Field of Science

#Microtwjc Why FRET about Biosensors ?

The latest paper for #microtwjc focuses on finding a new way to sense metabolites inside of living bacteria.  Bacteria need to regulate their nutrient intake, because like people, they don't want to get too fat or thin. 
If there isn't enough nutrient in the environment, they need to conserve what they have, and if more appears, they need to consume it as efficiently as possible, but if they did that all the time, it could cause them problems.

#Microtwjc A Salmonella of Doubt ?

The microbiology twitter journal club beckons, and it is now time to wade through the latest paper, on Salmonella, and how to spot different subtypes of this bacteria. This allows us to get a look at the recent evolutionary history of the bacteria, and to track new subtypes as they arise. In the past, the ways these new subtypes were tracked and analysed through serotyping. 

#microtwjc Do Electric Guts Dream of Android Burgers ? part 2

In part 1 of this post, I briefly described the key piece of equipment used in this study- the TIM2 machine, designed to model the large intestine.

Do Electric Guts Dream of Android Burgers? Part 1 #microtwjc

The next paper for #microtwjc raises some interesting questions about what effects probiotics have on the gut. If you want to study the gut, and the bacteria within it, there are a number of little problems. For instance, many of the bacteria in the gut are anaerobes, and will shrivel up the moment they get exposed to air. It is thought that the distribution of different bacteria varies throughout the gut, so just taking faecal samples won't cut it. 
So what can you do? There are animal models, where you can try and sample the bacteria in different areas of the intestine after dissection, or perhaps use techniques like bioluminescence to look at bacteria directly within the digestive tract. I remember hearing someone pitch a project to use magnetic resonance spectroscopy (using some fancy MRI technology) to analyse bacterial metabolites within the guts of human volunteers.
There is another way that researchers can try and work out what's happening in the gut. Through the creation of an artificial gut.
Consider for a second that in simple terms, your gut is basically a fancy bioreactor. It is a vessel in which enzymes, bile and bacteria all get mixed together to help you digest your food. So what if we tried to create this system artificially, and what would reveal about digestion
 Minekus et al (published in 1999) developed the system, where they essentially created an artificial model of the large intestine, which over the last ten years has been developed to the one seen in the week 6 #microtwjc paper.
So how does this machine replicate the way that the Large Intestine works ?

  • Peristalsis- Your gut moves food around through squeezing it's walls and pushing the food along. The inside of this machine has a series of flexible walled tubes, which have water pumped along the outside of them. The pumping of the water passing through the system causes periodic compressions to be transferred through the system, mirroring the peristaltic movement seen in actual human guts.
  • Temperature: The water passing through the gut is heated to body temperature, which is 37 °C.
  • Bile: Bile performs a number of functions, such as introducing a number of salts which act to emulsify fats. Another function it performs is neutralising gut acid, and keeping the pH of the large intestine stable. To ensure that the pH of the electric version of this system is stable,  pH sensors were present to control the infusion of sodium hydroxide, preventing it from getting too acidic.
  • Absorption: The main function of the gut is to absorb nutrients, such as short chain fatty acids. To replicate this, fibre membranes placed at strategic points along the machine allow for small molecules to pass through them. These are hooked up to pumps an pressure sensors to ensure that the pressure within the system remains constant. 
  •  Metabolites: In the human large intestine, partially digested food comes in from the small intestine. To replicate the present of this food, metabolites are added into this system, and because of the way the absorption works (via osmosis) the action of that system also acts to keep the metabolite levels within the gut fairly constant.
  • Anaerobic- It is generally thought that the human gut is mostly colonised by anaerobic bacteria*. So air was prevented from entering the system by flushing it with gaseous nitrogen.

This is the basis for the TIM2 system. Now, anyone can easily see that it isn't a perfect model for the gut. With any model, physical or computational, there are limitations. What you get is based off of your assumptions when creating it, and if you forget those, then you can be lead badly astray.
So the question is is it useful?

The only way to determine this is to validate the model.
In the initial paper, they found that the system absorbed short chain fatty acids, and maintained pH fairly well with "standard" fermenter flora and allowed them to survive in the system.
Also "Three successive experiments were carried out using fecal inocula from three diff€erent methane-excreting volunteers". They did not mention whether these people were chosen on the basis of their methane excretion. They looked at how well the faecal flora survived in the large intestine.
So from this first paper, they showed that this model of the gut could keep bacteria from the human gut alive, and that this system could absorb short chain fatty acids.

The point I would like to make about this model system is that yes, it does have limitations. It is not a perfect representation of the human gut.  Even though we can't extrapolate findings with this equipment directly into humans, we can still put this machine to good use. It can be use to grow bacteria with different nutrients, and furthermore elucidate some of the more complex relationships between them within the human large intestine. 
It is with that in mind that I shall look at the actual #microtwjc paper in part 2 of this post.

