Tag Archives: amoeba

Brain-eating amoeba infections expanding to Northern U.S.

Naegleria fowleri (commonly referred to as the “brain-eating amoeba” or “brain-eating ameba”), is a free-living microscopic ameba, (single-celled living organism). Credit: CDC.

A very rare, but almost invariably fatal infection of the brain caused by Naegleria fowleri, an amoeba found in soils and warm waters, is moving northward in the US. Historically, cases of Naegleria infections have been confined to the southern region of the United States, but a new study that mapped cases occurring in the country in the last four decades found that cases have started to appear farther north in recent years. Warming weather due to climate change may be to blame, scientists say.

Naegleria enters the central nervous system when infected water comes into contact with olfactory nerves through the nose. Once planted inside the olfactory bulbs of the forebrain, the amoeba causes an infection called primary amebic meningoencephalitis (PAM) and feeds on nerve tissue. The infection quickly spreads to other parts of the brain, causing extensive inflammation, necrosis, and hemorrhage.

The symptoms of PAM are indistinguishable from acute bacterial meningitis. The illness begins suddenly with the abrupt onset of fever, headache, nausea, and vomiting. Altered mental status occurs in about two-thirds of patients and is followed by rapid deterioration to coma and death.

About 95% of cases are fatal, but luckily there have been only 85 cases of PAM between 1978 and 2018, according to researchers at the Centers for Disease Control and Prevention (CDC) who linked recreational water exposure (i.e. swimming in lakes or rivers) toinfections with the brain-eating amoeba.

The vast majority of these cases (74) occurred in Texas, Florida, and other southern states. However, six cases were reported in Kansas, Minnesota, and Indiana, five of which occurred since 2010.

Locations of recreational water exposures associated with cases of primary amebic meningoencephalitis, United States, 1978–2018. Credit: CDC.

Although the sample size is very small, the trend suggests that infections are spreading northward. Generally, Naegleria infections occur when the water is untreated and warm, as this amoeba prefers high temperatures of up to 45°C, Live Science reported.

When the researchers plotted weather data from the date each case was reported, they found that daily temperatures in the 14 days leading up to each case were higher than the historical average. It may be possible that rising temperatures caused more people to swim in untreated waters, thereby contributing to the changing epidemiology of PAM, the CDC researchers wrote in the journal Emerging Infectious Diseases.

“In summary, our results show a suggested northward expansion of PAM and its potential association with higher temperatures warrants further investigation. Characterizing recreational water exposures could improve risk prediction and prevention strategies, helping to prevent cases, aid natural resource custodians, and reduce the burden on state and local health departments,” the authors concluded.

Newly discovered virus turns amoeba into stone

Scientists have discovered a new virus in the hot springs of northern Japan. It can turn amoebae into stone-like cysts and scientists have named it the Medusavirus.

Researchers led by Masaharu Takemura at Tokyo University of Science, Hiroyuki Ogata at Kyoto University, Japan National Institute for Physiological Sciences, and scientists from Tokyo Institute of Technology isolated the giant virus from a sample of mud and dead leaves collected from a Japanese hot spring. This was reported in the Journal of Virology.

Like the mythical monster from Greek mythology Medusa, this newfound virus can turn its host to “stone.” Thankfully, its hosts are not humans. The virus infects single-celled organisms known as Acanthamoeba castellanii, a type of amoeba. The virus infects amoebae and multiplies inside them, causing some to burst. Post-infection, other amoebae developed a hard outer coating or “shell” and enter a dormant state known as encystment. This prompted the researchers to name the virus after Medusa, the Greek mythological monster who turned onlookers to stone.

While the virus doesn’t have a head full of snakes, like Medusa, researchers found a unique feature on Medusavirus’ outer surface: on closer examination, researchers discovered that the virus’s genetic material is protected by 2,660 spherical-headed spikes. These unusual findings led the scientists to propose that the virus receive its own taxonomic family: Medusaviridae. Genomic and structural features indicate that Medusavirus is distantly related to other giant viruses.

