Posts Tagged ‘story’

The brewer’s yoke, the domestication of microbes

// July 15th, 2012 // Comments Off on The brewer’s yoke, the domestication of microbes // Recent Research

Something happened when I was spliced, something wrong. Some random event in my chromosomes, I suppose it was. In any event, I wound up lacking. My sister took all the toxin genes, and I was left with nothing.

It’s a scary world out there for a fungus without a toxin. How would I strike fear into the hearts of all animals who dared to eat the plants I was eating? How, without my precious aflatoxin to attack the liver, causing acute sickness or eventual cancer?

Quite simply, I’m surprised I lasted as long as I did before they found me.

Indeed, I’m not sure how they did find me. I had a pretty good disguise, growing colonies of blue along the endless islands of white rice grains, just like my toxic cousins always had. Safe from munching animals by my don’t-eat-me mimicry, the promise of sickness is the discoloured rice.

For some reason, these sake brewers saw past it all. I thought I was a goner when they lifted me up from the wild and plonked me into a house of wood.

Then I saw the food.

A. oryzae in heaven. Image by Forrest O.

It’s hard for mould like me to see, lacking in the eye department, but I knew it was there. An endless carpet of steamed rice. With my filamentous fronds I could touch it. Drill down into it and grow cottony soft, sprout fruiting bodies on the surface and spread on and on.

Call me legion, for we are many. Better yet, call me qū meí jūn in Pinwin, kōji-kin in Japanese, nulook-gyun in Korean or the grandiose Aspergillus oryzae in scientific circles. Back then, some 2000 years ago, I didn’t know who I was, or that I would one day be the National Fungus of Japan.

That’s when the changes happened.

I didn’t notice at first, I don’t know that there was ever a master plan. It felt… natural. Human hands, bristling with microbes and pitted with pores, dropped me into heaven. And when I had eaten the heaven for a time, they picked me up and dropped me once more into fresh heaven.

Incomprehensible! These hands must have spent hours polishing the rice to remove all the husks, then steamed it to perfection, cooled it so I didn’t burn my filaments, then spread it out – just for me! It was like being a king! King Kōji-kin!

I'm a national icon, and pretty cute too. Image by Ryoku Kasinn

As they fed me and I ate, we gradually adapted to please one another. Heaven grew ever more heavenly, until the temperature and humidity was just so.

For my part, I started growing much faster, hell, I had brilliant conditions for it and not a doubt in the world that I could grow as fast as I pleased. Fearlessly fast.

Over generations, they selected only the best for their purposes, which at that stage I knew nothing about. They selected the sons and daughters (hell, we’re all of one gender here) that could best turn rice starch to sugar. They also preferred fungi of least colour, but most smell and flavour. Each generation, the best of me would be plucked and propagated.

Turning starch to sugar is a tricky thing. I suppose the point of starch is to tie up the sugar molecules into a big, complex network so the plant can use them later. For me, kōji-kin I secrete the amylase enzymes, biological machine that chops starch into pieces of sweet. From a couple of recently-licked hands, I’ve learned humans make the same enzyme in their saliva. My amylases, however, not only make glucose, but a few other sugars that produce a wonderful flavour.

But why, pray tell? Have you worked it out yet?

Winemakers use yeast to turn the natural sugars in grapes into alcohol. Beer brewers must malt their barley, partially growing the seed to convert starch to sugar, to ferment it with yeast into alcohol.

And I, the humble fungus, plucked from the wild a millennia ago for a deficit in character. My non-toxic self excels, above all other moulds, in turning rice starch into sugars.

From the beds of heaven, me and my alchemical rice is transferred to the fermenting tank. Mixed with yeast, water and more rice, then left to stew in our own juices for a month.

This mash is pressed and filtered, and the sweet, alcoholic liquid that pours forth is bottled as sake.

Not to ring my own bell filaments, but I make soy sauce and miso too. That’s a whole meal – appetizer, main, and a drink.

Domesticated A oryzae (left) and wild A flavus (right). Image by John Gibbons, Vanderbilt University

These days I hardly recognise myself! So much of me has changed by growing with the sake brewers. Though I still share some 95% of my genome with my wild and toxic cousin A. flavus (and you, human reader, share 99% of yours with a chimpanzee), I am given all I could ever want to eat and praised world-over for my skill in sake making. While A. flavus, the wild thing, is targeted daily for a war against fungi with resistant crops and competitive yeasts.

What must the wolf think of the dog? Or the auroch of the cow? Well, to their accusations I say this: We may change our genes and appearance for protection and care, but, in doing so, we also mould the humans who cooperate with us. Through their attentions and skills, they, too, are domesticated.