  Minekus, M., Smeets-Peeters, M., Bernalier, A., Marol-Bonnin, S., Havenaar, R., Marteau, P., Alric, M., Fonty, G. & Huis in't Veld, J.H.J. (1999). A computer-controlled system to simulate conditions of the large intestine with peristaltic mixing, water absorption and absorption of fermentation products, Applied Microbiology and Biotechnology, 53 (1) 114. DOI: 10.1007/s002530051622

Part 2 is up here

* I should point out right now that I am not entirely certain whether the mammalian gut is entirely an anaerobic environment. For instance, I pointed out a study using bioluminescence to study bacteria as they invaded the gut. The bioluminescence reaction shown there requires oxygen to be present in order to function. So this indicates strongly that there is oxygen in the mammalian gut, but again, this conflicts with what is known about most of the microbiota present, which tend to shrivel and die at the mere mention of that element.

Cower Before Pretzlcoatlus !

The long neck of the Quetzlcoatlus always looked really odd to me, until I realised that all of the fossil conformations looked completely off.And when I zoomed in to the pictures of quetzlcoatlus fossils, I noticed that all of the structures were strangely square, almost like pixels. I propose that these are salt crystals ! Taking this new evidence into account,  I suggest an entirely new reconstruction for this beast. Ladies and Gentlemen, I present Pretzlcoatlus !

No, I'm not just overinterpreting every blemish on the paleontological images just to support my theory. I have verified it with tracing paper and crayon. And I need your support to get this new creature recognised by the paleontological community.
Ignore the unsavoury musings that can be found at tetrapod zoology
And the distasteful take found in Laelaps
And you should almost certainly disregard the  "lacking in snacky-goodness" views of the paleo king

Hail Pretzlcoatlus !


#microtwjc- What's living in your bathroom.. Weeee

And so dawns another week of the microbiology twitter journal club. This week we're discuss public toilets. WEEEEEEE!
Because the greatest concern when anyone goes to the restroom is the bacteria. Yes, you can't see them, but you know they're there.... watching...waiting...plotting.
But who are these mysterious bacteria? Can the 6 layers of two-ply really protect you as you sit straining atop your cushioned throne? This paper probably won't answer that.
This paper was an attempt to work out the identities of the bacteria in the restrooms, and where they come from.

Science, It's a meritocratic thing?

#sciencegirlthing meme confused me, because when I started at university, there was a 60:40 girl boy ratio on my science course. There seem to be plenty of girls going into science courses, but where do they go? This got me thinking about something that I wanted to blog about a while ago, but was too angry to do anything other than mash the keyboard with my own face.
In my early days working in the lab, I had the fortune to work with an amazing post doc. This post doc always knew what they were doing. Some days, they would be the first one in the lab, and last one out. Not because anyone told them to, not because they felt it gave them an air of arrogant superiority, but because the experiments demanded it. Through an extraordinary level of organisation, they managed to do a huge amount of work with very little time. It was an acknowledged fact in our lab that this post doc was some sort of superhero. Seeing that level of dedication, organisation and productivity affected me a lot, and I still am attempting to emulate their example.
So hearing that she wanted to get out of science sent my head spinning.
After which I was directed to look at the academics in higher positions. Most of them were men. It doesn't take a genius to see that something was going on.

There is a phrase that I've heard bandied about a number of places,  "Too smart for science". Occasionally a lab will be blessed with an amazing student who, despite being excellent at science decides that they'll be better off doing another career, because the job opportunities are so small. And they do well, because they are smart enough to excel at anything they do. But it is still a loss for science.
So when you present such a person with a game so stacked against them, is it any surprise when they cash their chips and go elsewhere ? Why go through the sacrifice and hard work of a career in science when there is very likely no pay off at the end of it. 

So seeing someone who had played such a key inspiration for me, decide that science wasn't the best use for her talents, was devastating. Hence the face/keyboard/laptop chewing implied earlier. Because I had my main preconceptions of science shattered.
 I realised that no matter how good I am as a scientist, some arbitrary crap that I have no control over can prevent me from pursuing a career. Actually we don't always have the best people solving our scientific problems because the system is tipped against a lot of them. This is a career where the smartest people don't get to the top, they get out. 
Can we really claim science is a meritocracy when we are haemorrhaging some of our best talent ? 

#Microtwjc EHEC strain 86-24 gives it 100%

It is time for me to again delve into the joyful quagmire that is the microbiology twitter journal club, to discuss "Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24", brought to you by the lab responsible for the best damn figure ever . So what are we waiting for ? Let's dive in!

#microtwjc ...Just Add Manuka Honey.

I tried. I really tried to avoid blogging, and to concentrate on my thesis. When the microbiology twitter journal club appeared, I thought that I may write a piece when I had finished with my thesis.
But then, they had to go and pick a paper about Streptococcus pyogenes, and I find myself drawn back into this blog. I tend to focus on the results sections of the paper , rather than the introduction and discussion, because frankly it's the whole point of the paper.

