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Posts Tagged bioluminescence

Monday Micro: living night lights Siouxsie Wiles Apr 29

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One of the latest Kickstarter projects to create a buzz is promising its backers a living nightlight that shines without electricity. Enter the Glowing Plant project, developed by a group of biohackers from BioCurious* in California. Launched just a few days ago, Antony Evans, Omri Amirav-Drory and Kyle Taylor have already exceeded their $65,000 target needed to create a genetically engineered plant that glows in the dark. In fact, they have already passed the $115,000 mark with over a month left to go. Their new goal is $400,000 to create a glowing rose. Check out their short video by clicking the link below:

Glowing plant vid

So how are they going to do it? Back in 2010, Alexander Krichevsky and colleagues published a paper in PLOS One showing that tobacco plants could be engineered to glow in the dark by incorporating the genes (known as the lux operon) which make the marine bacterium Photobacterium leiognathi** glow (1). The light generated by one of the plant lines they created could be detected by eye in a dark room after about 5-10 minutes suggesting they could make quite neat night lights. This was exciting stuff as previous attempts to make glowing plants had revolved around getting the plants to express the luciferase gene from the firefly, which required plants to be sprayed with luciferin, the substrate for the reaction, in order for light to be produced. In contrast, cells that express the whole bacterial lux operon glow without needing any additional cofactors.

Glowing tobacco plants

Glowing tobacco plants

Interestingly, Krichevsky declares in his PLOS One paper that he is founder of BioGlow Inc, a company which aims to develop commercially available glowing ornamental plants. BioGlow Inc is listed as a tenant of the Bio-Research & Development Growth (BRDG) Park at the Danforth Plant Science Centre in Missouri, but otherwise doesn’t have much of a web presence.

But back to the Glowing Plant project. Antony and his team say they are planning on building on the work of Krichevsky and colleagues, making a synthetic version of the bioluminescence genes so that they will be better expressed by the plant cells. Fingers crossed!

Reference:
1. Krichevsky A, Meyers B, Vainstein A, Maliga P, Citovsky V (2010) Autoluminescent Plants. PLoS ONE 5(11): e15461. doi:10.1371/journal.pone.0015461

*The BioCurious ethos is that innovations in biology should be accessible, affordable, and open to everyone. They have built up a complete working laboratory and training centre for citizen scientists and hobbyists to get together to do science.

**I’ve blogged about P. leiognathi before. They use their light to trick zooplankton into eating them. In a nutshell, the zooplankton ingest the glowing bacteria but are unable to digest them. The glowing bacteria mean the hapless zooplankton are then more visible to their own predators, nocturnal fish, who devour them. P. leiognathi are unfazed by all this, ending up in the fish’s digestive system which is where they wanted to be in the first place. Genius.

Astrosquid! Siouxsie Wiles Mar 27

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What is the value of blue-skies research?

This is a question often asked by politicians and the public. Why should public money be spent funding science that seems to have no obvious benefit beyond generating scientific knowledge? The simple answer is that it can be almost impossible to predict what new avenues that scientific knowledge will open up. Take the Hawaiian bobtail squid, for example. What could studying this little nocturnal hunter possibly lead to? Take a guess. No ideas? Let me help you out.

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It lead to the discovery that bacteria are able to communicate with each other, including how they sense when the time is right to turn on genes needed to cause disease. I’m not sure anyone could have seen that coming! Importantly, this research has provided scientists with another potential weapon with which to fight antibiotic resistant superbugs. In a world rapidly running out of antibiotics, we need all the weapons we can get.

This animation was produced with the support of a public engagement grant from the UK Society for Applied Microbiology, to engage the services of graphic artist Luke Harris and his team. Dr Siouxsie Wiles (@SiouxsieW) is a microbiologist and bioluminescence enthusiast who heads up the Bioluminescent Superbugs Group at the University of Auckland in New Zealand. She and her team make nasty bacteria glow in the dark to help understand and combat infectious diseases.

