Hexbyte Glen Cove Endangered rusty patched bumblebee is at the center of a legal challenge

Posted on March 31, 2021March 31, 2021 by Elroy Antes

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Credit: CC0 Public Domain

Conservation groups are making another push to protect habitat for the endangered rusty patched bumblebee, a creature that once buzzed throughout much of the United States and today is an insect you’re lucky to spot at all.

A federal lawsuit challenging a decision by the U.S. Fish and Wildlife Service to not designate critical habitat for the bee was filed last week by the Natural Resources Defense Council, the Center for Biological Diversity and Friends of Minnesota Scientific and Natural Areas. It’s the latest in a series of legal challenges in the lead-up to and aftermath of the bee’s listing under the Endangered Species Act.

The bee, which at one point existed in nearly 30 states including Illinois, is the first and only bumblebee listed under the act. A little more than two decades ago, its numbers began a sharp drop—crashing by at least 87%. The listing means the species was found to be at risk of extinction; recovery efforts are underway.

Like monarch butterflies, the bee is thought of as a species that can encourage conservation and open the door to creating pollinator habitat. Pollinators are responsible for a significant amount of food supply and the overall health of ecosystems. The rusty patched bumblebee might not be as flashy as the monarch, but it’s thick and fuzzy and adorable, as far as bugs go.

As the legal challenge moves ahead, local efforts to encourage habitat creation for the bee are picking up. And rusty patched hopefuls are still on the lookout for a rare sighting of a bumblebee with a tawny marking below black and yellow stripes.

In August 2018, Andrea Gruver was conducting graduate research as part of a joint program between Northwestern University and the Chicago Botanic Garden when she saw something she wasn’t expecting. And something she hasn’t seen since.

Gruver’s research involved the effects of urbanization on bees. She set up field sites, some more urban, some less, and waited to see which bees showed up.

“I was like, I don’t think that’s a rusty patched,” Gruver said. “The probability of it being a rusty patched bumblebee is very low.”

But two rusty patched bumblebees happened to be foraging around Rogers Park near the Metra station. Confirmation of the bee brought a sigh of relief.

“This is a really good sign that this bee is still here and it’s even in Chicago,” Gruver said. “Potentially, these could be areas that could really harbor a lot of bee diversity.”

Last year, the Fish and Wildlife Service determined that designating critical habitat for the bee was “not prudent,” arguing that its recovery didn’t depend primarily on specific habitat.

“As a habitat generalist, the rusty patched bumble bee can find the habitat it needs in a variety of ecosystems, including prairies, woodlands, marshes, agricultural landscapes and residential parks and gardens, all of which are abundant across the bee’s range,” said Lori Nordstrom, assistant regional director for Ecological Services in the Great Lakes region, in the agency’s news release announcing the decision.

But some conservation groups argue the bee should get a full suite of protections.

There can be instances in which the habitat designation, which offers another round of regulatory checkpoints, isn’t needed, said Lori Ann Burd, the Center for Biological Diversity’s environmental health director. But this isn’t one of those cases.

“This was a Trump-era decision,” Burd said. “I really hope that the Biden administration realizes that they have an opportunity to really make a difference in the pollinator crisis. Extinction is a political choice and the solutions to extinction are political choices. And this is just a question of mustering the political will to give the species what it is entitled to and what it needs to not go extinct.”

Burd said she’s hoping to see a shift in how the Fish and Wildlife Service takes action on endangered species, from the rusty patched bumblebee to the monarch butterfly. “I think they both tell the story of how these once-widespread generalists are tanking because of human action,” Burd said.

Some bumblebee populations are shrinking at a significantly more rapid pace than others. As is often the case with threatened species, there’s not one clear cause accepted as the definitive answer to the rusty patched bumblebee’s decline. There is a mix of hazards, which together can increase the potential for harm.

The Fish and Wildlife Service’s 2016 species status assessment, which helps inform the decision to list a species as endangered, identified some main concerns: pathogens, pesticides, habitat loss and degradation, climate change and problems caused by small populations.

The species’ reduction correlates with the spread of a fungus called nosema bombi. The pathogen may have “spilled over” into populations like the rusty patched bumblebee from commercial bees, but the link has not been proved.

Sydney Cameron, a professor in the department of entomology at the University of Illinois at Urbana-Champaign, led a study that found declining populations of some bumblebees, including the rusty patched, were more frequently infected with the fungus.

“I was actually not a believer, it seemed too simple a story,” Cameron said. “But everything just really seemed to converge strongly on that hypothesis.”

Researchers don’t know why the rusty patched bumblebee largely disappeared from the East but is still in pockets of the upper Midwest, Cameron said.

“I think the issue is that any factor that could help bring the species back is important,” Cameron said.