The Thesis / Paper Spiral

Step 7. Draw Comic. Step 10: Profit !

 Currently I can only describe my writing style as "Brute force" which is to go through every conceivable word combination in pursuit of the one which sucks the least. When I get out of the abyss, I will be sure to write about how it happened. Of course this pursuit of "moderately okay-ness" can be de-moralising. So I drew a cartoon to get this out of my system. When I get out of the abyss, I'll be sure to tell you how.

Who's Afraid of the Wasabi Fire Alarm ?

It was a strange series of events that lead me to having dinner with IgNobel awards maestro Marc Abrahams, former Monty Python Terry Jones and the inventors of the wasabi fire alarm. I had met Marc at the IgNobel show when it came to Imperial. I know I should have been writing up my PhD, but  one night surely wouldn't matter too much ?
 We ended up talking about this new fire alarm that had been invented by a couple of japanese researchers. This fire alarm was not like normal ones. Instead of ringing, it sprayed an infusion of wasabi into the air. Who could possible want a fire alarm that sprays you with wasabi. Isn't it bad enough being inside a burning building, and now they've invented a fire alarm and burns you from the inside too ?
This product was marketed to the deaf, which to me suggested a new horror was being inflicted on the disabled. I suggested that it would be useful for clearing out rooms in a night club when the music was too loud. Because I don't like nightclubs or the people who use them. So as we talked, Marc mentioned that the two IgNobel prize winners were coming into the country to exhibit their invention, and would I like to come along and discuss my ideas with them.
So that was how I ended up at the Science Museum to meet the inventors of the fire alarm. To my surprise Dr Makoto Imai was a friendly psychiatrist from Sapporo had helped test out the fire alarm, and his somewhat more subdued colleague, Hideako Gotou were not the vindicitive pranksters I had hoped for expected.
They had brought with them their new invention. It was quite simply a fire alarm with a wire attaching it to one of those automatic air fresheners you see in more upmarket public toilets. We were shown into the science museum, which was planning to exhibit the fire alarm. Marc and Steve Colgan  (of colganology) and I were treated to an enthusiastic tour of the museum by former New Scientist editor Roger Highfield. He had taken to the new role with aplomb, positively bouncing with excitement about all of the new exhibits and events happening at the museum.
After this, we ended up taking the inventors to the Knightsbridge fire station for a photo op.
Eventually a Tom Whipple, a journalist from the Times arrived, and displayed true dedication to his profession by making Dr Imai demonstrate the power of the alarm directly.

Immediately after he had finished dousing the choking journalist with wasabi spray, the inventor wryly noted that "This is a misuse of this system".
Whilst the effects are dramatic, and painful, the recovery was rapid.  Tom had to get quite close to the spray to get the worst effects. I was told this system would be mounted in such a way as to avoid situations where users get blasted in the face as demonstrated above.
Since the inventors were only going to be in London for a day, Marc had offered to show them around some of the best tourist attractions. As the Photo Op was drawing to a close, Marc said that he was taking the Inventors to meet Terry Jones at Centre Point, and whether Steve and I would like to come along. Whilst I still had a lot of writing to do for my thesis, I was not going to let it get in the way of meeting one of the Pythons.
So we ended up in a restaurant in one of the tallest buildings in the centre of london. If the day hadn't been so foggy, I would have been able to see my house from it. And so we sat down to dinner with our esteemed host and his wife. Later that day I would go home and be quizzed about the whole experience by my flatmates. They would ask whether he had eaten waffffer thin mints and look eachother knowingly as if this was a reference I should get.  I was spending too much time trying talking to Dr Imai, trying to decipher his motives for creating a wasabi spraying alarm.
  I asked him exactly how did this idea came into being?
 The original idea for the alarm came from the author Karin Matsumori. She had lost her hearing during her time at school, and had intially pitched the idea of an odour based alarm system to the perfume company Seems Inc.
At this point, Dr Imai noticed that I was feverishly writing all of this down on my arm. I had left the house without my note pad. So I had been writing notes on my hand since the museum. By the time we had reached the restaurant, my arm had begun to turn blue.
 Noticing this, He produced a business card, and wrote the pertinent details in neat handwriting. I asked him why the focus of his alarm system was on odour, rather than say, flashing lights.
There were a variety of problems with visual systems. What if the lighting system was not visible from wherever the person was?  And the most pressing concern was how to get someone to wake up quickly in the event of fire.
Conventional Fire alarms rely on triggering the startle reflex. When a human hears a loud unexpected noise, this reflex kicks into action to make you alert to possible danger. It can wake you up out of a deep sleep, and help you escape a fire. To demonstrate the startle response, watch this with the sound off, and then with the sound turned right up.

stereo skifcha from xgabberx on Vimeo.