What we couldn’t fit into 3 minutes…

The Hawaiian bobtail squid, Euprymna scolopes, is just 3 cm in length and lives in the shallow moonlit waters off Hawaii. It spends its days sleeping buried in the sand, emerging at night in search of food. It has a very cunning trick to hide its shadow from fish looking for a meal, or from creatures like shrimp that it feeds on. It houses a colony of glowing bacteria (Vibrio fischeri) in a special organ on its underside. These bioluminescent bacteria shine their light down so that to any creatures looking up, the squid just looks like the moon. What is even more clever is that the squid uses its ink sac to match the intensity of moonlight hitting its back, dimming the light from the glowing bacteria as needed. This is important not just for cloudy nights but as the squid moves through different depths of water.

Baby squid are born without V. fischeri or a light organ. Instead they just have a small opening in their mantle (the bulbous bit of their body) that is bathed by sea water. What is incredible is that only V. fischeri can colonise this opening – once they do, the squid cells start to change and the light organ forms. The ability to glow is crucial though – scientists have made versions of V. fischeri which can’t glow and they aren’t able to colonise either.

Adult squid have an ingenious way of ensuring that there is plenty of V. fischeri floating around in the water to colonise baby squid. Each morning, before they settle down in the sand to sleep for the day, they expel 99.9% of the bacteria from their light organ into the sea. This serves another purpose too, ensuring the bacteria left behind in their light organ are constantly growing and have plenty of nutrients. Bacteria that run out of nutrients start to shut down to save energy. Producing light takes quite a bit of energy and the last thing the squid wants is a mantle full of lazy dim bacteria!

When scientists first identified V. fischeri and grew it in the lab they noticed something quite interesting. The bacteria only switch on their light when they have reached a critical population size. This makes perfect sense. There is no point going to all the trouble of making light if it isn’t bright enough to be seen. Each bacterium produces a chemical, called the autoinducer, that diffuses out of the bacterial cell. The more bacteria there are, the more autoinducer is produced. If those bacteria are growing in a confined space like a flask, or the light organ of the squid, the autoinducer will accumulate. Once it reaches a critical concentration, the autoinducer triggers the bacteria to switch on the genes for producing light*. This phenomenon is called quorum sensing.

Scientists then used the bioluminescence reaction to see if other species of bacteria produce autoinducers. Surprise, surprise, it turns out that lots of different bacteria use quorum sensing to signal to each other that they are in the right numbers or environment to do something, which is not worth doing otherwise. From the bacterial form of sex, to swimming, to switching on the genes needed to cause disease in plants, animals and humans. Now we just have to find a way of exploiting this to our advantage!

You can hear me chatting about the squid and quorum sensing on Radio New Zealand’s Nine to Noon programme with Kathryn Ryan here (13’12”):

*For those who really want to know, the autoinducer is the product of the luxI gene. When it reaches a critical concentration, it interacts with the product of the luxR gene, and together this complex binds to a region of DNA upstream of the genes under their control called the lux box which then triggers their transcription.

Monday Micro Siouxsie Wiles Dec 03

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Welcome back to Monday Micro. Last week’s Monday was lacking in microbiology factoids as I was at the New Zealand Microbiology Society‘s annual meeting*. This year it was at the University of Otago in Dunedin. Highlights for me were keynotes by Rob Knight (microbiomes and Next Gen Sequencing), Eric Ruben (TB) and Steven Wilhelm (cyanobacterial blooms). Tweets of some of the talks are here.

Highlights for me:

Finding that lots of people flush public toilets with their feet, that cyanobacteria are a bad food source “like ordering pizza and only eating the box”** and that “we are all accidents of history”***.

Moving on, Round 3 of the SciFund Challenge is in full swing so if you fancy supporting some microbiology projects Amy Truitt wants so study butterflies and their sexually transmitted diseases, Will Helenbrook is studying the effects of infectious diseases on Mantled howler monkeys and Andy MacDonald is working on Lyme disease.

* The slides for my talk (Fireflies and superbugs: when science and nature collide) are up on slideshare. I started my talk with my Meet the Lampyridae animation….



