Tag Archives: nematode

Roundworms brought back to life after spending 42,000 years iced in permafrost

These creatures have set a new record for cryogenic survival.

The nematodes isolated from permafrost deposits of the Kolyma River Lowland. Image credits: Shatilovich et al.

The Kolyma River in north-eastern Siberia flows along over 2,129 kilometers (1,323 miles) before ultimately emptying into a part of the Arctic Ocean. For the most part (about 250 days each year), the Kolyma is frozen to depths of several meters. Similarly, most of the path it flows along is surrounded by thick ice — after all, this is the permafrost land we’re talking about.

A while back, Russian biologists dug up more than 300 samples of frozen soil from the area. They found that the samples are teeming with microscopic life: single-celled cyanobacteria, green algae, and yeasts. But among these samples, they also found some macroscopic organisms — namely, some nematodes (Panagrolaimus aff. detritophagus and Plectus aff. parvus) — or, as most people would call them, roundworms.

Some were found in what was likely a ground squirrel burrow some 32,000 years ago, but had since caved in and frozen over. The others were found in a bore sample at a depth of around 3.5 meters (about 11.5 feet). They were carbon dated and found to be 42,000 years old. There’s still the off chance of contamination, but researchers have detailed their strict practices, and peer-review also confirmed the sterility procedures.

After identifying the worms, biologists placed them in a room kept at a mellow temperature of 20 degrees Celsius (68 Fahrenheit). It didn’t take long before they started showing signs of life. Within weeks, they were moving around and eating, setting a new record for how long animals can survive frozen in ice.

[panel style=”panel-info” title=”Longest survival” footer=””]In 2000, scientists found bacteria spores inside 250 million-year-old salt crystals, and after careful processing, were able to bring them back to life.

However, it’s important to keep in mind that the tricks bacteria pull off to survive so long cannot be applied to macroscopic creatures, which are much more complex. Roundworms are remarkably sturdy creatures (related to tardigrades), but they don’t even come close to bacteria. Yet even tardigrades, these incredibly resilient creatures, have “only” been known to survive for decades after preservation.

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Aside from the main story, — that the creatures survived for 42,000 years, frozen — there are two ways to look at this. The first is optimistic and upbeat: by studying the mechanisms which allowed them to survive, we can learn more about cryomedicine and how creatures (potentially, alien creatures) survive in extreme environments.

“It is obvious that this ability suggests that the Pleistocene nematodes have some adaptive mechanisms that may be of scientific and practical importance for the related fields of science, such as cryomedicine, cryobiology, and astrobiology,” the researchers write in their study.

But there’s a darker side to the story. As global warming takes its course and much of the permafrost continues to melt, it could release a string of pathogens currently frozen. What the consequences will be is anyone’s guess.

This research was published in Doklady Biological Sciences.

C.elegans.

A worm’s brain was uploaded to a hard drive and put to the test — without a single line of code

Researchers from the Vienna University of Technology (VUT) have put a brain on a circuit board — specifically, the brain of the nematode C. elegans. They are now training it to perform tasks without a single line of human-written code.

C.elegans.

C. elegans worms.
Image credits PROZEISS Microscopy / Flickr.

C. elegans isn’t much to look at. Growing to just under one millimeter in length, it’s not just tiny, it’s also a very, very simple organism. But in one respect, this little nematode is unique and uniquely valuable for science — it’s the only living being whose neural system has been fully analyzed and mapped. In other words, its brain can be recreated as a circuit — either onto a circuit board or one simulated with software — without losing any of its function.

This has allowed researchers at the VUT to ‘copy-paste’ its brain into a computer, creating a virtual copy of the organism that reacts to stimuli the same way as the real thing. The researchers are now hard at work training this digi-worm to perform simple tasks, and it has already mastered the standard computer science trial of balancing a pole.

Worm in the software

So are your brains at risk of spontaneous copyfication? No. Researchers have been able to map C. elegans‘ neural systems precisely because it’s quite dumb — it can only draw on 300 neurons worth of processing power. However, that’s enough gray matter to allow the worm to navigate its environment, catch bacteria for dinner, and react to certain external stimuli — such as a touch on its body, which triggers a reflexive squirming-away.