The increased use of neonicotinoids, which act as insect neurotoxins, also correlates to the bee’s decline. Bumblebees are susceptible to the widespread crop and seed treatment, through exposure from plants and in the soil.

Habitat loss negatively affects the bees, the assessment said, but some researchers didn’t see it as the driving factor. The rusty patched once occupied native grasslands in the East and upper Midwest that scientists estimate are almost completely wiped out. The bees also need nesting sites and incoming queens require safe overwintering sites just below ground. And a major requirement is blooming flowers—the bee’s food.

In the Chicago area, local efforts to encourage habitat creation are underway.

Libby Shafer, an Evanston native and graduate student at DePaul University, is interested in what’s going on in our backyards and what our plants mean for the bigger picture.

“I think a lot of people don’t even really realize how their yards contribute to the urban ecosystem,” Shafer said. “The narrative of the rusty patched bumblebee struck me as something that might be compelling to organize people to transform their yards.”

Shafer is launching The Evanston Native Bee Initiative, a community science project in partnership with Natural Habitat Evanston. The project will be based in Evanston, but participation isn’t exclusive to the north suburb. Participants are asked to assess existing plants, grow new plants and document any visiting pollinators through the iNaturalist site. Shafer will then use that data to create maps of each blooming period for the bee and see which host plants might be missing throughout the bee’s lengthy season.

“One yard space can contribute but really what’s most beneficial is having a network of yards,” Shafer said. “The city can serve as a mosaic of habitat patches.”

One group of Evanston neighbors is working to do just that, joining together to create pollinator habitat on the block with grant funds. They’re trying to recruit some new participants so habitat stretches around the corner.

Sarah Abu-Absi, an Evanston resident, said she hopes the project is a way for neighbors to learn from one another.

“I think that residential properties are a crucial component of providing habitat for pollinators and being part of the fight against climate change,” Abu-Absi said.

As she’s learned about bees, Abu-Absi said she wa

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Hexbyte Glen Cove Is battery recycling environmentally friendly?

Posted on March 31, 2021March 31, 2021 by Larisa Mote

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With new solution-based recycling processes, more raw materials can be recovered from batteries. In the picture, a red cobalt salt and a blue-green nickel salt have been obtained from a battery cell. Credit: Valeria Azovskaya/Aalto University

The EU will be home to 30 million electric cars by 2030 and the European Commission is preparing tough targets for recycling these and other batteries. Yet the impacts of battery recycling, especially for the sizeable lithium-ion batteries of the electric cars soon filling our streets, has been largely unstudied.

In a new study, researchers at Aalto University have investigated the environmental effects of a hydrometallurgical recycling process for electric car batteries. Using simulation-based life-cycle analysis, they considered energy and water consumption, as well as process emissions.

“Battery recycling processes are still developing, so their environmental footprints haven’t yet been studied in detail. To be beneficial, recycling must be proven to be more ecological than producing raw materials– we can’t just assume recycling is automatically better, even though we know mining the raw materials has large environmental impacts, like high energy and water consumption,” says Mari Lundström, Assistant Professor at Aalto University.

Battery recycling often uses smelting, which typically loses lithium and other raw materials. Novel hydrometallurgical processes, which separate battery metals from waste by dissolution, enable the recovery of all metals but consume large amounts of energy and chemicals, and often produce contaminated wastewaters.

According to the results, the carbon footprint of the raw material obtained by the recycling process studied is 38% smaller than that of the virgin raw material. The difference is even greater if copper and aluminum recovered during mechanical pre-treatment are included. The results also point to problem areas.

“Life-cycle analysis identifies the areas where recycling can be improved. For example, we noticed that using sodium hydroxide as a neutralizing chemical significantly increases the environmental load of our process,” says Marja Rinne, a doctoral student at Aalto University.

This kind of analysis, which the researchers say has been rarely done for battery recycling, can also be done before new processes are taken into use. It is useful for determining how certain choices or process parameters affect the environmental impacts of a process, so it can be a beneficial decision-making tool for both industry and policymakers.

“Simulation-based life-cycle analysis can be used even at the design stage of recycling processes to assess the environmental impacts and find the best possible options,” says Lundström.

The potential benefits of finding the best recycling processes are substantial; the EU aims to recycle 70% of the mass battery waste by the end of the decade. It is also setting targets for specific metals used in batteries: 95% of cobalt, nickel and copper, and 70% of lithium must be recycled by 2030. It is estimated that the global lithium battery recycling market will be worth 19 billion by 2030.

According to Lundström, now is the time to develop alternative recycling methods, as the amount of battery waste will skyrocket with the rapid growth of electric cars.

“We will have a massive need for recycling, and we have to find the most viable and ecological recycling processes. Research into technological innovations and their environmental impact go hand in hand,” she says.

