A Schooner of Science

The red queen, sex and nematode worms

// July 28th, 2011 // 1 Comment » // Recent Research, Sex and Reproduction

Alice and the Red Queen by John Tenniel

In Lewis Carroll’s Through the looking-glass- a whacky book if I ever read one – the laws of physics don’t really apply. Hills can become valleys, straight can become curvy, and forward is really backward.

In one scene, Alice chases after the Red Queen, both running as fast as they can, but when they stop Alice realises they are still right where they started. “Now, here, you see, it takes all the running you can do to keep in the same place” says the Red Queen.

And it might be the same with the evolution of predator and prey, host and parasite. Running doesn’t get you anywhere. So says the Red Queen Hypothesis.

C elegans embryo. Image by Monica Gotta

As the host adapts to fight the parasite, the parasite evolves to infect the host. It’s an endless race, and extinction faces the first organism to stop running.

So what’s this got to do with sex? Sex is evolution on turbo. Mixing and matching genes increases genetic diversity, giving a species more opportunities to outlast in the ultimate game of survivor.

Field data supports the Red Queen Hypothesis as describing an adaptive advantage of sex. Models and maths support the idea that coevolving species could select for rare genes and unusual combination randomly created by sex. Direct experimentation of coevolution and nookie is tricky business.

New research, published in Science, grew several populations of nematode worms (C. elegans, roundworms) which are usually asexually, but reproduce sexually 20% of the time.

The populations were differently exposed to bacterial parasites (Serratia marcescens) as shown.

C Elegans image by Bob Goldstein, University of Carolina, Chapel Hill, remixed by Science Journal. Creative Commons License

One population was given the parasites and left to their own devices. They and their bacteria could evolve together. These nematode worms increased their rate of sexual reproduction to 80-90% over time, and maintained a high level of sexy-times.

The other nematodes were given frozen stocks of bacteria every generation, so the parasites weren’t evolving as the worms did. At first, sexual reproduction increased in the worms, but then it dropped back down to 20% – the same level as nematodes which hadn’t been exposed to the bacteria at all.

Parasites on their own don’t increase sex – coevolution does.

A second experiment supported their conclusion. Nematodes mutated to be unable to reproduce sexually (asexual obligates) became extinct after 20 generations when exposed to the parasites. But mutants that always required sex to reproduce (sexual obligates) never became extinct.

When it comes to coevolution, it’s fall behind and be left behind.

Never stop running.

Morran, L. et al (2011). Running with the Red Queen: Host-Parasite Coevolution Selects for Biparental Sex Science, 333 (6039), 216-218 DOI: 10.1126/science.1206360
Brockhurst, M. (2011). Sex, Death, and the Red Queen Science, 333 (6039), 166-167 DOI: 10.1126/science.1209420

Bacteria solve sudoku

// November 17th, 2010 // 1 Comment » // Just for Fun, Recent Research

Image by UT-Tokyo for iGEM

Nobody loves sudoku like my granddad, unless it’s these Tokyo scientists. They genetically engineered e-coli to let them solve sudoku puzzles.

The puzzle was a 4×4, not quite the 9×9 that we’re used to. An example is shown in the picture. Each number was assigned a colour, so a red colony was the number one, and blue was two. The bacteria had to become the right colour to fit into the sudoku solution.

To solve the puzzle, the bacteria have to know what numbers are around it. For example, the position in the top left has the following data: There is a one in the column, a three in the row and a two in the box. Therefore it needs to be a four.

To become a number four, it needs to receive signals for one, two and three which makes it flip on a switch to say “four.” The switch works only when it receives three different signals.

Signals were transferred between bacteria using phage – viruses that infect bacteria. For example, a number one bacteria would produce a phage which says “Yo, I’m number one.” When that phage infects bacteria around it, they know they are in the presence of a number one. That helps flip the right switch for the bacteria to solve the puzzle.

More details on the project, which was part of the iGEM competition, can be found here.