So visual cues just don't have the same impact. So the question is whether the addition of an olfactory cue would make this type of alarm more effective.But this reflex is based solely on sound. A deaf person cannot react to these cues, so they would not be awakened. So how could they get a fire alarm for the deaf that could wake them out of a deep sleep. The solution was to use a different sense altogether. The sense of smell.
 Seems Inc tried out a number of different fragrances, such as the smell of dirty old socks, and others to see what would work. At some point, they contacted Dr Imai and asked him to conduct a trial with wasabi to see if it could wake people up.
Then  it occurred to me that since Dr Imai was a clinical psychiatrist, there was one key question that I needed to ask. What has this research told him about the brain?
He told me that the way the brain processes the smell of wasabi is quite different to how it treats most other smells. Most of the things you smell are processed by an area of your brain called the olfactory bulb which cuddles up against the back of your nose. When sensory neurones detect smells, they relay this information to the bulb, which can interpret these signals and relay this information to the rest of the brain. Pretty much everything that you can smell goes through this region. However, there is a problem.When you sleep, the olfactory system becomes dormant as well.  This may have been a problem for the inventors of the odour alarm.
But there are certain chemicals which don't limit themselves to using the olfactory system. For instance, when you fry chillis you will no doubt notice that the smell stings the nostrils somewhat. When cutting onions, your eyes will often betray you and start to weep. These are examples of smells which activate pain receptors in mucus membranes in the eyes. When Dr Imai took electro encephalogram readings of the brains of volunteers exposed to wasabi, he noticed this manifest as trigeminal nerve activation.
The trigeminal nerve is not the most famous of the cranial nerves, but it is important. It controls the muscles around the face and mouth, and processes pain in these areas. This is why you get a stinging sensation in addition to flavour when you eat spicy food.
If you happen to be ill, and are bunged up with a stuffy nose, whilst most of the sensory neurones associated with olfaction get knocked out, the trigeminal system is still in working condition. Most importantly, the trigeminal system doesn't go to sleep when you do.  So odours that can have an effect on this system will be able to wake you up from a sleep.
As I noted earlier there are a number of different odours which can activate this system, to different extents.  One viable candidate was capsaicin, the primary component of pepper spray. So why aren't we talking about an alarm that pepper sprays you ? In a word, boiling points.
Capsaicin has a higher boiling point than the odorant in Wasabi. This basically means that unless the fire was already too hot to survive, the fire alarm would have to physically squirt you with the liquid. If you are out of its range, it is pretty much useless.
 The chemical that gives wasabi it's smell however has quite a low boiling point, and exists as a gas. That is why when you have wasabi, it hits you in the nose, whereas a chilli exerts most of its fire in the mouth.
I asked whether this odour could travel faster than say the smell of smoke, and whether it would wake people up before the fire had gotten out of control. The solution here would be to have multiple odour dispensers in a house linked to a smoke detector system, so that no matter where you were, the smell of wasabi would reach you before the smell of smoke.
Is it possible to get used to the smell ? Hypothetically it's possible, if unlikely. Because of the way it acts to elicit pain, it would be harder for people to get used to its smell, in the same way that you can get used to the smell of a fart after a while. However, it's your olfactory system that controls how you adapt to smells, and is the reason why people are mostly unaware of their own body odour. However, the pain sensing system does turn itself off in the same way. However, if people eat enough wasabi on a regular basis , it is possible for them to become less sensitised to the stinging sensation. Of course the only way to test whether this were true would be to find wasabi eating champions, test whether they need more spray to wake them up.
Speaking of which, it turns out that there is someone working on an alarm clock that will sprays wasabi. That's something to look forward to.
But despite my initial skepticism about the practical uses of the wasabi fire alarm, I was slowly won over. These weren't just a pari of eccentric inventors who had decided to add another terror to being trapped in a burning building. They had identified a specific safety concern for the deaf. And to solve this problem, they had come up unique and well thought out solution to this problem.  In spite of myself, I was surprised. While their research had made me laugh, and it was now getting me to think. What else should I have expected from IgNobel prize winners ?

Three Pieces of Advice I've found useful for writing up

It has been a month now since I've embarked on the whole writing up process. Before I started, I asked around for advice from other people who've gone through the same experience. So here is a list of the tips that I've found useful:-

Start with the Results section, and the rest will write itself
This piece of advice has been given by a number of people, likely because it is good advice. The data is the story of the paper, and starting off writing by familiarising oneself with it is a good way to see what shape the rest of the paper will turn out. Once I got that done, the methods section could be constructed accurately, and from their discussion and introduction are a downhill slope.

