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.

References:
Internet:
 http://www.donny.co.uk/Doncaster/news/index.php3?ID=1175

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

Papers

Elkington F (1844). Observations on the Contagiousness of Puerperal Fever, and Its Connection with Erysipelas. Provincial medical & surgical journal, 7 (172), 287-8 PMID: 20793370

Storrs, R. (1842). History of a Puerperal Fever in Doncaster: Illustrated by Ten Cases, with Remarks BMJ, s1-4 (3), 45-51 DOI: 10.1136/bmj.s1-4.3.45

Dunn PM (1998). Dr Alexander Gordon (1752-99) and contagious puerperal fever. Archives of disease in childhood. Fetal and neonatal edition, 78 (3) PMID: 9713041

Storrs, R. (1843). Observations on Puerperal Fever: Containing a Series of Evidence Respecting Its Origin, Causes, and Mode of Propagation BMJ, s1-7 (166), 163-169 DOI: 10.1136/bmj.s1-7.166.163

De Costa CM (2002). "The contagiousness of childbed fever": a short history of puerperal sepsis and its treatment. The Medical journal of Australia, 177 (11-12), 668-71 PMID: 12463995

Adriaanse, A. (2000). Semmelweis: the combat against puerperal fever European Journal of Obstetrics & Gynecology and Reproductive Biology, 90 (2), 153-158 DOI: 10.1016/S0301-2115(00)00264-5

Dunn, P. (2005). Ignac Semmelweis (1818-1865) of Budapest and the prevention of puerperal fever Archives of Disease in Childhood - Fetal and Neonatal Edition, 90 (4) DOI: 10.1136/adc.2004.062901

Colebrook, L. (1956). The Story of Puerperal Fever--1800 to 1950 BMJ, 1 (4961), 247-252 DOI: 10.1136/bmj.1.4961.247

Review of the Year

The time of the year has arrived, where we all collectively look back, and go, what the hell was that ?
 I remember starting this year, with the absolute certainty that it was going to be terrible. VAT increases, job losses, public service cuts. 2010 was a year of extreme worry.
My Blogger traffic statistics hates 2010 so much that it has been completely expunged from the timeline.

But the traffic statistics also tell another story.
When I started this blog, nearly five years ago, it was purely as a revision aid, to help me set down my thoughts about certain subjects that I was studying. I didn't seek readership, and naturally I didn't get any, Then I started my PhD, and promptly forgot the damn thing existed.
Then in November 2010, I found myself directed to "science of blogging", and once again , enthused, I decided to start a blog. And then I found that Memoirs of a Defective Brain was still here. Everything was just as I left it, even though it had been such a long time. All of the posts that I published, all of the drafts that I intended to publish, but never did. I blew out the cobwebs, tightened up the site design, and started writing posts for research blogging, and for the MolBio carnival.
And something weird happened. People actually started reading. Every spike in my pageview statistics correlated with a spike in dopamine.  Of course finding the time to write the kind of blog posts I wanted was (and still is) time consuming. Nevertheless, when the Blogmaster solicited applications for new bloggers to join field of science, I signed up. Probably one of my best decisions ever.
That big spike in my stats in August came from a collaboration of multiple bloggers, where we each discussed the question "Are we doomed ?", and we got some excellent and creative posts about how dangerous viruses, Uncontrolled populations, Incredible Human Stupidity, and the universe is in general trying to kill us. I drew a silly comic where everyone had funny legs.
And since then , I've managed to keep a minimum of about 1,000 page views per month. My proudest achievement has my series on the history of scarlet fever. These have been in the works for a very long time, with many spare moments reading centuries old papers on scarlet fever and streptococci finally paying off. I learned about characters like Johann Weyer, Daniel Sennert and of course Thomas Sydenham, all of whom were interesting in their own right, and each of whom played a role in the History of Scarlet Fever.
And the process of researching and writing for this weblog has helped me innovate my own research, and those of my colleagues. But that's a story I'd like to tell another day, when I (or my colleagues) publish on it.
But it was not all happiness and blog writing. In the wider world, the year was not always so great.