** Steven Wilhelm
*** Unknown kilted MC of conference dinner :)

Antibiotic myths Siouxsie Wiles Sep 10

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Dr Michael Addidle, a clinical microbiologist with Pathlab in Tauranga, has written a very nice article* in the Clinical Microbiology Journal, debunking some of the urban myths around antibiotic resistance. Alas the article is behind a pay wall so I thought I would summarise a few of the myths here.

Myth 1: Antibiotics were invented in the 1930s

Nope. We didn’t invent antibiotics, we merely ‘discovered’ them. Antibiotics are substances produced by microbes to kill other microbes and so its likely they have been around for almost as long as the microbes themselves have been. So unless you are a creationist, that is a very long time indeed.

One of my favourite examples is of the glowing bacterium Photorhabdus luminescens. This bug is part of a deadly duo: it pairs up with a small worm and together they kill various insect larvae. P. luminescens lives in the worms gut. When the worms are eaten by larvae, they regurgitate their bacterial passengers who then start to produce toxins which kill the insect, and enzymes which turn it into a soup of nutrients. P. luminescens also start to glow, possibly to attract other unsuspecting lavae to the show, as well as produce antibiotics, presumably to stop any other bacteria enjoying the delights of the rotting cadaver which the worms are now feeding on. Anyway, bacteria and worms multiply, re-associate and burst forth in search of new prey. I’ve often read that injured soldiers in the Crimean War (1853-1856) who had glowing wounds were more likely to survive their injuries than those whose wounds didn’t glow. If this is true, an explanation could be that the ‘glowing’ wounds contained P. luminescens and the antibiotics they produced stopped other much nastier bacteria contaminating the wounds and killing the soldiers.

Myth 2: Antibiotic Resistance Developed Soon After the Invention of Antibiotics

Nope. Its likely antibiotic resistance has been around for almost as long as bacteria have been producing antibiotics. In fact E. coli were found to produce an enzyme capable of degrading penicillin before penicillin went into clinical use.

Myth 3: Inappropriate Antibiotic Use Creates Antibiotic Resistance

Dr Addidle argues that this is a misleading statement and in fact all antibiotic use selects for resistant bacteria. While this is true, Dr Addidle is putting it in the context of treating a patient with a broad spectrum antibiotic when a narrow spectrum one might do. When I think of an inappropriate use, I’m thinking more of feeding broad spectrum antibiotics to poultry so they can be housed in less than ideal conditions and not all die from infection! Ideally these antibiotics could be removed completely by less intensive farming practices.

Myth 4: Finish Your Course of Antibiotics to Prevent Emergence of Resistance

I’m not sure I agree with this statement being a myth. Dr Addidle argues that a longer than necessary course of antibiotics prolongs the selective pressure for resistant organisms to thrive, promoting antibiotic resistance. Instead he says the real message should be that antibiotic courses should be long enough to deal with the infection at hand, but not so prolonged that they unnecessarily promote selection of resistant bacterial strains. My assumption has always been that the prescribing doctor is giving you the appropriate length course of antibiotics and that you should finish them else your course is too short! Not taking antibiotics for long enough is one of the factors that in my understanding has lead to the rise of antibiotic resistance in M. tuberculosis, which is a global health disaster.

Myth 5: No New Antibiotics Are Being Developed

Let’s end on this myth which is most definitely a myth. While the majority of big pharma are not interested in antibiotic development (too little reward for too little effort) there are still plenty of labs around the world trying to develop new treatments. Its clear though, that in order to limit resistance emerging, what we need are entirely synthetic antibiotics like nothing ever seen in nature. And that’s a big ask!

*Addidle M (2012). Antimicrobial resistance: urban myths. Clinical Microbiology Journal, 34 (18):147–150.

Melons and glowing eggs Siouxsie Wiles Aug 20

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Yesterday’s post on the current melon Salmonella outbreak reminded me of an old paper I read once. Alas, its not open access so it will cost you US$37 (+ tax it says…) if you want to read it, but you can get the gist from the abstract.

