Tag Archives: biology

Scientists create the most complex map yet of an insect brain’s ‘wiring’

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Researchers understand the structure of brains and have mapped them out in some detail, but they still don't know exactly how they process data — for that, a detailed "circuit map" of the brain is needed. 

Now, scientists have created just such a map for the most advanced creature yet: a fruit fly larva. Called a connectome, it diagrams the insect's 3016 neurons and 548,000 synapses, Neuroscience News has reported. The map will help researchers study better understand how the brains of both insects and animals control behavior, learning, body functions and more. The work may even inspired improved AI networks.

"Up until this point, we’ve not seen the structure of any brain except of the roundworm C. elegans, the tadpole of a low chordate, and the larva of a marine annelid, all of which have several hundred neurons," said professor Marta Zlatic from the MRC Laboratory of Molecular Biology. "This means neuroscience has been mostly operating without circuit maps. Without knowing the structure of a brain, we’re guessing on the way computations are implemented. But now, we can start gaining a mechanistic understanding of how the brain works." 

To build the map, the team scanned thousands of slices from the larva's brain with an electron microscope, then integrated those into a detailed map, annotating all the neural connections. From there, they used computational tools to identify likely information flow pathways and types of "circuit motifs" in the insect's brain. They even noticed that some structural features closely resembled state-of-the-art deep learning architecture.

Scientists have made detailed maps of the brain of a fruit fly, which is far more complex than a fruit fly larva. However, these maps don't include all the detailed connections required to have a true circuit map of their brains. 

As a next step, the team will investigate the structures used for behavioural functions like learning and decision making, and examine connectome activity while the insect does specific activities. And while a fruit fly larva is a simple insect, the researchers expect to see similar patterns in other animals. "In the same way that genes are conserved across the animal kingdom, I think that the basic circuit motifs that implement these fundamental behaviours will also be conserved," said Zlatic.

This article originally appeared on Engadget at https://www.engadget.com/scientists-create-the-most-complex-map-yet-of-an-insect-brains-wiring-085600210.html?src=rss

Researchers created a sticky drone to collect environmental DNA from forest canopies

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Swiss scientists have developed a proof-of-concept method to collect environmental DNA (eDNA) from high-arching forest canopies, an under-observed habitat. Rather than hiring skilled climbers to risk their lives to grab a little bug and bird DNA, the team flew a collection drone into the trees to capture genetic material — giving them a clearer picture of the area’s organic breakdown.

The researchers used a quadcopter equipped with a sticky collection cage. But since tree branches can bend at the slightest touch — and the drone needs to touch the branches to collect DNA — it has a haptic-based control scheme using force sensors to measure the pressure between the drone and the branch. Then, it adjusts its landing accordingly, leaning against the branch gently enough to avoid flinging valuable material to the ground.

The drone’s cage then grabs samples with a sticky surface made from “adhesive tape and a cotton gauze humidified with a solution of water and DNA-free sugar.” The cage spends around 10 seconds leaning on each branch and collecting eDNA before zipping back to the base, where the scientists retrieve the samples and ship them to a lab. The experiment’s drone successfully collected enough genetic material to identify 21 animal classes ranging from insects and mammals to birds and amphibians.

Illustrated diagram showing an eDNA collection drone approaching a tree branch, collecting material and returning to base.
Science

However, the scientists make it clear this is a work in progress. For example, on the last research day, the team noticed a drop in eDNA detection because of rainfall the night before — suggesting the method only tells them which creatures visited since the last downpour. Additionally, they noted unexplained differences in the performance of their two collectors, highlighting the need for more research on equipment variations.

The researchers hope their work will make it easier and cheaper for environmental biologists to learn which critters live in some of the hardest-to-reach places. The approach could eventually help the scientific community understand how environmental changes affect biodiversity, perhaps helping identify endangered or vulnerable species before it’s too late.

Researchers created a sticky drone to collect environmental DNA from forest canopies

Posted on by

Swiss scientists have developed a proof-of-concept method to collect environmental DNA (eDNA) from high-arching forest canopies, an under-observed habitat. Rather than hiring skilled climbers to risk their lives to grab a little bug and bird DNA, the team flew a collection drone into the trees to capture genetic material — giving them a clearer picture of the area’s organic breakdown.

The researchers used a quadcopter equipped with a sticky collection cage. But since tree branches can bend at the slightest touch — and the drone needs to touch the branches to collect DNA — it has a haptic-based control scheme using force sensors to measure the pressure between the drone and the branch. Then, it adjusts its landing accordingly, leaning against the branch gently enough to avoid flinging valuable material to the ground.

The drone’s cage then grabs samples with a sticky surface made from “adhesive tape and a cotton gauze humidified with a solution of water and DNA-free sugar.” The cage spends around 10 seconds leaning on each branch and collecting eDNA before zipping back to the base, where the scientists retrieve the samples and ship them to a lab. The experiment’s drone successfully collected enough genetic material to identify 21 animal classes ranging from insects and mammals to birds and amphibians.

