Saturday, March 18, 2023

Scientists complete 1st map of an insect brain

In the quest to understand how we think, ‘everything has been working up to this’

Peer-Reviewed Publication

JOHNS HOPKINS UNIVERSITY

Diagram of neuron connectivity 

IMAGE: A DIAGRAM DEPICTING THE CONNECTIVITY, WHERE NEURONS ARE REPRESENTED AS POINTS, AND NEURONS WITH MORE SIMILAR CONNECTIVITY ARE PLOTTED CLOSER TOGETHER. LINES DEPICT CONNECTIONS BETWEEN NEURONS. THE BORDER OF THE FIGURE SHOWS EXAMPLE NEURON MORPHOLOGIES. view more 

CREDIT: JOHNS HOPKINS UNIVERSITY/UNIVERSITY OF CAMBRIDGE

Researchers have completed the most advanced brain map to date, that of an insect, a landmark achievement in neuroscience that brings scientists closer to true understanding of the mechanism of thought.

The international team led by Johns Hopkins University and the University of Cambridge produced a breathtakingly detailed diagram tracing every neural connection in the brain of a larval fruit fly, an archetypal scientific model with brains comparable to humans.

The work, likely to underpin future brain research and to inspire new machine learning architectures, appears today in the journal Science.

“If we want to understand who we are and how we think, part of that is understanding the mechanism of thought,” said senior author Joshua T. Vogelstein, a Johns Hopkins biomedical engineer who specializes in data-driven projects including connectomics, the study of nervous system connections. “And the key to that is knowing how neurons connect with each other.”

The first attempt at mapping a brain—a 14-year study of the roundworm begun in the 1970s, resulted in a partial map and a Nobel Prize. Since then, partial connectomes have been mapped in many systems, including flies, mice, and even humans, but these reconstructions typically only represent only a tiny fraction of the total brain. Comprehensive connectomes have only been generated for several small species with a few hundred to a few thousand neurons in their bodies–a roundworm, a larval sea squirt, and a larval marine annelid worm.

This team’s connectome of a baby fruit fly, Drosophila melanogaster larva, is the most complete as well as the most expansive map of an entire insect brain ever completed. It includes 3,016 neurons and every connection between them: 548,000.

“It’s been 50 years and this is the first brain connectome. It’s a flag in the sand that we can do this,” Vogelstein said. “Everything has been working up to this.”

Mapping whole brains is difficult and extremely time-consuming, even with the best modern technology. Getting a complete cellular-level picture of a brain requires slicing the brain into hundreds or thousands of individual tissue samples, all of which have to be imaged with electron microscopes before the painstaking process of reconstructing all those pieces, neuron by neuron, into a full, accurate portrait of a brain. It took more than a decade to do that with the baby fruit fly. The brain of a mouse is estimated to be a million times larger than that of a baby fruit fly, meaning the chance of mapping anything close to a human brain isn’t likely in the near future, maybe not even in our lifetimes.

The team purposely chose the fruit fly larva because, for an insect, the species shares much of its fundamental biology with humans, including a comparable genetic foundation. It also has rich learning and decision-making behaviors, making it a useful model organism in neuroscience. And for practical purposes, its relatively compact brain can be imaged and its circuits reconstructed within a reasonable time frame.

Even so, the work took the University of Cambridge and Johns Hopkins 12 years. The imaging alone took about a day per neuron.

Cambridge researchers created the high-resolution images of the brain and manually studied them to find individual neurons, rigorously tracing each one and linking their synaptic connections. 

Cambridge handed off the data to Johns Hopkins, where the team spent more than three years using original code they created to analyze the brain’s connectivity. The Johns Hopkins team developed techniques to find groups of neurons based on shared connectivity patterns, and then analyzed how information could propagate through the brain.

In the end, the full team charted every neuron and every connection, and categorized each neuron by the role it plays in the brain. They found that the brain’s busiest circuits were those that led to and away from neurons of the learning center.

The methods Johns Hopkins developed are applicable to any brain connection project, and their code is available to whoever attempts to map an even larger animal brain, Vogelstein said, adding that despite the challenges, scientists are expected to take on the mouse, possibly within the next decade. Other teams are already working on a map of the adult fruit fly brain. Co-first author Benjamin Pedigo, a Johns Hopkins doctoral candidate in Biomedical Engineering, expects the team’s code could help reveal important comparisons between connections in the adult and larval brain. As connectomes are generated for more larva and from other related species, Pedigo expects their analysis techniques could lead to better understanding of variations in brain wiring. 

