The Project

TO DO: project in a nutshell.

Context


Cholera

Cholera has been a scourge to civilizations the world over since ancient times. According to the World Health Organization’s estimates, there are 3-5 million cholera cases and 100,000-120,000 deaths every year worldwide. Caused by the bacterial pathogen Vibrio cholerae, the disease has been responsible for seven global pandemics in recorded history, plus countless localized outbreaks (World Health Organization, 2014). These outbreaks are triggered by V. cholerae when present in water sources or food even at very small cell densities, and can have devastating effects, with mortality rates reaching up to an alarming 50% and causing death in a matter of hours if left untreated (Public Health Vigilance Group, 2011). The disease is most prevalent in low-income populations with inadequate health services and water management infrastructure (Public Health Vigilance Group, 2011). Although no cases have been confirmed in Colombia for a decade, some of the greatest risk factors are widespread across the country’s rural–and even urban–areas (Public Health Vigilance Group, 2011). Proof of this vulnerability is the impact generated by the arrival of the deadly El Tor V. cholerae strain in 1991, which caused 30,000 cholera cases in two years.

Due to the disease’s alarmingly quick onset upon infection and the fact that rapid access to medical care is often not available in affected areas, prevention is a key factor in combating cholera. Careful monitoring of water sources and food stocks in areas of potential contamination is vital, especially during outbreaks. In spite of this need, there currently is no cost-effective way of detecting V. cholerae easily in environmental samples (Wang et al., 2010). The most effective ways of detecting the pathogen are culturing environmental samples in selective enrichment media in the lab and real-time PCR, which require a lab, trained personnel, and enough time to grow cultures. Rapid detection systems such as immunomagnetic beads or DNA probe hybridization can be unspecific and are based on molecular techniques that can be expensive or difficult to use (Wang et al., 2010). Recent research in environmental cholera detection has focused on improving upon existing techniques, such as adapting immunochromatographic dipstick tests used for stool samples (Chakraborty et al., 2013). Although there have been interesting synthetic biology projects aimed at preventing V. cholerae infection by meddling with the pathogen’s quorum sensing mechanism (Duan & March, 2010), there have been no attempts to build an environmental cholera biosensor using synthetic biology to date.

In light of this, our project aims to use synthetic biology to develop a V. cholerae sensor using a new technique. Instead of trying to detect the cholerae toxin, specific sequences of nucleic acid, or antigens, we propose detecting V. cholerae Autoinducer 1 (CAI-1), the bacteria’s species-specific quorum sensing molecule. If we rewire V. cholerae’s own quorum sensing mechanism –used in nature to gauge population levels and regulate pathogenicity– in a harmless E. coli chassis, we can build a cheap and easy-to-use biosensor that gives a color output when it senses the pathogen. This prototype can serve as a proof-of-concept for future quorum sensing-based pathogen biosensors.

Quorum Sensing Mechanism

To Sherlock Holmes she is always the woman. I have seldom heard him mention her under any other name. In his eyes she eclipses and predominates the whole of her sex. It was not that he felt any emotion akin to love for Irene Adler. All emotions, and that one particularly, were abhorrent to his cold, precise, but admirably balanced mind. He was, I take it, the most perfect reasoning and observing machine that the world has seen; but, as a lover, he would have placed himself in a false position. He never spoke of the softer passions, save with a gibe and a sneer. They were admirable things for the observer—excellent for drawing the veil from men’s motives and actions. But for the trained reasoner to admit such intrusions into his own delicate and finely adjusted temperament was to introduce a distracting factor which might throw a doubt upon all his mental results. Grit in a sensitive instrument, or a crack in one of his own high-power lenses, would not be more disturbing than a strong emotion in a nature such as his. And yet there was but one woman to him, and that woman was the late Irene Adler, of dubious and questionable memory.

I had seen little of Holmes since the singular chain of events which I have already narrated in a bold fashion under the heading of The Sign of Four. My marriage had, as he foretold, drifted us away from each other. My own complete happiness, and the home-centred interests which rise up around the man who first finds himself master of his own establishment, were sufficient to absorb all my attention; while Holmes, who loathed every form of society with his whole Bohemian soul, remained in our lodgings in Baker Street, buried among his old books, and alternating from week to week between cocaine and ambition, the drowsiness of the drug, and the fierce energy of his own keen nature. He was still, as ever, deeply attracted by the study of crime, and occupied his immense faculties and extraordinary powers of observation in following out those clues, and clearing up those mysteries, which had been abandoned as hopeless by the official police. From time to time I heard some vague account of his doings: of his summons to Odessa in the case of the Trepoff murder, of his clearing up of the singular tragedy of the Atkinson brothers at Trincomalee, and finally of the mission which he had accomplished so delicately and successfully for the reigning family of Holland. Beyond these signs of his activity, however, which I merely shared with all the readers of the daily press, I knew little of my former friend and companion.