Illustrated diagram showing an eDNA collection drone approaching a tree branch, collecting material and returning to base.
Science

However, the scientists make it clear this is a work in progress. For example, on the last research day, the team noticed a drop in eDNA detection because of rainfall the night before — suggesting the method only tells them which creatures visited since the last downpour. Additionally, they noted unexplained differences in the performance of their two collectors, highlighting the need for more research on equipment variations.

The researchers hope their work will make it easier and cheaper for environmental biologists to learn which critters live in some of the hardest-to-reach places. The approach could eventually help the scientific community understand how environmental changes affect biodiversity, perhaps helping identify endangered or vulnerable species before it’s too late.

Scientists got lab-grown human brain cells to play ‘Pong’

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Researchers who grew a brain cell culture in a lab claim that they taught the cells to play a version of Pong. Scientists from a biotech startup called Cortical Labs say it's the first demonstrated example of a so-called "mini-brain" being taught to carry out goal-directed tasks. ''It is able to take in information from an external source, process it and then respond to it in real time," Dr. Brett Kagan, lead author of a paper on the research that was published in Neuron, told the BBC.

The culture of 800,000 brain cells is known as DishBrain. The scientists placed mouse cells (derived from embryonic brains) and human cells taken from stem cells on top of an electrode array that was hooked up to Pong, as The Age notes. Electrical pulses sent to the neurons indicated the position of the ball in the game. The array then moved the paddle up and down based on signals from the neurons. DishBrain received a strong and consistent feedback signal (effectively a form of stimulus) when the paddle hit the ball and a short, random pulse when it missed.

The researchers, who believe the culture is too primitive to be conscious, noted that DishBrain showed signs of "apparent learning within five minutes of real-time gameplay not observed in control conditions." After playing Pong for 20 minutes, the culture got better at the game. The scientists say that indicates the cells were reorganizing, developing networks and learning.

“They changed their activity in a way that is very consistent with them actually behaving as a dynamic system,” Kagan said. “For example, the neurons’ ability to change and adapt their activity as a result of experience increases over time, consistent with what we see with the cells’ learning rate.”

Future research into DishBrain will involve looking at how medicines and alcohol affect the culture's ability to play Pong, to test whether it can effectively be treated as a stand-in for a human brain. Kagan expressed hope that DishBrain (or perhaps future versions of it) can be used to test treatments for diseases like Alzheimer's.

Meanwhile, researchers at Stanford University cultivated stem cells into human brain tissue, which they transplanted into newborn rats. These so-called brain organoids integrated with the rodents' own brains. After a few months, the scientists found that the organoids accounted for around a third of the rats' brain hemispheres and that they were engaging with the rodents' brain circuits. As Wired notes, these organoids could be used to study neurodegenerative disorders or to test drugs designed to treat neuropsychiatric diseases. Scientists may also look at how genetic defects in organoids can affect animal behavior.

Scientists got lab-grown human brain cells to play ‘Pong’

Posted on by

Researchers who grew a brain cell culture in a lab claim that they taught the cells to play a version of Pong. Scientists from a biotech startup called Cortical Labs say it's the first demonstrated example of a so-called "mini-brain" being taught to carry out goal-directed tasks. ''It is able to take in information from an external source, process it and then respond to it in real time," Dr. Brett Kagan, lead author of a paper on the research that was published in Neuron, told the BBC.

The culture of 800,000 brain cells is known as DishBrain. The scientists placed mouse cells (derived from embryonic brains) and human cells taken from stem cells on top of an electrode array that was hooked up to Pong, as The Age notes. Electrical pulses sent to the neurons indicated the position of the ball in the game. The array then moved the paddle up and down based on signals from the neurons. DishBrain received a strong and consistent feedback signal (a form of stimulus) when the paddle hit the ball and a short, random pulse when it missed.

The researchers, who believe the culture is too primitive to be conscious, noted that DishBrain showed signs of "apparent learning within five minutes of real-time gameplay not observed in control conditions." After playing Pong for 20 minutes, the culture got better at the game. The scientists say that indicates the cells were reorganizing, developing networks and learning.

“They changed their activity in a way that is very consistent with them actually behaving as a dynamic system,” Kagan said. “For example, the neurons’ ability to change and adapt their activity as a result of experience increases over time, consistent with what we see with the cells’ learning rate.”

Future research into DishBrain will involve looking at how medicines and alcohol affect the culture's ability to play Pong, to test whether it can effectively be treated as a stand-in for a human brain. Kagan expressed hope that DishBrain (or perhaps future versions of it) can be used to test treatments for diseases like Alzheimer's.