In the study, the team also assessed the industrial scalability of the process and made recommendations on how to best modify the process accordingly.

More information:
Marja Rinne et al, Simulation-based life cycle assessment for hydrometallurgical recycling of mixed LIB and NiMH waste, Resources, Conservation and Recycling (2021). DOI: 10.1016/j.resconrec.2021.105586

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Is battery recycling environmentally friendly? (2021, March 31)
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Hexbyte Glen Cove ‘Designer’ pore shows selective traffic to and from the cell nucleus

Posted on March 31, 2021March 31, 2021 by Elida Badon

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The team reduced the complexity of nuclear pores down to a single, artificial Nucleoporin that they call ‘NupX’. This protein is based on the average properties of a class of Nucleoporins rich in the amino acid motif Glycine-Leucine-Phenylalanine-Glycine. In these simulation snapshots, each particle represents a whole amino acid. Credit: University of Groningen

The nucleus is the headquarters of a cell and molecules constantly move across the nuclear membrane through pores. The transport of these molecules is both selective and fast; some 1,000 molecules per second can move in or out. Scientists from the University of Groningen and Delft University of Technology, both in the Netherlands, and a colleague from the Swedish Chalmers University of Technology, have developed an artificial model of these pores using simple design rules, which enabled them to study how this feat is accomplished. Their results were published on 31 March in Nature Communications.

Nuclear pores are extremely complicated structures. The pore itself is a big protein complex and the opening of the pore is filled with a dense network of disordered proteins called nucleoporins. These proteins regulate selective transport, but exactly how they do this is still unclear. “The nuclear pore complex is one of the biggest protein structures in the cell,” explains Patrick Onck, professor of Micromechanics at the University of Groningen. “We previously studied the pores in all their complexity, but for this study, we created a drastically simplified ‘designer’ pore to investigate the essential physical mechanisms of transport.”

Nanopore

First, the team analyzed the composition of the nucleoporins to design a simplified, ‘average’ version, which they termed nucleoporin X, or NupX for short. These proteins are made up of domains comprising phenylalanine (F) and glycine (G) amino acids in tandem, and these play an essential role in transport. These FG repeats are separated by ‘spacers’ of other amino acids. In addition to the FG repeats, some nucleoporins also contain domains of glycine, leucine, phenylalanine and glycine, or GLFG repeats. The team designed proteins that contain both domains, separated by spacers of ten amino acids.

NupX was tested in two different systems: it was studied experimentally, attached to a surface and added to artificial nanopores that were ‘drilled’ in a ‘membrane’ of silicon nitride, and through molecular dynamics simulations. The experiments were performed at Delft University of Technology, while the simulations were prepared and executed in Groningen, mostly by Henry de Vries, a Ph.D. student in Onck’s laboratory.

Snapshot of the computer simulations, showing that nanopores filled with NupX-proteins allow specific transport proteins (chaperones) to pass. At the same time, the pores efficiently block any non-specific molecules. Credit: University of Groningen

Transport ticket

The nucleoporins were tested for interactions with non-specific proteins and with chaperones, which are proteins that act as transport tickets through the pore. In the cell, large molecules that must be transported into or out of the nucleus can only do so when they are attached to such a chaperone. The artificial nucleoporins selectively interacted with the chaperones but not with the non-specific proteins. This demonstrated that the NupX pores are fully functional: they are able to facilitate selective transport. De Vries: “However, the experiments showed that transport through the artificial pores occurs but not what happens inside the pore. With our simulations, we showed what exactly happens inside the pore as the chaperones translocate, while the non-specific proteins do not interact with the pore at all.”

The simulations also revealed how the FG and the GLFG nucleoporins were distributed inside the pore. “Recent studies suggested that they would be in different places in nuclear pores and that this might help to create selectivity,” says De Vries. “However, we found that they were homogenously distributed and yet we still saw selectivity.” Another suggestion was that the amino acids that make up the spacers are important for the selectivity. “Our results showed that the specific sequence of amino acids in the spacer doesn’t matter since we used random sequences. The only important part is the ratio of charged amino acids to hydrophobic amino acids within the spacers, which determines the stickiness of the proteins.”

Redundancy

The final conclusion of the study is that a very simple system in nucleoporins that has limited variation still produces a selective pore. “What is needed is a certain density of these FG nucleoporins,” says Onck. “These form a barrier, which can only be breached by the chaperones.” This begs the question of why the pores contain a very large number of different nucleoporins in nature. Onck: “We know that nature doesn’t always come up with optimized solutions. However, their redundancy could very well have a function in natural pores.”

The fact that the very simple artificial system already reproduces selective transport mechanisms means that the scientists now have an excellent tool to study the physical principles that regulate nuclear pore function. Onck: “This could lead to new fundamental insights but also to new applications, for example in creating filtration systems, or in the design of artificial cells.”