Design


Overview

One night—it was on the 20th of March, 1888—I was returning from a journey to a patient (for I had now returned to civil practice), when my way led me through Baker Street. As I passed the well-remembered door, which must always be associated in my mind with my wooing, and with the dark incidents of the Study in Scarlet, I was seized with a keen desire to see Holmes again, and to know how he was employing his extraordinary powers. His rooms were brilliantly lit, and, even as I looked up, I saw his tall spare figure pass twice in a dark silhouette against the blind. He was pacing the room swiftly, eagerly, with his head sunk upon his chest, and his hands clasped behind him. To me, who knew his every mood and habit, his attitude and manner told their own story. He was at work again. He had risen out of his drug- created dreams, and was hot upon the scent of some new problem. I rang the bell, and was shown up to the chamber which had formerly been in part my own.

Receptor and transduction pathway

His manner was not effusive. It seldom was; but he was glad, I think, to see me. With hardly a word spoken, but with a kindly eye, he waved me to an armchair, threw across his case of cigars, and indicated a spirit case and a gasogene in the corner. Then he stood before the fire, and looked me over in his singular introspective fashion.

Signal processing: Inverter

‘Wedlock suits you,’ he remarked. ‘I think, Watson, that you have put on seven and a half pounds since I saw you.’ ‘Seven,’ I answered. ‘Indeed, I should have thought a little more. Just a trifle more, I fancy, Watson. And in practice again, I observe. You did not tell me that you intended to go into harness.’ ‘Then, how do you know?’

Output: Fluorescent color protein

‘I see it, I deduce it. How do I know that you have been getting yourself very wet lately, and that you have a most clumsy and careless servant girl?’ ‘My dear Holmes,’ said I, ‘this is too much. You would certainly have been burned had you lived a few centuries ago. It is true that I had a country walk on Thursday and came home in a dreadful mess; but, as I have changed my clothes, I can’t imagine how you deduce it. As to Mary Jane, she is incorrigible, and my wife has given her notice; but there again I fail to see how you work it out.’ He chuckled to himself and rubbed his long nervous hands together.

Results

‘It is simplicity itself,’ said he; ‘my eyes tell me that on the inside of your left shoe, just where the firelight strikes it, the leather is scored by six almost parallel cuts. Obviously they have been caused by someone who has very carelessly scraped round the edges of the sole in order to remove crusted mud from it. Hence, you see, my double deduction that you had been out in vile weather, and that you had a particularly malignant boot-slitting specimen of the London slavey. As to your practice, if a gentleman walks into my rooms smelling of iodoform, with a black mark of nitrate of silver upon his right fore-finger, and a bulge on the side of his top hat to show where he has secreted his stethoscope, I must be dull indeed if I do not pronounce him to be an active member of the medical profession.’

References

1. Chakraborty, S., Alam, M., Scobie, H. M., & Sack, D. A. (2013). Adaptation of a simple dipstick test for detection of Vibrio cholerae O1 and O139 in environmental water. Frontiers in microbiology, 4.



2. Duan, F., & March, J. C. (2010). Engineered bacterial communication prevents Vibrio cholerae virulence in an infant mouse model. Proceedings of the National Academy of Sciences, 107(25), 11260-11264.



3. Public Health Vigilance Group. (2011) Plan de contingencia del sector salud para la prevención y control de cólera en Colombia [Health sector contingency plan for the prevention and control of cholera in Colombia]. Ministry of Social Protection, Republic of Colombia. Accessed 8 june 2014 from



4. Wang, D., Xu, X., Deng, X., Chen, C., Li, B., Tan, H., ... & Kan, B. (2010). Detection of Vibrio cholerae O1 and O139 in environmental water samples by an immunofluorescent-aggregation assay. Applied and environmental microbiology, 76(16), 5520-5525.



5. World Health Organization. (2014) Cholera: Fact sheet No. 107. Media Center Fact Sheets. Retrieved 8 june 2014 from .