This story was inspired by this recent research by Vanderbilt University into the domestication of microbes. “Although people don’t often think about it, we haven’t only domesticated animals and plants, but we have also domesticated dozens of different microbes.” – Assistant Professor of Biological Sciences Antonis Rokas in the press release. You can find more information on brewing sake here, and a beautiful description of koji pampering by interns at a sake house in Japan who blogged their experiences.

ResearchBlogging.orgGibbons, J. et. al. (2012). The Evolutionary Imprint of Domestication on Genome Variation and Function of the Filamentous Fungus Aspergillus oryzae Current Biology

Fever dreams – the true tale of Richard Spruce

// March 26th, 2012 // 4 Comments » // Drugs

Richard Spruce had seen some strange villages since arriving in South America in 1849, but this one took the cake. It was a ghost town. Every door was shut tight against the hot, humid jungle, while inside people slumbered away the sunlight.

Being the adventurous sort, he couldn’t comprehend such laziness, not, that is, until he mopped his clammy brow. His hand returned smeared with squashed mosquitoes and his own bright red blood.

He reflected, not for the first time, that life in the jungle wasn’t all it was cracked up to be, all things considered. Charles Darwin had joyfully described the Brazilian rainforest as “a great wild, untidy, luxuriant hothouse.” The tales of Alfred Wallace, a fellow young botanist, absolutely dripped with adventure.

Money truly did grow on trees here – there was a fortune to be made by transporting unusual plant species to England, where new novelties for Victorian gardens fetched a pretty penny.

Plus, the trailblazers in taxonomy whispered, it was delightfully warm, warm being a most thrilling word to Brits.

Had they mentioned the innumerable insects? If so, he still hadn’t expected the particular, primal discomforts of living in a cloud of whining and dining mosquitoes. Likewise, he hadn’t realised that breathing the air’s rich humidity would be as drinking tepid whisky through a straw. Nor how hot the nights were, wrapped tight as a flower bud in his stockings and blanket with a handkerchief over the face to ward away bloodsucking bats.

Nonetheless, Richard Spruce was not one to fret. He was of unfazeable stock, and though inch of his bare skin was soon in welts (not to mention his unmentionables), he followed the river and its plethora of plants to plunder. The cloud of mosquitoes followed too.

It’s not surprising what happened next.

The fever came on suddenly; a shivering, sweating, aching fever that rendered him helpless, striking him down mid-step on the border of Venezuela and Colombia.

His guides carried him shaking to a village. He knew the symptoms, hell he’d seen it before, but he denied his own diagnosis. Though he had the cure in his pocket, quinine from the bark from the Cinchona tree, he was loath to take its bitter rescue. He didn’t want it to be malaria.

Like a pot of swamp water on the boil, was his brain, his temperature climbing like lianas, curling like fern fronds, perching like epiphytic orchids. Images sprung forth from his fertile mind. The first two days he flashed on those damn mosquitoes, a haze of infected blood cells bursting. It didn’t make sense! The mosquitoes had left him three days ago. Certainly it wasn’t malaria, certainly, for it had been weeks since he was around the bad air of stale water, giving the Italian term mal’aria. Still he kept seeing mosquitoes.

As the fever broke into freezing chills, Richard’s guides began to mutter. When those chills turned once more to fever, they sensed his impending demise and sold his scientific equipment for rum. The patient was in no condition to care.

Spruce was stuck on mosquitoes, thriving in stagnant water and stale air, their droning drilled through his brain. He shrunk to the size of a grain of pollen and was sucked up like whisky through a mosquito’s straw. Inside the mosquito gut (it sure was hot and sticky) blood cells burst to release hideous parasites. These sex cells, for he identified them thus as surely as an anther and stigma, combined inside the mosquito. In the gut wall they formed cysts full of eggs. Or were they seeds? Or ferns?

Whatever they were, they grew for over a week, and exploded (much like his mind) yielding youngsters that frolicked freely.

Richard wasn’t frolicking. By the twinges in his aching joints, he knew the pangs of an elderly mosquito carrying young parasites, which had moved to his salivary gland to yield virulent juices. Next time he ate, dipping his mosquito’s double straw through the skin, spitting and sucking simultaneously, he would administer his chemical cocktail – anaesthetics to dull the pain, anti-blood clotting agents and, of course, the parasites.