Do not get distracted, immerse yourself in the writing process
This piece of advice was given by a number of students who took full time work while writing up, and told me that it was not the best idea, and to not do it if possible. The words "Living Hell" were often used. I'm glad I took this advice. Whilst I've had to reduce my expenses a lot, It also means that I don't have to worry about getting distracted. Living on a diet of lentils and bread is worth that at least.

Don't be a perfectionist, Just bloody get on with it
This is probably the last bit of advice I would expect to get, but it is the kind of advice that I can see myself giving... about blogging. The first draft of any of my writing is not going to be the best. When I'm writing something for the first time, I have no idea what the best structure is for presenting my ideas. I may agonize over the wording of a single sentence, only to find that that beautifully constructed sentence fits better elsewhere, and should probably have been split into two sentences anyway. The process of writing changes the way you write, so when you are finished and look at your work, it's going to be crushingly uneven anyway. So why waste time?
Write like you're digging for the gold at the bottom of your keyboard, and you can sift out the precious nuggets from the slag afterwards, and if you are truly talented, you can arrange them into pleasing jewellery. There's no need to make the process of digging harder for yourself.

Now I'd better get back to my thesis. It gets angry if I don't pay attention to it.

Write Up Mode : Activate !

Use Thundershock you Fool! Books are weak to Electric !

It's over, and I'm overwhelmed. I've finished my last set of experiments. My feelings upon leaving the lab are difficult to sum up. There is so much more I could've done ! If I'd worked smarter, if I'd planned some experiments better, or if I'd gotten luckier. But the lab work had to stop sometime.
It only hit me how much work I still had ahead of me when I packed away all of the various papers, notes and lab diaries that had accumulated on my desk. It all looked fine, neatly packed into a large duffel bag, until I did my back in trying to lift the damned thing. Distilling a thesis from all of that may take up a lot of my time.
I don't know how this will effect my blogging yet. I reckon I can still find the time to do it, considering how I was still able to do it when spending most of my time in the lab, so in theory I should be able to find time to write/ draw for this blog. But I've never written a PhD thesis before so I don't know for sure. I'm toying with the idea of blogging about the thesis writing process as it happens, but I'll have to wait and see.

The Beetle to Beat TB

Over at Infectious Thoughts, Siouxsie Wiles has a video up about her research, which makes a great introduction to a paper that I've wanted to blog about for some time.


The goal of this research was to create a glowing strain of mycobacteria, and looking at this video, one may be fooled into thinking that this research was "simple". This is far from the truth. In fact , the route to getting a bioluminescent strain of mycobacteria was fraught with difficulty.

Getting any bacteria to express genes from other organisms is a difficult process. In nature, bacteria are often subject to attack from foreign genes from viruses. Some bacteria have defenses against this, others simply don't react well at all. many a synthetic biologist has created a "perfect" construct, only to find that it immediately kills all bacteria that express it.
The way in which genes are introduced into bacteria using a plasmid. Plasmids are circular pieces of DNA that can replicate in their host. With the inclusion of special sequences, they can integrate into the genome of the host. different plasmids can do ifferent things. Some of them can replicate a lot in their host, so each bacterium can have lots of plasmids, and therefore lots of copies of a gene. Conversely, you can have plasmids that copy themselves less often. The most extreme form is actually getting the plasmid to integrate within the chromosome, so that there is only one copy, that only replicates when the host cell replicates.
The number of plasmids containing your gene can affect the level to which it is expressed. More plasmids = more gene copies, and therefore more expression of that gene.

And then one needs to think about the gene to be used.
Firstly, whilst this video focuses on the firefly, this video could easily have featured a number of different organisms in its place. In nature, bioluminescence is surprisingly common, and a number of different organisms use different methods to glow. So when setting out to make mycobacteria luminescent, they had three candidates:
Firefly: The beetle that is shown in this video. Firefly bioluminescence is known to require a Luciferase enzyme (called Luc), and a compound known as D-Luciferin. Whilst we know that D-luciferin is needed for bioluminescence, the actual genetic system that creates this compound is not fully understood.
Gaussia Princeps: This tiny marine copepod glows in the dark of the deep sea. It's bioluminescence system requires a compound known as coelentarazine, and is one of the few systems that doesn't require oxygen as a substrate. The copepod itself doesn't make it's own coelentarazine. Instead, it often hunts other marine organisms to obtain it, and it is not known specifically what organisms are producing this compound. So the genes encoding it are not known.
Photorhabdus Luminescens : A nematode/ caterpillar pathogen. When it feeds on a caterpillar, it causes it's carcass to glow to attract more nemotode hosts. The luminescence system for this bacteria is simpler than those found for the eukaryotic organisms, with the genes encoding both the luciferase enzyme, and it's substrate are both known.
These facts will come in useful when thinking about taking these genes out, and actually using them in a practical situation.

