Scientists complete first map of an insect brain

 

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, appeared 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."

(Image credit: Johns Hopkins University and University of Cambridge)

https://cutt.ly/B53lDus

How intricate Venus’s-flower-baskets manipulate the flow of seawater

 

The Venus’s-flower-basket is a sea sponge found at depths of 100 to 1,000 meters in the Pacific Ocean near the Philippines. A new study shows how the creature’s porous, glassy skeleton alters the flow of seawater.

AGEFOTOSTOCK/ALAMY STOCK PHOTO

By Nikk Ogasa

Simulations show that this deep-sea glass sponge’s skeleton is more than just pretty

A Venus’s-flower-basket isn’t all show. This stunning deep-sea sponge can also alter the flow of seawater in surprising ways.

A lacy, barrel-shaped chamber forms the sponge’s glassy skeleton. Flow simulations reveal how this intricate structure alters the way water moves around and through the sponge, helping it endure unforgiving ocean currents and perhaps feed and reproduce, researchers report online July 21 in Nature.

Previous studies have found that the gridlike construction of a Venus’s-flower-basket (Euplectella aspergillum) is strong and flexible. “But no one has ever tried to see if these beautiful structures have fluid-dynamic properties,” says mechanical engineer Giacomo Falcucci of Tor Vergata University of Rome.

Harnessing supercomputers, Falcucci and colleagues simulated how water flows around and through the sponge’s body, with and without different skeletal components such as the sponge’s myriad pores. If the sponge were a solid cylinder, water flowing past would form a turbulent wake immediately downstream that could jostle the creature, Falcucci says. Instead water flows through and around the highly porous Venus’s-flower-basket and forms a gentle zone of water that flanks the sponge and displaces turbulence downstream, the team found. That way, the sponge’s body endures less stress.

Ridges that spiral around the outside of the sponge’s skeleton also somehow cause water to slow and swirl inside the structure, the simulations showed. As a result, food and reproductive cells that drift into the sponge would become trapped for up to twice as long as in the same sponge without ridges. That lingering could help the filter feeders catch more plankton. And because Venus’s-flower-baskets can reproduce sexually, it could also enhance the chances that free-floating sperm encounter eggs, the researchers say.

It’s amazing that such beauty could be so functional, Falcucci says. The sponge’s flow-altering abilities, he says, might help inspire taller, more wind-resistant skyscrapers.

This simulation shows how water flows around and through a Venus’s-flower-basket (gray). Ridges that spiral across the outside of the sponge cause water inside to somehow slow and swirl, forming particle-trapping vortices. And the sponge’s shape creates a gentle zone of slower water that forms immediately downstream, buffering the creature against turbulence. Vertical cross sections contrast the flow activity of the calm zone (nearer the sponge) and the turbulent zone (downstream).G. FALCUCCI ET AL/NATURE 2021

CITATIONS

G. Falcucci et al. Extreme flow simulations reveal skeletal adaptations of deep-sea sponges. Nature. Published online July 21, 2021. doi: 10.1038/s41586-021-03658-1.

https://bit.ly/3yjA1bF

Siberian unicorns lived alongside humans

A reconstruction of what a Siberian unicorn might look like, by Heinrich Harder in 1908Heinrich Harder/Wikimedia Commons

Ancient rhinos were basically magic.

By Sara Chodosh

All rhinos are unicorns, really—they just aren't pearly white and magical the way our myths say they should be. These powerful beasts get their strength from stocky muscles and keratinized body armor instead of rainbows and magic, but they're the only unicorns we've got. And one extinct species is named accordingly: the Siberian unicorn.

Elasmotherium sibericum was the last remaining survivor of the Elasmotherium genus, which was once a large, diverse group of giant rhinos. Siberian unicorns were once thought to have gone extinct during a broad "background extinction" that occurred during the early and middle Pleistocene, which covers a period from around 126,000 to 2.5 million years ago. The species hadn't been studied much, but it was previously thought that E. sibericum died out roughly 100,000 to 200,000 years ago.

