Scientists took a rare chance to prove we can quantify biodiversity by ‘testing the water’

Scientists took a rare chance to prove we can quantify biodiversity by 'testing the water'
EA team operating at the fishery farm during fish translocation. Credit: Dr. Watson H.V.

Organisms excrete DNA in their surroundings through metabolic waste, sloughed skin cells or gametes, and this genetic material is referred to as environmental DNA (eDNA).


As eDNA can be collected directly from water, soil or air, and analysed using molecular tools with no need to capture the organisms themselves, this genetic information can be used to report biodiversity in bulk. For instance, the presence of many fish species can be identified simultaneously by sampling and sequencing eDNA from water, while avoiding harmful capture methods, such as netting, trapping or electrofishing, currently used for fish monitoring.

While the eDNA approach has already been applied in a number of studies concerning fish diversity in different types of aquatic habitats: rivers, lakes and marine systems, its efficiency in quantifying species abundance (number of individuals per species) is yet to be determined. Even though previous studies, conducted in controlled aquatic systems, such as aquaria, experimental tanks and artificial ponds, have reported positive correlation between the DNA quantity found in the water and the species abundance, it remains unclear how the results would fare in natural environments.

Scientists took a rare chance to prove we can quantify biodiversity by 'testing the water'
Drained pond after fish translocation. Credit: Dr. Watson H.V.

However, a research team from the University of Hull together with the Environment Agency (United Kingdom), took the rare opportunity to use an invasive species eradication programme carried out in a UK fishery farm as the ultimate case study to evaluate the success rate of eDNA sampling in identifying species abundance in natural aquatic habitats. Their findings were published in the open-access, peer-reviewed journal Metabarcoding and Metagenomics.

“Investigating the quantitative power of eDNA in natural aquatic habitats is difficult, as there is no way to ascertain the real species abundance and biomass (weight) in aquatic systems, unless catching all target organisms out of water and counting/measuring them all,” explains Cristina Di Muri, Ph.D. student at the University of Hull.

During the eradication, the original fish ponds were drained and all fish, except the problematic invasive species: the topmouth gudgeon, were placed in a new pond, while the original ponds were treated with a piscicide to remove the invasive fish. After the eradication, the fish were returned to their original ponds. In the meantime, all individuals were counted, identified and weighed from experts, allowing for the precise estimation of fish abundance and biomass.

Scientists took a rare chance to prove we can quantify biodiversity by 'testing the water'
Environmental DNA sampling using water collection bottles. Credit: Dr. Peirson G.

“We then carried out our water sampling and ran genetic analysis to assess the diversity and abundance of fish genetic sequences, and compared the results with the manually collected data. We found strong positive correlations between the amount of fish eDNA and the actual fish species biomass and abundance, demonstrating the existence of a strong association between the amount of fish DNA sequences in water and the actual fish abundance in natural aquatic environments”, reports Di Muri.

The scientists successfully identified all fish species in the ponds: from the most abundant

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In Monterey Bay, California, scientists grab the chance to study white sharks up close

Growing over six meters (20 feet) long and armed with hundreds of serrated, razor-sharp teeth, white sharks are the world’s largest predatory fish.



a fish swimming under water


© Stanford University


In late summer and fall, up to 250 white sharks congregate in Monterey Bay, off the central Californian coast, to feast on marine mammals — including elephant seals and sea lions — that gather here to breed.

From a shark’s perspective, “think of Monterey Bay as having one of the best fast food restaurants on the planet,” says shark expert and Stanford professor, Barbara Block.

Block also travels to Monterey Bay because the annual marine mammal “buffet” offers her an ideal opportunity to study the sharks up close. She and her team lure the “curious” sharks alongside their small boat, attach electronic tags to their dorsal fins, and then track the sharks as they swim out to the open ocean and dive to depths of 2,000 meters (6,500 feet).

