowed climate change in driving historical broad-scale biodiversity dynamics.

Map of the northern boundary of Asian elephant (Elephas maximus) in the study area over the past four millennia, based on multiple archaeological and historical sources. The distribution dynamics were inconsistent with the trend of mean annual temperature across the study area. Oracle bone scripts were used for divination by a cultural group recognized as Chinese ancestors ruling much of the North China Plain. The significant similarity between these scripts and their modern forms for the large mammals supports the past wide distribution of these taxa in ancient China.
 
Credit: Shuqing Teng

By mining the deep Chinese administrative records in relation to culturally important wild megafauna species as well as sociocultural development, the researchers identified the millennia-long spread of agricultural land and agricultural intensification, as well as the specific expansion of the Han culture, as the main cause of the extirpation of five megafauna species from much of China, with little or no direct importance of climate.

Cultural evolution, not climate change, as the main driver

"China's well-preserved written records for more than 2000 years provide a unique opportunity to reconstruct long-term dynamics of culture-nature interactions across large geographical extents," says senior author Professor Jens-Christian Svenning, director of Center for Biodiversity Dynamics in Changing World (BIOCHANGE), Aarhus University. The five studied megafauna taxa include Asiatic elephant (Elephas maximus), Asian rhinoceroses (Rhinoceros sondaicus, R. unicornis and Dicerorhinus sumatrensis), tiger (Panthera tigris), Asiatic black bear (Ursus thibetanus), and brown bear (Ursus arctos), all of which were widely distributed across the study area and have played an important role in ancient China's cultural activities.

The Sumatran rhinoceros (Dicerorhinus sumatrensis) was widely distributed in eastern China in historical times, but was extirpated due to increasing human pressure -- and process that has continued to the present day in its remaining range in southeast Asia, threatening to cause the complete extinction of this species, with likely less than 80 individuals surviving, all in Indonesia.

Credit: Drawing by Friedrich Wilhelm Kuhnert, https://commons.wikimedia.org/wiki/File:Rauhohr-Nashorn-drawing.jpg, CC0 Public Domain

"Ancient China used to host a highly biodiverse assemblage of large mammals even in its nowadays densely populated areas such as the North China Plain and the Middle-Lower Yangtze Plain. Our research shows that the relatively recent loss of this rich megafauna in large part can be attributed to the southward expansion of intensified agricultural practices with the Han culture, which originated in North China," explains postdoc Shuqing Teng from Aarhus University and Nanjing University, the first author of the study.

Regional extirpation of these taxa from the study area were consistent with the sociocultural dynamics described above, but inconsistent with climate change. There were at least two conspicuous cooling-warming cycles during the last two thousand years, including the Medieval Warm Period and the Little Ice Age, with fluctuations of mean annual temperature around 1 to 1.5 °C, but neither had a conspicuous effect on the megafauna range dynamics.

Importance of cultural filtering

The study provides clear evidence that cultural evolution historically has overshadowed past climate change in shaping broad-scale megafauna patterns, in contrast to the common belief that human societies were unimportant in driving biodiversity dynamics at such large spatiotemporal scales until recent time frames such as the Industrial Revolution or the Great Acceleration of the 20th century.

This finding highlights the importance of culture's role in filtering current ecological assemblages from historical species pools. Perspectives through the lens of cultural filtering should also stimulate thoughts on what is natural - notably helping to overcome the Shifting Baseline Syndrome, the tendency to accept an already degraded state as natural due to lacking recognition of earlier declines - and which natural world we aim to conserve or restore.

Furthermore, modification of cultural filters will be key to respond to the challenges of the Anthropocene biodiversity crisis, as it is fundamentally culturally driven, as shown by this study of historical China, and how to achieve this is an important research challenge.




Contacts and sources:
Jens-Christian Svenning
Aarhus University

Citation: Long-term effects of cultural filtering on megafauna species distributions across China Shuqing N. Teng, Chi Xu, Licheng Teng, and Jens-Christian Svenning. PNAS first published December 23, 2019 http://dx.doi.org/10.1073/pnas.1909896116 https://www.pnas.org/content/early/2019/12/17/1909896116