But new research dating the fossilized molars of these ancient unicorns shows that they lasted all the way to the late Quaternary megafaunal extinction. That's the scientific name for the event you know as the end of the last ice age when many retroactively beloved animals—saber-toothed tigers and woolly mammoths, for instance—died out as the climate changed. The paper, published this week in the journal Nature Ecology & Evolution, dates the most recent fossils to around 35,000 to 39,000 years old. Humans started widely dispersing just before the megafaunal extinction, so there's been a lot of debate in the past about whether the widespread deaths of various species are due to overhunting or to climate change.

First published restoration of Elasmotherium sibiricumRashevsky, under supervision of A.F. Brant

In this case, though, it looks like the increase in temperature is what killed off these giant beasts. The researchers note in this recent paper that Siberian unicorns had some extreme adaptations that limited their diet, so when vegetation began to change E. sibericum simply couldn't change fast enough to survive. The lineages that begat modern antelopes and rhinos survived this extinction by evolving to eat a different diet, which they could do because they browsed and grazed on a variety of plants. Siberian unicorns couldn't. Based on the angle between the back of their head and their palate (the bone on the roof of your mouth), researchers think Siberian unicorns held their heads even lower than modern rhinos. This allowed them to eat vegetation very close to the ground. But when their ecological niche disappeared, so did they.

The authors point out that extinction was especially likely because E. sibericum had a highly restricted geographic range, a small population size, and a low reproductive rate. Rhinocerotinae, the group that includes modern rhinos, survived while their Elasmotherium cousins died out. This paper also shows that the two groups had split long before, somewhere around 43 million years. Though they looked superficially similar, ancient rhinos were mostly part of a highly specialized group that simply couldn't survive a massive shift in climate.

We know all of this now because this group of researchers decided to actually look at the evidence they already had in front of them. The 25 specimens they performed radiocarbon dating on were in various museum collections, but as they wrote in the study, no dating or genetic analysis had been done for the species. At last, these real-life unicorns are getting their day in the sun.

These are the top 10 emerging technologies of 2018

Oliver CannHead of Media Content, World Economic Forum

What do lab-grown meat, a holographic museum guide and a supercharged version of Amazon’s Alexa have in common?

They’re all breakthrough technologies that are likely to shape our lives in the near future, according to a list published by the World Economic Forum. Selected by a panel of scientists and experts, each one has been identified as having the potential to be disruptive by altering deep-rooted practices or shaking up whole industries.

While we’ve all heard how technologies like artificial intelligence and quantum computing are set to transform our everyday lives, the coming change can seem like a nebulous concept that’s hard to define. In this list, experts seek to pinpoint the breakthroughs that will take effect within three to five years.

Here are the technologies generating the most excitement among experts this year:

Augmented reality

Overlaying information and animation on to real-world images is set to go mainstream. While the technology isn’t new - many of us have used a car display with guides to aid parking or played the game PokémonGo - it’s set to take a leap forward in terms of sophistication and everyday use. In the future, augmented reality will help surgeons visualize tissues beneath a patient’s skin in three dimensions and conjure up holographic-like guides to take you through a museum.

Personalised medicine

Advanced diagnostic tools are set to tailor your medicines to you, detecting and quantifying multiple signs of a disorder to decide how likely you are to contract a disease. Several advanced diagnostic tools are already in use for cancer. One helps women with certain types of breast cancer avoid chemotherapy. It can also be used to diagnose endometriosis, without the need for surgery, as well as brain disorders, like autism, Parkinson's and Alzheimer’s, that are currently diagnosed by an assessment of symptoms.

AI-led molecular design

The days of science relying on educated predictions - or guesses - to create new drugs and materials may become a thing of the past as artificial intelligence takes over. Instead of messy experiments, machine-learning algorithms will analyse all known past tests, discern patterns and predict what new molecules are likely to work. As well as speeding up the process and reducing chemical waste, it will help the pharmaceutical industry identify and develop new drugs at a rapid pace.