Through the whisky straw Richard swirled, straight to the liver. His own liver, human and wracked with heat. From the liver, parasites paraded to the blood cells. Inside they ate oxygen-carrying haemoglobin and ran round after round of asexual reproduction, like spores or strawberry runners, each strawberry red and juicy, dripping. Each round took three days to replicate, feast and rupture the blood cells, like clockwork, and his body followed the same ticking cycle, burning fever following freezing chills following fever. Tick. Tick. Tick.

Richard shivered.

From outside he heard the nurse employed for his care, drunkenly yell “die, you English dog, that we may have a merry valorio with your dollars.” Well may she want a valorio, or watch night, but Richard was no a corpse.

After fifteen days of dreaming fever, he relented. Malaria it was. He took the bark of Cinchona trees, which kept him alive (just) by reducing his extreme body heat and causing the haemoglobin-chomping parasites to choke on their own waste. Such sweet relief from such bitter bark.

Thirty-eight days after his collapse, Richard was alive, but exhausted. His full recovery took many months more though, naturally, he kept collecting plants once he found new equipment.

Trudging onwards, Richard felt naught but respect and gratitude for the fine tree, Cinchona (though he preferred moss as a general rule).

Ten years later, having bushwhacked his way through saucer-sized tarantulas and marching fire ants, Richard found himself in the Andes. Gone were the South American rainforests, here roamed high altitude winds and freezing snows. After so long in the heat, the extreme chilliness didn’t suit him at all. But, onwards and upwards, as they say, and he was here to hunt Cinchona trees.

The trees were in high demand by the British and Dutch, both needing supplies for their malaria-wracked colonies. They had no steady supply, as the species had never been cultivated. There were sincere concerns that people would harvest it into extinction.

Richard spent a cold, windswept year collecting seeds and growing young plants. Almost 700 seedlings, well wrapped in moss, were tended all the way to England by a gardener assigned to their care. From the survivors, more than two hundred thousand precious plants were sent on to grow in Indian plantations.

Richard’s success with the species that saved his life did nothing less than change the world, making the heart of Africa habitable and saving millions of lives – but in the end he paid for it with his own health. Another disease cost him the use of his limbs, and he spent the rest of his days on a small pension in Britain.

Today, malaria kills around two million people each year and infects 200 million more. It has quite possibly killed more people throughout history than all our wars and plagues combined. Quinine, along with other chemicals, is still used for cures and prevention, and is gathered from the decedents of Richard Spruce’s trees.

Drinking notes: Enjoy this true tale with warm whisky or gin and tonic. Small quantities of Quinine are added to some brands of tonic water for flavour. Fluorescent, the chemical glows under black light. Many thanks to highly informative Flower Hunters by Mary and John Gribbin for the biography of Richard Spruce.

Nubia, irrigation and parasitic worms, a tale told by a Mummy

// June 8th, 2011 // Comments Off on Nubia, irrigation and parasitic worms, a tale told by a Mummy // Recent Research

A few months ago I wrote about Ancient Nubians and their antibiotic beer, delivering a dose of tetracycline in every brew.

Now bioarcheologist George Armelagos has co-authored a study showing that early irrigation channels changed how humans were affected by parasites.

I’ll describe the research at the end, but first – a story! Make yourself a cup of tea and come back to read it.

Nubia, 500AD

Cotton. Image by Martin LaBar

Since he’d taken his first wobbly steps on Nubian soil, Alara had been pulling his then insubstantial weight on the family farm. He’d pull up weeds with grubby fingers under the watchful eye of his older cousins by day. Lunch was often a paltry loaf of flat bread to share between the lot of them, supplemented with whatever local edible plant was in season, eaten hastily and followed by a brief break in which he built dirt pyramids with other children.

Now 30, Alara remembered his childhood as carefree and unplanned. His memories swam together like waves billowed out from boats on the Nile. Only small moments stood out with any clarity. A snarling dog snapping at his leg. The taste of bread warmed by the sun, seasoned with hunger. Buzzing with disbelief at the stories told by his cousins of things adult and forbidden.

A life in the sun had baked him hard and capable, and he still worked on the same farm he had as a toddler. His extended family shared the plot of land, shared the work, shared the harvest, shared the income. Shared the good years and the bad. He was a cotton farmer through and through, born and raised to the plough.

A friendly slap on the should shook Alara out of his reverie. “Wake up, brother, you are asleep on your feet! It’s time for lunch and then I need to walk to the river and check the channels. The water is not flowing as it should. Will you go with me?”

“Lunch already, Arty? I didn’t notice the sun was so high. Of course I’ll come with you.”

The midday meal of onion and lentils served with flat bread for eating with was waiting hot on the table. They ate quickly and had a weak cup of tea before walking to the Nile.