Greece was caught out on it's tax returns, revealing the fragility of the european constitution, and bringing us to the precipice. We still don't know whether the european single market will collapse, and what effect that will have on the UK, but it's out of our hands, since we vacated our seat at the table.
Riots and protests have erupted worldwide. And when these riots turned up on my doorstep, I was surprised, worried and (shamefully) slightly thrilled.
But that same swell of global anger has shaken the foundations of governments worldwide. The Arab spring is the story of the year, with the Tunisian, Egyptian and Libyan revolutions toppling dictators. And every blow was filmed, tweeted and blogged. The power of protest had been demonstrated, and suddenly others worldwide found their voice. If they weren't happy about the way things were, there was something they could do about it. Suddenly financial centres worldwide began to attract occupiers. The idea of popular revolution, remixed and spread throughout the world.
And this is why I have hope for the next year. As hard as times get, humanities propensity for innovation will prevail. The ability to take one idea, re-assess it, improve it and develop and progress is our greatest strength.
And I can show one event that demonstrated this incredible ingenuity, of people taking one idea, and making it their own.



So what do we expect for 2012 ?

More posts on Scarlet Fever's History. You can look forward to learning about great doctors, like Francis Russell Elkington, and Robert Storr.
More Phylomon ! I have been lacking in inspiration lately, but next year I hope to start drawing more bacteria.
And of course, we can expect the giant space god of the Mayans to come down and say "Hey, you guys need a new calendar ? We heard your last one ran out".
And London 2012 will be so bad that the world will end out of sheer embarrassment.

Do you hate slow walkers? So does the Grim Reaper !

Researchers in Sydney, Australia were analysing mortality statistics, when they found an intriguing trend. They found that slow walkers tended to have a higher chance of dying early. Could this be a sign of an underlying lack of fitness in slow walkers? Or perhaps that laziness really can kill you ?
None of these explanations were satisfying. But then they realised the one unifying factor in these mortality statistics. Everyone had died. And as you well know, when you die, it is as a result of meeting that fabled entity, The Grim Reaper.

The Grim Reaper, the Harbinger of Souls, Friend to the Friendless, is known to stalk the halls of many a hospital. Despite the fact that this creature is believed to be responsible for 100% of all mortality statistics, it has barely been studied in the scientific literature.

So they did the sensible thing. They set up a study, and enlisted a number of participants, and measured their walking speed. They kept in touch with their participants, checking up on their health and ultimately recorded when they died.

They analysed the relationship between the average walking speed, and the likelihood of encountering the Grim Reaper. And they found that faster walkers do seem to outrun the Grim Reaper. To quote the paper
"Faster speeds are protective against mortality because fast walkers can maintain a safe distance from the Grim Reaper."
"The Grim Reaper prefers to walk at 0.82 m/s (2 miles (about 3 km) per hour), with a maximum estimated speed of 1.36 m/s (3 miles (about 5 km) per hour)"
Older men wishing to outrun the Grim Reaper should maintain walking speeds above these levels. The researchers did say "However, as it is possible that Death’s walking speed varies between work and leisure time,"
In terms of study limitations, they highlighted other problems:
"A further limitation is that we were unable to collect data on the presence of resources that have been reported as enabling people to avoid Death, such as invisibility cloaks, resurrection stones, and elder wands (collectively known as the Deathly Hallows)

They recognise that it is possible to trick, and /or outwit the grim reaper, and to investigate this they propose future work.
"Future research could investigate whether a person’s level of cunning, measured on a suitably developed scale such as the potential CCATBS (the Cunning, Conniving and All-round Tricky Bastard Scale), enables them to walk at slow speeds while still avoiding Death."

So avoid tragedy this Christmas. Walk Faster !

Stanaway FF, Gnjidic D, Blyth FM, Le Couteur DG, Naganathan V, Waite L, Seibel MJ, Handelsman DJ, Sambrook PN, & Cumming RG (2011). How fast does the Grim Reaper walk? Receiver operating characteristics curve analysis in healthy men aged 70 and over. BMJ (Clinical research ed.), 343 PMID: 22174324

When Phylomon fall from the sky

The winter winds are blowing. These cold winds whip bacteria up into the atmosphere. These tiny specks of life, unaware of the vast sphere turning beneath them, feel only the cold. 