Data on white shark population sizes, life histories and migratory patterns, can be used to inform marine protection policy, says Block, adding that sharks play a vital role in maintaining ecological balance in the ocean. “We need these apex predators to keep our ecosystems healthy.”

Watch the video above to find out more.

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Stanford University Report Ranks Vice President of Academic Affairs Dr. Mohammed Cherkaoui Among the World’s Top 2% of Scientists

In the discipline of “materials” science, Dr. Cherkaoui ranked in the top 3,000 of the world’s more than 177,000 researchers in the field. He is best known for his pioneering work in micromechanics and nuclear engineering, and he has authored more than 200 publications including the first-ever micromechanics textbook. His international accolades include the France Medal from the National Center for Scientific Research, the Obama Award under the Material Genome Initiative, and the Lorraine Award for Excellence in Technology Transfer. He has also achieved a tenured professorship at Georgia Institute of Technology and a Boeing Endowed Chair and professorship at Mississippi State University.

“I am humbled by this recognition, and I owe a debt of gratitude to all of my co-authors and the vast network of Ph.D. students and contributors who have supported my work throughout my career,” said Dr. Cherkaoui. “I am proud to bring LIU to the forefront of global research as we strive to become a world-leading, pioneering university of the future.”

Dr. Cherkaoui was a pioneering influence of the International University of Rabat in Morocco, the International Joint Units (UMI) research institution between the French government and the Georgia Institute of Technology, and the France National Center for Scientific Research. He is a member of the European Commission material science division, and he is the associate editor of the American Society of Mechanical Engineers Journal of Engineering Materials and Technology.

“Dr. Cherkaoui’s visionary leadership and collaborative approach to interdisciplinary research across LIU has led to some of our most forward-thinking initiatives such as our Digital Health Institute and competitive artificial intelligence program,” said LIU President Dr. Kimberly R. Cline. “I am proud to see him recognized as one of the world’s greatest scientists; an honor he truly deserves.” 

About Long Island University
Long Island University, founded in 1926, continues to redefine higher education, providing high quality academic instruction by world-class faculty. Recognized by Forbes for its emphasis on experiential learning and by the Brookings Institution for its “value added” to student outcomes, LIU offers close to 265 accredited programs, with a network of 267,000 alumni that includes industry leaders and entrepreneurs all across the globe. Visit liu.edu for more information. 

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Tropical reef fish, 81, is the oldest ever discovered by scientists

The octogenarian fish, which is old enough to have lived through World War II, was found by the Australian Institute of Marine Science at the Rowley Shoals, about 300 kilometers (186 miles) west of Broome, as part of a study into the longevity of tropical fish.

Researchers looked at three species they said were not commonly targeted by commercial or recreational fishing in Western Australia and the Chagos Archipelago in the central Indian Ocean. The species included red bass, midnight snapper and black and white snapper.

Long in the tooth: Greenland shark named longest-living vertebrate

The 81-year-old midnight snapper was identified alongside 10 other fish over the age of 60, including a 79-year-old red bass that was also caught in the Rowley Shoals — an area spanning three coral reefs at the edge of Australia’s continental shelf.

Marine scientists determined the age of the fish by dissecting them and studying their ear bones, or otoliths, which contain annual growth bands that can be counted in a similar way as tree rings.

Brett Taylor, a fish biologist who led the study, said the midnight snapper beat the previous record holder by two decades.

“Until now, the oldest fish that we’ve found in shallow, tropical waters have been around 60 years old,” he said.

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“We’ve identified two different species here that are becoming octogenarians, and probably older.”

Taylor said the research would help scientists understand how fish length and age will be affected by climate change.

“We’re observing fish at different latitudes — with varying water temperatures — to better understand how they might react when temperatures warm everywhere,” he said.

The octogenarian fish is not the oldest sea-dwelling creature to exist.

Greenland sharks, which are native to Arctic seas, are the longest-living vertebrate on Earth. University of Copenhagen researchers estimated that these sharks live to at least 400 years, nearly two centuries longer than the whales.