They could hear the river well before they could see it. The sound of saqiya irrigation was like music that infiltrated the whole valley, though they were so used to it they barely heard it. As they approached their saqiya, they called out a greeting to Nala who was driving the cow.

“Nala! We have brought food for you.”

“Thank you uncle,” she called back. “I’ll come down to eat.”

Al-Jazari's Water-raising-device ca 1205AD

The saqiya was the heart of the farm, pumping the water of life from the river to the fields where it was needed. Made of wood, it consisted of cogs and a large open-spoked wheel. The cow, encouraged by young Nala, moved a wooden arm around, turning the wheels and cogs to move a pulley.

That pulley was studded with jars which dipped down into the water and lifted up to the farm’s main channel. Each jar then deposited its precious load which ran to the farm and branched out into smaller channels, delivering water for the cotton.

Alara inspected the cow and saqiya while Nala ate lunch. Despite a slightly thirsty cow, everything seemed to be working fine. The problem must lie in one of the channels.

Walking along the main channel, he stopped now and then to check the water level. Sometimes silt and aquatic plants collected at the bottom, blocking the flow of water. When he and Arty came to the first branch in the channel, they separated to cover more ground. Following his channel through several other branches, Alara found one that was a problem.

The side of the channel must have collapsed recently. Mud clogged the small stream, causing water to dam up behind it and overflow. Alara reached in and started to pull up clumps of the stuff. The water became turbulent and muddy, and he noticed more than a few of the fresh-water snails that liked to live in the slowly flowing channels. As he cleared it, the water began to run clean again and move into the farm. He spent the rest of the afternoon checking other channels, clearing several that were silting badly.

Though he didn’t know it, those snails were responsible for the troubling, itchy spots many adults had on their arms and feet. Well, it wasn’t the snails exactly, it was the tiny worms inside them.

Several species of trematode of the genus Schistosoma could infect humans. These tiny parasitic worms hatched in water and quickly found snails to infect, burrowing into their large feet. They moved through the life stages of miracidia and sporocyst inside that host, emerging as free swimming cercariae which needed a mammal host to continue to the next stages.

In contact with humans, or for some species other animals, they penetrated the skin and lost their tails, moving through the circulation as schistosomulae. In the liver they would mature into adults, pair, and migrate so the eggs they produced would be shed in stool. Those eggs would make their way to water to repeat the cycle.

Two weeks later, Alara woke in the night with a pain in his stomach which sent him running to the toilet area. By morning he was exhausted and feverish. Though the disease didn’t kill him, researchers would later find evidence of the parasitic worms in his mumified remains.

The research

Schistosomiasis, the chronic disease caused by these worms, is thought “the most important water-based disease from a global public-health perspective” in modern populations. It infects an estimated 200 million people per year. It has a low mortality rate, but causes development problems in children and damages internal organs.

Modern irrigation systems, particularly slow moving ones, boost the disease by providing habitats to the snails. But what about ancient populations?

To find out, Armelagos, Hibbs, Secor and Van Gerven studied dessicated remains (aka mummies) from two Nubian populations. Wadi Halfa (N = 46) lived in 500AD when the Nile was lower, and used saqiya irrigation on their crops. Kulubnarti (N = 191) lived 300 years later, during a time when Nile flooding was good and irrigation was less critical. They hypothesised the Wadi Halfa population would have more Schistosoma mansoni, and it would be more prevalent in children and men due to differential water contact.

One out of three ain’t bad. Indeed, Wadi Halfa people had more of the parastic worms: 26% to Kulubnarti’s 9%. However peak prevalence of infection did not occur at a younger age in the Wadi Halfa, and there was no sex difference.

ResearchBlogging.orgHibbs AC, Secor WE, Van Gerven D, & Armelagos G (2011). Irrigation and infection: The immunoepidemiology of schistosomiasis in ancient Nubia. American journal of physical anthropology, 145 (2), 290-8 PMID: 21469072

Note: I tried to be accurate about life in Nubia, 500AD, but please correct me in the comments

(Also, I want to be a bioarcheologist! Should I apply for one of these Graduate Programs at Emory University?

Death of a hive, a science story

// February 1st, 2011 // 1 Comment » // Recent Research, Science Communication

Apis bee in honeycomb

Image by By Richard Bartz

It was late afternoon, and Aethina could smell a hive in danger.

Heavy with eggs she felt compelled to investigate. The scent wafted softly though the hot and hazy air, so faint it was barely discernible.