Hat tip to The Loom.

Microbes, photographic film and a self portrait

// November 4th, 2010 // 1 Comment » // Science Art

Image by Erno-Eric Raitanen

This art is made of film degraded by bacteria.

It’s a self-portrait of the artist Erno-Eric Raitanen. The bacteria was harvested from his own body and cultivated on the gelatin surface of photographic film.

It’s a similar process to growing bacteria on a plate of agar. As the bacteria gnaw away at the gelatin, the film starts to degrade and creates some interesting patterns. He calls them bacteriograms.

I recommend you flick through his online gallery. I like to think I could make some myself one day, except with added science. Maybe add some antibacterials to part of the film and influence the pattern. OR add a mild antibacterial to the whole surface and make a picture of antibiotic-resistant bacteria!

I know I’ve got some scientist readers out there who are into bacteria. What would you make a bacteriogram of? What about virologists, how could you get some viral action happening on film?

World’s sweetest antibiotic? The five ways honey kills bacteria.

// July 13th, 2010 // 5 Comments » // Drugs, How Things Work, Recent Research, Science at Home

You’re at the doctors with a suspected infection, but instead of offering penicillin or erythromycin, they prescribe honey. Would you switch toast toppings? Take a honey pill? How about letting the doctor smear medical grade honey over the infected area?

People have been using honey (not mad honey) as medicine since ancient times, but until now we have never fully understood how it works. Research lead by Dr. Paulus Kwakman from the University of Amsterdam and his team have finally identified the key elements which give honey its antibacterial activity.

Bacteria are becoming resistant to drugs faster than we’re developing them. Honey might help because it works when other drugs don’t. Studies show it has good activity in vitro against antibiotic-resistant bacteria. An older study reports successful treatment of a chronic wound infections not responding to normal medicine.

So how does it work? It’s a combination of five factors.

1. Hydrogen peroxide, a kind of bleach. The honey enzyme called glucose oxidase makes hydrogen peroxide when honey is diluted with water. We clean toilets with bleach, and it’s pretty good at killing bacteria.

2. Sugar. Honey has so much sugar there’s hardly any water for bacteria to grow in.

3. Methylglyoxal (MGO), an antibacterial compound found in New Zealand Manuka honey a couple of years ago. It’s also found in medical grade honey which is made in controlled greenhouses, albeit in smaller amounts.

4. Bee defensin 1, a protein found in royal jelly (special food for queen bee larva.) This report is the first time bee defensin 1 has been identified in honey, and it works as an antibiotic.

5. Acid. Diluted honey has a pH of around 3.5, the acidic environment slows down bacterial growth.

These five things work together to provide a broad spectrum activity against bacteria. For example, S. aureus is vulnerable hydrogen peroxide, while B. subtillis is challenged only if MGO and bee defensin 1 are working simultaneously. Honey has the right mix for maximum destruction.

So that’s how bees keep their honey fresh and unspoiled by bacterial growth. Perhaps with this information we’ll create enhanced honey to guard against infection, improving on nature like we did with penicillin. Until then, I know what I’m having on my toast.

A Schooner of Science could be named Australia’s best science blog. If you enjoyed reading, please vote for me.

Kwakman, P., te Velde, A., de Boer, L., Speijer, D., Vandenbroucke-Grauls, C., & Zaat, S. (2010). How honey kills bacteria The FASEB Journal, 24 (7), 2576-2582 DOI: 10.1096/fj.09-150789

What is the synthetic cell?

// May 22nd, 2010 // 1 Comment » // How Things Work, Recent Research

Two days ago scientists at J. Craig Venter announced the creation of the first self-replicating synthetic cell, a bacteria with DNA made in a lab. How did they do it, and what does it mean for us in the future?

First up, the scientists didn’t make life out of nothing, and they didn’t make a new species. They recreated a bacteria that already existed, and developed the techniques to do it.

