Category Archives: Bacteria

The eye-opening parasite that can get in through your contact lens

A recent eye infection suffered by 18-year-old Nottingham University student Jess Greaney is the kind of story that fills us with horror. Greaney had keratitis, an inflammation of the cornea, caused by Acanthamoeba castellanii, a parasite that was living and feasting on her eye.

A. castellanii is a ubiquitous organism, found in many eco-systems worldwide. It is able to survive in harsh environmental circumstances – even in some contact lens solutions – and this is not the first occurrence of A. castellanii appearing in the eye. Acanthamoeba keratitis (AK) is a neglected malady frequently associated with contact lens wear and it is thought Greaney caught the bug after splashing tap water on her contact lenses.

Not a great friend to have

Acanthamoeba infection of the cornea causes severe inflammation, intense pain and impaired vision, which is blinding if left untreated. Infection begins when the parasite is at its active feeding trophozoite stage and sticks to the corneal tissue before penetrating the lower stromal layer. The resulting opacity leads to less sharp vision and eventually blindness.

Even more worrying is that besides the painful progressive sight-threatening corneal disease, the parasite can cross the blood brain barrier and cause granulomatous amoebic encephalitis, a progressive disease of the central nervous system) that often results in death.

Greaney was lucky – if you can put it that way – because she was able to receive treatment. After a week her eye was red, painful and bulged, “it looked like a huge red golf ball,” she said. Treatments included clamping her eye open, keeping her awake, scraping off layers of tissue and repeated eye drops.

How does it get in?

Lenses can be contaminated by exposure to water during swimming, using a hot tub, washing with tap water or as a result of poor personal hygiene or inappropriate disinfection regimes, which can promote the growth of bacteria on lenses onto which amoebae in turn adhere and proliferate. In the case of Greaney it was suggested that the parasite was trapped between the eye and the lens before it burrowed.

As contact lenses continue to gain popularity (including for recreational purposes) the proportion of the population at increased risk of developing Acanthamoeba keratitis may rise.

Other Acanthamoeba infections

Acanthamoeba infections (not just in the eye) are being detected by clinicians with increasing frequency, especially as opportunistic infections in patients whose immune system is already compromised. This at-risk population is expanding as a result of increasing use of immune-suppressing therapies for cancer treatment and the global HIV/AIDS pandemic.

No vaccine is available, and the current drugs used to treat these inflammatory infections is largely insufficient, has undesirable side effects and doesn’t work well in the later chronic stage of infection. Treatment also requires the application of a mixture of drugs for prolonged periods, with mixed results. New drugs, either for this or for other neglected parasitic illnesses that afflict millions of people worldwide, are not being developed. The development of cheaper and more efficient, preferably A. castellanii-specific, chemotherapies would be highly advantageous.

Practice good hygiene

When it comes to contact lens wearers, there have been previous efforts looking at whether contact lens care solutions can counter against Acanthamoeba. Contact lenses treated with an antimicrobial peptide have also been developed and tested in human and rabbits, but more clinical trials are still needed before they can be worn by humans.

However, there are some cardinal rules for contact lens wearers: always wash your hands and follow all instructions in handling and storing contact lenses properly. Reusable lenses should be cleaned and disinfected with powerful lens disinfecting solutions every day. Contact lens wearers should also apply make-up only after lenses are put in to avoid contact with eyeliner or mascara and lens. These are some of the “golden rules” that contact lens wearers should stick to.

Millions of people use contact lenses to improve their vision and to enhance the ability to focus or to do activities unencumbered by glasses. And overall, the risk of Acanthamoeba keratitis – and other infections – is low with proper hygiene and care. In the very near future we might even see smart lenses that can monitor the body’s health conditions and measure glucose levels in the tear fluid of the eyes of diabetes patients. So don’t let the horror story lead you to ditch them just yet.

Hany Elsheikha is Associate Professor of Parasitology at University of Nottingham.

This article was originally published on The Conversation.
Read the original article.

Meet Loki – one of our oldest, primeval ancestors

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The Arctic might seem like a desolate place, but in fact new research suggests a lot of vibrant activity beneath its rapidly diminishing sheets of ice, with a rather surprising find hidden rather deep within the hydrothermal vents at the floor of the Arctic Ocean, where scientists discovered a new and unusual organism which may finally bring to light a significant evolutionary link from the days when life on Earth was simple, comprised of a single cell to when cells became multiple and further complex life forms first took shape.

The recently discovered microbe along with its relatives belonged to the group Lokiarchaeota, named for the trickster god from Norse mythology. They were described in depth in the latest issue of the journal Nature – single-celled organisms who display a rather unusual mix of traits more commonly found among eukaryotes — the taxon that consists of all complex cellular life forms on Earth – including all species of animals, plants and fungi. Even the single-celled protozoan such as amoebas are eukaryotes.

Evolutionary biologists have estimated that the earliest line of the eukaryotes first evolved some two billion years ago, in what was perhaps the most significant transition in the history of life on this planet – the moment at which it was determined beings like us would one day exist. However, until now there has been very little evidence of when these events began to take place, with few fossilized remains to help them map out the gradual process along the way, and a lack of transitional forms from prokaryotic to eukaryotic.

On Wednesday, a team of scientists changed all this when they proudly announced the discovery of such a transitional form. In the far depths of the Arctic Ocean, where just enough heat circulates to encourage life, the scientists discovered microbes which contain many — but not all — of those features which had previously only been singular in eukaryotes. These microbes could provide us with an indication of what the precursors of complex cellular organisms actually looked like.

“This is a genuine breakthrough,” said Eugene Koonin, an evolutionary biologist at the National Center for Biotechnology Information who did not partake in the research. “It’s almost too good to be true.”