Meanwhile, researchers at Stanford University cultivated stem cells into human brain tissue, which they transplanted into newborn rats. These so-called brain organoids integrated with the rodents' own brains. After a few months, the scientists found that the organoids accounted for around a third of the rats' brain hemispheres and that they were engaging with the rodents' brain circuits. As Wired notes, these organoids could be used to study neurodegenerative disorders or to test drugs designed to treat neuropsychiatric diseases. Scientists may also look at how genetic defects in organoids can affect animal behavior.

Crab-inspired artificial vision system works on land and underwater

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There had been many previous attempts to develop cameras that mimic the eyes of insects, fish and other living creatures. However, development of artificial vision systems that can see both underwater and on land has apparently been pretty limited. Further, biomimetic cameras are usually restricted by their 180-degree field-of-view. Now, a team of scientists from MIT's Computer Science and Artificial Intelligence Laboratory (CSAIL), the Gwangju Institute of Science and Technology (GIST) and Seoul National University in Korea have developed a new artificial vision system with a 360-degree field-of-view that can work on amphibious machines.

The team was inspired by the semi-terrestrial fiddler crab, which has a 3D omnidirectional field-of-view. They evolved to be able to look at almost everything at once on land and underwater to avoid attacks and to see communicate with fellow fiddler crabs. Scientists have apparently been having issues finding a way to sustain a camera's focusing capability when the environment changes, which is why this team has decided to take a closer look at the fiddler crab. 

The resulting artificial eye is a nondescript black ball that combines various materials and lenses. Its configuration allows light rays from multiple sources to converge at the same spot regardless of the refractive index of its surrounding — in other words, whether the device is underwater or not. The team tested the technology by conducting in-air and in-water experiments: To be specific, they projected "cutesy" objects in the shape of a dolphin, an airplane, a submarine, a fish and a ship at different distances and in various angles onto the artificial vision system. The result? They found that their camera was successfully able to see the objects whether they were or weren't submerged in water.

Young Min Song, professor of electrical engineering and computer Science at GIST, said:

"Our system could be of use in the development of unconventional applications, like panoramic motion detection and obstacle avoidance in continuously changing environments, as well as augmented and virtual reality."

Other potential applications Song didn't mention include population surveillance and environmental monitoring, which could make the technology an invaluable tool for keeping a close eye on endangered, vulnerable and threatened species. You can check out the scientists' paper with more details about the new vision system in Nature.

The largest bacterium discovered is visible to the naked eye

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When you hear the word "bacteria," you probably picture organisms that couldn't be seen unless they're placed under a microscope. A bacterium that has now been classified as the largest in the world ever discovered, however, needs no special tools to be visible to the naked eye. Thiomargarita magnifica, as it's called, takes on a filament-like appearance and can be as long as a human eyelash. As the BBC notes, that makes it bigger than some more complex organisms, such as tiny flies, mites and worms. It was first discovered by marine biologist Olivier Gros living on sunken mangrove tree leaves in the French Caribbean back in 2009. 

Due to the organism's size, Gros first thought he was looking at a eukaryote rather than simpler prokaryotic organisms like bacteria. It wasn't until he got back to his laboratory that he found out that it wasn't the case at all. Years later, Jean-Marie Volland and his team at the Lawrence Berkeley National Laboratory in California took a closer look at the bacterium using various techniques, such as transmission electron microscopy, to confirm that it is indeed a single-cell organism. They've recently published a paper describing the centimeter-long bacterium in Science.

Volland said T. magnifica is "5,000 times bigger than most bacteria" and is comparable to an average person "encountering another human as tall as Mount Everest." One other information Volland's team has discovered is that the bacterium keeps its DNA organized within a structure that has a membrane. In most bacteria, DNA materials just float freely in their cytoplasm. Further, it has around 6,000 billion bases of DNA. "For comparison, a diploid human genome is approximately six giga (billion) bases in size. So this means that our Thiomargarita stores several orders of magnitude more DNA in itself as compared to a human cell," said team member Tanja Woyke. 

While the scientists know that T. magnifica grows on top of mangrove sediments in the Caribbean and that it creates energy to live using chemosynthesis, which is similar to photosynthesis in plants, there's still a lot about it that remains a mystery. And it'll likely take some time before the scientists can discover its secrets: They have yet to figure out how to grow the organism in the lab, so Gros has to gather samples every time they want to run an experiment. It doesn't help that the organism has an unpredictable life cycle. Gros told The New York Times that he couldn't even find any over the past two months. 

Volland and his team now aim to find a way to grow T. magnifica in the lab. As for Gros, he now expects other teams to go off in search of even bigger bacteria, which like T. magnifica, may also be hiding in plain sight.