The bacteria is Mycoplasma mycoides. It’s a parasite which lives in cows, and some subspecies cause cow lung disease. It has a circular chromosome made of just under 600,000 base pairs, making it a small genome.

The scientists had the genome sequence of M. mycoides and split it into bite-size portions and then synthesised. Synthesising DNA is nothing new, scientists have been able to write DNA code for quite a while, and can write whatever code they want to.

These little chunks were put into yeast, which can be forced to absorb little bits of DNA. Inside the yeast, the chunks can be sewn together. It’s called recombination. The resulting medium chunks were taken out and put into more yeast to be sewn together making large chunks. There were 11 large chunks were put into more yeast, and sewn together into one complete genome.

Along the way and at the end they checked the code was right by doing PCR tests, genetic fingerprinting made famous by CSI.

Result: A synthetic genome, written by a computer and put together in yeast sweatshops.

Now they had to get it into a bacterial cell. At first they tried to put the DNA into bacterial cells of a similar species, M. capricolum. They ran into trouble at first, because the DNA they had was unmethylated (lacking methyl groups) and the bacteria destroys DNA which is unmethylated. It’s a clever defense mechanism, and they got around it by methylating the DNA before putting it in.

Finally success. The synthetic genome was put into an M. capricolum bacteria where it replaced the normal genome. The bacteria were controlled by the new, synthetic chromosome and were able to replicate billions of times.

What does it mean for us in the future? The technology these guys have developed could be used to alter the DNA of bacteria and make them do new things. From medicine to clean water, the benefits could be huge. We already have this ability to some extent, but it opens up some new doors.

Some organisations have raised concerns about the work. Could a new bacteria be unleashed and take over the world? Probably not. It’s hard to predict how new genes will work in cells, and everything is linked together in a way we don’t understand now. Too much tinkering to the genome will probably not be tolerated by the cell. And if it did get outside, it would probably be extinct pretty quickly because it doesn’t have thousands of years of evolution to prepare it for the world.

If it did get out, we could track it back to the company in charge. These guys watermarked their genome by adding some quotes into the DNA/protein code. Now that’s just epically geeky!

Gibson, D., & et al (2010). Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome Science DOI: 10.1126/science.1190719

Some (bacteria) like it hot

// May 13th, 2010 // No Comments » // How Things Work, Science in the Movies, The Realm of Bizzare

New video up!

I started this video back in January and 95% finished it before I moved to Canberra and bought a laptop. I haven’t had a chance to complete it and upload it… until now.

The montage part is my favourite.

Art in a plate of agar – designs made with bacteria

// December 27th, 2009 // 1 Comment » // Science Art

Bacteria and fungi are not generally thought of as attractive pieces of art, indeed I know the times I have lapsed in used-by-date judgment I have beheld them with disgust. Disgust, followed by destruction – straight to the bin or a boiling hot death.

Still, they have a certain something… especially when dressed up like this.

These two piratey concoctions were created by the Gregory Lab at the University of Guelph. They were made with e-coli plated onto green agar. I’m not 100% on the process, but if it was me I would print out a design and place a plate of green agar over it – then with an inoculator (sterilised wire loop on a stick) trace the outline onto with e-coli culture, then let it grow for a while. It might not smell great (blegh, e-coli always smells like ass), but at least it LOOKS cool.

Niall Hamilton counters with a range of plates made using fungi and bacteria. I particularly like the way the texture of the grass vs the mushroom head, either the different varieties grow at a different rate or he plated the grass a few hours after the mushroom. Using fungi gives you a range of colours to choose from (I think the pink is Aureobasidium pullulans), for e-coli to grow in different colours you need to genetically engineer them.

Speaking of genetically engineering bacteria, here is Salmonella typhimurium made to express fluorescent and carotenoid pigments. This was created by iGEM Team Osaka, who work on a range of projects, including art of an almost-alcoholic bacterial cocktail. Yum!

These images were found at Microbial Art, and they have plenty more on show. As the role of microbiology becomes larger in society, I think we’ll be seeing more and more microbial artwork. I hope we do, anyway.