Back in the 1970s, scientists picked up the first major piece of evidence about how life evolved from a single cell to many. Carl Woese, a microbiologist from the University of Illinois, along with his colleagues looked at the genetic material across different species in order to reconstruct the tree of life, an effort that would later become the scientific practice of phylogenetics. This analysis broke life forms down into three major branches.

The first branch included bacteria, with such familiar species as E. coli, located in the intestines of living animals. A second branch was described by Dr. Woese as archaea, consisting of the lesser-known species of microbes, extremophiles, which thrive in high stress environments such as bogs or hot springs. Eukaryotes, which comprise the third branch, have much more in common with archaea than they do with bacteria, and are more closely related to the former.

Over the last four decades, during which scientists identified new species of microbes and created powerful new ways for comparing their DNA, Woese’s tree of life has become clearer. Many of the most recent studies now indicate that eukaryotes are in fact not a third individual branch. Rather, they evolved from the archaea.

Thijs J. G. Ettema, a microbiologist at Upssala University in Sweden, was particularly enamored by the fact that many species of archaea closely related to eukaryotes grew colonies on the deep sea floor. It remains likely that in the near future, scientists could discover even closer relatives between the two, hiding near the hydrothermal vents.

It was discovered quite by accident, when Steffen L. Jorgensen, a microbiologist from the University of Bergen, was digging up samples of sediment at a full two miles beneath the surface of the Arctic Ocean. An initial glimpse of this sediment revealed several types of archaea living among the layers. Dr. Jorgensen then offered some of his samples to Dr. Ettema so he could take a closer look.

Dr. Ettema and his colleagues took it a step further, attempting to extract DNA out of the sediment for further analysis, which is quite a risky undertaking.

Dr. Jorgensen was only able to provide a teaspoon size amount of the sediment, one that Dr. Ettema was sure couldn’t contain too many microbes.

As the environment they are used to is cold and dark, the microbes barely grow. If you offered a spoonful soil out of your own backyard, it would likely contain a million times the amount of microbes.

It soon became clear that Dr. Ettema and his colleagues would have to spend just about every bit of the sediment just to get enough DNA for an accurate analysis. Any accidents that might happen along the way would leave them nothing to study.

“There was just one shot,” Dr. Ettema recalled.

Luckily, Dr. Ettema and his colleagues were successful in their experiment. It so happened that this particular sample of the sediment held DNA carried from a lineage of archaea that was unlike any kind ever discovered before. The scientists decided to call it Lokiarchaeum, for the hydrothermal vent near where it was found, which is known as Loki’s Castle.

Analyzing the DNA, the researchers found that Lokiarchaeum is far more closely related to eukaryotes than any other known species of archaea. But even more surprising was that it had genes for many traits that had only been found previously in eukaryotes.

Among the bundles of genes they discovered were ones that coded for special compartments within eukaryote cells. These compartments, which are known as lysosomes, allow the eukaryote cells to eliminate any defective proteins.

All eukaryotes also possess a cellular skeleton which is constantly being rebuilt and torn apart as their shape changes. Dr. Ettema, along with his colleagues found that many of the genes in Lokiarchaeum code for the same type of proteins necessary for building such a skeleton.

It could be likely that the Lokiarchaeum use their skeletons for crawling over surfaces in the same way that protozoans do. Lokiarchaeum’s genes also indicate that they may be able to swallow up molecules or smaller microbes just as eukaryotes do.

At the present time, Lokiarchaeum appears to be far more complex than other archaea and bacteria, although not as complex as true eukaryotes. The new study indicates that they lacked a nucleus and mitochondria.

But Dr. Ettema’s discovery sheds light on how a creature resembling the Lokiarchaeum may have subsequently evolved into the first full-blown eukaryotes.

After the ancestors of eukaryotes had developed a complex skeleton, the second major step could have been the beginning of mitochondria, which provides energy to the cell.

Scientists have long known that mitochondria evolved from bacteria. They carry their own DNA, which more closely resembles the genetic strands found in free-living bacteria than the genes within the cell’s nucleus.

A number of the researchers propose that the common ancestors of all eukaryotes consumed some free-living bacteria. The bacteria became mitochondria, providing fuel for their host cell.

Lokiarchaeum, which holds the potential to graze for microbes, may be exactly the type of microbe needed for this scenario.

Once the early eukaryotes developed mitochondria, they acquired the energy needed for fueling a much larger and more complex cell. In 2006, Drs. Koonin and William Martin at the University of Düsseldorf suggested that the development of mitochondria encouraged the gradual evolution of the cell’s powerhouse – a nucleus.

The two different sets of genes could cause a whole host of damage, were they to interfere with each other. Drs. Koonin and Martin suggested that eukaryotes gradually build a barrier to keep them separated.

As much as the Lokiarchaeum’s genes may reveal, there are limits on how many clues they can give the scientists. “We don’t even know how big the cells are,” said Dr. Ettema.

Dr. Ettema and his colleagues are now focusing on the Lokiarchaeum microbes. They’ve acquired some new sediment samples, and they are now able to determine how many microbes are inside them. Unfortunately, due to the pressure and harsh lighting of a laboratory setting, the microbes often die out before the scientists are able to find out much about them.

So the researchers have another task lying ahead: how to best recreate the conditions suitable for the growth and survival of these microbes will replicating the extreme temperatures and high pressure that the Lokiarchaeum have grown accustomed to. Before they can do that, however, they still need to determine some other factors necessary for the survival of the microbes, such as the type of carbon necessary for their survival.

“It’s definitely not easy,” said Dr. Ettema, “but we’re not giving up. There are so many questions — this is a whole new biology we have to study.”

James Sullivan
James Sullivan is the assistant editor of Brain World Magazine and a contributor to Truth Is Cool and OMNI Reboot. He can usually be found on TVTropes or RationalWiki when not exploiting life and science stories for another blog article.