More information:
Alessio Fragasso et al, A designer FG-Nup that reconstitutes the selective transport barrier of the nuclear pore complex, Nature Communications (2021). DOI: 10.1038/s41467-021-22293-y

Citation:
‘Designer’ pore shows selective traffic to and from the cell nucleus (2021, March 31)
retrieved 31 March 2021
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Hexbyte Glen Cove Astronomers inspect black hole X-ray binary MAXI J1348–630

Posted on March 30, 2021March 30, 2021 by Laine Lupo

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X-ray and radio light curves of MAXI J1348–630 during its 2019/2020 outburst. Credit: Carotenuto et al., 2021.

An international team of astronomers has carried out a comprehensive radio and X-ray monitoring of a black hole X-ray binary known as MAXI J1348–630. The observational campaign provided important insights into the evolution of the source’s compact and transient jets. The study was presented in a paper published March 22 on arXiv.org.

Black hole X-ray binaries (BHXBs) are binary systems consisting of a black hole orbited by a stellar companion, typically a low-mass, evolved star. In BHXBs, X-rays are produced by material accreting from a secondary companion star onto a black hole primary. Such systems are usually detected in outbursts when the X-ray flux increases significantly.

MAXI J1348–630 was initially detected on January 26, 2019 as a bright X-ray transient by the Monitor of All-sky X-ray Image (MAXI) aboard the International Space Station (ISS). Further observations of this source confirmed that it is a BHXB with a black hole mass of about seven solar masses at a distance of some 7,170 light years away from the Earth.

Almost immediately after the bursting activity of MAXI J1348–630 started, a group of astronomers led by Francesco Carotenuto of the University of Paris, France, commenced a monitoring campaign of this source with the aim of shedding more light on its nature. They observed MAXI J1348–630 in the radio band with the MeerKAT telescope in south Africa and the Australia Telescope Compact Array (ATCA), and also in the X-rays using MAXI and NASA’s Swift spacecraft.

“In this work, we have presented the X-ray and radio monitoring of MAXI J1348–630 during its 2019/2020, discovery outburst. With our X-ray monitoring, we have been able to follow the whole outburst,” the researchers wrote in the paper.

The observations show that during the outburst MAXI J1348–630 exhibited a rather typical X-ray evolution in the first part, completing a whole cycle in the hardness-density diagram (HID), and then showcased a complex sequence of hard-state-only re-brightenings in the second part.

During the outburst, Carotenuto’s team observed the rise, quenching, and re-activation of the compact jets. They also identified two single-sided discrete ejecta, launched about two months apart and traveling away from the black hole. These ejecta had proper motion at a level of some 100 mas/day—the highest proper motion measured so far for such features in BHXBs.

The astronomers found that the first ejection happened during the hard-to-soft state transition of the source, before a strong radio flare. When it comes to the second ejection, it was launched during a short excursion from the soft to the intermediate state.

According to the authors of the paper, the results suggest that MAXI J1348–630 appears to be inside a low-density cavity in the interstellar medium (ISM).

“After traveling with constant speed, the first component underwent a strong deceleration, which was covered with unprecedented detail and suggested that MAXI J1348–630 could be located inside a low-density cavity in the interstellar medium, as already proposed for XTE J1550–564 and H1743–322,” the researchers concluded.

More information:
The black hole transient MAXI J1348–630: evolution of the compact and transient jets during its 2019/2020 outburst, arXiv:2103.12190 [astro-ph.HE] arxiv.org/abs/2103.12190

Citation:
Astronomers inspect black hole X-ray binary MAXI J1348–630 (2021, March 30)
retrieved 30 March 2021
from https://phys.org/news/2021-03-astronomers-black-hole-x-ray-binary.

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Hexbyte Glen Cove Shampoo ingredient could wash diesel out of soil

Posted on March 30, 2021March 30, 2021 by Johnathon Pepper

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Credit: Pixabay/CC0 Public Domain

A plant more commonly used for herbal shampoos could be used to clean oil-contaminated soil, according to a new report.

Soapnut, from the soapberry tree, is known for its foaming and antimicrobial properties, but a team of scientists in Edinburgh found it could be a low-cost way to decontaminate soil in industrial areas.

Diesel oil contamination of soil and groundwater can occur due to pipeline leakages, accidental spills or leakage from storage tanks and automobiles.

Any diesel oil spill has serious, adverse effects on soil and plants, making it difficult to grow crops. The high risk of groundwater contamination poses a serious health risk for people living nearby.

Professor Bhaskar Sen Gupta from Heriot-Watt University tested three materials to find out how effective they were at removing oil from soil: soapnut, rhamnolipid, a commercially-available microbial product and EDTA, a synthetic industrial cleaning chemical.