Animal to Human Transplantation

// December 13th, 2009 // 3 Comments » // How Things Work, Recent Research

As I gazed out over the undulating ocean I could feel a twinge of phantom pain in my lost leg, it always twinges so when the beast is near. Perhaps some part of it’s spirit was not cleaved so sharply from my body, and it can sense its physical counterpart is close and yearns to be reunited again. Perhaps it hungers for revenge against the monster. Perhaps it is a prosthetic it desires, carved out perhaps from the fleshy appendages of the monster itself, a leg for a leg if you will. The beast today is nowhere to be seen, but still I stand and ruminate on such matters of animal to human transplantation.

Australia, my home port, decided on Thursday to lift their ban on animal to human transplantation clinical trials and join countries such as New Zealand and the USA. The ban was started five years ago due to concerns diseases could spread from animals to humans during transplant, but the evidence now shows that this is an unlikely outcome and the possible benefits (curing diabetes, an alternative to stem cells) outweigh the possible dangers.

Animal diseases can rarely enter humans, because we have different cells and physiology. A microbe which can happily infect a cat is stumped when it comes to infecting a human (where’s the tail? Where the hell am I?) and the further the animal gets from a human the less likely they are to cross-infect (worm microbes are unlikely to jump to humans.)

However there are some exceptions. The flu is a big one, owing to the fact that it has eight pieces of RNA that are packaged into a single virus particle, and if an animal (usually a pig or a bird) catches both human flu and pig/bird flu at the same time, and both kinds infect the same cell, there can be mistakes in packaging that creates a new strain of virus UNLIKE ANYTHING WE’VE SEEN BEFORE. It’s called an antigenic shift, and if the packaging creates something that is very good at infecting humans then we’re in trouble. Our immune system doesn’t like being confronted with weird things. Other exceptions include HIV which swapped from monkeys to humans, and Yersinia pestis which can infect rats and humans and caused the Black Plague.

Pandemic flu, HIV, the black plague… microbes may not jump animal to human often, but when they do the results can be severe. Perhaps this is why Jacqueline Dalziell had this to say: “The public, who had no say in this discussion whatsoever, will be the first to be directly affected if a new pandemic like AIDS … is introduced into Australia through the ban being lifted,” she said. “The whole of Australia is currently taking part in an experiment without their consent.”

On the other hand, perhaps it is because she is project co-ordinator for Animal Liberation and has other reasons against the decision. I disagree with the statement anyway, asking the general public what they think of the subject is a bit ridiculous, most people only know what they hear from the media and we all know what sensationalist bs that can be (if you don’t, check out Bad Science), an effort to educate people before the vote would probably be limited to a pissy brochure about the risks and benefits which most people wouldn’t bother reading anyway.

Not that I have a negative view on the public and science, I know you my fair readers are interested and educated on the science world, and I’m a science communicator at heart. But people, there’s a reason to do ENQUIRIES to make an INFORMED decision rather than tossing a question like this to the masses and saying “well this way if it goes bad, at least we can say they voted for it.” Whatever.

Notes on the virus, pirate of the cell

// December 13th, 2009 // No Comments » // How Things Work

Viruses are on the cusp of life and non-life. On one hand they have genetic material and use it to make more of themselves and evolve, on the other hand they don’t do anything outside of a host cell, they don’t breathe, grow, or move. If we count them as living, they are the most primitive form of life on Earth, but they certainly evolved after other forms of life because their existence depends on other cells. Viruses are custom designed to invade archaea, bacteria, animals and everything in between. In humans they are responsible for the common cold, chicken pox, influenza, polio and a host of sexually transmitted diseases like genital warts, HIV, herpes, and plenty others.