More capable digital helpers

If you’re becoming reliant on Siri and Alexa to switch on your music or give you the weather forecast, you’ll soon be able to access far more sophisticated digital aides. Powered by AI, the latest technology will mine the cloud and outline various arguments on topics that are important to you, without prior training. And it’s not difficult to think of all the ways this technology could help in the workplace: for example helping doctors find research relevant to a complicated medical case and then debating the merits of the different ways of treating it.

Implantable drug-making cells

For people who have to take medicine regularly, the idea of having a tiny drug factory implanted in the body is probably very appealing. At some point in your life you’ve probably needed to take a course of drugs and struggled to remember when to take them. Until now, implant use was limited because users also needed to take immune-suppressing drugs to prevent their bodies attacking the implant. Now the technology is sophisticated enough to work without being rejected by the immune system and could transform the treatment of long-term conditions, such as cardiovascular disease, tuberculosis, diabetes, cancer and chronic pain.

Gene drive

Changing genes knowingly can be controversial and often goes hand-in-hand with ethical questions. And while gene drives - natural or engineered genetic elements that spread through populations quickly - are no different, they offer enormous power to fight disease or eliminate species of pests such as mosquitoes that transmit malaria. Such efforts got a shot in the arm in recent years with the introduction of CRISPR gene-editing, which makes it easy to insert genetic material into specific spots on chromosomes.

Algorithms for quantum computers

Computers that use quantum mechanics to perform calculations can solve some problems far more efficiently than a conventional computer. While early use was held back by disruptions to their function, the latest research has improved that and a growing number of academics are developing programmes and quantum software. Once refined, powerful quantum computers could simulate nature and help design materials.

Plasmonic materials

Is this the technology that will make Harry Potter’s invisibility cloak a reality? While that is probably still a way off, plasmonic devices that manipulate electron clouds and light at the nanoscale are set to increase magnetic memory storage and the sensitivity of biological sensors. Several companies are developing new products, including a device that can distinguish viral from bacterial infections and a heat-assisted magnetic recording device. Light-activated nanoparticles are also being investigated for their ability to treat cancer without damaging healthy tissue.

Lab-grown meat

Would you eat a burger that you knew had been grown in a lab? Meat grown from cultured cells could cut the environmental costs of producing meat and eliminate the unethical treatment suffered by animals that are raised for food. Start-ups like Mosa Meat, Memphis Meats, SuperMeat and Finless Foods have already attracted millions in funding, even though the production costs remain very high and taste-test results have been mixed. With the technology improving all the time, duck, chicken, and beef produced without slaughter could be on its way to a kitchen near you sooner than you think.

Electroceuticals

Could we cut down our reliance on drugs to treat most health conditions? Some say yes, with electroceuticals offering the ability to treat ailments using electrical impulses. One approach, targeting the vagus nerve - the system that sends signals from the brain to most organs - is poised to transform care for many conditions, since it has the potential to regulate the immune system. This has been used to treat epilepsy and depression for more than a decade, and now looks set to aid sufferers of migraines, obesity and rheumatoid arthritis.

Read more about each of the top 10 emerging technologies of 2018 here.

Gut bacteria's shocking secret: They produce electricity

Date:

September 12, 2018

Source:

University of California - Berkeley

Summary:

To date, most electricity-generating bacteria have come from weird environments, but researchers have found more than 100 in the human microbiome, both pathogenic and probiotic. They were unsuspected because they employ a different and simpler extracellular electron transfer system, which may prove useful in creating bacterial batteries. Their electrogenic ability may be important in infectivity, or in how they ferment cheese and yogurt.

Listeria bacteria transport electrons through their cell wall into the environment as tiny currents, assisted by ubiquitous flavin molecules (yellow dots).

Credit: Amy Cao graphic. Copyright UC Berkeley

While bacteria that produce electricity have been found in exotic environments like mines and the bottoms of lakes, scientists have missed a source closer to home: the human gut.

University of California, Berkeley, scientists discovered that a common diarrhea-causing bacterium, Listeria monocytogenes, produces electricity using an entirely different technique from known electrogenic bacteria, and that hundreds of other bacterial species use this same process.