Professor Sen Gupta said: “We showed that soapnut is comparably effective at removing diesel from contaminated soils—it removed 39.3% of the oil in a single wash from a soil column.

“It’s a very attractive option for washing contaminated soil.

“It’s a low-cost plant material that’s completely safe for humans and animals, so agriculture or gardening is possible immediately after the cleaning phase.

“It’s biodegradable and doesn’t corrode the soil or alter its pH.

“EDTA, on the other hand, is globally popular as a remediation and cleaning agent, but it degrades soil and harms its microbial community.”

The team tried batch and column experiments to mimic ex-situ and in-situ cleaning methods. While batch washing could be twice as effective, reaching up to 88% oil removal, it has very high costs due to material handling and transport of the soil.

In fact, column washing could achieve the same success by repeating the process, and it means the soil doesn’t have to be moved anywhere.

Professor Sen Gupta said: “Batch washing removes the most diesel, but it may not always be a realistic option due to the enormous costs of removing and transporting soil from the contaminated site.

“There are brownfield sites around the world that could be remediated and restored, not only for environmental benefits but to safeguard public health.

“Sustainable, safe materials like soapnut could help communities reclaim contaminated land, and it’s critical we continue to investigate and perfect soil washing techniques.”

More information:
A comparative study on effectiveness of soapnut, rhamnolipid and EDTA in cleaning diesel oil contaminated soil from a commercial site in Edinburgh. pure.hw.ac.uk/ws/portalfiles/p … Idika_et_al_2020.pdf

Citation:
Shampoo ingredient could wash diesel out of soil (2021, March 30)
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Hexbyte Glen Cove Oil-eating bacteria could help to tackle spills

Posted on March 30, 2021March 30, 2021 by Alejandro Pepper

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Credit: Unsplash/CC0 Public Domain

A team of scientists from Heriot-Watt University has created an underwater observatory in the Faroe-Shetland Channel—and found its waters are teeming with oil-eating bacteria that could help deal with future oil spills.

It is the first observatory of its kind in the northeast Atlantic, an area with a high level of oil and gas and shipping activity.

It’s still unknown if the abundance of the oil-degrading bacteria is evidence of chronic spillage, but indicates they are primed and ready to deal with blowouts or pollution from the industrial activity nearby, says Dr. Tony Gutierrez from Heriot-Watt University.

“Oil-degrading bacteria play a vital role in cleaning up oil spills—we found them strongly enriched during the Deepwater Horizon spill, for example. These types of microbes thrive on oil as a food source.”

Gutierrez and his team monitored the Faroe-Shetland channel’s water over two years, at different depths and locations, to establish a baseline for the microbes when there is no spill.

“Overall, we detected a higher than usual abundance of these bacteria. They comprised about 15-20% of the total community of microbes, when quite often you find them at less than 1% abundance.

“We’re not sure why this is the case—it could be due to natural seepage of oil from the seafloor, or the release of produced waters from oil rigs.

“Establishing a baseline in these waters is critical so that we can monitor the impact of future spills and the success of any clean-up efforts, as well as other issues such as ocean acidification and ocean warming.”

The team is planning to extend its monitoring in the Faroe-Shetland channel and hopes to better understand why these types of bacteria are in such atypically high abundance.

They also have other locations in mind for similar observatories.

“Creating microbial observatories in other ocean regions at potential risk of pollution and climate change effects, like the Arctic, is one of our goals,” said Gutierrez.

The research was funded by the Royal Society, the Society for Applied Microbiology and the Marine Alliance for Science and Technology for Scotland (MASTS).

The research was published in mBio, an American Society for Microbiology journal.

More information:
Angelina G. Angelova et al. Inter- and Intra-Annual Bacterioplankton Community Patterns in a Deepwater Sub-Arctic Region: Persistent High Background Abundance of Putative Oil Degraders, mBio (2021). DOI: 10.1128/mBio.03701-20

Journal information:
mBio

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Hexbyte Glen Cove ‘Animal-stress’ signal improves plant drought resilience

Posted on March 29, 2021March 29, 2021 by Diego Schewe

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Credit: Pixabay/CC0 Public Domain

A team of Australian and German researchers has discovered a novel pathway that plants can use to save water and improve their drought tolerance.

The research published today in Nature Communications shows that the molecule GABA (gamma-aminobutyric acid), most commonly associated with relaxation in animals, can control the size of the pores on plant leaves to minimise water loss.

Matthew Gilliham, Director of the Waite Research Institute at the University of Adelaide, who led the research team, said they found: “GABA minimised pore openings in a range of crops such as barley, broad bean and soybean, and in lab plants that produce more GABA than normal. This led to the lab plants using less water from the soil and surviving longer in the drought experiments.”