Medusavirus holds many distinguishing features compared with other giant viruses. Its DNA codes for all five types of histones, the key proteins that help compact DNA within the nucleus. In fact, no other known virus has all five types. Further, Medusavirus encoded neither RNA polymerase nor DNA topoimerase II, whereas all other giant viruses encode at least one.

Source: National Institute for Physiological Sciences, Japan

In addition, several genes in Medusavirus were also found in its amoeba hosts suggesting that Medusavirus has infected these amoebas millions of years (or more) ago and the two microorganisms (amoeba and Medusavirus) have exchanged genes over the course of evolution possibly through lateral gene transfer going both directions — host-to-virus and virus-to-host.

“Medusavirus is a unique giant virus that still preserves the ancient footprints of the virus-host evolutionary interactions,” the researchers said in a statement. The team of experts in virus hunting, molecular biology, structural biology, bioinformatics intends to study the infection process of Medusavirus in more detail, including the role of the viral histones and learn more about how the billion years’ co-evolution occurred between giant viruses and eukaryotes.

Bacteria knives

Scientists use the world’s smallest chisel to investigate dagger-wielding bacteria

A new paper describes how one species of bacteria learned to not only stay safe but profit from their greatest enemies, amoeba. The secret is wielding a lot, a lot of knives.

Bacteria knives

Image credits me / ZME Science.
Free to use with attribution.

Bacteria usually steer as clear of amoeba as they possibly can — because amoeba like to snack on them. They’re bigger and usually faster than bacteria, and will envelop any they can catch in pseudopodia to be digested at a later date. Not the nicest of fates.

Some of the bacteria have learned to defend themselves in pretty spectacular ways. One such species is known as Amoebophilus, and was discovered by researchers at the University of Vienna a few years back. It doesn’t only survive inside amoeba but is so well adapted to thrive in there that they’ve have become this species’ favorite habitat.

Now, working together with the Viennese researchers that discovered the bacterium, scientists from ETH Zurich have uncovered the mechanism that guarantees the bug’s survival inside amoeba. And it would make Arya Stark proud: the bacteria has (possibly poison-coated) dagger-launcher devices built into its membrane that allows it to shred their predators from inside and avoid digestion.

Bringing a knife to a bug fight

To find the bacteria’s secret, the researchers used a novel method developed at ETH that’s currently in use only in a handful of labs worldwide. They froze amoeba that had absorbed bacteria at minus 180°C (-292°F). Then João Medeiros, a doctoral student at ETH and paper co-author, used a focused ion beam to cut away at the specimens, much like archaeologists chip away at soil and rock around an artifact with chisels. After milling away the amoeba and most of the bacteria, Medeiros was able to extract the bug’s defensive mechanism and produce a three-dimensional electron tomogram of it.

The mechanism consists of several sheaths affixed onto the bacterium’s inner membrane by a baseplate and an anchoring platform. Their purpose is to shoot molecular-sized “daggers” at the amoeba. Each sheath “is spring-loaded and the micro-dagger lies inside it,” explains João Medeiros, a doctoral student at ETH and paper co-author.

Clusters of daggers.

A cluster of the spring-loaded daggers inside Amoebophilus. Green ones are ‘loaded’, red shows them after the dagger has been launched.
Image credits Leo Popovich / ETHZ.

“When the sheath contracts, the dagger is shot outwards extremely quickly through the bacterial membrane.”

This comes in really handy for the tiny Amoebophilus, as amoeba surround their pray into a stomach-like digestive vesicle (a pocket of membrane inside the amoeba filled with digestive fluids). The daggers shred through these vesicles and allow the bacteria to escape the very unfriendly conditions of the digestive bubble. But it doesn’t escape all the way — once safe, Amoebophilus stays inside the amoeba and takes advantage of its host to feed and even multiply.

We don’t really know why these digestive vesicles get destroyed so easily. It may be that it’s simple mechanical force that does it, but the team suspects there’s more at play here. Their theory is that Amoebophilus’ daggers are also coated in ‘poison’ in the shape of membrane-degrading enzymes. The theory looks to be right, based on bits of genetic code that researcher at the UOV have shown to encode information for such enzymes.