Many of these sparking bacteria are part of the human gut microbiome, and many, like the bug that causes the food-borne illness listeriosis, which can also cause miscarriages, are pathogenic. The bacteria that cause gangrene (Clostridium perfringens) and hospital-acquired infections (Enterococcus faecalis) and some disease-causing streptococcus bacteria also produce electricity. Other electrogenic bacteria, like Lactobacilli, are important in fermenting yogurt, and many are probiotics.

"The fact that so many bugs that interact with humans, either as pathogens or in probiotics or in our microbiota or involved in fermentation of human products, are electrogenic -- that had been missed before," said Dan Portnoy, a UC Berkeley professor of molecular and cell biology and of plant and microbial biology. "It could tell us a lot about how these bacteria infect us or help us have a healthy gut."

The discovery will be good news for those currently trying to create living batteries from microbes. Such "green" bioenergetic technologies could, for example, generate electricity from bacteria in waste treatment plants.

The research will be posted online Sept. 12 in advance of Oct. 4 print publication in the journal Nature.

Breathing metal

Bacteria generate electricity for the same reason we breathe oxygen: to remove electrons produced during metabolism and support energy production. Whereas animals and plants transfer their electrons to oxygen inside the mitochondria of every cell, bacteria in environments with no oxygen -- including our gut, but also alcohol and cheese fermentation vats and acidic mines -- have to find another electron acceptor. In geologic environments, that has often been a mineral -- iron or manganese, for example -- outside the cell. In some sense, these bacteria "breathe" iron or manganese.

Transferring electrons out of the cell to a mineral requires a cascade of special chemical reactions, the so-called extracellular electron transfer chain, which carries the electrons as a tiny electrical current. Some scientists have tapped that chain to make a battery: stick an electrode in a flask of these bacteria and you can generate electricity.

The newly discovered extracellular electron transfer system is actually simpler than the already known transfer chain, and seems to be used by bacteria only when necessary, perhaps when oxygen levels are low. So far, this simpler electron transfer chain has been found in bacteria with a single cell wall -- microbes classified as gram-positive bacteria -- that live in an environment with lots of flavin, which are derivatives of vitamin B2.

"It seems that the cell structure of these bacteria and the vitamin-rich ecological niche that they occupy makes it significantly easier and more cost effective to transfer electrons out of the cell," said first author Sam Light, a postdoctoral fellow. "Thus, we think that the conventionally studied mineral-respiring bacteria are using extracellular electron transfer because it is crucial for survival, whereas these newly identified bacteria are using it because it is 'easy.'"

To see how robust this system is, Light teamed up with Caroline Ajo-Franklin from Lawrence Berkeley National Laboratory, who explores the interactions between living microbes and inorganic materials for possible applications in carbon capture and sequestration and bio-solar energy generation.

She used an electrode to measure the electric current that streams from the bacteria -- up to 500 microamps -- confirming that it is indeed electrogenic. In fact, they make about as much electricity -- some 100,000 electrons per second per cell -- as known electrogenic bacteria.

Light is particularly intrigued by the presence of this system in Lactobacillus, bacteria crucial to the production of cheese, yogurt and sauerkraut. Perhaps, he suggests, electron transport plays a role in the taste of cheese and sauerkraut.

"This is a whole big part of the physiology of bacteria that people didn't realize existed, and that could be potentially manipulated," he said.

Light and Portnoy have many more questions about how and why these bacteria developed such a unique system. Simplicity -- it's easier to transfer electrons through one cell wall rather than through two -- and opportunity -- taking advantage of ubiquitous flavin molecules to get rid of electrons -- appear to have enabled these bacteria to find a way to survive in both oxygen-rich and oxygen-poor environments.

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Story Source:

Materials provided by University of California - Berkeley. Original written by Robert Sanders. Note: Content may be edited for style and length.

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Journal Reference:

1. Samuel H. Light, Lin Su, Rafael Rivera-Lugo, Jose A. Cornejo, Alexander Louie, Anthony T. Iavarone, Caroline M. Ajo-Franklin, Daniel A. Portnoy. A flavin-based extracellular electron transfer mechanism in diverse Gram-positive bacteria. Nature, 2018; DOI:10.1038/s41586-018-0498-z