“We found plants that produce lots of GABA reduce how much their pores open, thereby taking a smaller breath and reducing water loss.”

In an earlier study, members of the team found that GABA—known as a nerve signal in animals—could act as plant GABA receptors. This led to renewed speculation that GABA could be a signal in plants as well as in animals.

Lead author on the study, Dr. Bo Xu, a Postdoctoral Researcher at the Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology adds: “Both plants and animals produce GABA and they put it to different uses. Plants don’t have nerves, instead they appear to use GABA to match their energy levels with their response to the environment.”

“GABA doesn’t close pores on leaves like other stress signals, it acts in a different way—how much a plant accumulates GABA when it is stressed determines how much it applies the brake pedal to reduce the pore opening the following morning, and water loss that day—like a stress memory of the day before.”

During drought, the signalling molecule GABA is produced and inhibits the opening of leaf pores (left). If the enzyme GAD2, which converts glutamate to GABA, is genetically switched off, the pores remain open even during drought – the plants lose more water (centre). If the gene for GAD2 is reintroduced into the closing cells, the defect is reversed. The experiment shows that the sphincter cells autonomously perceive stress and react to it with GABA production. Credit: Rainer Hedrich / University of Wuerzburg

Professor Rainer Hedrich at the University of Würzburg, a pioneer in studying how plants regulate water loss, led the German component of the study.

“I’ve been studying how plants regulate their stomatal pores for over 35 years. To find a completely new and unexpected way that they are regulated has certainly been one of our most surprising discoveries. I look forward to seeing how this translates out in the field.”

The team recently received a new grant from the Australian Federal Government to partner with researchers at the University of Cambridge, UK, and are looking for new Ph.D. students to join the team to discover new components of the signalling pathway and to trial its impact in crops.

More information:
Nature Communications (2021). DOI: 10.1038/s41467-021-21694-3

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‘Animal-stress’ signal improves plant drought resilience (2021, March 29)
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Hexbyte Glen Cove Study reports six novel variants for CRISPR-Cas12a in plants, expanding genome engineering

Posted on March 29, 2021March 29, 2021 by Rebecka Mayoral

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Associate professor of Plant Science at the University of Maryland Yiping Qi continues to innovate genome editing and engineering in plants, with the ultimate goal of improving the efficiency of food production. His new work contributes six novel variants of CRISPR-Cas12a in plants, testing first in rice as a major global crop. In addition to broadening possible gene editing targets, these tools can edit many different sites at once, or even repress gene expression. Credit: National Institutes of Health, public domain

In a new publication in Nature Communications, associate professor of Plant Science at the University of Maryland Yiping Qi continues to innovate genome editing and engineering in plants, with the ultimate goal of improving the efficiency of food production. His recent work contributes six novel variants of CRISPR-Cas12a that have never before been proven in plants, testing them first in rice as a major global crop. In addition to allowing for a much broader scope of possible gene editing targets, these new tools can edit many different sites in the genome at once, or even repress gene expression to tone down undesirable traits. These patent-pending tools greatly expand the scope of what CRISPR-Cas12a can do in plants, which can help to produce food more effectively to feed a growing global population.

“We are excited about this paper because we’ve contributed two major breakthroughs,” says Qi. “First, we’ve reported multiple Cas12a tools with genome editing capabilities in plants for the first time, and found one [Mb2Cas12a] that hugely broadens the targeting range of Cas12a. Second, we’ve developed a very efficient system that can edit many different sites at once [multiplexed editing], and that allows us to edit 16 different genes in rice in a single generation.”

As Qi explains, Cas12a (like other CRISPR systems) has typically been tied to targeting a specific short sequence of DNA known as a PAM sequence. The PAM sequence is what CRISPR systems typically use to identify where to possibly make their molecular cuts in DNA. However, the new Mb2Cas12a variant introduced by Qi works under relaxed PAM requirements, broadening the scope of what can be targeted for editing the way Qi’s lab recently did for CRISPR-Cas9.

In addition to this discovery, the multiplexed editing system introduced for Cas12a in plants provides specific strategies for efficiently editing multiple sites across the genome all at once. For this proof-of-concept, Qi’s team first targeted six different sites in the genome to enhance rice yield and disease resistance. But when this was successful, the team didn’t stop there.

“I wanted to add more targets to see if there is any limit,” explains Qi. “So we added 10 more and tried to target 16 sites, and we found that across almost all rice chromosomes, we had an amazingly high efficiency with all sites being edited all at once in one generation. And that doesn’t even represent the upper limit necessarily, but it is the most genes in a plant that has ever been recorded as being edited all at once in one generation for Cas12a.”