Driven by survival, she flew as fast as she could. Weak as the smell was it was hard to tell which direction to go. Through trial and error she travelled across small hills covered with brown grass, wilting seedlings, and huge angular mounds of dirt.

Finally she reached an ocean of bright yellow flowers heads pointed towards the sun. Interspersed between the identical tall and bristled stems were smaller flowers in purples and whites.

Like islands in the sea, these were safe havens for bees, providing a delicious variety to an otherwise blandly repetitive diet. But Aethina wasn’t hungry for nectar. The hive was close, she could smell it.

As a larva, Aethina had heard stories of her ancestors. Generations upon generations ago they had moved across an ocean too. Their land was dry like this, but filled with foreign flowers. They had travelled, said the stories, inside sweet melons.

Suddenly Aethina could see it, the hive. The smell radiated from it, a beacon of hope and danger.

She alighted and walked through the entrance.

At once the guards sprang upon her. Stinking of bee, they buzzed angrily and tried to push her outside. Her own smell must have set them off. To fend off the aggressive attack, Aethina turtled her head and legs under her hard shell. The guards could find no purchase on her smooth surface, and their suicidal stinging could not penetrate her armor.

With small steps, Aethina sneaked deeper into the hive, avoiding the cracks that riddled the tunnels. Below she could hear the cry of her kin, trapped below. As she watched, hunched under her shell, an apparently very stupid bee dripped honey down the crack, feeding her kind as though they were bee grubs.

One step at a time, slowly, slowly, Aethina forced her way though the tunnels. The attacks continued as she inched her way along, turning this way and that along the chambers.

Suddenly the attacks stopped. Poking out one antennae, and then two, she investigated her surroundings. The bees seemed to be gone, perhaps called on another mission.

There was no time to lose. Silently Aethina laid her eggs as quickly as possible, hiding them near the honey-filled pots that rose like ornamental ponds in mosaic. When they hatched, her larvae would have plenty of food nearby. It would be enough for them to molt into adulthood and find their own hives.

Unless removed by the bees, her children had a good chance of surviving. Eating, growing fat on sweet sugar and proteins, they would gradually destroy the hive. No place lasted long after becoming a Small Hive Beetle Nursery. It was only fair. After all, bees had killed her mother, and would kill her in a heartbeat.

Bees were nasty insects, particularly in this melon-founded land. There were other species of bees, natives with a barbaric tendency to catch her kind and mummify them alive. Armed with balls of sticky resin during the day, they created a lacy resin curtain every night that was impossible to get through. The old saying came back to her “Always lay near Apis, never Austroplebeia.”

For good measure, she dusted spores from her six legs. Yeast. It would consume the honey to produce more of the attractive alarm scent that guided her to the hive. Soon there would be even more beetles, and as the larva fed, the yeast would eventual turning the hive from it’s well-ordered structure into a slimy mess. It would seal the fate of this hive.

Served the bitches right, thought Aethina viciously, as she crawled into a crack to take advantage of idiot-bee hospitality.

This story is based on scientific fact. Since their accidental introduction in 2002, African Small Hive Beetles (Aethina tumida) have been decimating Australian hives of honey bees (Apis mellifera). Their larva consume the hives, while the yeast they bring in converts hives to slime. But the native bee (Austroplebeia australis) destroy the beetles with resin balls and build resin curtains.

Further reading
Stingless bees entomb beetle invaders by Anne Dolin at Aussie Bee.
Beetle and yeast team up against bees by Not Exactly Rocket Science.
Ellis, J., Hepburn, H., Ellis, A., & Elzen, P. (2003). Social encapsulation of the small hive beetle ( Aethina tumida Murray) by European honeybees ( Apis mellifera L.) Insectes Sociaux, 50 (3), 286-291 DOI: 10.1007/s00040-003-0671-7

Oh, Oh OMG I’m included in Open Lab 2010!

// January 10th, 2011 // 1 Comment » // Jibber Jabber, Science Communication

Open Lab 2010The finalists of Open Lab have been announced. I’m all a-quiver with excitement because I’m included in the list!

That means I’m going to be PUBLISHED in an ANTHOLOGY of science writers. Among the list of those included are some big names like Scicurious, Ed Yong, Carl Zimmer, Kevin Zelnio and many more excellent bloggers.

Many thanks to Jason Goldman for his work as the editor, and to the reviewers and everyone else in the project who give up their time (and probably sleep) to put Open Lab 2010 together. The book will be published in early February and available online and in some stores.

Here’s my award winning post How aqua regia saved Nobel Prize medals from the Nazis.






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