Beards don’t actually have feces in them

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Clickbait headlines claiming there is poop in people’s beards whipped around social media this week. It’s junk science based on common misconceptions about bacteria.

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These headlines are shite: “Some beards contain more poo than a toilet shocking study reveals” – the Mirror “Shock new research reveals some beards contain more poo than a toilet” – news.com.au “Some beards are so full of poo they are as dirty as toilets” – metro.co.uk

Of course, I wanted to read the evidence for myself, like I do with all outrageous, suspicious claims. I couldn’t even find a study cited in any of the articles. All I found was some pretty crappy journalism~!

If there was no legitimate study by respected microbiologists and no instances of unintentional poop in people’s beards, where did this story even come from? As far as I could tell, the story originated from a local tv news segment out of New Mexico, wherein a reporter swabbed some random men’s beards and sent it to a microbiologist to culture for microbes.

To some readers that might sound like legit science. Here’s why it isn’t:

That’s a very small sample size. The reporter pretty much stayed vague about how many beards he swabbed but it was a “handful”. All it would take is a couple unwashed faces to make a petri-dish grow some gross stuff. So, yeah… bad science.

Just because a microbe lives in the guts doesn’t mean it isn’t on your face. Microbiologist, John Golobic called some of the bacteria found “enterics”, meaning bacteria that normally live in the intestines, “the types of things you’d find in faeces,” he said, without telling the reporter or audiences how unbelievably common it is to find these microbes on various surfaces in everyday life, including shaved and unshaven faces. That’s all it took to get the rumor started and people rewrote, retweeted and reshared the story.

Most of the headlines and editorials about this left out that it was merely a bacteria that can also be found inside the intestine, and reported that actual poop was on people’s face, which has nothing to do with the original story and beyond bad science – it’s bad reporting.

Scientists in the microbiology field and pretty much anyone who has followed current thought on the subject know that the human body is home to vast diversity of microbes. Bacteria like E. coli is commonly found all over the body, inside and out.

Readers might remember a similar viral story about unidentified DNA found on swabbed subway cars, implying there are millions of unknown microbes people are being exposed to. In reality everything in the world is covered in millions of microbes, and there isn’t any real danger from being exposed to them everyday.

If you are looking for media that debunks the dangers of microbial paranoia, check out NPR’s articles about probiotics and Mythbuster’s entertaining critique of the “five second rule”.

Jonathan Howard
Jonathan is a freelance writer living in Brooklyn, NY

How Bacteria May Be Our Allies in the War on Climate Change

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A recent report from the United Nations has revealed some unsettling figures, warning that our planet could experience a 40 percent shortage of usable water by the year 2030 unless countries begin to substantially cut back on its usage. Because 70 percent of fresh water in the world is used on irrigation and agriculture, the most practical approach would be to change the ways in which people farm. The need is a rather ubiquitous one. Throughout California’s Central Valley, farmers have begun drilling for water, and they are now tapping into stores that are over 30,000 years old. Kenya is now being faced with its worst drought since 2000, and farmers have begun hand-digging wells in order to gain hold on the receding water table, meanwhile, it’s estimated that as many as one-in-ten Kenyans are going hungry.

This might seem to be as much that both of these regions have in common, but that means that a game-changing solution could easily be put into place in both economies, making use of a resource we hardly knew was there. Beneath the soil, surrounding the roots of plants are swarms of helpful bacteria that number in the billions. These microbiomes can be found in soil all across the globe: along the hard-hit Kenyan coast, right to New England’s notoriously rocky soil.

In each shovelful of dirt, there are armies of bacteria, along with microscopic fungi and protozoan, all of which carry out life processes that the soil is dependent upon for yielding crops, but bacteria substantially outnumber the other microorganisms. Even in bygone centuries, bacteria effectively provided us with a number of products – from cheeses, wines, and vinegars, to laundry detergents and even medicine. Now, it could seem that aside from a food source, they could be helpful allies in actually the growth of standard produce. Actinomyocytes – which are just one type of the diverse microscopic ecosystem found in the dirt, have been used to synthesize a number of modern day antibiotics, such as erythromycin, used to treat bronchitis and whooping cough, among many other infections.

Another type of bacteria known as pseudomonas, is able to metabolize a number of chemicals and fertilizers into useful nutrients for the soil, while clostridium is able to thrive despite an absence of oxygen, breathing anaerobically from the soil’s nitrogen supply as it feeds the plants their nutrients. Not only does this trait make it important, but it’s also an important sign that the bacteria, with their incredibly short lifespans, are among the few organisms that can adapt quickly to an ever changing climate. Manipulating them to our advantage could be a primary means of our species’ own survival.

At the time of this writing, there are scientists throughout the five continents that are regularly digging up evidence for the beneficial symbiotic relationships that exist among microbes and crops such as corn, cotton, tomato and peppers, even varieties that have been genetically modified. Plants typically give off a liquids rich in carbon, providing sustenance for the microbes. Some of these liquids are the result of the plants responding to environmental stressors such as attacks from insects, another rising concern as we are seeing an increase in invasive insect species. Other chemicals are produced due to increases in water following a deluge. The soil bacteria are sensitive to these chemical messages, and they then secrete chemicals of their own which can strengthen the already complex defenses of the plants.

As an example, there are studies done that have shown the right combination of beneficial microbes exposed to the seeds directly can be as effective as commercial pesticides against one particular type of worm known as the rice leaf-folder, which will wraps itself inside and then eat away the leaves of younger plants. Other studies have demonstrated that there are soil microbes that will significantly increase the overall growth and yields of important crops. One study from Germany, observed the same field over a 10-year period, learning that beneficial microbes have increased the rate of growth in maize plants but also boosted the prevalence of phosphorous as well as other elements that are critical to the growth of crops in the soil. In Colombia, where the effects of famine due to climate change are already being experienced, microbiologists have begun to mass-produce bacteria to colonize cassava plants, an economic staple. The result was an increase in the yields of cassava by 20 percent.