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The Milky Way and beyond: Scientists publish new data on nearly 2 billion stars

As of today (Dec. 3), scientists have 1.8 billion local stars at their fingertips.

That bounty is thanks to the European Space Agency’s Gaia mission, which has spent 6.5 years tracking stars in our Milky Way galaxy and beyond. Using the spacecraft’s observations, scientists can create a precise 3D map of stars and find patterns playing out across the galaxy.

“Essentially all of astronomy benefits from this one way or another because it’s very fundamental data,” Anthony Brown, an astronomer at the University of Leiden in the Netherlands and chair of the Gaia Data Processing and Analysis Consortium Executive team, told Space.com. “It’s a very, very broad survey mission.”

Related: This 3D color map of 1.7 billion stars in the Milky Way is the best ever made

This image shows the paths of 40,000 stars located within 326 light-years of our Milky Way galaxy over the next 400,000 years based on measurements and projections from the European Space Agency’s Gaia spacecraft.. (Image credit: ESA/Gaia/DPAC; CC BY-SA 3.0 IGO. Acknowledgement: A. Brown, S. Jordan, T. Roegiers, X. Luri, E. Masana, T. Prusti and A. Moitinho.)

Studying 1.8 billion stars is impressive, of course, but the heart of the mission’s science is the statistical analysis that such large amounts of data facilitate. “I think the precise number doesn’t matter so much,” Brown said. “We’re still only observing probably about 1% of all the stars in the Milky Way, even with this enormous number.”

Although today is scientists’ first chance to access the data publicly, Gaia team members have already dug through it to conduct some initial analyses. One result of that work is that scientists have measured how the solar system is accelerating in its orbit of the Milky Way, a tiny phenomenon.

To do so, Gaia studied more than a million quasars — bright objects at the hearts of galaxies — located so far away that they shouldn’t appear to move. But they do, and in a pattern that points to the center of the center of the Milky Way and reflects all the different tiny tugs that the solar system experiences from neighboring objects.

The result is a value that’s a fraction of a fraction of a meter, measured with a precision still smaller, an eye-wateringly tiny number that couldn’t be calculated meaningfully until the new data release.

“It’s amazing that one can do this,” Brown said of the measurement.

And that’s just the beginning. Today’s data is the Gaia spacecraft’s third trove and includes nearly three years’ worth of observations, less than half of what has been gathered so far. (The disconnect stems from the sheer bulk of data Gaia collects and the processing work that 400 team members spread across Europe must do to turn it into the public results.) And at least two more data releases are planned, potentially more if Gaia’s mission is extended to last a full decade.

Among plenty of other research, the previous data release allowed scientists to track the formation history

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Puerto Rican scientists, shattered by collapse of Arecibo Observatory, push to rebuild

Génesis Ferrer had dreamed of working in the Arecibo Observatory ever since she first met some of its astrophysicists during a high school trip in Puerto Rico.

After hearing them use terms such as “radiation” and “emission,” Ferrer, 21, said she “just fell in love with the entire idea of being able to understand things so far away.” Like many scientists in the U.S. territory, Ferrer can trace back her interest in astrophysics, biophysics and space to that school trip.

The fourth-year physics student from the University of Puerto Rico, Río Piedras campus, had recently earned a fellowship from the Puerto Rico NASA Space Consortium to study emissions from red dwarf stars using the giant radio telescope in Arecibo. Because of coronavirus restrictions, Ferrer has been accessing the data she needs from the Arecibo Observatory remotely, hoping she would soon be able to finish her investigation in the place where it all started.

Those hopes faded away Tuesday morning when the Arecibo Observatory collapsed. The telescope’s 900-ton receiver platform and the Gregorian dome — a structure as tall as a four-story building that houses secondary reflectors — fell onto the northern portion of the vast reflector dish more than 400 feet below after the main cables holding up the structures broke overnight.