And one particular species of bacterium does something quite special. This bacterium is known as Pseudomonas syringae.

Usually, this unassuming life form lives in plants. It has a number of strategies to attack its plant host, to break apart the cells of a plant to release the delicious nutrients within. Usually, this involves a number of virulence factors, lethal proteins which it injects into the cells. But as winter sets in, this becomes more difficult. The bacterium begins to freeze. But this bacterium still has a trick up it's metaphorical sleeve.

It uses winter as a weapon. As winter sets in, it produces special proteins. These proteins allow ice to form around them, such that they grow out like daggers. These pierce into it's host, ensuring that there will be a nutrient rich bounty waiting for the bacterium when the thaw comes.

But occasionally, a strong wind will blow the bacterium away.  And as the bacterium gets higher in the atmosphere, it senses the chill. And, just as it would on a plant, it produces nucleation proteins. Ice crystals begin to form around it. It becomes encased in the heart of a snowflake, and returns to earth.

Hat tip- Scripture of science

Olfactory Reference Syndrome: My attempt at self diagnosis

When one is in their first relationship, mistakes are made. There are certain unspoken rules that a novice can accidentally break. Forgetting to hold the door open, laughing at the wrong moment, or believing them when they say "I don't want a Valentines day gift". I had watched many colleagues fall foul of these errors, and vowed to not make these errors with my first girlfriend. I was young, naive and almost certainly scared.
You see, my first girlfriend had several burly, older brothers, which as you may imagine, raised the stakes somewhat.

So the situation is thus. After a day at her place, her mother kindly decided to drop me off at the station so that I could go home. Of course my girlfriend decided to ride along, because it was the decent thing to do. 

 A perfectly innocent situation, the only risk being the necessarily stilted conversation with the mother. Keep to short sentences. The less words said, the less chance of causing offence.

But then the worst thing that could possibly happen in an enclosed space with both my girlfriend and her mother. But soon, there was something else in the room. It announced it's presence in the most subtle of ways. It was barely audible.
The sound of a zipper being pulled very slowly. As it got louder, it's pitch deepened. Soon, we were regaled with the wet baritone creak of a troubled colon. I didn't, and still don't understand how such a small girl could have created such a noise. I may have been able to keep my composure, if I hadn't had to cope with the humid stench that enveloped the car.
"Did you just fart ?!" I exclaimed.

"No" she responded, with an angelic expression.

"I'm pretty sure...." 

" No, I think that was you" With absolute conviction.

At this point , my subconscious began to ring alarm bells. I was about to get into an argument in front of her mother. If I came across as too confrontational, her mother would probably assume that I was a wife beater, and I would have to go to prison, where I would get the stuffing kicked out of me by the aforementioned brothers.*
Just by giving into the juvenile impulse of naming and shaming those who loudly produce gas, I had stumbled into minefield. 

What could I do? I could simply keep telling the truth and call her a liar. I could accuse her mother, who was also another person in the car who didn't fart. Only one other option remained.

"oh, err, my mistake" were the words that I probably mumbled. Perhaps this was another one of those unwritten chivalric rules that are alluded to but never mentioned. Maybe all men take responsibility for whatever untoward smells that emanate from their partners. Unless there's a dog present .Then blame the heck out of it**. Dogs don't care. 

Or maybe I actually did emit the horrible fart. That would make far more sense*. Perhaps in it's eternal plots against me, my rectum finally devised a way to sneak odours past me without my knowledge. Worst of all, it had learned to throw it's voice. This one incident may have triggered a disorder knonw formally as "Olfactory Reference Syndrome".
This disorder has been recognised in psychiatry under a number of different names since the 1890's, and a recent systematic review set out to examine this as a disease in it's own right.
They set out three diagnostic criteria:

1) The belief that one emits a malodourous smell ("it does not have to be delusional")
2) This belief causes clinically significant distress
3) This is not a manifestation of another disorder, and that this was a unique condition in it's own right.