There are a number of farmers across the globe who strive to adapt to climate change, a sensitive issue as many established farms, both family and commercial, were plotted based on their precise ability for growing crops. As warming trends advance, dry areas are projected to become drier, and wet areas wetter. Those who have been hit hardest are small-scale farmers who grow their own crops with limited resources. A simple increase in their yield may benefit them economically as boosted crop sales generate cash and higher yields also allow them room to grow other crops. A study conducted using GMO cotton in India over a ten year period, ending in 2013, showed improved nutrition in the diets of subsistence farmers who grew the cotton for this reason – that they could grow more vegetables for themselves, while those who continued growing standard crops ate a diet primarily consisting of cereal. Additional revenue from the crops may then be invested in a wide array of “climate-smart” farming efforts geared towards the further conservation of water and soil.

There’s more good news, however, as to how these microbes may help guard against droughts. Some new studies have shown that microbes have a direct role to play in helping soil bacteria shield crops from harsh dry seasons while also improving their growth and ability to absorb nutrients from rapidly drying soil. If the crops are beneficial to the bacteria, they may help them adapt to extreme highs and lows as well as massive flooding events.

In one such study, the scientists observed that pepper plants cultivated within arid desert-like conditions can function as “resource islands” wherein they attract and manage to trap in any bacteria that sustain plant development during the periods when water is scarce. At present, we know that our bodies are dependent in many ways on microbes as well, which aid in processes like digestion, and may even control traits that we once attributed to genetics, such as body weight. Perhaps, this relationship with plants is not all that different. There was another study which identified soil bacteria that can actually signal the plants to temporarily open and shut the water absorbing pores on their leaves. Not only does this guard against fungi and other bacteria that may cause disease, but it can also keep the moisture trapped inside the plant.

So what’s the best way to go about cultivating this new biotechnology? Particularly at a time when many people believe GMO’s themselves to be harmful.

As we speak, companies involved in the production of foods and medicine, such as Nozozymes, Monsanto and Bayer Crop Sciences, are already launching their own investigation in to how we may go about the commercialization of soil bacteria. In their stead, are also several start-up companies that work tirelessly around the clock in order to commercialize microbial cocktails for growing food, but in all, we are only at the dawn of what may be an exciting new era of realizing the full potential that microbes have to offer.

The United Nations has officially designated 2015 as its International Year of Soil, part of a systematic plan to focus on not only climate change, but one of the problems it brings along with it – the issue of world hunger. Therefore, governments, funders and researchers of all stripes have been taking a serious look into the function of healthy soil in helping the United Nations reach its goal of achieving food security, while the population continues to climb past the seven billion mark, and the prolonged droughts of climate change continue to lower the yields of important food crops. While these initiatives often do a good job looking at the big picture, considering the potential that crop surpluses will have on communities and farmers, one thing that is so often overlooked is hidden in the soil itself, many species of which have evolved over the last six thousand years with their crops, part of a functioning ecosystem in which the crops themselves are essential to the life processes of the soil microbes.

At the end of the day, however, the use of soil microbes for producing better harvests may just be a single phase out of a trying and complex journey as we continue to improve the quality of our food. Even maintaining the quality of the natural resources may be a continuous battle, with climate change expected to worsen by the mid-21st century. Already there are efforts underway to cultivate new GMO’s capable of thriving in drier climates, extracted from beans.

As the climate is changing and unnatural changes like a continuous increase of CO2 continues to build up, risking the destruction of countless natural sanctuaries such as the Amazon River basin, now one of the most important climate sinks on the map, perhaps our best hope in offsetting the impending devastation may lie within nature itself – harvesting what the Earth already offers, in order to preserve our planet for the future.

Bleeding Glacier Mystery of Antarctica Solved

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If you were ever pressed to make a list of the planet’s most extreme desert regions, Antarctica probably would be one of the last places you’d look, but your list wouldn’t quite be complete without making mention of the McMurdo Dry Valleys. It’s one of the few regions in the Antarctic that remains untouched by ice throughout the year, an area almost 2,000 square miles wide with high mountains that prevent most forms of precipitation from entering, as they block off the ice that flows seaward from the East Antarctic Ice Sheet.

What’s even more surprising, if you’ve never heard of this region of mostly loose gravel, with winds traveling at speeds of up to 200 miles per hour, is that despite its harrowing low humidity, new research suggests that underneath the rock region there lies a basin filled with salty, and ice cold groundwater. This underground basin may be a tributary that connects with the surrounding lakes, linking them into one massive network, and, as has already been spotted on this strange continent, the basin likely hosts a myriad of never before seen microbial lifeforms.

These new findings were reported on Tuesday in the journal Nature Communications.

There always seemed to be something unsettling about the place. McMurdo is the home of the gloriously eerie Blood Falls, the name given to a phenomenon in which strange red ooze, resembling dried blood, which shines bright atop what is an unsettlingly desolate surface of rock. It appears as though the rocks are bleeding, which momentarily makes the place seem like something only H.P. Lovecraft could imagine for his novel At the Mountains of Madness, which describes an expedition to the Antarctic gone horribly wrong.

For a long time, many scientists had thought that it was red algae, similar to the kind found in red tides along the West Coast, that caused the coloration of this strange, bloody ooze. While iron oxide is a primary ingredient in the ooze, and gives it its vibrant color, a deeper analysis has revealed that the Blood Falls do harbor some unusual bacterial lifeforms.

