Field of Science

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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