This behavior is encoded in the worm’s nerve cells, and governed by the strength of the connections between these neurons. When recreated on a computer, this simple reflex pathway works the same way as its biological counterpart — not because it’s been programmed to do so, but because this behavior arises from the structure itself.

“This reflexive response of such a neural circuit, is very similar to the reaction of a control agent balancing a pole,” says co-author Ramin Hasani.

Pole balancing is actually a typical control trial in computer science. It involves a pole, fixed on its lower end on a moving object, which the device has to keep in a vertical position. It does this by moving the object slightly whenever the pole starts tilting, in a bid to keep it from tipping over.

Worm test pole.

The worm’s natural behavior is very similar to that required in this test.
Image credits TU Wien.

Standard controllers don’t have much trouble passing this test. The trial is functionally similar to the processes the nematode’s neural system has to handle in the wild — move when a stimulus is registered. So, the team wanted to see if it could solve the problem without adding any extra code or neurons, just by tuning the strength of connections between cells. They chose this final parameter based on the fact that shifting synaptic strength is the characteristic feature of any natural learning process.

After some tweaking, the network managed to easily pass the pole trial.

“With the help of reinforcement learning, a method also known as ‘learning based on experiment and reward’, the artificial reflex network was trained and optimized on the computer,” explains first author Mathias Lechner.

“The result is a controller, which can solve a standard technology problem — stabilizing a pole, balanced on its tip. But no human being has written even one line of code for this controller, it just emerged by training a biological nerve system,” says co-author Radu Grosu.

After establishing that the method works, the team plans to probe the capabilities of similar circuits further. Still, the research does raise some very impactful questions — are machine learning and our brain processes fundamentally the same? If so, is silicon intelligence any less valuable or ‘alive’ than biological intelligences?

For now, however, we simply don’t know — C. elegans doesn’t know or care whether it lives as a worm in the ground or as a virtual collection of 1’s and 0’s on a computer in Vienna.

The paper “Worm-level Control through Search-based Reinforcement” has been published in the preprint server arXiv.

earthworm-686592_1920

Why worms can actually taste sunshine

Nematodes lack eyes, and why would they have any in the first place? Worms spend their lives inside the soil with little to no contact with sunlight. Yet, despite lacking eyes, worms do detect light — with their nose, sort of.

earthworm-686592_1920

Credit: Pixabay

Inside the tissue of roundworms, researchers at the University of Michigan found a photoreceptor protein called LITE-1 that’s about 50 times more efficient at capturing light than rhodopsin — the photoreceptor protein found in the human eye. LITE-1 was first discovered among a family of taste receptors in invertebrates and it’s only the third type of photoreceptor found in animals.

“LITE-1 actually comes from a family of taste receptor proteins first discovered in insects,” said Shawn Xu, a faculty member of the U-M Life Sciences Institute, who is also a professor in the Department of Molecular and Integrative Physiology at the U-M Medical School. “These, however, are not the same taste receptors as in mammals.”

Credit: CELL

Xiu and colleagues were first hinted that the worms must somehow sense light after they flashed the eyeless, slithering critters and found these moved away. It could be that the nematodes sensed chemical reactions triggered by light interaction but eventually it was shown using spectrophotometric analysis that LITE-1 absorbs light. That’s strikingly different to the other two animal photoreceptors which react to photons (light particles) and do not simply absorb them.

“Photoreceptors convert light into a signal that the body can use,” Xu said. “LITE-1 is unusual in that it is extremely efficient at absorbing both UV-A and UV-B light—10 to 100 times greater than the two other types found in the animal kingdom: opsins and cryptochromes. The next step is to better understand why it has these amazing properties.”