Blood Falls has come from quite a distance, seeping from all the way at the end of the Taylor Glacier towards Lake Bonney.

While scientists had known that this ooze had a source, they were quite pleasantly surprised to discover the overwhelming extent contained by the valley’s briny waterways.

“I’ve been studying Blood Falls for quite some time, and it’s always been a mystery,” said the study’s lead author Jill Mikucki from the University of Tennessee. Being a microbiologist, she has had a longtime interest in the microbial ecosystems that thrive within the oozy brine.

In order to survey the area, Mikucki and her colleagues made use of an electromagnetic sensor mounted on top of a helicopter, which then tested the electrical conductivity of the ground beneath their feet. As water begins to freeze, it increases in its resistivity, meaning that it’s less conductive of electrical currents. Salty water, however, is capable of remaining in liquid form at much lower temperatures and has a very low degree of resistivity.

“We found, as expected, that there was something sourcing Blood Falls,” Mikucki said, “and we found that these brines were more widespread than previously thought. They appear to connect these surface lakes that appear separated on the ground. That means there’s the potential for a much more extensive subsurface ecosystem, which I’m pretty jazzed about.”

It is also a good possibility that this substantial amount of brine is not unique to the dry valleys, Mikucki explained. Therfore, it is likely that these subsurface ecosystems made up of extreme microbes may be interconnected to visible lakes on the surface, and perhaps they may even have interaction with the ocean.

Microbiologists call this type of bacteria extreme because those are the types of conditions in which they flourish – intense cold, salinity, or heat. A prime example of the latter is Thermus brockianus, discovered in Yellowstone National Park, where it established colonies around the geyser Old Faithful. Since then, industrialists have domesticated the bacteria which is used to take the hydrogen peroxide out of treated wood, bleaching it to make paper products. Less than a year ago, scientists working in Antarctica sampled water from one of the continent’s subglacial lakes, discovering a well adapted colony of bacteria that exists half a mile beneath the ice.

Extremeophiles aren’t unique to bacteria either. Some species of tree lichen brought to outer space have been seen to undergo photosynthesis and rapidly adapt to the sunlight cycles of other planets on an experiment aboard the International Space Station.

“It turns out that as beautiful and visceral as Blood Falls is in these valleys, it’s actually just a blip. It’s a little defect in this much more exciting feature,” she said.

Mikucki is hoping that soon the team shall be able to return and survey more extensively with the electromagnetic sensor, giving them a bigger picture of how much connection exists among the lakes of Antarctica, and therefore how often the subsurface brines come into contact with oceans along the coast. In addition to being the perfect setting for a horror or pulp adventure novel, all scientific research done in the Dry Valleys has another purpose too, as everything done by the research team does is just as practical for future space explorations as it is for learning more about Earth and the continent of Antarctica, which during the Meosozoic Era was actually a vast tropical region.

“Scientists have been using the Dry Valleys to test instruments since the Viking missions,” Mikucki said. “So how we detect the brines and access them is relevant to work on places like Mars.”

Indeed, there is already some evidence suggesting that brines may exist on Mars, responsible for some unusual, jagged features in the mountains of the red planet. It could be a likely sign that at one time, life thrived throughout the planet, in an era when its geographical features were not much different from our own. There may even be microbes on Mars already, the Tersicoccus phoenicis, which has been isolated in spacecraft assembly cleaning rooms and develops resistance to most cleaning fluids. The fact that they might be resistant to space travel raises questions about how well they may interact with alien forms of bacteria. Russian cosmonauts last summer also reported finding large numbers of sea plankton outside the windows of the International Space Station, indicating that they were able to thrive in the extreme cold of space.

If we are to discover interplanetary life in the near future, it will most likely resemble the life we have recently discovered in Antarctica. The subsurface Lake Vostok, which is currently believed to hold some extensive (and rather unusual) life forms, is also considered to be a prime example of what our technology may soon discover on Europa, the ice-and-ocean covered moon of Jupiter, or Enceladus, which may contain a frigid ocean beneath its surface. On our own planet, these types of subsurface waters are able to support only the most extreme forms of life, and some things close to life – such as large viruses that thrive on bacterial microbes alone. Elsewhere in our solar system, however, these same extreme conditions could be as supportive as planets get when it comes to hosting life.

“The subsurface is actually pretty attractive when you think about life on other planets. It’s cold and dark and has all these strikes against it, but it’s protected from the harsh environment on the surface,” Mikucki said.

Easter Plays a Part in Deconstructing Myth About Ulcers

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Today, scientists aren’t just celebrating Easter, they are commemorating the emergence of a quite modest bacterium called Helicobacter pylori. The bacterium contaminates more than 50 percent of the entire globe’s population – most who will never experience or even recognize any of the symptoms that characterize the infection. Yet, it is the perpetrator behind a majorty of the ulcers people develop as well as the culprit behind a number of stomach cancers. H. pylori actually remained concealed and unidentified in human stomachs for thousands of years until 33 years ago. The bacterium is believed so ancient that it tagged along with humans out of Africa. Today, many credit the Easter holiday with its unveiling for reasons soon to be explained here…

The story begins about 35 Easters ago with a pathologist at the Royal Perth Hospital in Australia, Robert Warren. The doctor observed that of all the biopsies he obtained from patients with ulcers and stomach cancers, about half of them simultaneously carried a corkscrew-shaped bacterium later termed Helicobacter pylori.

It wasn’t long before Warren began collaborating in the early 1980s with Barry Marshall, an eager young scientist in mid-training for internal medicine, in an attempt to grow H. pylori for the purpose of studying it further. To begin, the duo had trouble replicating the bacterium which they were trying to cultivate in the agar dishes customarily used for growing Campylobacter, a bacterium responsible for causing food poisoning in human beings. After about two days of zero growth, Warren and Marshall tossed the dishes in trash bins in the lab.