Tiny stabbings

It’s not the first time we’ve seen such daggers in biology. Bacteriophages, viruses which specialize in preying on bacteria, use similar systems to inject their genome past their defenses. Some species of bacteria are known to use similar micro-weapons to pepper their surroundings in ‘ow’ and deter competing microorganisms from a source of food, for example.

What sets these findings apart is the sheer fidelity and resolution the team managed to get on the mechanisms. They’re also the first to create the complete 3D structure of such mechanisms inside cells in their natural context and the first to show the details in the baseplate and membrane anchor.

“In the past, cell biologists investigated the function of such systems and structural biologists elucidated the structure of individual components,” says ETH Professor Martin Pilhofer, the paper’s corresponding author.

“With the cryo-focused ion beam milling and electron cryo-tomography technologies that we have established at ETH Zurich, we can now close the gap between cell biology and structural biology.”

Another new discovery the team can boast is finding these mechanisms arranged in clusters. All previous known micro-dagger weaponry we’ve found is deployed as individual devices. Amoebophilus, however, is not shy of escalating the conflict, using heavy batteries or clusters of up to 30 dagger-launching systems.

“You could call them multi-barrel guns,” Pilhofer adds.

The team also used genomic comparisons to peek into how Amoebophilus evolved its daggers. Their results show that “the relevant genes are very similar to bacteriophage injection systems,” which led the team to believe that these genes are originated from an ancestor of today’s bacteriophages that left bits of its code in the bacteria’s genome long ago. The results also suggest that many other bacterial strains in at least nine of the most important groups should have similar dagger arsenals. It’s not yet known whether they serve the same purpose or not, but the team says their next steps will be to find out.

They also plan to use the new method of cryo-focused ion beam milling to look at other complex molecular systems.

The full paper “In situ architecture, function, and evolution of a contractile injection system” has been published in the journal Science.

This one amoeba could hold the secret to fixing immune deficiencies in humans

Our immune system’s phagocytes use two mechanisms to protect our bodies: they attack and destroy pathogens either internally or externally. These mechanisms are well-studied and established in medicine, but it was believed that only humans and other complex organisms possess such defense mechanisms.

Microbiologists from the University of Geneva Switzerland (UNIGE) have now stumbled upon a species of social amoeba living in the soil of temperate forests that also employs these defensive mechanisms, and has been doing so for over a billion years. Since the amoebas employ defensive behaviors similar to the ones seen in human cells while being genetically modifiable, researchers plan to study them to understand and fight genetic diseases of the immune system.

Working in tandem with researchers from Baylor College of Medicine in Huston, USA, Professor Thierry Soldati’s team studies the social amoeba Dictyostelium discoideum. These predatory amoebas are usually very good at finding enough to eat by themselves, but when food is short they do something astonishing.

Amoeba slug

Close to 100,000 amoebas will come together into a single “mini animal,” known as a slug. This them turns into a “fruiting body” made up of a mass of spores and a central stalk. The spores can survive without food until the wind or another force carries them to a new area where they can germinate and find breakfast.

This is a slug made up of social amoebae. Reactive oxygen species produced by the sentinel cells, which are necessary for the generation of DNA nets that defend the slug, are colored in red.
Image credit Thierry Soldati, UNIGE.

In this way, the amoebas assure their survival through trying times. But it does come at a cost: around 20% of cells sacrifice themselves to create the stalk and 80% will become spores. To make sure the amoebas cash out on their investment, up to 1% of amoebas retain their phagocytic functions.

This 1% is what got the team’s science-bone a’tingling.

“This last percentage is made up of cells called “sentinel” cells. They make up the primitive innate immune system of the slug and play the same role as immune cells in animals,” explains Thierry Soldati, last author of the study.

“Indeed, they also use phagocytosis and DNA nets to exterminate bacteria that would jeopardize the survival of the slug. We have thus discovered that what we believed to be an invention of higher animals is actually a strategy that was already active in unicellular organisms one billion years ago,”

Our body’s bodyguards

Scanning electron micrograph of a neutrophil phagocytosing anthrax bacilli (orange). Photo by Volker Brinkmann.