The fruit fly larva work showed circuit features that were strikingly reminiscent of prominent and powerful machine learning architectures. The team expects continued study will reveal even more computational principles and potentially inspire new artificial intelligence systems.

“What we learned about code for fruit flies will have implications for the code for humans,” Vogelstein said. “That’s what we want to understand—how to write a program that leads to a human brain network.”

Authors included: Michael Winding, Christopher L. Barnes, Heather G. Patsolic, Youngser Park, Tom Kazimiers, Akira Fushiki, Ingrid V. Andrade, Avinash Khandelwal, Javier Valdes-Aleman, Feng Li, Nadine Randel, Elizabeth Barsotti, Ana Correia, Richard D. Fetter, Volker Hartenstein, Carey E. Priebe, Albert Cardona, and Marta Zlatic.

The complete set of neurons in an insect brain, which were reconstructed using synapse-resolution electron microscopy.

Neurons of a Baby Fruit Fly Brain 

CREDIT


Complete map of baby fruit fly [VIDEO] |

Agricultural certification stimulates compliance with environmental legislation by coffee farms in Brazil


The researchers analyzed data for more than 500 coffee farms in areas of Atlantic Rainforest and Cerrado, Brazil’s savanna-type biome, in 84 municipalities in the states of São Paulo and Minas Gerais.


Peer-Reviewed Publication

FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO

Agricultural certification 

IMAGE: THE RESEARCHERS ANALYZED DATA FOR MORE THAN 500 COFFEE FARMS IN AREAS OF ATLANTIC RAINFOREST AND CERRADO, IN 84 MUNICIPALITIES IN THE STATES OF SÃO PAULO AND MINAS GERAIS view more 

CREDIT: VALTER CAMPANATO/AGÊNCIA BRASI

Agricultural certification can act as an incentive for coffee growers and other farmers to comply with laws designed to protect the environment, promoting their alignment with the current demands of society and the market, although it does not necessarily contribute to a reduction in deforestation or an increase in natural regeneration of plant cover in rural properties, according to a study conducted in Brazil and reported in an article recently published in the journal Biological Conservation

The study was conducted under the aegis of the FAPESP Biodiversity Conservation, Restoration and Sustainable Use Program (BIOTA-FAPESP) and funded via two projects (13/23457-6 and 18/22881-2). The authors of the article are researchers at Brazil’s SOS Mata Atlântica Foundation and the University of São Paulo’s Luiz de Queiroz College of Agriculture (ESALQ-USP) and Institute of Biosciences (IB-USP).

With almost 40% of world production certified, coffee is an example of the growing use of certification seals to show that producers are committed to best practices in terms of sustainability and environmental protection. However, statistical and methodological difficulties have prevented researchers from determining whether agriculture is in fact becoming more sustainable as a result of certification and exactly how environmental legislation affects biodiversity in the areas concerned.

“We didn’t observe a direct cause-and-effect relationship between certification and deforestation or natural regeneration, but certification can apparently serve as an additional incentive to comply with the legislation, confirming that the synergy has beneficial effects,” said Francisco d’Albertas Gomes de Carvalho, first author of the article and currently a postdoctoral researcher in data science at the International Institute for Sustainability (IIS Rio). At the time of the study, he was affiliated with IB-USP's Department of Ecology. 

“In Brazil, certification can be a worthwhile tool to strengthen compliance with the Native Vegetation Protection Act, also known as the Forest Code, given the lack of interest among landowners and weak enforcement by the government,” he said.

The researchers began by analyzing data from IMAFLORA, the main Brazilian certifier, and SICAR, the national rural environmental register, for 84 municipalities in the states of São Paulo and Minas Gerais, to obtain a list of 537 coffee farms in protected areas classified as Atlantic Rainforest (172 farms) and Cerrado, the savanna-type biome (362 farms). They then defined and calculated a set of characteristics that could influence the probability of certification, including the size of the property, the amount of natural plant cover, and the rate of deforestation or regeneration, in order to arrive at a group of certified farms and uncertified controls.

They chose the first certification as the cutoff date. “We analyzed the changes to the farms in the previous five years to see if the advent of certification had caused variations in factors relating to public policy, such as a reduction in deforestation and an increase in native plant cover,” D’Albertas said. They concluded that it had not, partly because the certified properties analyzed in the study were in “consolidated” agricultural areas, where land use has not changed significantly for a considerable period. 