“Anything that didn’t grow in two days didn’t exist. But Heliobacter is slow-growing, we discovered,”

reported Marshall to Discover magazine in 2010. It was the Easter holiday that kept the researchers out of the laboratory for the following four days, only to return to find colonies of H. pylori growing in the lab.

Having an ulcer has been stereotyped as being the result of an unhealthy, overly-stressful lifestyle marked also by bingeing on too much spicy food. That perception has lingered as current thought. However, thanks to Warren and Marshall who were once scoffed at for their contrasting notion, the perception has gradually grown into a medical myth. The doctors were able to support their theory that ulcers are actually caused by infection with succeeding experiments such as one that entailed Marshall infecting himself with H. pylori by drinking a consomme made with the bacteria which caused him to come down with gastritis. Via further experiments, the doctors were also able to prove the correlation between the bacterial infection with some stomach cancers. Flash forward to current times, and scientific journals and academic papers galore have been published on H. pylori.

By closely examining the bacteria’s assorted strains, scientists have tested their theories about how humans colonized Pacific islands about 30,000 years ago. Recent studies indicate that H. pylori may have actually played a significant role in ridding the elder portion of a population to make way for the young. Traces of the microbe have been unearthed in the gastric tissues of 600-year-old Mexican mummies.

Marshall and Warren won the 2005 Nobel Prize in physiology or medicine because of their discoveries, and nowadays peptic ulcers can be treated with short courses of antibiotics or over-the-counter acid-relieving medications.

Janice Bevilacqua

Why is CRISPR the Science Buzzword of Early 2015?

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CRISPR isn’t just the cutting edge of genetic modification – it is re-framing our understanding of evolution.

What is CRISPR?

CRISPR is a DNA sequence that can do something most other genes can’t. It changes based on the experience of the cell it’s written in. It works because of a natural ability for cells to rewrite their own genetic code, first discovered in 1987. The name CRISPR was coined in 2002, and it stands for “clustered regularly interspaced short palindromic repeats”. They function as a method of inserting recognizable DNA of questionable or dangerous viruses into DNA strands so that the offspring of the cell can recognize what its ancestors have encountered and defeated in the past. By inserting a CRISPR-associated protein into a cell along with a piece of RNA code the cell didn’t write, DNA can be edited.A 2012 breakthrough involved, in part, the work of Dr. Jennifer A. Doudna. Doudna and the rest of the team at UC Berkley were the first to edit human DNA using CRISPR. Recently, in March 2015, she warned this new genome-editing technique comes with dangers and ethical quandaries, as new tech often does. Dr. Doudna in a NYT article, she called for a planet-wide moratorium on human DNA editing, to allow humanity time to better understand the complicated subset of issues we all now face.

CRISPR-related tech insn’t only about editing human genes, though. It affects cloning and the reactivation of otherwise extinct species. It isn’t immediately clear what purpose this type of species revival would have without acknowledging the scary, rapidly increasing list of animals that are going extinct because of human activity. Understanding and utilizing species revival could allow humans to undo or reverse some of our environmental wrongs. The technique may be able to revive the long lost wooly mammoth by editing existing elephant DNA to match the mammoth‘s, for instance. Mammoths likely died out due to an inability to adapt to natural climate change which caused lower temperatures in their era, and are a non-politically controversial choice but the implications for future environmentalism are promising.

Each year, mosquitoes are responsible for the largest planetary human death toll. Editing DNA with CRISPR bio-techniques could help control or even wipe out malaria someday. The goal of this controversial tech is to make the mosquito’s immune system susceptible to malaria or make decisions about their breeding based on how susceptible they are to carrying the disease. The controversy around this approach to pest and disease control involves the relatively young research behind Horizontal Gene Transfer, where DNA is passed from one organism to an unrelated species. A gene that interferes with the ability of mosquitoes to reproduce could end up unintentionally cause other organisms to have trouble reproducing. This info is based on the work of , , http://www.biorxiv.org/content/early/2014/12/27/013276

Even more controversial are the startups claiming they can create new life forms, and own the publishing rights. Austen Heinz’ firm is called Cambrian Genomics which grows genetically-controlled and edited plants. The most amazing example is the creation of a rose species that literally glows in the dark. Cambrian is collaborating with the rose’s designer, a company called Glowing Plant, whose projects were eventually banned from kickstarter for violating a rule about owning lifeforms. Eventually, Heinz wants to let customers request and create creatures: http://www.sfgate.com/business/article/Controversial-DNA-startup-wants-to-let-customers-5992426.php#photo-7342819

The final example in an ongoing list of 2015 breakthroughs involving CRISPR is this CRISPR-mediated direct mutation of cancer genes in the mouse liver might be able to combat cancer. It’s the second cancer-related breakthrough in 2015 that affects the immune system, the first was on Cosmos about a week back: Accidental Discovery Could Turn Cancer Cells Into Cancer-Attacking Immune Cells.

Other Related Cosmoso.net articles:

Pre-Darwinian Theory of Heredity Wasn’t Too Far Off

Wooly Mammoth Poised to be the First De-Extincted Animal, Son~!

Jonathan Howard
Jonathan is a freelance writer living in Brooklyn, NY

Accidental Discovery Could Turn Cancer Cells Into Cancer-Attacking Immune Cells

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Unexpected results are sort of the point of lab experiments. Laboratory studies reveal the unforeseen and if they didn’t, there would seldom be a reason to perform lab studies. It can be problematic when scientists don’t get the results they wanted or thought to expect but other times new data can be the result of the unexpected, and lead to discoveries no one thought to check for in the beginning. Some famous discoveries happened on total accident throughout scientific history. The latest unintentional discovery might make one of the most aggressive types of cancer more treatable than ever before.