This system has major implications for precision breeding and the efficiency of food production, says Qi. “For precision breeding, how many genes you can edit at once is really practically important because you can target almost anything and really tailor the product. We targeted disease resistance and yield, but you can add more traits like nitrogen use efficiency, climate resilience traits such as temperature tolerance, and more. It is really a robust system.”

Qi is currently doing work to examine the off-targeting effects of editing more genes at once with more relaxed target site requirements. But in addition to these contributions, this paper also demonstrated Cas12a’s utility as a synthetic repressor of genes in the model plant Arabidopsis as another tool for genome engineering.

“You can regulate activation or repression of certain genes by using CRISPR not as a cutting tool, but instead as a binding tool to attract activators or repressors to induce or suppress gene expression to engineer desirable traits. In this case, Cas12a is acting as glue, not as scissors. You use an inactivated form of Cas12a to inactivate the expression of other genes. It’s a great new tool for the industry and for future research.”

Future work will expand these tools out of rice and Arabidopsis, and into all kinds of plants and crops. “This type of technology helps increase crop yield and sustainably feed a growing population in a changing world,” says Qi. “I am very pleased to continue to expand the impacts of CRISPR technologies.”

This paper, entitled “Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems,” can be found in Nature Communications.

More information:
“Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems,” Nature Communications, DOI: 10.1038/s41467-021-22330-w

Citation:
Study reports six novel variants for CRISPR-Cas12a in plants, expanding genome engineering (2021, March 29)
retrieved 29 March 2021
from https://phys.org/news/2021-03-variants-crispr-cas12a-genome.html

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Hexbyte Glen Cove Racial diversity within a church is associated with higher average attendance over time

Posted on March 29, 2021March 29, 2021 by Qiana Kazmierczak

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Credit: CC0 Public Domain

United Methodist churches—whether the congregation is white or not—have higher attendance when located within white neighborhoods. But racial diversity within a church is associated with higher average attendance over time, according to a new study.

“This is a startling contrast to previous research that reported multiracial congregations are less stable,” said lead author Kevin D. Dougherty, Ph.D., associate professor of sociology at Baylor University.

The study is published in the journal Social Forces.

Previous research has found that it is difficult for congregations to build and sustain racially diverse memberships, but little research has been done to explore the overlap of racial changes in congregations and neighborhoods over time.

The research also found that white churches in nonwhite neighborhoods fare the worst in attendance.

“Overall, our understanding of racial diversity and congregational participation remains ambiguous,” said co-author Gerardo Martí, Ph.D., L. Richardson King Professor of Sociology at Davidson College. “In this study, we consider: What does the history of demographic change in local churches and their neighborhoods tell us about the potential for congregational survival over time?”

Researchers tracked data from more than 20,000 United Methodist Church (UMC) congregations over 20 years—from 1990 to 2010—and paired that information with census tract data for that time frame to investigate the effect of demographic change on congregations.

The racial composition of the United States is changing, with a majority of the population to be nonwhite by 2035, according to U.S. Census Bureau projections. Congregations in this country are voluntary organizations, and their growing number, along with advances in transportation, gives people more options for where they attend. The growth also increases churches’ competition to attract and keep members, researchers noted.

While neighborhoods are generally becoming more diverse, congregations are not. Only one in four American adults attends a multiracial congregation, defined as one in which no single racial or ethnic group has more than 80 percent representation.

Changing demographic conditions can threaten the survival of congregations. The number of all-white neighborhoods has fallen sharply since 1980; attendance at United Methodist churches also has declined, and Methodist churches with a higher percentage of whites have had increasingly lower average attendance over time.

“As one of the largest religious denominations in the United States, with more than 6 million U.S. members, the United Methodist Church is a wonderful test case to explore how changes in neighborhood demographics impact local congregations,” said third author Todd W. Ferguson, Ph.D, assistant professor of sociology at the University of Mary Hardin-Baylor.

Here are the researchers’ three hypotheses and findings:

Racial uniformity inside congregations will be associated with higher attendance. Findings did not support this hypothesis. Instead, Methodist churches with more racial diversity had higher attendance.
Neighborhood racial uniformity will be associated with higher congregational attendance. This hypothesis was supported in the study. Specifically, Methodist churches in neighborhoods in which 100 percent of residents were white had more people attending worship services than Methodist churches in racially mixed or predominantly non-white neighborhoods.
When the racial makeup of a congregation matches that of a neighborhood, this will correspond with higher church attendance. Contradicting the hypothesis, attendance levels were highest for nonwhite Methodist churches in 100 percent white neighborhoods as well as racially diverse Methodist churches in neighborhoods with racial uniformity. The authors speculate that nonwhite or racially diverse Methodist churches may attract more participants because they offer an attractive alternative to typical white Methodist churches found in white neighborhoods.