“In these areas, where coffee has been produced for decades, there’s no deforestation to speak of, especially compared with the scale of ongoing deforestation along the agricultural frontier in the Amazon, or in parts of the Cerrado where soybean plantations are expanding,” he said.

Legislation and certification as allies

The researchers next refined the analysis to see if certified properties complied more thoroughly with the environmental legislation, detecting only a general tendency for increased compliance, with no significant difference between certified and uncertified farms.

Because many landowners begin complying with the legislation before applying for certification, the researchers also analyzed land-use changes in the three years prior to certification, finding a considerable increase in native vegetation on certified farms only in areas of Atlantic Rainforest, which mostly complied with the obligation to protect plant cover in Permanent Conservation Areas (APPs). The authors attribute this difference to more efficient law enforcement and higher civil society awareness in the region, as well as more technical expertise in forest restoration.

About São Paulo Research Foundation (FAPESP)

The São Paulo Research Foundation (FAPESP) is a public institution with the mission of supporting scientific research in all fields of knowledge by awarding scholarships, fellowships and grants to investigators linked with higher education and research institutions in the State of São Paulo, Brazil. FAPESP is aware that the very best research can only be done by working with the best researchers internationally. Therefore, it has established partnerships with funding agencies, higher education, private companies, and research organizations in other countries known for the quality of their research and has been encouraging scientists funded by its grants to further develop their international collaboration. You can learn more about FAPESP at www.fapesp.br/en and visit FAPESP news agency at www.agencia.fapesp.br/en to keep updated with the latest scientific breakthroughs FAPESP helps achieve through its many programs, awards and research centers. You may also subscribe to FAPESP news agency at http://agencia.fapesp.br/subscribe.

Scientists call for global push to eliminate space junk

Peer-Reviewed Publication

UNIVERSITY OF PLYMOUTH

Scientists call for global push to eliminate space junk 

IMAGE: DR IMOGEN NAPPER, RESEARCH FELLOW AT THE UNIVERSITY OF PLYMOUTH view more 

CREDIT: ELEANOR BURFITT/UNIVERSITY OF PLYMOUTH

Scientists have called for a legally-binding treaty to ensure Earth’s orbit isn’t irreparably harmed by the future expansion of the global space industry.

In the week that nearly 200 countries agreed to a treaty to protect the High Seas after a 20-year process, the experts believe society needs to take the lessons learned from one part of our planet to another. 

The number of satellites in orbit is expected to increase from 9,000 today to over 60,000 by 2030, with estimates suggesting there are already more than 100 trillion untracked pieces of old satellites circling the planet.

While such technology is used to provide a huge range of social and environmental benefits, there are fears the predicted growth of the industry could make large parts of Earth’s orbit unusable.

Writing in the journal Science, an international collaboration of experts in fields including satellite technology and ocean plastic pollution say this demonstrates the urgent need for global consensus on how best to govern Earth’s orbit.

They acknowledge that a number of industries and countries are starting to focus on satellite sustainability, but say this should be enforced to include any nation with plans to use Earth’s orbit.

Any agreement, they add, should include measures to implement producer and user responsibility for satellites and debris, from the time they launch onwards. Commercial costs should also be considered when looking at ways to incentivise accountability. Such considerations are consistent with current proposals to address ocean plastic pollution as countries begin negotiations for the Global Plastics Treaty.

The experts also believe that unless action is taken immediately, large parts of our planet’s immediate surroundings risk the same fate as the High Seas where insubstantial governance has led to overfishing, habitat destruction, deep-sea mining exploration, and plastic pollution.

The article was co-authored by researchers from the University of Plymouth, Arribada Initiative, The University of Texas at Austin, California Institute of Technology, NASA Jet Propulsion Laboratory, Spaceport Cornwall, and ZSL (Zoological Society of London).

They include the academic who led the first ever study into marine microplastics, also published in Science almost 20 years ago, and scientists who contributed to the commitment to develop a Global Plastics Treaty signed by 170 world leaders at the United Nations Environment Assembly in March 2022.

Dr Imogen Napper, Research Fellow at the University of Plymouth, led the newly-published study with funding from the National Geographical Society. She said: “The issue of plastic pollution, and many of the other challenges facing our ocean, is now attracting global attention. However, there has been limited collaborative action and implementation has been slow. Now we are in a similar situation with the accumulation of space debris. Taking into consideration what we have learnt from the high seas, we can avoid making the same mistakes and work collectively to prevent a tragedy of the commons in space. Without a global agreement we could find ourselves on a similar path”.