Scientists at Stanford recently discovered a way to force leukemia cells to become mature immune cells do something amazing. The researchers were actually trying to stabilize cancer cells so they could keep them alive longer in order to study them. The method of keeping the cells alive allowed the cells to develop into immune cells that may one day help the immune system attack cancerous tumor cells!

You can read the study in full at Proceedings of the National Academy of Sciences.

Acute lymphocytic leukemia (ALL) is the name for a particularly rapidly-progressing cancer where the immature cells that should differentiate and become white blood cells or lymphocytes instead become cancerous. ALL has several classifications based on which kind of lymphocyte (B cell or T cell) the mutated cancer cell originated from.

The scientists were simply investigating a common type of lymphoblastic leukemia, an acute cancer called precursor B cell ALL, aka B-ALL. B-ALL starts as a rogue B cell mutating away from usefulness during an early part of its maturation. The immature cells can’t fully differentiate and become the B cells they were otherwise destined to be. The flawed B cells lack the transcription factors required for normal development. Transcription factors are basically proteins that attach themselves to sections of DNA and are then supposed to switch designated genes on or off, depending on the type of transcription factor. Did you follow that? It’s a bit technical for the layman but most of us understand DNA. Transcription factors are basically a DNA reader than helps the cell decide which part of your DNA it should use to become a specific type of cell.

So, when a transcription factor messes up and activates the wrong section of DNA or doesn’t activate the correct section, it can cause mutations where the cell doesn’t develop or develops poorly. B-ALL is one of the most nasty types of cancer and the prognosis for victims is not good. The Stanford U team wanted to study this villain but had trouble keeping the cancer cells alive outside of the victims body.

Lead researcher Ravi Majeti reported in the lab’s news release: “We were throwing everything at the cells to help them survive.”

One of the techniques they used to attempt to keep the cancer cells from dying involved exposure to a certain transcription factor. The exposed cells began to grow and change shape, and the new morphology was a type of white blood cell called a macrophage, normally responsible for attacking damaged, mutated cells or foreign material.

The team recognized the cancerous cells behaved the same as macrophages in various ways such as surrounding and engulfing bacteria. Most notably, the pseudomacrophages from the cancer cells of mice added back into the cancerous mouse did not behave as a cancer cell, and the mice who did not have cancer did not develop cancer after being exposed.

The Stanford researchers believe the newly converted cells are no longer cancerous. Furthermore, they might even help the body’s immune system regroup and attack other, still cancerous cells. It could work because macrophages normally collect DNA tags from abnormal cells they encounter and also mark foreign material so that other cells in the immune system know what to attack. Since the false macrophages were originally cancerous cells, they will, in theory, already possess the correct signals that recognize the same kind of cancer.

Now that this principle has been identified as a possible method of treating one cancer, it might open the door to helping the immune system combat other cancers.

Related Cosmoso article: Pre-Darwinian Theory of Heredity Wasn’t Too Far Off

Jonathan Howard
Jonathan is a freelance writer living in Brooklyn, NY

Scientists Re-create 170-year-old Beer

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Back in 2010, some archaeologists investigating a 19th century Baltic Sea shipwreck found something more unusual than treasure in the ship’s cargo – four beer bottles fully intact, with the brew still sealed inside. The amber ale was likely brewed in Belgium back in the 1840s, and was on its way to ports in Scandinavia.

You might wonder how well it held up, but surprisingly not too badly for being nearly two centuries old. “These bacteria were still alive,” said Brian Gibson, a senior scientist from the VTT Technical Research Centre in Espoo, Finland, not far from where the bottles were discovered. While beer has been around for at least 7,000 years, being brewed by the ancient Mesopotamians in Iraq, and many breweries have worked to recreate beers from the Middle Ages and American colonial era, Gibson believes this batch is likely the oldest bottle of beer in the world that’s still intact.

Gibson and his colleagues from the University of Munich did an in-depth chemical and microbiological analysis of the beer recently, publishing their work this week in the Journal of Agriculture and Food Chemistry. Despite the inevitable contamination from salt water, they were able to learn quite a bit about the processes of mid-19th century brewing.

“We have a reasonably good idea about what kind of hops were used, different ones than today,” said Gibson. “These hops would have been harsher, these days they are quite mild. The one surprising thing is the beers were quite mild. The original alcohol level was 4.5 percent, nothing extreme.”

Shortly after their retrieval from under the sea, the discovery was celebrated with a monumental beer tasting, consisting of beer experts throughout Finland who came to sample the 170-year-old brew. Rather than using a novelty talking bottle opener, they inserted a thin needle through the cork, taking their samples from two different bottles, in order to avoid exposing the contents to open air. However, the taste testing ended up being something of a disappointment in the end. The researchers described the ancient beer’s scent fairly vividly in their paper, as a cross between “autolyzed yeast, dimethyl sulfide, Bakelite, burnt rubber, over-ripe cheese, and goat with phenolic and sulfery notes.” During its time under the sea, water leaked through the cork of the bottle, rendering the contents about 30 percent salt water.

Despite how good it looked, the beer was considerably degraded. Like modern beers, this beer had a shelf life – a sell by date that had long since come and gone. Aside from the taste of sea water, the tasters had another issue. According to Gibson: “For the analysis, it was difficult to pick out the original flavors. We invited some of the most experienced beer tasters in Finland. The flavors were from bacterial contamination and not the original flavors of the beer.”

Therefore, Gibson and his team had to rely on a further chemical analysis to be taken on the sugars that remained, as well as the alcoholic compounds in order to get a better idea of how the beer was made – their primary interest being the practice of pre-Industrial distilleries.