One of the problems is the mycobacterium itself. The main purpose of this research was to develop bioluminescent strains of the bacterium Mycobacterium tuberculosis. However, it is probably not a good idea to expose themselves to TB on a daily basis, and moreover, it takes a long time to grow the bacteria. So instead of moving straight into TB, the researchers tested out their bioluminescent constructs in Mycobacterium smegmatis. M. smegmatis is generally non-pathogenic, and grows a lot faster than other strains of Mycobacterium. So it can be more easily used to test out these bioluminescent constructs.

So the author took three plasmids, one which has a high copy number, one with a low copy number, and one which integrates, and then partnered them up with the three different luciferase systems, shown above.
So you'd expect that with more copies of the gene, you would see more light production. What was found was in fact quite different.
 In fact the bacteria with just one copy of the luciferase genes glowed better than the bacteria with multiple copies. This same effect was found for the firefly luciferases , and for the bacterial luciferases. 
Whilst this initially surprising to me, my synthetic biologist friend simply made some derisive noises along the lines of "well duh". Bioluminescence is an energy intensive reaction. So a bacteria using up a lot of energy for bioluminescence will not have much energy for other important processes, like nutrient acquisition. And so the system feeds back on itself, setting up the paradoxical situation where less really is more.

But this was not the end of it. The amount a certain gene is expressed is also dependant on something known as a promoter. This is a section of gene sequence which controls how much a gene is expressed, by attracting proteins which "open up" the DNA strand, allowing the sequence to be read. They tried a number of different promoters, and found the best one to express the luminescent signal.

Using these techniques, the maximum amount of messenger RNA is made in the cell. But at some level, the decoding of these genes into actual proteins is limited. In order for protein to be made from messenger RNA, each segment of the DNA sequence needs to be partnered up with an amino acids. This decoding wis performed by transfer RNA, which binds to an amino acid, and to a three base pair sequence on the messenger RNA
There are 21 different amino acids which can be used to make up proteins, but 64 different combinations of codons. So some tRNAs that bind to different DNA sequences can bind to the same amino acid.
However, different organisms have different amounts of tRNA. So a firefly cell may have more of one type of tRNA than another, but a bacterial cell may have different number of tRNA.
If you take a gene directly from one and put it into the other, you may find that the protein takes longer to form, and therefore you get less of it.

However, if you take the amino acid sequences for the firefly luciferase, and then translate it into the DNA code according to the most abundant tRNA present in a cell, you can increase the chances of the right tRNA binding to the right area, and thus increase the rate of transcription. This technique is known as "codon optimisation". So the researchers performed this "codon optimisation" and found that it did indeed make the bacteria glow brighter.

So now that they had made sure that their genes worked in Mycobacterium smegmatis, they put them into Mycobacterium tuberculosis and found that they glowed just as brightly. The brightest signal came from the bacteria with the firefly luciferase.

Now that we have this glowing bacteria, we can see where it goes and what it does during an infection, without the need to kill animals at every single time point. And using this technique, the bacteria can show us where they go during infection. This is an unprecedented opportunity to find out, not only how this bacteria causes infection, but also to reveal new treatments to combat it. And all because of one beetle.

Andreu N, Zelmer A, Fletcher T, Elkington PT, Ward TH, Ripoll J, Parish T, Bancroft GJ, Schaible U, Robertson BD, & Wiles S (2010). Optimisation of bioluminescent reporters for use with mycobacteria. PloS one, 5 (5) PMID: 20520722

History of Scarlet Fever: The Fight against Childbed fever, and it's many casualties

It was 1790,when Dr Alexander Gordon, a retired naval physician, decided to settle down in the scottish town of Aberdeen .  He had had an esteemed career , and a wide experience in treating malady.  So when the town was struck by a horrible epidemic, he was the man the local physicians looked to for guidance.
This epidemic of was of a very tragic kind. It affected mothers immediately after giving birth. This childbed fever was usually fatal.  The locals referred to it as weeds. Doctors tended to call this "puerperal fever" .This kind of fever has been recorded since the time of Hippocrates, and is referenced in the Ayurveda.  But it was never very common. But as the 19th century dawned, this disease became more common. The practice of midwifery was in flux as well. Historically, the main practitioners were women who had deep practical knowledge of their craft, but this was changing. Doctors and surgeons, backed by scholarship and a grounding in anatomy started to practive midwifery. Inventions such as obstetrics forceps revolutionised the field of midwifery. in the mid 1700s, "Lying in" maternity hospitals were established.
for this reason, Alexander Gordon would have been asked to preside over pregnancies as part of his general practice. Most doctors assumed that puerperal fever was a natural consequence of pregnancy, and paid it no mind.
Dr Gordon was different.  He did not have any pre-conceived assumptions about this disease. Much in the way as had been set out by Thomas Sydenham, he checked the facts before resorting to theory. He noticed that patients who succumbed to the disease tended to share contacts with eachother, or the midwives that tended to them. Through careful observation, he found that medical practitioners, including himself, were spreading contagion to their patients. In fact, he noted in his publication that the epidemic had not spread to a town outside of Aberdeen specifically because the midwife tending those areas had not become infected.  He was the first person to recognise that puerperal fever could be transmitted. And that the main medium of transmission was through doctors.