“Our findings challenge the popular assumption of the Church Growth Movement that churches grow by focusing on a single racial or ethnic group,” Martí said. “For Methodist churches, reaching across racial lines proves a better strategy for growth.”

Other influences on church attendance were region of the country and population size. The study found that Methodist churches in the Midwest and West had higher attendance, as did Methodist churches in more populated neighborhoods.

“More research is needed on race and attendance over time in other denominations,” Dougherty said. “Neither congregations nor neighborhoods stay the same indefinitely. Understanding how change in one impacts change in the other is a crucial task for researchers and religious leaders.”

More information:
Kevin D Dougherty et al, Racial Dynamics of Congregations and Communities: A Longitudinal Analysis of United Methodist Congregations, 1990–2010, Social Forces (2020). DOI: 10.1093/sf/soaa124

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Hexbyte Glen Cove Functional consequences of global biodiversity loss guide future nature conservation

Posted on March 28, 2021March 28, 2021 by Joan Pepper

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The ginkgo, the western gorilla, the gharial, the European sturgeon, and the Andean condor are classified as species in danger of extinction by IUCN. These species exhibit peculiar functional traits such as large size, long lifespan, and late sexual maturity (All photos CC-BY-SA) Credit: Ginkgo biloba; photo: Marzena PGorilla gorilla; photo: Philip KromerGavialis gangeticus; photo: Jonathan ZanderAcipenser sturio; photo: Hans BraxmeierVultur gryphus; photo: Emilio del Prado

One million species are under threat of extinction worldwide, primarily due to adverse human impact. The loss of a species is an ethical tragedy, but additionally, it can have dramatic effects on the functioning of ecosystems on Earth. In each ecosystem, species have their roles. These roles depend on the characteristics of the species, like their size, weight, shape, reproductive capacity or the food resources they use. If some species are similar, they can sometimes substitute each other and keep the ecosystem going even if one of them is lost. However, the accumulated loss of many species can lead to ecosystem degradation with a direct adverse effect on human well-being.

There are so many species that it is extremely difficult to generalize the global functional variation and understand the functional consequences of biodiversity loss. A research group from the University of Tartu took the challenge and compiled data on characteristics of more than 75,000 species of plants, mammals, birds, amphibians, reptiles, and freshwater fish. The unprecedented global summary of organisms’ functions was just published in Science Advances.

All species were projected onto a so-called functional space—a mathematical abstraction of their form and function. In this functional space, similar species are located close to each other, and dissimilar species are far apart. Overall, the functional space has some “regions” with plenty of species and others with just a few. The leading author, Dr. Carlos P. Carmona, says, “A very interesting result that we found is that, in all these groups, more than half of the species are responsible for less than 20% of the functions performed by the group, therefore implying that 80% of the remaining functions are performed by few species which are functionally unique.”

Some particular functions performed by a taxonomic group, such as plants, mammals or freshwater fish, may be shared among many species or only supported by a few species. For example, on a global scale, there are many species of grasses that have similar features and perform similar functions, but there are not many species with the features of a redwood. In the case of functions performed by many species, it is unlikely that the extinction of some of these species will strongly affect the functions of the whole group. On the contrary, if certain functions are performed by only one or a few species, their disappearance will lead to a reduction in the range of functions performed by the entire group.

The research group also explored how much we can lose from the functional space if these one million threatened species do go extinct. Dr. Carmona continues, “We wanted to explore how extinctions will affect the functioning of different groups of organisms. We found that large, long-lived, and low-fertility species are universally more likely to be threatened. This is bad news because we know that the largest plants and animals play a hugely important role in functions such as soil fertility, seed dispersion or carbon storage. Their extinction would therefore cause an overall reorganization of the range of functions performed.”

Since many species can substitute each other’s roles, the functional decline would be up to 5%, with the most dramatic losses happening to freshwater fish. This percentage is lower than the potential loss of species numbers. Still, it can have a major influence on the ecosystem services to humans, like clean air and water, soil fertility, our own food, medicines, building material, or good physical and mental health. In addition, a very large part of the functional space will rely on a much lower number of species, and possible subsequent biodiversity loss will already have a much more dramatic effect.

Dr. Carmona also has a clear suggestion to nature conservation authorities: “We propose that species providing unique trait combinations should have a top conservation priority because losing them would imply the complete disappearance of their functions from Earth.”

More information:
“Erosion of global functional diversity across the tree of life” Science Advances (2021). advances.sciencemag.org/lookup … .1126/sciadv.abf2675

Carlos P. Carmona et al, Mapping extinction risk in the global functional spectra across the tree of life, (2020). DOI: 10.1101/2020.06.29.179143

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Functional consequences of global biodiversity loss guide future nature conservation (2021, March 26)
retrieved 28 March 2021
from https://phys.org/news/2021-03-functional-consequences-global-biodiversity-loss.html

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