Ok, let me give you some background. Phagocytes are one kind of immune-system cells floating around in your body. They get their name from the process of phagocytosis, which describes the act of one cell enveloping another then “digesting” it. This is done using reactive species of oxygen (hydrogen peroxide, ozone, etc) synthesized by the NOX2 enzyme.

But this hinges on the ability of a cell to envelop the pathogen. If the invader is too large to be captured, cells instead resort to the external attack method. They eject genetic material in the form of DNA that forms sticky, toxic nets called “neutrophil extracellular traps” (so the acronym for these nets is literally NETs — very handy.)

Armed with these NETs, phagocytes can bite more than they chew — pathogens get covered in these, are attacked by the same oxygen species and die, allowing our immune cells to take out threats much larger than themselves.

But immune systems don’t always work as intended. Patients suffering from granulomatous disease (CGD), for example, can’t express the functional NOX2 enzyme, so their phagocytes can’t destroy the pathogens they find. Because their cells can’t take out the invaders, they suffer from a host of recurring infections.

The team’s discovery might help researchers understand such immune system deficiencies in humans. By genetically modifying Dictyostelium discoideum, UNIGE microbiologists are able to conduct experiments on the mechanisms of their innate immune system. The team hopes that this microorganism can therefore serve as a scientific model for the research on defects in these defense processes, opening the way to possible treatments.

The full paper, titled “Social amoebae trap and kill bacteria by casting DNA nets” has been published online in the journal Nature Communications and can be read here.

Bacterial infections turns amoebae into the world’s tiniest farmers

In 2011 the Queller-Strassmann lab, then at Rice University, made a surprising announcement in Nature Letters.

They had been collecting single-celled amoebae of the species Dictyostelium discoideum from the soil in Virginia and Minnesota. While laboratory grown strain of Dicty happily fed on the bacteria provided for it by its keepers, roughly one third of the wild strains showed a green (or maybe bacterial) thumb. When food was short, they gathered up bacteria, carried them to new sites and seeded the soil with them.

Dictyostelium Aggregation
Image via wikimedia

Pretty smart for something you (usually) can’t even see with a naked eye, right? News of the discovery of the “world’s smallest farmer” went viral. At the time most people assumed that the amoebae were somehow in charge in this relationship. They were, after all, bigger, their spores sometimes contained bacteria, and they ate the bacteria. The theory was that the farming amoebae had different genes than their “hunter-gatherer” brethren.

Who’s teaching them to sow?

The lab has since moved to Washington University in St. Louis, where David Queller, PhD, is the Spencer T. Olin Professor in Arts & Sciences, and Joan Strassmann, PhD, is the Charles Rebstock Professor of Biology, also in Arts & Sciences.

In the August 24 issue of Proceedings of the National Academy of Sciences, they published their work revealing that things are a bit more complicated than they first seemed. They were joined by postdoctoral research associate Susanne DiSalvo, PhD in their research.

Their paper suggests that bacteria, not amoebae, may be in charge; not the bacteria the amoebae are farming, but a third member of this symbiotic relationship. Surveying the bacteria found in association with their stable farmer clones, they found both both edible and inedible bacterial species, but the assemblage always included bacteria of the Burkholderia genus. This was intriguing because this is not a genus of bacteria they find edible; amoeba raised on a lawn of Burkholderia die.

They learned that when a nonfarmer amoebae was infected with Burkholderia, it brought out its plow and started exhibiting behaviors consistent with primitive farming practices; they began to pick up and carry bacterial passengers, such as the tasty Klebsiella pneumoniae bacteria, and “planting” them in more productive areas of the cultures.

It's a farmer's life for me. -Amoeba, Infected.

“It’s a farmer’s life for me.”
-Amoeba, Infected.

When treated with antibiotics that killed the Burkholderia bacteria, they reverted to the non-farming type and no longer picked up or carried food bacteria.

The scientists concluded that Burkholderia has both pathogenic and beneficial properties; pathogenic ones that facilitate infection and beneficial ones that promote the maintenance of a relationship once established.