“I was very sad, very disappointed,” Ferrer told NBC News. “I worked so hard to finally get accepted to work in the Arecibo Observatory. And now that I got accepted, I can’t work in it. I felt very sad, not only individually, but I also saw it as a very sad thing for Puerto Rico and the science in Puerto Rico.”

The Arecibo Observatory was the largest radio telescope in the world and a point of pride for Puerto Ricans, whether they were in science or not. About 90,000 islanders and tourists visited the observatory every year, a boon to the region.

During its almost 57 years in operation, the observatory built with money from the U.S. Department of Defense has been at the forefront of space research — and a crucial training ground for space science students.

In August, the observatory started crumbling after an auxiliary cable snapped, causing damage to the telescope’s dish and the receiver platform that hung above it, according to the U.S. National Science Foundation, the federal agency that owns the observatory. In an attempt to prevent “an uncontrolled collapse” in order to “safely preserve other parts of the observatory that could be damaged or destroyed,” the agency said it began its plan to decommission the telescope in mid-November.

“The NSF was taking a long time to do this because they have a series of protocols they have to follow,” said Abel Méndez, director of the Planetary Habitability Laboratory at the University of Puerto Rico, Arecibo campus, and a planetary astrobiologist. “We thought they had an emergency plan that could speed things up.”

But the cables failed before the agency was able to preserve the telescope.

Dreams to do science in Puerto Rico

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Scientists discover new way to measure turbulence of large planets and exoplanets

Scientists discover new way to measure turbulence of large plan
The planet Jupiter. Credit: NASA/JPL-Caltech/SwRI/MSSS/Gerald Eichstadt/Sean Doran

The swirls, eddies, and wavy bands of Jupiter and Saturn may remind us of a soothing, starry, starry night—but they reveal these two gas giants to be stormy, turbulent places. The turbulence produces energy cascades, a non-linear transfer of energy between different scales of motion. These are as fundamental to understanding planetary dynamics as the cardiovascular system is to understanding the human body.


But scientists haven’t had a reliable way to quantify planetary turbulence—until now.

A global team led by scientists at the University of Rome, which included Boris Galperin, Ph.D., a professor at the USF College of Marine Science, described the advance in Geophysical Research Letters. The results show that the rate of the turbulence energy transfer—until now a black box of mystery—can be calculated relatively easily from a variable related to the planetary rotation and known as potential vorticity (PV).

The method was first developed by Galperin and his graduate student, Jesse Hoemann, and tested in the experiments conducted at the University of Rome during Jesse’s visit there. The method was confirmed using real velocity data extracted from images of Jupiter’s clouds movement captured by the 20-year-long Cassini mission, additional laboratory results performed in a rotating tank at the University of Rome in Italy, and computer simulations for Saturn.

Based on the calculations of PV, the team showed for the first time that the rate of the energy transfer in Jupiter’s atmosphere is four times greater than that in Saturn’s.

Scientists discover new way to measure turbulence of large plan
Banded flows on Jupiter and Saturn (from Cassini), and in a rotating tank experiment by Cabanes et al. (2020), showing non-monotonic PV profiles. Credit: University of South Florida

“Now you can see why I was really excited about this work,” said Galperin, who developed the original idea for the experiments several years ago.

Since the laws of turbulence, as any fundamental physical laws, are universal, the method can now be applied to other natural environments such as the ocean, Galperin said. Eddies in Earth’s ocean that look like the swirls on Jupiter, for example, come in different strengths, sizes, and lifetimes, and are critical to understanding Earth’s balances of energy, heat, salt, carbon dioxide, and more.

“This is the first estimate of Saturn’s turbulent power from observations, and this study paves the way for future data analysis in other planetary atmospheres,” said lead author Simon Cabanes, Ph.D., a post doc at the Department of Civil and Environmental Engineering (DICEA) of the University of Rome La Sapienza.