The largest bacterium discovered is visible to the naked eye

Posted on by

When you hear the word "bacteria," you probably picture organisms that couldn't be seen unless they're placed under a microscope. A bacterium that has now been classified as the largest in the world ever discovered, however, needs no special tools to be visible to the naked eye. Thiomargarita magnifica, as it's called, takes on a filament-like appearance and can be as long as a human eyelash. As the BBC notes, that makes it bigger than some more complex organisms, such as tiny flies, mites and worms. It was first discovered by marine biologist Olivier Gros living on sunken mangrove tree leaves in the French Caribbean back in 2009. 

Due to the organism's size, Gros first thought he was looking at a eukaryote rather than simpler prokaryotic organisms like bacteria. It wasn't until he got back to his laboratory that he found out that it wasn't the case at all. Years later, Jean-Marie Volland and his team at the Lawrence Berkeley National Laboratory in California took a closer look at the bacterium using various techniques, such as transmission electron microscopy, to confirm that it is indeed a single-cell organism. They've recently published a paper describing the centimeter-long bacterium in Science.

Volland said T. magnifica is "5,000 times bigger than most bacteria" and is comparable to an average person "encountering another human as tall as Mount Everest." One other information Volland's team has discovered is that the bacterium keeps its DNA organized within a structure that has a membrane. In most bacteria, DNA materials just float freely in their cytoplasm. Further, it has around 6,000 billion bases of DNA. "For comparison, a diploid human genome is approximately six giga (billion) bases in size. So this means that our Thiomargarita stores several orders of magnitude more DNA in itself as compared to a human cell," said team member Tanja Woyke. 

While the scientists know that T. magnifica grows on top of mangrove sediments in the Caribbean and that it creates energy to live using chemosynthesis, which is similar to photosynthesis in plants, there's still a lot about it that remains a mystery. And it'll likely take some time before the scientists can discover its secrets: They have yet to figure out how to grow the organism in the lab, so Gros has to gather samples every time they want to run an experiment. It doesn't help that the organism has an unpredictable life cycle. Gros told The New York Times that he couldn't even find any over the past two months. 

Volland and his team now aim to find a way to grow T. magnifica in the lab. As for Gros, he now expects other teams to go off in search of even bigger bacteria, which like T. magnifica, may also be hiding in plain sight.

Scientists sequence the most complete human genome yet

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A team of almost 100 scientists part of the Telomere-to-Telomere (T2T) Consortium has successfully sequenced the most complete human genome yet. If you're thinking "Wait a minute — didn't scientists produce the complete human genome sequence almost two decades ago?" Well, you wouldn't be wrong. The Human Genome Project finished sequencing 92 percent of the human genome back in 2003, but the techniques available at the time left the remaining 8 percent out of reach until recent years. Thus, 200 million DNA bases remained a mystery for the longest time. 

In a series of papers published in Science, the T2T Consortium has reported how it managed to fill in almost all of the missing spots except for five, leaving only 10 million and the Y chromosome only vaguely understood. After the papers went out, the consortium's scientists have revealed on Twitter that they have figured out the correct assembly for the Y chromosome and that they will publish another paper with the latest results.

Research lead Evan Eichler from the University of Washington likened sequencing a DNA to solving a jigsaw puzzle. Scientists have to break the DNA into small parts and then use sequencing machines to piece them together. Older tools could only sequence small sections of DNA at once, so it's like solving those unnecessarily tough puzzles with tens of thousands of repetitive, almost identical pieces. Newer tools can sequence longer segments of DNA, which makes finding the correct sequence much more achievable.

To make the process less complicated, the team used a cell line from a failed pregnancy called a mole, wherein the sperm enters an egg that doesn't have its own set of chromosomes. That means the team only had to sequence one set of DNA instead of two. Then, they used a technique called Oxford Nanopore to complete assemblies of centromeres, which are dense knobs in the middle of chromosomes. Oxford Nanopore has a relatively high error rate, however, making it less than ideal for sequencing sections with repetitive DNA. For those regions, the team used another technique called PacBio HiFi, which can sequence shorter sections with 99.9 percent accuracy. 

Eichler said the previously unknown genes include ones for immune response that help us survive plagues and viruses, genes that help predict a person's response to drugs and genes responsible for making human brains larger than other primates'. "Having this complete information will allow us to better understand how we form as an individual organism and how we vary not just between other humans but other species," Eichler said. 

The consortium's work cost a few million dollars to achieve, but sequencing is getting cheaper and cheaper with new technologies. Adam Phillippy, another lead author for the studies, said the hope is for individual genome sequencing to cost as little as $1,000 within the next decade. That could make DNA sequencing a part of routine medical tests, which might help doctors create tailor-made treatments for individuals. 

A ferret is the first North American endangered animal to be cloned

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Animal cloning might just become a valuable tool in preserving species that might otherwise go extinct. BBC News says US Fish and Wildlife Service has successfully cloned a black-footed ferret — the first genetic copy of a North American endangered s...