That’s not all. Photoreceptors typically found in animals have two main components: a base protein and a light-absorbing chromophore. if you break the photoreceptors apart, the chromophore is still functional. When LITE-1 is broken into its constituents, however, the components’ ability to absorb is completely halted rather than simply diminished. Xu says this is proof that we’re dealing with a whole different photoreceptor model. The worm might be unique, at least in this regard. Perhaps other animals used LITE-1 but we’ve yet to found others.

Writing in the journal Cell, the researchers think LITE-1’s phenomenal ultraviolet absorption efficiency could make it a great ingredient for new, better sunscreens. Artificial photoreceptors used in sensors could also be developed based on the worm’s protein.

Not to worry, the sunscreen industry won’t have to farm millions of worms just so you can catch some rays in peace. Xu and colleagues found having the amino acid tryptophan in two places was critical to its function. When these residues were added to GUR-3, a taste protein from the same family, it began to strongly react to ultraviolet light with about a third the sensitivity to UV-B as LITE-1.

“This suggests scientists may be able to use similar techniques to genetically engineer other new photoreceptors,” Xu said.

c. elegans nematode brain activity

What a worm’s brain looks like fired up

These aren’t Christmas lights, but the actual neural activity of Caenorhabditis Elegans, a parasitic nematode. The brain imaging was done by researchers at Princeton University, and no worm had to be cut open. Instead, the researchers used a special protein which  fluoresces in response to calcium.

c. elegans nematode brain activity

When scientists tap the brain, they’re looking for one prime indicator: electrical activity. When a neuron is active, it fires an action potential which is basically a depolarization made between a neuron’s axon to another neuron it signals to. Now, traditionally neuroscientists use a technique called electrophysiology to study the patterns of neuron electrical activity. It’s precise, yet the analysis is limited to a handful of neurons at a time. A more interesting method exploits the fact that when a neuron is active (again, depolarized), calcium flows into it. Using special dyes (proteins) that fluoresce in response to whether or not they bind to calcium, scientists can monitor these calcium dynamics and in turn the depolarization.

That’s exactly what the Princeton researchers achieved, allowing them to monitor in real time  77 of the nematode’s 302 neurons as they light up. These have been shared in this amazing video, split into four frames. In the upper left, we see the location of the neurons, while the upper right shows a simulation of the calcium signaling which is analogous to neural electrical patterns. In the lower two panels we zoom out: the worm itself (left) and the location of the brain (right).

Using this data, the researchers would like to devise a mathematical model that will allow them to simulate and control the worm’s brain. Previously, other efforts identified how C. elegans can identify magnetic fields, while a more ambitious team from Harvard  targeted laser pulses at the worm’s neurons, and directed it to move in any directions they wanted,  even tricking the worm in thinking there’s food nearby.

New Hookwork Vaccine Passes Clinical Trials in Brazil

A permanent vaccine for hookworm has passed clinical trials. The hookworm is one of the most pervasive parasites, affecting over 600 million people worldwide. The virus is also known for affecting mostly poor populations.

The hookworm is a parasitic nematode (roundworm) that lives in the small intestine of its host, which may be a mammal such as a dog, cat, or (often times) a human. Affecting over half a billion people worldwide, it is the leading cause of maternal and child morbidity in the developing countries of the tropics and subtropics. In susceptible children hookworms cause intellectual, cognitive and growth retardation, intrauterine growth retardation, prematurity, and low birth weight among newborns born to infected mothers. The worm is especially prevalent in developing tropical countries; studies showed incredibly high figures of infection in areas in India (42.8% in Darjeeling), Brazil (62.8% in Minas Gerais), Vietnam (52% in the northern parts of the country) and even China (60% in the Xiulongkan Village).

For all the high infection rates, hookworms are also especially nasty. The parasites mainly live in the small intestine, feeding on blood leached from the intestine walls they hook into; they can also live in the lungs. But the problem is manageable with adequate medical treatment – getting rid of an infection takes between a few days and (at the very most) a couple of weeks. But sadly, in many parts of the world, people either can’t afford the treatment, or they simply aren’t aware of it (in many cases, they aren’t even aware they’re infected). This is why a lifetime vaccine would definitely come in hand.