“We looked at esters, which give beer a fruity or flowery taste. Most of the compounds that we would expect were there. In terms of the fruitiness, probably similar to modern beers. High level of 2-phenyl ethanol which gives a rose or floral aroma.”

In comparison to modern day craft brews, Gibson said their batch was similar to an amber or lambic style ale, which are normally brewed with wild hops. One of the beers had a fairly pronounced hops flavor, while the other likely had more of a fruit flavor, similar to modern summer beers. In many ways, the ingredients in the beers were fairly similar to modern ones, although it was likely that 19th century beer was much more sour, as they did not have a way of keeping acid-producing bacteria from the brew during fermentation.

Sam Calagione, who is the founder and president of Dogfish Head brewery in Milton, Del., has already shown great intrigue in their finds, as his company has worked to recreate historic beers since 1998 with recipes obtained from archaeological digs.

Dogfish’s “Midas Touch,” named for the fabled Greek king, was based on a jar found in a 2,700-year-old tomb uncovered in Turkey, a Bronze Age drink made from barley, saffron and white muscat grapes.

“The whole idea of looking backward for creative inspiration and culinary adventure is really catching on,” Calagione said. “All (the scientists) can give us is a laundry list of ingredients. It is up to us to come up with a creative recipe. What the alcohol content is, whether it’s filtered or carbonated. We have a lot of creative input in bringing these creative beers back to life.”

Stallhagen Brewery of the Aaland Islands in Finland has recently imitated the Baltic Sea beer, under the label “1843.” In addition to the beer bottles, the divers also found 150 bottles of champagne in the wreckage.

Study Could Extend the Lives of People Living with Cystic Fibrosis

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Cystic fibrosis (CF) has proven an enigma for medical researchers and professionals – and patients – for years. There is still a lack of knowledge when it comes to the exact cause of the disease. Despite the missing puzzle pieces however, new medical treatments and courses for controlling the disease and enhancing the quality of life for those living with the illness come in great strides year after year while the prognosis for patients takes consistent turns for the better. Following in the trend of some trailblazing work is a study currently taking place at Aston University in the UK. The study’s researchers are referring to their work as potentially life-prolonging for people with the CF.

WHAT IS CYSTIC FIBROSIS?

Cystic fibrosis is a life threatening, more often than not fatal genetic disease that affects primarily the respiratory and digestive systems, and other bodily systems, depending upon the patient. “CFers” possess a malfunctioning gene that creates a protein which causes the body to produce an atypically thick and sticky mucous. This mucous obstructs the lungs and airways which leads to a lifetime of lung infections, and plugs up the pancreas so that natural enzymes which aid in the breaking down of food cannot be produced. Consequently, vital nutrients cannot be absorbed leading to severe malnourishment and in many cases either lifetime dependence on feeding tubes, or death.

A LOOK AT THE STUDY

Led by Dr. Lindsay Marshall, scientists at Aston University are investigating under the premise that preventing lung infections during childhood can fend off life-threatening infections later in the lives of those with cystic fibrosis. The study entails proving the theory that bacteria pinpointed in children with the illness can disable their natural defense mechanisms, making these children more susceptible to attracting virulent bacteria that can infect airways.

One of the nasty milestones of the disease when it comes to the ravaging of a CF-infected body is the development of a deadly bacterial strain known as Pseudomonas aeruginosa (P. aeruginosa). This specific strain is notorious for being the almost-impossible to treat “superbug” that ultimately creates enough lung damage to kill a CFer. In order to determine the extent to which P. aeruginosa can be halted in its steps, Dr. Marshall and her team have created an impeccable replica of a human CF airway, made completely of human cells in order to examine the treatment of early childhood infections with a spectrum of antibiotics. The model can mimic the functions of an actual human airway and show the deadly progression of cystic fibrosis.

Observing the deterioration process will help Marshall and her crew learn information that can prove critical to developing new and revamped treatments that can actually prolong the lives of people with the illness and carry the CF community in great leaps towards a cure. Marshall claims that the project will allow for establishment of just how accurately their layered human cell prototype can be used to assess its extent for studying the body’s natural defenses and how they are affected by a whole range of inflammatory and infectious conditions – which can lead to the development and assessment of the effectiveness of new and enhanced treatments for CF and other diseases in the future.

ANOTHER DIMENSION TO THE STUDY

With financial support of the a Human Research Trust grant, Marshall’s study is able to take on another objective: that of coming up with new experimental techniques for decreasing the number of animals used to perform respiratory studies. According to an article written in the online magazine Science Daily, last year in the UK more than 115,000 animals were involved in studies for analyzing respiratory conditions like smoke-related lung diseases and asthma. However, since animals do not naturally have CF, it is not only an inaccurate avenue for testing, but quite expensive to genetically alter them for having the disease and is certainly not as effective as using a human model that can be manipulated to have actual CF. In the article, Dr. Marshall states:

“We simply cannot use animals to model the decline in lung function seen in people with CF, the infections typical of people with CF or the administration and dosage of drugs required to treat the condition. Our human CF model…is extremely representative of what happens in human airways and is both ethically and scientifically an improvement upon current animal models.”

THE GOOD NEWS

Cystic Fibrosis is amongst the most common life-threatening inherited diseases in the United States, affecting an approximate 30,000 children and adults in the country and 70,000 worldwide. To demonstrate the benefit of the research when it comes to cystic fibrosis including the aggressive project underway at Aston University, it is important to note that in the 1950s, the disease was strictly a pediatric disease and most children did not live long enough to even attend elementary school. Today people living with the disease can look forward to living well into their 30s, 40s and beyond. Indeed, courtesy of the development of new treatments and therapies, today the average life expectancy of people with cystic fibrosis has risen to 41 years of age.

Janice Bevilacqua