To summarise, bacteria can fall victim to viruses just like us. These viruses are often called phage or bacteriophage. The interaction between phage and host is very specific with a particular phage only infecting a single or very closely related species of bacteria. Jinru Chen and Mansel Griffiths added the genes for bioluminescence to a phage that specifically infects Salmonella.

Because viruses highjack the machinery of the invaded cell to make their proteins, the phage don’t produce light until they have infected a Salmonella bacterium. The authors showed that this elegant system could be used to detect Salmonella from within contaminated eggs – just inject in a preparation of the phage and if the bacteria are present the eggs glow!

Reference: Chen, J & Griffiths, MW. (1996). Salmonella Detection in Eggs Using Lux+ Bacteriophages. Journal of Food Protection, 59 (9): 908-914.

The Innovate TB contest Siouxsie Wiles Jun 14

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The Stop TB Partnership and Working Group on New TB Drugs are currently running the Innovate TB Contest where people where asked to submit their videos showing how innovations are revolutionising tuberculosis (TB) prevention, treatment and advocacy. Submissions are now closed and the public have just a couple of days left to vote. The three videos with the most votes will then be evaluated on their overall message, relevance to the theme, and creativity by an expert panel of TB stakeholders.

My firefly animation, Meet the Lamypridae, which shows how bioluminescence is being used to speed up TB drug discovery, is currently sat in 5th place. Please help it get into to top three by clicking on the link to the video and voting by clicking on the Facebook, Twitter and LinkedIn buttons underneath it.

Thanks for your help!

SciFund Challenge – Target achieved! Siouxsie Wiles May 20

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Glowing bacteria attract over $3000 for science in 15 days!

For those who don’t know, this month I am taking part in the SciFund Challenge, raising money for my research using the RocketHub crowdfunding platform. My project, Evolution in Action, involves studying how infectious microbes evolve to cause disease and I am raising money to sequence the genomes of my evolved bacteria to unravel the genetic basis of their evolution. It costs about $100 per genome, so the more money I raise the more genomes I can sequence.

So it took just over 2 weeks to reach my $3000 target. I’m currently at $3,288 – that’s almost an extra 3 genomes. Whoohoo! And there is still more than a week to go! I’m really looking forward to doing a little analysis of all my contributors when the challenge is over to find out how many I actually know and how many are strangers, and how those strangers found me.

So a huge thanks to all who have contributed and everyone who helped spread the word. I couldn’t have done it without you guys. And for those who still want to contribute, there is still time, and we have no shortage of evolved bacteria whose genomes we would like to sequence so the more money we raise, the better!

Now we are getting on to preparing our rewards, which includes writing our contributors names/logo’s in glowing bacteria. Watch this space!

Ummm, it should say "science rocks" but the bugs in our 'e' didn't grow properly.... YouTube Preview Image

*In addition to those listed here and here, contributors to date are:

Jon Woods
Stippy
Marius Rowell
Richard Cornford
Dr Alan Koslow
K. Gilbert
Ian
Sefton Billington
Simon Clendon
Dan
Barbara Vanhoeke
Gingiber Theginge
Conor Reilly
Rob Heighway

SciFund Challenge Day 13! Siouxsie Wiles May 14

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So with 18 days still left to go, the 75 projects which make up round 2 of the SciFund Challenge have raised over 58,000 US dollars for scientific research using the RocketHub crowd funding platform.

My own project, Evolution in Action, is just 387 dollars away from reaching its target. So I just wanted to say a big thanks to all my contributors* and everyone who has helped to spread the word.

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*In addition to those listed here, contributors to date are:

Alan Brown
Judy Morris
Ged Hayward
Robin Capper
Cassandra Baker Lee
Ian Hovander
Lorna Strachan
Karen Toast Conger
Kalani Hausman
Samantha Sampson
Sam Egli
Victoria Galbraith
Doug & Wendy
Martin Kennedy
Maria Connor
Celia
Simon Young
Don & Louise Galbraith
Graham & Hazel
Robert van Leeuwen
Bob Sellars
Garrett Butt
Alan Reader
Moira Statham
Ana Elisa Garcia
Cate Macinnis-Ng
Aleks Ksiazkiewicz
Mark Martin
Greg Crowther
Stephen Hawley
Heather Galbraith
Dave Guerin

Round 2 of the SciFund Challenge is now live! Siouxsie Wiles May 01

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I’ll be spending the next 31 days trying to raise money for my research using the crowd funding model on the RocketHub platform, where contributors exchange small donations (in the 10-100 dollar ballpark) in return for ‘rewards’. As a microbiologist who makes glow-in-the-dark bacteria for a living, my rewards are things like sending donors a picture of their name written in glowing bacteria or naming one of my bacteria after them.