So they scoured the literature, and found 180 reported examples of this disorder between the years of 1890, to 2009. Of these, only 82 cases were suitable for analysis. Of these, the majority of the victims were male, and the median age of onset was 15.
Often, this disorder would be triggered by a precipitating event, such as the one I described above. So perhaps this psychological trait could explain why I spent the rest of my teenage years doused in aftershave.
On the basis of this trawl through the literature, the authors suggest that this should be recognised as it's own disorder. However, It should be noted that a large proportion of the cases excluded from this study were done so because the delusional odour manifested as a part of different psychiatric disease.
But here is the thing. Whilst I may have gotten slightly paranoid over this event, it never got to the point where it caused significant distress. The "significant cause of distress" in my life dumped me soon after this event. Whilst I woried about it, it never spilled over into the kind of pathology seen in real sufferers from this disease. People who genuinely smell odours that are not there, people who end up obseesively trying to manage odours that aren't present. In some cases, it ended up getting to the point where their doctors had to prescribe medical treatments to get them to stop.
My technique of occasionally dousing myself in aftershave before meeting people seems tame by comparison. Like many psychological traits, this syndrome can manifest at many levels of severity, and only a relatively small portion of people express it severely enough to actually qualify as sufferers. My case was easy enough to get over. I now have a huge collection of aftershave that I no longer use. Although people still keep giving them to me at birthdays, Christmas, Easter, Thanksgivng, and Ohmygodgetyourarmpitoutofmypostcode day.

* this was what passed for logical thinking when I was a teenager.

** For a long time I suspected this was the real reason rich girls carry dogs around in handbags.

Begum M, & McKenna PJ (2011). Olfactory reference syndrome: a systematic review of the world literature. Psychological medicine, 41 (3), 453-61 PMID: 20529415

History of Scarlet Fever : Dancing fever, Civil War and a Revolutionary Scientist

Once upon a time, there was a wicked and vain queen with a strong desire to murder her stepdaughter. However, through a convoluted series of events involving a huntsman, seven dwarves and a handsome prince, the stepdaughter survived. In fact she ended up engaged to the handsome prince. As a wedding present to his new bride, the prince invited the queen to the wedding. A show of forgiveness? Not exactly.
As part of the nights entertainment, the queen is forced to wear a set of red hot iron shoes and dance for the amusement of all the guests. Until she drops dead. The moral of this story?


 Don't f*ck with Snow White.


Whilst this may seem like a cruel and unusual punishment for us, dancing yourself to death was a genuine fear for people when the Snow White legend came into being.
A medieval medic, known as Felix Platerus records a curious case involving a young lady. She appeared to have a supernatural compulsion that forced her to dance. Guards had to attend to her for a whole month to prevet her hurting herself, or others. She danced  until her feet were rubbed raw, and she could no longer stand. And then when she could stand, she started dancing again. A few of the writers of the time make references to Arabic descriptions of "Jumping limbs" and palsy, and a number of writers tended to notice the convulsiveness that characterised these dances.


In northern europe, it was believed to be caused by some form of demonic possession, and sufferers had to pray to St Vitus (the patron saint of dancers) to be relieved of this disease.  In Italy and Greece, it was believed that the cause of the disease was from the bite of a wolf spider. The remedy for this disorder was a frenzied dance which eventually became known as a tarantella.


It was not only these nations that took up dancing as the cure for this disease. In parts of Germany, magistrates employed people to play music for these people, and for others to act as dancing partners. This was to allow them to "dance out" their disease.
Choruses of sufferers roamed the streets. Musicians followed them, attempting to soothe their disease by providing rhythm. The greatest challenge in managing this chorus was ensuring the safety of the people who ended up collapsing from exhaustion.


In Strasbourg 1518, an outbreak of this fever prompted the council to set up a guildhall especially for the dancers, and paid people to dance with them, and others to play music for them. Yet still, many danced themselves to exhaustion, and death. Eventually, the Strasbourg council realised  this treatment was not working. Still unaware of the cause of the disease, and wanting to prevent contagion, the city banned all dancing. The sufferers who still danced in spite of the ban were sent on a pilgrimage to the shrine of St Vitus. Once they arrived they received holy oil, and red shoes.
 These choruses of dances lead to a particular name being ascribed to the disorder-  a Chorea. The literature documenting this disease is so littered with allusion and innuendo that it is difficult to get to the truth of the source of this illness.