Heather Koldewey, ZSL’s Senior Marine Technical Advisor, said: “To tackle planetary problems, we need to bring together scientists from across disciplines to identify and accelerate solutions. As a marine biologist I never imagined writing a paper on space, but through this collaborative research identified so many parallels with the challenges of tackling environmental issues in the ocean. We just need to get better at the uptake of science into management and policy.”

Dr Moriba Jah, Associate Professor of Aerospace Engineering and Engineering Mechanics at The University of Texas at Austin, said: “Ancient TEK (traditional ecological knowledge) informs us how we must embrace stewardship because our lives depend on it. I’m excited to work with others in highlighting the links and interconnectedness amongst all things and that marine debris and space debris are both an anthropogenic detriment that is avoidable.”

Dr Kimberley Miner, Scientist at the NASA Jet Propulsion Laboratory, said: “Mirroring the new UN ocean initiative, minimizing the pollution of the lower Earth orbit will allow continued space exploration, satellite continuity, and the growth of life-changing space technology.”

Melissa Quinn, Head of Spaceport Cornwall, said: "Satellites are vital to the health of our people, economies, security and Earth itself. However, using space to benefit people and planet is at risk. By comparing how we have treated our seas, we can be proactive before we damage the use of space for future generations. Humanity needs to take responsibility for our behaviours in space now, not later. I encourage all leaders to take note, to recognise the significance of this next step and to become jointly accountable."

Professor Richard Thompson OBE, Head of the International Marine Litter Research Unit at the University of Plymouth, said: “I have spent most of my career working on the accumulation of plastic litter in the marine environment; the harm it can bring and the potential solutions. It is very clear that much of the pollution we see today could have been avoided. We were well aware of the issue of plastic pollution a decade ago, and had we acted then the quantity of plastic in our oceans might be half of what it is today. Going forward we need to take a much more proactive stance to help safeguard the future of our planet. There is much that can be learned from mistakes made in our oceans that is relevance to the accumulation of debris in space.”

Island-inhabiting giants, dwarves more vulnerable to extinction

Human arrival on islands catalyzed disappearance of iconic animal species

Peer-Reviewed Publication

UNIVERSITY OF NEBRASKA-LINCOLN

Island footprint 

IMAGE: ISLAND-DWELLING MAMMAL SPECIES OFTEN EXPAND OR CONTRACT IN SIZE, BECOMING GIANT OR DWARF VERSIONS OF THEIR MAINLAND COUNTERPARTS. A NEW SCIENCE STUDY FROM A GLOBAL TEAM SHOWS THAT THOSE GIANTS AND DWARVES HAVE FACED EXTREME RISK OF EXTINCTION — AN EXISTENTIAL THREAT EXACERBATED BY THE ARRIVAL OF HUMANS. view more 

CREDIT: SCOTT SCHRAGE | UNIVERSITY OF NEBRASKA–LINCOLN

Forget the sci-fi trappings of ray guns, Pym Particles and gamma radiation: For animals both supersized and miniaturized, look no further than islands, where rodents can swell to 100 times their mainland mass and mammoths once shrank from 20,000 pounds to 2,000.

Those same island-dwelling giants and dwarves contend with far greater risks of disappearing from the planet than do other species, says a new study in the journal Science. Yet it’s not so much the size that counts, the researchers concluded, as how much that size varies between mainland and island.

Island inhabitants, even those of standard size, face more than their share of existential peril. Roughly 75% of the documented extinctions over the past 500 years took place on water-encompassed patches of land. About half of the animal species now listed as threatened by the International Union for Conservation of Nature live on islands, too.

But ecologists from the German Centre for Integrative Biodiversity Research (iDiv), Martin Luther University Halle-Wittenberg, the University of Nebraska–Lincoln and elsewhere found that island-dwelling mammal species larger or smaller than their continental counterparts are even more likely to be endangered — or have already gone extinct.

Extinction risks generally rose in tandem with the size disparities between mainland and island species, meaning that the most extreme giants and dwarves were dealt the longest survival odds, the team discovered. Island-inhabiting mammals whose evolution multiplied or divided their mass by at least four were 75%-plus likely to be classified as threatened. Those that evolved to be 10 times larger or smaller than their mainland peers, meanwhile, faced at least a 75% chance of going extinct.

“We think it has to do with the associated ecological changes that go along with the morphological changes on islands,” said Kate Lyons, associate professor of biological sciences at Nebraska. “Islands are generators of evolutionary novelty. You get all sorts of weird things on islands that you don’t get on the mainland.”