Weather on Jupiter and Saturn may be driven by different forces than on Earth


More information:
Simon Cabanes et al. Revealing the intensity of turbulent energy transfer in planetary atmospheres, Geophysical Research Letters (2020). DOI: 10.1029/2020GL088685
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Scientists discover new way to measure turbulence of large planets and exoplanets (2020, December 2)
retrieved 2 December 2020
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Scientists just mapped 1 million new galaxies, in 300 hours

Astronomers in Australia have just mapped 83% of the observable universe, in just 300 hours.



a traffic light sitting on the beach: The ASKAP radio telescope array, located in the Australian outback, just mapped 3 million galaxies in less than a month.


© Provided by Live Science
The ASKAP radio telescope array, located in the Australian outback, just mapped 3 million galaxies in less than a month.

This new sky survey, which Australia’s national science agency (CSIRO) described in a statement as a “Google map of the universe” , marks the completion of a big test for the Australian Square Kilometre Array Pathfinder (ASKAP) radio telescope –- a network of 36 antennas rooted in the remote Western Australia Outback. While astronomers have been using ASKAP to scour the sky for radio signatures (including mysterious fast radio bursts) since 2012, the telescope’s full array of antennas has never been used in a single sky survey –- until now.

By harnessing the telescope’s full potential, researchers mapped roughly 3 million galaxies in the southern sky, according to a paper published Nov. 30 in the journal Publications of the Astronomical Society of Australia. As many as 1 million of these distant galaxies may be previously unknown to astronomy, the researchers wrote, and that’s likely just the beginning. With the success of this first survey, CSIRO scientists are already planning even more in-depth observations in the coming years.

Related: Scientists unveil largest 3D map of the universe ever

“For the first time, ASKAP has flexed its full muscles, building a map of the universe in greater detail than ever before, and at record speed,” lead study author David McConnell, a CSIRO astronomer, said in a statement. “We expect to find tens of millions of new galaxies in future surveys.”

Many all-sky surveys can take months, even years, to complete. CSIRO’s new effort, which they’ve labeled the Rapid ASKAP Continuum Survey, only took a few weeks of stargazing. While each of the telescope’s 36 receivers took vast, panoramic pictures of the sky, a dedicated network of supercomputers worked double-time to combine them. The resulting map, which covers 83% of the sky, is a combination of 903 individual images, each containing 70 billion pixels. (For comparison, the highest-definition cameras for sale snap a few hundred million pixels per image).

Each of these images will be made publicly available through CSIRO’s Data Access Portal, as scientists analyze the results and plan for their next sky-charting adventures.

Originally published on Live Science.

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To study aging, scientists are looking to outer space

As anyone who has experienced middle age will know, the process of growing old can be extremely hard on the body. Your bones begin to leak calcium, your muscles begin to shrivel, the immune system weakens, and arthritis can set in. Poor posture and balance affect how you move about the world, while cataracts and deteriorating eyesight impair how you see it. Heart problems and declining cognitive function eventually set in as people approach the end of their lives.



Mark Kelly in a blue shirt: Former NASA astronauts and identical twins Scott Kelly (right) and Mark Kelly. Scott spent a year on the ISS from 2015 to 2016 while Mark stayed on Earth, allowing scientists to study the effects of living in space on Scott's body and compare the changes to Mark.


© Photograph by ROBERT MARKOWITZ, NASA

Former NASA astronauts and identical twins Scott Kelly (right) and Mark Kelly. Scott spent a year on the ISS from 2015 to 2016 while Mark stayed on Earth, allowing scientists to study the effects of living in space on Scott’s body and compare the changes to Mark.


These symptoms, however, can also be caused by something less common: space travel.

Spaceflight influences biology in dramatic ways, and people in space appear to experience the effects of aging faster than people on Earth. Now, scientists have gained a better understanding of space travel’s influence on living beings than ever before. A slew of 29 papers recently published in the journals Cell, Cell Reports, iScience, Cell Systems, and Patterns examine the biological hazards of spaceflight in 56 astronauts—more than 10 percent of all the people who have ever been to space.