“Developing lasting solutions for hookworm and other NTDs trapping people in poverty requires comprehensive collaboration, cutting-edge science and leadership among health and policy leaders in endemic countries,” Peter Hotez, president of Sabin, has said.

The vaccine itself, as most vaccines, is made with some ingredients from the culprit themselves – namely a protein from the hookworm. When your body is exposed to the protein, it starts to generate antibodies, without having to actually fight the infection. Should the body be infected at some later time, it will recognize the parasite and adequately fight it.

While the vaccine itself shows immense promise, it may still be a while before it actually starts hitting the shelves or before it is implemented in the nations’ vaccination policy system. Even though phase 1 trials were successfully completed, it may take until 2020 for the vaccine to get a license.

Fruit Fly

Mere presence of opposite sex triggers premature aging in fruit flies and worms

Ever found yourself in a hazardous relationship in which your spouse makes your hair go white? Well, if the answer’s yes then you’re not alone. A new study provides new evidence that key aspects of the social environment of some animals significantly influence life span after researchers found that sexually frustrated fruit flies and “haunted” hermaphrodite nematodes died earlier than expected.

Fruit Fly

(c) frankieflowers.com

Environmental cues play pivotal rules in an organisms’ development and health. It’s not only about the space and objects around an animal that influence it however, interactions with other members of the species also have an effect on longevity.  For instance, female fruit flies face a dramatic cut in life expectancy after mating since the male fruit fly’s seminal fluid contains toxins. Now, a group of researchers led by Scott Pletcher, a geneticist at the University of Michigan, Ann Arbor, found that sexually frustrated fruit flies live a shorter life.

An unshared love

Pletcher and colleagues played a most cruel prank on male fruit flies. The researchers genetically modified some male fruit flies to expel female pheromones that typically invite male for mating. To normal flies’ surprise they found they couldn’t mate  with these strange “females”.  This sexual frustration caused the males flies to lose fat, become stressed, and decrease in life span by 10%.

After dwelling deeper into the physiological processes sparked by the psychological sexual frustration, the researchers found that some neurons that signal the production of a certain protein which enable the flies to respond to rewards or mating were destroyed. So, basically living in a delusional world was too much for the fruit life as it never got to have a piece (reward) of what it was expecting (anticipation). Similar results were measured after female flies were modified to release male pheromones; this trickery caused female flies to also live shorter lives.

[RELATED] Promiscuous female mice breed sexier male offspring

Elsewhere,  Anne Brunet, a geneticist at Stanford University in Palo Alto, California, found that nematodes significantly lived less just after sensing the presence of the opposite sex. Now, for this particular nematode species, sex may not be the word to describe them since 99% of all specimens are hermaphrodites (lay eggs and produce sperm at the same time), while only 1% are males.

Simply smelling the opposite sex kills the roundworm

The researchers placed the tiny male roundworms in culture dishes for up to 2 days and then ejected them. In the same dishes, they introduced hermaphrodite worms. Even though the males were gone, the hermaphrodites could still sense them fact which significantly affected their life span. Like in fruit flies, the worms differentiate between sexes using pheromones and in this case, the males’ scent persisted in the dishes causing the hermaphrodites to experience   premature aging—the worms slow down or become paralyzed, and their muscles and internal organs begin to degenerate.  Genetically modified hermaphrodites engineered not to smell pheromones anymore had a normal life span – as in much higher than if they could sense male worms.

“We’ve known for a long time that mating can be harmful,” says Patrick Phillips, an evolutionary geneticist at the University of Oregon in Eugene. But these papers show that “you can have the effects without direct physical contact.”

What about mammals? The researchers say mammals are far more complicated, however I’ve read before of some studies that suggest castration increases lifespan in males. A very interesting  Korean study examined the genealogy records and lifespan of 81 Korean eunuchs to find that their average lifespan is ~14-19 years longer than that of non-castrated men of similar class.  Now, the data range is rather narrow but the life expectancy compared to the control general population is so great that it can only make you wonder. Want to live more? Well… you know what to do now.