After making impassioned pleas for change, he was accused as being the cause of the outbreak. He was driven out of Aberdeen, and  eventually fell back into Naval service, where he would eventually die from tuberculosis far from home. His work was never fully conveyed to the medical establishment, and it faded into obscurity.
Nearly fifty years later, a doctor from Doncaster by the name of Robert Storr noticed a worrying trend in his patients. In the winter of 1840, there were outbreaks of scarlet fever and erysipelas. And suddenly, he noticed an epidemic of childbed fever.  More worryingly, he noticed that if he saw a pregnant woman soon after attending to a sufferer of childbed fever, they too would succumb to the disease. At these instances, he became incredibly anxious. He recognised the one factor that linked all of these patients: himself.
So he began a strict regimen of cleaning himself, and changing his clothes in between patients. So concerned was he that he decided to leave his practice, and take some time out in Wales, with the hope that the fresh air would help rid him of the "poison".
He returned to his practice, and to the treatment of his patients. Within a week of returning, he was called to attend to two pregnancies happening within a day of eachother. And both of those pregnancies resulted in the deaths of the mothers.
The good doctor was distraught. It was his colleague, Dr Thompson who suggested that perhaps Dr Storrs may have re-acquired the "poison" from another of the patients he saw. It was then that Dr Storr recalled that before each outbreak, he had attended one woman, a Mrs Richardson for erysipelas.
Erysipelas is another form of scarlet fever, a fact that had been recognised since the time of Daniel Sennert. In it's most severe form, it can manifest as necrotizing fasciitis. In the case of Mrs Richardson, it had caused massive build up of pus in her leg,  making it painful for her to move. Dr Storrs had been alleviating her pain it by draining off the pus. And Dr Storr realised that every time he attended a pregancy after draining off this pus, that pregnancy would lead to a case of fever.
He immediately handed over the treatment of Mrs Richardson to one of his colleagues, and found that his preventative measures began to work. And so he dug deeper. He asked around his medical colleagues, and found that many had similar experiences. One would note how doctors who attended mothers after dissecting corpses would often see those mothers die of childbed fever. And often, this fever would appear linked to cases of Erysipelas. He noted previous work had showed that it was possible to contract erysipelas from puerperal fever, and Storr realised that it could work both ways. He published his observations in the Provincial and Medical Journal. He was the first to realise that the disease of erysipelas, and scarlet fever was also the disease that was the cause of childbed fever. It was well read amongst the physicians of Britain, and soon other physicians came forward with their own stories.
Dr Francis Elkington of Birmingham wrote in support of Dr Storr, having noticed a similar pattern at his local practice in the preceding decade. He had begun to enforce strict hygienic practice when dealing with pregnant women, ensuring that he only wore clean clothes, and always cleaned himself. And as a result, for the past seven years, the numbers of patients who had died of childbed fever fell precipitously. There were only two cases. One happened when he was hurrying home after draining pus from a man by the name of Perry, and he was urgently needed for a woman who was "dangerously ill" and not supposed to be in labour. The second case happened at the house of Perry, where it was likely that he had transmitted the disease to the sufferer.
More physicians in Britain came forward, and soon Dr Storr found himself contacted by an American physician by the name of Oliver Wendell Holmes. He too had been investigating this problem for some time.