Symbiosis apparently benefits all three partners. Dicty that carry edible bacteria are better able to survive starving times; and bacteria that hitchhike on Dicty are dispersed more widely. Dicty sometimes eat the edible bacteria, but the Burkholderia sometimes eat the Dicty.

“Now we know that Burkholderia are the drivers,” said DiSalvo, “likely to benefit by exploiting new terrain and sometimes harming their vehicle in the process.”

Amoebas revolutionize our understanding of sex

Amoebas caught in the act


Amoebas are the first eukaryotic creatures, they’re about years old, and still exist today, with a myriad of forms and evolutionary tweaks, interspersed with familiar lineages like animals and plants. The general consensus regarding them was that they are asexual, meaning that they just divide on their own and not engage in sexual activities. But now, researchers are forced to rethink that whole idea, after gathering evidence that amoeboid sex.

“It changes how we interpret the evolution of organisms” says study researcher Daniel Lahr, of the University of Massachusetts. “If the last common ancestor of eukaryotes was sexual, then there is in practice no evolution of sex.”

Amoeba sex was probably missed because when they were grown in the lab, they generally didn’t seem to indicate any sexual activity whatsoever, and probably even when they did, the behaviour was labeled as just weird.

“When discussing the sex of amoeboid protists, the existing evidence does not evoke chastity but rather Kama Sutra,” Lahr writes in the paper, published in the March 23 issue of the journal Proceedings of the Royal Society B: Biological Sciences.

It is this reason that made biologists believe that amoebas, all eukaryotes, and subsequently, us, evolved from the same asexual ancestor, but they are now forced to start rewriting some books. The thing with asexuality is that in the short run, it is better; it’s faster, you can do it whenever or wherever you want, without needing any other conditions. But in the long run, it’s not a great idea on its own, as mistakes tend to accumulate in the offsprings, which become weaker and weaker, and eventually die – this is the main reason why sex evolved in the first place. When genomes are splitting and recombining, offspring can shed these mistakes.

“The bring-home message to the biology community: In general, they have to look more widely than they have been if they really want to talk about theories about sex and the roles of sex,” said Fred Spiegel at the University of Arkansas, who wrote a commentary about the study for the same issue. The last common ancestor of all living eukaryotes had to be sexual,” Spiegel conckudes. “Sex is the rule and not the exception.”

Yeah, well, you can just go ahead and insert your jokes about that last remark here.

Smart amoebas reveal origins of primitive intelligence

Intelligence is very hard to define as a trait, as it’s usually a simplified term used to describe a quantum of related abilities, such as the ability to solve problems, to understand abstract issues, to learn and to plan. But the notion of intelligence should (by any means) be understood at a whole new level, even different than that of human intelligence.

For example, if anybody claimed that amoebas have the slightest trace of intelligence, even a primitive one, the first reaction would be to laugh in the man’s face; and that would be very wrong. Because amoebas are more intelligent than they seem to be at a first glance. A team of US physicists built a simple electronic circuit that helped define how amoebas “think”, and how they adapt.

In some previous studies, a team of Japanese scientists had shown that the Physarum amoeba adapts to shifts of temperature. It was well known that the cells tend to become more sluggish when it gets colder, but they showed that it slows down even in anticipation of cold conditions when there are no changes in the temperature. But what was even more intriguing about this was that despite the fact that the Physarum anticipated the cold spikes in the experiment, after a few repetitions they “learned” that the cold spike would not actually come and continued their existence as usual.

In the study conducted by the Americans, they pointed out to what could be a storage device. The amoebe contains a watery sol within a gel, which creates some low-viscosity channels which are grouped in a network. These channels adapt to the conditions of the moment, but they retain a certain memory of the previous conditions.

“It appears that our model describes pretty well the experiments on amoebas’ learning,” says Di Ventra. He cautions there is a huge gap between the cognitive abilities of single-celled animals and those of developed species, but adds there is no doubt that a combined set of simple circuit models will have more complex behaviour. “This is in fact what we are now interested in studying,” he says.