Your name in lights!

Your name in lights!

The challenge came about partly as a result of the lack of funding for basic science (success rates stand at about 20% in the USA, while for New Zealand’s only blue skies research pot, the Marsden Fund, they are about 8%). But perhaps more importantly, the SciFund Challenge is also about getting the public more interested and involved in science.

So why did I get involved? I want to tell the world how amazing bacteria are. They are masters at adapting to their environment, rearranging their genetic material or gaining new genes from their surroundings. This has allowed them to colonise pretty much every conceivable environment. From boiling hot geysers to human beings. While many are harmless or pretty beneficial, plenty have evolved to cause us serious harm. Bacterial adaptation is how we get antibiotic resistance and new diseases emerging.

So what I want to know is, how do bacteria evolve to cause disease? And that’s where my SciFund project comes in. I need your to help unravel how these amazing microbes keep outsmarting us. For more information, check out my project, Evolution in Action. Wish me luck!

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For those unfamiliar with RocketHub:
• RocketHub is a legitimate site, used mainly by artists and musicians to launch their projects.
• RocketHub is not an investment or charity. It is a site that allows the project owner to exchange rewards for contributions.
• RocketHub is based in the USA so all the rewards are listed in US dollars. For those outside of the US, 10 US dollars are roughly equivalent to: 6.20 UK pounds/ 7.60 EUROs/ 10 AUS dollars/ 12 NZ dollars/ 10 Canadian dollars. For an up to date currency conversion check here.
• RocketHub is an ‘all and more’ funding mechanism. If I don’t reach my financial goal I get to keep what I raise. And if I raise more than my goal I get to do even more cool science.
• RocketHub take a 4% cut of whatever I raise if I make my target, and 8% if I don’t. In addition to this, there is a 4% credit card transaction fee.
• All contributions are handled by RocketHub, and the money raised (minus fees) will not be sent directly to me, but to the University of Auckland like a traditional science grant.

Survival of the brightest Siouxsie Wiles Mar 04

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Regular readers will be well aware of my obsession with bioluminescence, that beautiful light produced by things like fireflies and glow worms. So I was excited to see this paper in the Proceedings of the National Academy of Sciences.

Margarita Zarubin and colleagues have discovered why so many non-symbiotic marine bacteria are bioluminescent. It turns out that the light gets the bacteria to where they ultimately want to be, inside the digestive tract of fish. While it may not appeal to you or me, fish guts are some bugs idea of bacterial nirvana – all the food you can eat, a safe haven from predators and a convenient means of transport.

Here’s how it seems to work. Using the bioluminescent marine bacterium, Photobacterium leiognathi, Zarubin and colleagues found that zooplankton, attracted by the light, ingest the bacteria but are then unable to digest them. Unfortunately for the zooplankton, the bacteria continue to glow, revealing the presence of the hapless zooplankton to their own predators, nocturnal fish, who were now able to easily spot the glowing zooplankton in the dark water, and devour them. Zarubin and colleagues also showed that fish weren’t attracted to zooplankton who had ingested mutated P. leiognathi that no longer glowed. P. leiognathi were also found to survive the transit through the fish digestive system. Hey presto, they’ve reached nirvana! How neat is that? Survival of the brightest indeed.

Reference: M. Zarubin, S. Belkin, M. Ionescu, A. Genin (2011). Bacterial bioluminescence as a lure for marine zooplankton and fish. Proceedings of the National Academy of Sciences 109 (3): 853 DOI: 10.1073/pnas.1116683109.

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