And into this quagmire strolls the hero of this particular story. His name was Thomas Sydenham. He was a physician of the practical sort, whose personality and career was wrought in the events of the English civil war.


The English Civil War can be said to have begun with one man.  When King Charles came to the throne, he had high ambitions. He wanted to finish his father's work, to bring unity between Scotland, England and Ireland. Furthermore, he wanted to enter the brutal "Thirty Years" war that had been raging on the continent.
But what was more controversial was how he dealt with parliament. At the time, parliaments control was far less than it was today. It collected taxes, and controlled how they were spent. If the king wanted to use any of that money, he needed to consult with parliament. Charles however, was believed in the king's "Divine Right" to rule over his subjects, and that he should answer to no-one but God himself. Needless to say, there was some friction between the King and his parliament.


One example is when Charles demanded funding for an expensive military campaign on the continent. Parliament, initially supportive of this course of action, questioned him over putting one of his friends in command, instead of more competent individuals. Their fears were confirmed when the war ended in an expensive defeat. When parliament attempted to bring charges against the man responsible, Charles dissolved parliament.
 Such exchanges began to characterise the King's rocky relationship with his kingdom. Charles needed parliament to fund him, but in return they would want a say in how the money was spent.  So the king stopped convening parliament, and attempted to rule the kingdom as an autocracy. He levied new ( and illegal ) taxes upon the populace, as a replacement for the parliamentary purse. He instilled a new religious doctrine, and began to persecute those who did not adhere to it. For those in religious minorities, this was a worrying chain of events. Puritans, such as Thomas Hooker, sick of the religious persecution, emigrated to America.
  The Scot's also did not take these changes lightly. Soon, they were in open rebellion, and the King didn't have the money to fight them.  So after eleven years of "personal rule" , Charles was forced to convene parliament again, to secure more funds.
 Various members of parliament saw this as an opportunity to bring their king under control, and introduce more reforms. It did not turn out that way. Predictably, this resulted in another quarrel, and in less than a month, parliament was once again dissolved.
The king went to war anyway with what little funds he could muster. The ensuing fiasco ended with Scotland in control of the North of England. The Scots, magnanimous in victory, promised they wouldn't burn all of the cities in their possession so long as Charles paid them a ransom.
 The King couldn't just let the north burn. He needed to reconvene parliament . In return for the money, reforms were enacted that aimed to end the king's autocratic habit. But Charles would not crack so easily.
 By the time Thomas Sydenham began his studies in Oxford, events had come to a head. In January 1642 King Charles had marched with 400 men to parliament with the intention of arresting 5 of it's members, but without success.
Across the country, towns and constituencies began declaring fealty to either king or parliament. War was brewing.  Parliament began recruiting an army to do the unthinkable. To fight against their own king.
In the early stages of the war, Sydenham's mother was killed when Royalists raided their home. This act which drew the whole family deeper into the conflict.
Sydenham left Oxford, and joined his family to declare loyalty to parliament.  Their exploits during the war lead them to be known as"The Fighting Sydenhams".

Thomas's older brother, Francis Sydenham  became a legend in the Parliamentarian army. When attacking the seemingly impregnable town of Corfe, it was Francis who oversaw the construction of tank, which was used to great effect to assail the city.
 At one point, Francis pretended to defect to the Royalist side against his own family. In doing so, he tricked Royalist forces into entering a devastating ambush in Poole. And during that battle, by chance he encountered the man responsible for the death of his mother, and killed him on the spot*.


   Thomas's role in the war is largely overshadowed by those of his brothers and his father. It is known that he was wounded in a cavalry charge at the battle of Weymouth as the war was drawing to a close.  By the time the royalists had surrendered and the king executed. Two of his brothers, including Francis, were dead. It was a new England, with Oliver Cromwell and parliament in charge.
Thomas Sydenham returned to Oxford to take up his studies once more, and found it a much different place. It had been one of the last royalist strongholds to fall, and Parliamentary forces aimed to keep it under strict control.   Parliament had put "visitors" in place, who enforced parliament's political will on campus. They expelled anyone who spoke out against the new government.