NASA astronauts Terry Virts (right) and Scott Kelly perform experiments for Rodent Research-2, a commercial investigation of the effects of spaceflight on the muscles, skeletons, and nervous systems of mice that were launched to the ISS on April 14, 2015.


© Photograph by NASA

NASA astronauts Terry Virts (right) and Scott Kelly perform experiments for Rodent Research-2, a commercial investigation of the effects of spaceflight on the muscles, skeletons, and nervous systems of mice that were launched to the ISS on April 14, 2015.


The new studies bring us a step closer to identifying the mechanisms underpinning the biological responses to living in space. More than 200 scientists demonstrated that space upends the genes, mitochondrial function, and chemical balances in the cells to trigger a cascade of broader health effects in spacefaring humans and animals.

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“The entire body is affected, because [space] is such a different and extreme environment,” says Susan Bailey, a radiologist at Colorado State University who participated in multiple of the new studies.

The health effects associated with spaceflight have several similarities to aging-related disorders, such as cancer and osteoporosis. While spaceflight’s parallels to aging are a concern for long-term crewed missions—such as those that would be required on a voyage to Mars—the unique space environment also presents a unique opportunity to study the physiology of aging.



NASA’s Rodent Habitat, shown here with one of the two access doors open, provides long-term housing for rodents aboard the International Space Station.


© Photograph by Dominic Hart, NASA
NASA’s Rodent Habitat, shown here with one of the two access doors open, provides long-term housing for rodents aboard the International Space Station.

It’s estimated that the heart, blood vessels, bones, and muscles deteriorate more than 10 times faster in space than by natural aging. This means to study the aging process, scientists don’t have to wait for their biological subjects to naturally mature on Earth—they can harness the accelerated health effects by running experiments on the International Space Station (ISS).

Scientists stress that the symptoms of space

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Scientists map ‘new atlas of the universe’



The new telescope has already mapped a million new galaxies


© CSIRO
The new telescope has already mapped a million new galaxies

Australian scientists say they have mapped a million new galaxies using an advanced telescope in the desert.

The CSIRO, the national science agency, said its new telescope had created “a new atlas of the universe” in record time – showing unprecedented detail.

It mapped three million galaxies in total, with pictures revealing twice the level of detail of previous surveys, the study said.

Astronomers hope the images will lead to new discoveries about the universe.

The CSIRO said the mapping took just 300 hours, whereas previous all-sky surveys had taken years.

With the data publicly available, scientists around the world would be able to study “everything from star formation to how galaxies and their super-massive black hole evolve and interact”, said lead author Dr David McConnell.

“We expect to find tens of millions of new galaxies in future surveys,” he added.

The initial results were published on Tuesday in the Publications of the Astronomical Society of Australia.

What is this telescope?

The Australian Square Kilometre Array Pathfinder (Askap) is a collection of 36 dish antennas which work together to take panoramas of the sky.

The system is located in the southern hemisphere in remote outback Western Australia. It is spread across a 6km (3.7 miles) area at the CSIRO’s Murchison observatory about 700km north of Perth.



a close up of a boat: The Askap telescope consists of a collection of dishes across the Western Australia desert


© CSIRO
The Askap telescope consists of a collection of dishes across the Western Australia desert

By combining signals from smaller dishes, the telescope creates high-resolution images at a fraction of the cost of one very large dish, said the CSIRO.

The huge volumes of data – generated at a faster rate than Australia’s entire internet traffic – are then sent to supercomputer processing facility in Perth to create the images.

What has it found?

Askap conducted its first all-sky survey this year, covering 83% of the sky and covering three million galaxies all up.

The map was stitched together using just 903 highly detailed images. Previous surveys have needed tens of thousands to complete a picture of the sky.

Astronomers said the depth and scale was exciting because by cataloguing the millions of galaxies beyond the Milky Way, they can conduct statistical analyses. These can help with understanding of how the universe evolved and is structured.

The Askap telescope is one of the precursors to an international project to build the world’s largest radio telescope – the Square Kilometre Array, to be located in South Africa and Australia.

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