During a meeting of the Boston Society for Medical improvement, a peculiar case was discussed. A woman had died of childbed fever, and during the autopsy, the attending physician had sustained a wound. He soon developed Erysipelas, and died. It was said that in the week before he succumbed to this disease. It was said that before he had died, every pregnant woman to whom he had attended developed childbed fever. After fervent discussion, it was determined that more research was needed before they made any decisions as to how to change medical practice. One of the members in attendance, Dr Oliver Wendell Holmes, decided to take up this case. In 1842, he began to scour the literature, to see whether any other doctors had seen anything like this before.
What he found astonished him. He managed to find the first accounts by Dr Gordon published in 1795. As he interrogated the literature, he saw many more cases where physicians, upon suspecting themselves of "poisoning" their patients, enacting hygienic practices to prevent this happening again.
He catalogued a large number of cases, ranging over fifty years, and published his recommendations in the New England Quarterly Journal of Medicine and Surgery.
In England, Dr Storr seized upon this publication as further support for the guidelines he himself had been developing. However, Dr Storr's efforts in promoting these new guidleines ended abruptly with his death in 1847, due to fever.
 The New England Quarterly journal never got very much circulation, and Holmes's work only appeared in the final issue. Apart from it's strong support in England, it was not well read. But enough people had read it to find significant disagreement with its findings.
 Many physicians in europe and the US maintained that childbed fever could not be contagious, and that it was a separate disease from erysipelas and scarlet fever. In the US, the chief opposition came from two eminent physicians based at the Philadelphia medical school. Dr Hugh Hodges published a provocative article ,describing the "Non-contagiousness of puerperal fever", and was supported by his colleague, Charles Meigs.  They suggested that these cases were due to pure chance, or bad luck.  They did their utmost to suppress these findings. In fact, Charles Miegs took this evidence very personally,saying that "Doctors, are gentleman. and a gentleman's hands are clean".
On continental Europe, the situation was very much similar. Whilst the USA had Oliver Wendell Holmes to plead it's case, such voices in europe were largely absent. At least, until a physician based in vienna changed this.
Jakob Kolletschska was a professor of forensic pathology. As part of his work, he would routinely perform autopsies on cadavers. He would get his students to help him, pointing out details and abnormalities as they worked. It was during one of these exercises that one of the students accidentally cut him with an unlcean scalpel. The wound became septic, and he died as a result. He was no expert on childbed fever, but his death had a profund effect on his friend at that same institution, Ignaz Semmelweis.
  Ignaz Semmelweis had been appointed the head of obstetrics in the Vienna Lying-in hospital, and he was immediately appalled by the numbers of deaths from childbed fever at the hospital. Almost immediately, he set about trying to find a solution to this problem. Semmelweis noted that women who gave birth before reaching hospital tended to not to get this disease.
As the head of obstetrics, he was also aware that every morning, medical students and doctors would perform autopsies on women who had died the previous day. It was these sorts of dissections that Jakob Kolletchska performed on a regular basis, and it was on one of these were he had received his mortal wound.
In 1847,  disgusted with his inability to prevent these outbreaks, he took a holiday in Venice. It was while he was in Venice that he recieved word of the death of his friend. When he evenutally got around to reading the autopsy report, he was struck by how similar it was to those of the dead pregnant women whom he had dissected nearly every morning.
He realsied that if it was possible for his friend to have contracted a disease from a cadaver, then it was also possible that he, and his students could transfer this disease to the young mothers in their care. In that same year, he instituted new guidelines to the people workign under him: everyone should wash their hands before they start ont he wards, and before they examined patients.
The results were extraordinary. The numbers of patients contracting this disease fell from 18% to just 3%. But, just as his western counterparts, he faced strong opposition from the medical establishment.  Amongst his critics was the "Father of Modern Pathology" Rudolf Virchow, who exerted much influence amongst the medical establishment.
Semmelweis found himself passed over for promotions, and for work as a result of his strong views on handwashing. In the end, he returned to his native Hungary a bitter man. He was appointed to an unpaid position in St Rochus hospital, where he successfully enforced hygiene, and saved lives. He went on to obtain a professorship from the University of Pest and went on to publish his work in 1861, providing crucial statistical grounding to his theories . But he never forgot the insult he was dealt in Vienna.
Whilst some accepted his views, many did not, and they would often recieve a torrent of invective as a result. Semmelweis would publish open letters to his detractors, branding them as "Medical Neros" and "Murderers" in the popular press. He steadily became more unstable, until in 1864, he was committed to an Asylum. He died within weeks, tragically being felled by the very disease he had fought so hard against. But his work lived on afterwards, and his fervour in promoting hygiene was not forgotten.
Many would point to Semmelwies as the founder of hygienic practices in hospitals, but the story is more complex. In fact, the guidelines set out by Semmelweis had been discovered independently by a number of physicians in the west, who were mostly ignorant of each other's work. And the main reason for this was the strong opposition to these findings. The medical establishment didn't want to be told that they were killing their patients, or that their hands were dirty. Many doctors who had seen the effects of hygiene first hand, such as Francis Russell Elkington, implemented changes without telling anyone, and saw their patients improve. But people like Alexander Gordon, Robert Storr, Oliver Wendell Holmes and Ignaz Semmelweis fought hard to get their message out to the rest of the medical establishment. It was not enough for them to be better than their medical companions. We never heard them shrug and say "what's the harm" when they saw their fellow physicians blunder and kill their patients. They went out to change the world for the better, and they paid for it. Most of them ended their lives with their careers in ruin, and lives in tatters. But the lives they saved more than made up for it. They had reached enough people to provoke a groundswell of change. But it was slow and incremental. Whether we remember their names or not, there are people alive today who owe their existence to these men.
 Oliver Wendell Holmes was one of the few of them who managed to live long enough to see his work vindicated. Ten years before his death, he met the man whom he held responsible for that. He referred to as "one of the truest benefactors of his race". That man was Louis Pasteur.


The works of Oliver Wendell Holmes:  Medical Essays 1842-1882


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