 Thomas, being a leading member of the revolution, thrived in this environment. Parliament were eager to bestow some commendation upon him for his family's role in the war. As a result,  ended up with a doctorate within his first year of study. In addition to this, he may also have played a role in helping Cromwells "visitors" in expelling professors on the basis of their royalist leanings. This removal of old academics aided the careers of younger academics such as John Locke and Robert Boyle, both of whom were friends of Sydenham.


Nevertheless, the army was not yet done with Sydenham. Whilst Cromwell had successfully won the civil war, winning the peace was a different matter. After returning from a brutal and bloody campaign in Northern Ireland, Cromwell turned his eyes north. The Scottish parliament were jockeying for more power in the new order, and recruited the heir to the throne, Prince Charles II to force the issue. In 1651, Cromwell answered with an army of seasoned veterans. Once again, Thomas Sydenham found himself at war. He was put in charge of his own battalion, where he used his medical knowledge to fortify his troops against the northern frosts. But this didn't stop him from being left for dead on a battlefield and nearly shot at point blank range by a drunken trooper from his own side. When Scotland was defeated, Thomas left the army, never to return.


 He devoted the rest of his life to the study and the application of medicine, and managed to revolutionise the way it was practised in England. At the time, there were many explanations of diseases, and often doctors would prescribe treatments accordingly.  The vast increase in anatomical knowledge lead physicians to prescribe bleeding to balance the "humours" that allegedly controlled the body. Various beliefs on matter, and findings in chemistry lead to mercury being used as a purgative. The best "treatment" for a convulsive jerking disorder at the time was to "dance" the demons out.


When the founder of the British museum, Hans Sloane applied to be a student of Sydenham, he presented the physician with a letter of introduction . Sydenham glanced at the letter. It indicated that Sloane was "a ripe scholar, a good botanist, a skillful anatomist".
"This is all very fine," Sydenham cried "but it won't do! Anatomy ? botany! Nonsense! Sir, I know an old woman in Covent Garden who understands botany better, and as for anatomy, my butcher can dissect a joint fully as well. No, young man, all this is stuff; you must go to the bedside; it is there alone you can learn disease."


He recognised that many of the findings of anatomy and science were very much in their infancy. The application of their principles when they were so poorly understood was foolhardy. He staunchly believed that evidence was the guiding factor at the bedside.


"It is my nature, to think where others read; to ask less whether the world agrees with me than whether I agree with the truth" he says in one of his works.  He flatly states that to speculate on the causes of diseases was a "difficult and perhaps inexplicable affair; and I choose to keep my hands clear of it".


He was one of the few men of the day who recognised that they simply didn't have the tools to speculate on the causes of disease, and that the bedside was a far better teacher than the library.
What Sydenham frequently found was that the application of unproven theories to the treatment of patients did more harm than good, and that often the best thing to do was to let nature take its course.


Sydenham had very little patience for nonsense. So one wonders what he thought when he first heard of the dancing fever. When he first encountered a patient,  He did not speculate on whether it was caused by demonic possession, or by a spider bite.  He focused on collecting as much information as possible about the disease, and then letting the evidence speak for itself.  He described the patients as exhibiting convulsive movements out of their control,** . Instead of prescribing dancing, or prayer, he simply let the disease run its course, and found that patients would eventually get better without interference. The deaths attributed to this disease were probably caused by the forcing of sufferers to "dance out" their disease. Whilst he did not know it at the time, this dancing disease was related to another disease he studied, the disease that is the subject of this series.


 It was Thomas Sydenham who gave scarlet fever it's name***. His initial studies on epidemiology in 1666 are where he first describes the disease, although the actual name “Scarlet Fever” only appears in the 1683 edition. . He noted the seasonality of this disease, and made key observations on it's disease course, and that the treatments of the time were at best ineffective.
Unfortunately, his description of the fever leaves out many of the essential details that were catalogued by Sennert. Sydenham's failure to recognise the more severe forms of this disease (such as the dropsy and arthritis) meant that subsequent physicians often confused it with measles. Such was Sydenham's repute that his word was deemed to be the last one on this issue for over a century.