Gigantism and dwarfism are notable symptoms of what ecologists call “island syndrome,” which frequently affects animal species — from the enlarged but endangered Komodo dragon to the extinct pygmy mammoth — that either immigrate to islands or originate there. Smaller mammals, like mice, generally encounter fewer predators and, having less reason to hide or flee, may evolve into giant versions of their mainland species or sister species. Larger mammals, including buffalo and hippopotamuses, tend to confront more constraints — less territory on which to forage for vegetation or prey, and smaller quantities of both — that limit their growth and ultimate size.

Species emigrating from a mainland often exhibit another trait: Being unfamiliar with the meat-eaters on their newfound home, they may lack appropriate fear of the neighbors most motivated and best equipped to kill them. The fact that some of the mammal species most prone to expanding or contracting in size also make for unsuspecting prey could help explain why island-confined giants and dwarves are so vulnerable, the researchers said.

“They’re going to be really naïve to predators, especially any large primate predator, like us, that shows up,” Lyons said. “So they’re going to be much easier to catch and kill and eat. And because islands are isolated, and there’s no source population for them, it’s also going to be easier for a new predator to drive them to extinction.

“If you think about what we know from the recorded history of what happened to a lot of these islands when sailors arrived,” she said, “they would just easily catch and eat animals with no issues.”

Data from 1,231 surviving mammal species, and fossils from 350 extinct ones, allowed Martin Luther’s Roberto Rozzi, iDiv’s Jonathan Chase and the global team to take stock of those very human footprints across 182 current and former islands. For as much danger as giants and dwarves already faced on islands, the arrival of modern humans, or Homo sapiens, multiplied the probability of extinction by 16. That far outweighed even the impacts of earlier, less advanced Homo species, whose appearance coincided with a doubling in extinctions.

Those rises in human-linked extinctions manifested as pulses in the fossil record that together represent a “protracted extinction event” stretching back roughly 100,000 years, when the first pulse occurred. Another emerged about 16,000 years ago, near the end of the last ice age, with a third arising just 2,000 years ago. That latest pulse yielded an extinction rate about 88 times higher than that of the first.

“The reason they’re pulsed like that is because Homo sapiens got to different islands at different times,” said Lyons, whose prior research has linked the extinction of large mammals with human encroachment. “It’s similar to how we got to different continents at different times — except that for islands, it took us much longer to get to some of them, especially the really remote ones.”

The pulses also help illustrate differences in how humans and other predators alter the food webs of ecosystems — differences that can lead not just to the thinning but the snipping of threads that make up those webs. Most predators, Lyons said, will not drive their prey to extinction. When the population of prey plummets due to hunting, predators have less to eat and eventually see their own numbers drop. That allows the prey population to rebound, with predators following suit, and so on.

“Humans (historically) don’t do that,” she said. “We switch prey constantly. We eat something until it’s gone, or until it’s hard to catch, and then we eat something else until it’s gone. But we don’t stop eating the thing that we were first eating. If we come across it, we’re going to continue eating it, so the pressure on that population is still there.”

Efforts to prevent the further disappearance of species might benefit from incorporating the study’s findings, Lyons said. Current conservation policies do prioritize so-called endemic species that, by inhabiting only one small part of the world — often an island — are more vulnerable to extinction. Many conservationists also triage species according to genetic diversity, so that those featuring more distinct blueprints receive more attention and resources.

“So they do tend to look at various axes of diversity that they want to try to preserve. But they don’t take into account what this study shows,” Lyons said, “which is that the species that get onto islands, and either dwarf or get giant, are at particular risk.”

Rozzi, Chase and Lyons authored the study with Mark Lomolino, from the State University of New York; Alexandra van der Geer of the Naturalis Biodiversity Center in the Netherlands; Daniele Silvestro, from Switzerland’s University of Fribourg; Pere Bover, from Spain’s University of Zaragoza; Josep Alcover, from Spain’s Mediterranean Institute for Advanced Studies; Ana Benítez-López of the Spanish National Research Council; Cheng-Hsiu Tsai of National Taiwan University; Masaki Fujita, from Japan’s National Museum of Nature and Science; Mugino Kubo, from The University of Tokyo; Janine Ochoa, from the University of the Philippines; Matthew Scarborough, from the University of Cape Town; Samuel Turvey, from the Zoological Society of London; and Alexander Zizka, from the Philipps University of Marburg in Germany.