They are made of genetic material (single stranded or double stranded DNA or RNA) wrapped up in proteins. On their own, a virus can’t replicate themselves, they don’t have the machinery, the energy, or the building blocks. They get around this by sneaking into a cell and holding it at ransom, forcing it to make more and more viruses until they break the cell apart or sneak out one by one to infect other cells. Instead of a lust for gold, viruses have a lust for machinery and energy. They will board, hijack, rape, ravage and destroy to get what they want.

Cells aren’t fond of viruses, after all they screw up the well-organised operations that a good cell is proud of, so if a virus was to knock on the membrane and say “Hey, I’m a virus, can I come in please” the cell would likely sound an alarm for the immune system to come and kick some viral ass. Good thing for viruses (and not us) they are crafty indeed, and will decorate themselves with proteins that say “Hi, I’m full of food, come and eat me” or “Hi, I bear an important message from the brain. Let me in and I’ll tell you all about it” or they say nothing, just dock onto the outside of the cell and inject their genetic material. After all, it’s the genes that are important, the external proteins are just the boat.

Bacteriophages are viruses that infects bacteria, and there are buttloads of them, around 900 million bacteriophage in a milliliter at the surface of the sea, where bacteria are busy exhaling oxygen as they sun themselves. T4 (which infects e-coli) does it through the last method, and does it very effectively. They also look like a spider from Mars.

I’m gonna eat you. Yee!

Those legs attach to the outside of the bacteria, then it screws down and breaks through the membrane where it pumps out the genetic matter located in the head. Once inside the virus may either go lytic – launch a full attack, take over cellular process and devote all energy to making more viruses until SPLOOF! the cell ruptures and releases all the babies to start the process again, or go lysogenic – the viral DNA will slip into the bacterial chromosome and act like it belongs, hiding in plain sight and being carried through the generations until it launches a mutiny and starts the lytic cycle again. Some viruses just go for the lytic cycle all the way, and they be the truest pirates of the cell (the others being ninja pirates.)

So next time ye are coughing and sickly with a viral infection, be glad ye are not e-coli with a big spider thing attached to you, and spare a thought for the pirates of the cell. Though they may not be strictly alive, they are just making a living and don’t mean to make you ill, after all a dead host is no use to them. We wage war against the pirates near every day, getting sick is nothing more than collateral damage.

Gift Ideas for a Microbiologist or Pathologist

// November 20th, 2009 // 5 Comments » // Just for Fun, Science Art

Christmas is coming up (freak out!) so here are some funky gift ideas for someone obsessed with bacteria, a microbiologist, pathologist, or anyone interested in science and medicine.

Giant Microbes make a crazy selection of bacteria, viruses and human cells in soft plushy goodness. I’m a sucker for teh cute and fluffies! They’ve just released six new products, including yoghurt, bird flu and this platelet cell.

Swine flu is also available which might be a good (or annoying) get well soon present. Nothing says “I care” like a big cuddly version of the virus making you feel like crap. They also have little ones packaged in a petri dish for some of the fancier viruses, like Hepatitis C and Tuberculosis.

Or how about a cheesy shirt, cap or cup from Cafe Press? Check out this bacteria-inspired wall clock.

Or a book about microbiology like this one I blogged about here. Small Wonders was written by a microbiologist, and is full of the amazing things bacterias do told with utmost humour. You can by it on Amazon.

Or a new lab coat with added sexy. Check out this one by buffalonerdproject OMG OMG OMG it has the SKULL AND CROSSBONES!

It’s only $50 US and you can buy it here. It’s pretty awesome. She also make a bacteria style tie called Mr. Euglena. SO cool! She combines science with sewing and has plenty of other unique creations.

I should totally jazz up my old lab coat pirate-style.

This Paramecium Felt Keychain is pretty amazing. The same etsy store makes magnets, brooches and all sorts. Check out this microscope and beaker magnet set while you’re there.

If you have any other ideas for Christmas gifts, post them in the comments.

You might also like:
Gift Ideas for a Chemist or Chemistry Grad
Gift Ideas for a Biochemist, Medical Scientist, or Neuroscientist