Nevertheless, his work was revolutionary. The Dancing fever would eventually be named after him, and called Sydenham's Chorea, and the wide regard of his work raised awareness about Scarlet Fever.
Unbeknownst to him, the two diseases are linked. Previously, I talked about how Sennert was amongst the first to recognize that scarlet fever can trigger other diseases, such as "dropsy" and rheumatism.
Today we know that these occur because the bacteria that causes scarlet fever, Streptococcus pyogenes, often uses a variety techniques to hoodwink the immune system. In some cases it can turn the immune system against the rest of the body. These immune reactions are what cause these "disease sequels".


In the case of Sydenham's chorea, the immune system has a bad reaction with the nervous system, causing damage. This manifests itself as the juddering dancing motions characteristic of the disease. It usually resolves of its own accord after the underlying bacterial disease is cleared. So Sydenhams basic treatment of "Wait and See", or even the religious method of "Wait and Pray" would have worked far better than other treatments available at the time.


But what Sydenham did for medicine was not limited to his descriptions of diseases. Indeed, in many of his writings he often proclaims his ignorance on many subjects. It was the way he practiced medicine that secured his place in history. His re-introduction of Hippocratic methods of evidence gathering were the key to his success.  After his death, the following was written of the great practitioner;


"The great merit of Sydenham, was to proclaim the great truth that science was, and always must be incomplete; and that danger lurks in the natural tendency to act upon it as if it were complete. A practical man has to be guided not only by positive knowledge, but by that which is imperfectly known. He must listen to the hints of nature, as well as to her clear utterances. to combine them may be difficult; but the difficulty is solved in minor matters by the faculty called common sense; in greater affairs by the synthetic power of Genius " ***




Footnotes

* In one account , it was said to be Thomas himself who avenged his mother, but sources that are more reliable indicate that it was actually Francis.
** There seems to be a bit of controversy over the actual causes of the medieval dancing disease. Whilst  the diagnosis of Sydenham's Chorea may make sense in the context of the devastating streptococcal outbreaks pushing their way through Germany at the time (as documented by Weyer and Sennert), it does not explain everything.
The medieval descriptions of the sufferers of Chorea differ much from Sydenhams own account. They talk of sufferers leaping and so forth. It is the impreciseness of language that makes it hard to definitively describe the disease. It appears that only arabic accounts agree with Sydenham's description, but I have not been able to source the relevant documents to back this up, and even if I did, I can't read arabic.
It is also likely that hysteria may have played a role, especially where people were employed to dance with these victims. In fact, the dancing bans in Strasbourg likely helped to quell the spread of this hysteria.
There are also theories that a rye fungus outbreak spread hallucinogenic substances on foodstuffs, although nothing in the accounts I read indicates that these dancers were actually hallucinating.
The truth is that there is no truly satisfactory explanation for this disease. Sydenham's explanation was good enough for those who lived contemporaneously with the disease, so I decided that it was good enough for me.


***Samuel Pepys is probably the first person recorded to use the term "scarlet fever" to describe a disease, it is unlikely to refer to the disease we know today. It may have been used interchangeably with measles, and other diseases that produced a red rash. It should also be noted that colour based adjectives were often imbued with some form of emotion, with "scarlet" and "black"  being not only descriptive, but emotional terms. When researching these articles, I was struck by how almost every disease was described as a "black plague", including those which exhibited streptococcal symptoms. But in some cases, the writers may have well have said "terrible plague" or "scary plague". This use of language makes investigating diseases in the past a very confusing affair to the novice.


*** I have scoured the internet for the source of this quote, and came up with zip. Any help with this would be appreciated.


References

Google Books

"A History of Madness in Sixteenth-Century Germany" By H. C. Erik Midelfort

"Anatomy of Melancholy," by Robert Burton

"The continuum companion to Locke", by Sami-Juhani Savonius-Wroth, Paul Schuurman, Jonathan Walmsley


Dr Thomas Sydenham- by Unknown.


Journals

Rolleston, J. (1928). THE HISTORY OF SCARLET FEVER BMJ, 2 (3542), 926-929 DOI: 10.1136/bmj.2.3542.926

Fischer WJ (1913). THOMAS SYDENHAM, THE ENGLISH HIPPOCRATES: (1624-1689). Canadian Medical Association journal, 3 (11), 931-46 PMID: 20310434