PHOTORHABDUS: A LUMINESCENT HUMAN PATHOGEN

1. INTRODUCTION: A BIT OF SCIENCE FICTION," PHOTL++", A BACTERIA MAKING EYES GLOW AND THEN ROT...!

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In "We Share", the novel on bacteria I am writing, the cave-living colony of bacteria which I call a bactorg will feel threatened by changes in its environment. To defend itself, it will launch a series of attacks on humans and animals outside the cave.

This will be seen initially as a bioterrorist attack. Soon, considering the variety of viruses and bacteria used and their complete strangeness, the scientists in the novel will understand that there is more at work than just "plain", human-invented bioterrorism... Indeed, they will be confronted with attacks devised by an organism, the bactorg, which has acquired, over its millions of years, a total mastery of cellular bioengineering at the evolutionary time scale.

It has built all sorts of strange bacterial and viral mutants and has enslaved many insects and higher animals. It is a frightful enemy. However, it is a bit naïve too, It does not really know the world outside the cave and does not really understand what we are or what are the constraints of massive terrestrial and airborne bioterrorism agents dissemination.

To build my directory of potential bactorg weapons, I have thus, at this stage, to find in the literature on "bacterial emerging pathogens", "viruses" and "bacterial curiosa", a set of dramatic infections using insects and animal vectors, bacterial and viral pathogens. I need my pathogens to induce nightmarish (yet plausible) illnesses. It is also mandatory that they use advanced and original signalling and logical processing methods, they need to be intelligent weapons.


I have thus to select carefully my pathogens for scientific interest and drama potential.

In this post, I'll present one of my favourites "Photarhabdus luminescent". In the novel, I modify it of course to amplify its effects and I call it PhotL++.

The real PhotL it is a bacteria living in nematodes (small worms) which infect the guts of many insects. The nematodes release the bacteria into the insect blood circulation and then the bacteria kill the insect. From my point of view, the real PhotL it has three interesting characteristics:

• It is the only terrestrial bacteria which is luminescent... the question is why ??? This will be a big question in "WE SHARE"
  
• Until recently, it was known to infect only insects but it is now emerging as a human pathogen.
  
• It secretes many powerful toxins and also antibiotics

Just extrapolating a little bit, I will thus invent "PhotL++", a nicely dramatic mutant.

PhotL++ causes awful abscesses in humans and make them glow in the dark. It also attacks the eyes creating strong conjunctivitis and keratitis (inflammations of the conjunctiva -the outermost layer of the eye and the inner surface of the eyelids- and the cornea). The inflammated eyes present first an abundant, opaque purulent discharge and tears. Then they become red and glowing in the dark (very bright green light). Finally, they rot and the brain is attacked; the infected animal or person dies. Is that sufficiently awful? I guess so. As you will see, temporal lobe epilepsy is high drama stuff.

I will add one more twist: the emission of photoluminescence by PhotL++ will be influenced by electromagnetic radiations which can make its intensity pulsate

(I have a literature reference proposing this, see later).

Moreover, a PhotL colony will use its light signal to coordinate its actions and those of its symbiont, the nematode.

But enough on science fiction. When I had my initial nightmare about luminous bacteria, I was quite excited, here was an ideal weapon... Imagine, your eyes glowing in the dark, pulsating and then rotting...

Then I went hunting for it in the real world (I mean on the WEB) and as usual, I was flabbergasted... Reality is almost always better than fiction... My brainchild was almost existing. The real PhotL is known as Photorhabdus luminescent. In the following sections, I will just present the facts about it... just plain facts.


2. PHOTORHABDUS LUMINESCENT, THE FACTS

Meet Nick Waterfield, from Bath University, a microbiologist studying phosphorhabdus and many other microbes (sorry for the distorsion of the photo, for some reason, I can't get it right).

One of its many ideas is that insects are a neglected field of study when it comes to microbiology. They are an enormous reservoir, harboring many potentially harmful species. Their immune systems is, strangely enough (at least to me), quite close to ours. So the bacteria which have adapted to them have just small evolutionary steps to take to get their metaphorical teeth into us. So Nick's idea is that we should study more closely the bacteria infecting insects and that's what he does.
What follows is closely inspired from a text on his website on one of his pet subject, Photorhabdus (PhotL). It is the only known terrestrial bioluminescent bacterium. It is a pathogen of insects. It lives in the gut of a nematode. An ideal candidate for the "WE SHARE" casting.

Click here to have a link to Nick's site.

2.1 THE LIFE OF PHOTL: Infective young nematodes carrying PhotL search in the soil for their insect prey until they encounter one (often a larva). Then, they scratch their way into the insect's blood circulation and "vomit" up Photorhabdus into the blood where it secretes toxins and virulence factors that rapidly kill the insect.

Studies on the insecticidal-complex produced by PhotL have revealed that several extracellular macromolecules such as proteases, lipases and broad-spectrum antibiotics confer its insecticidal ability which is wide ranged (PhotL is proposed as a pesticide but that raises important security concerns. Its killing ability is wide ranging and it might very well kill useful insects). Imagine a few mutations and we have a fearful human pathogen.

The bacteria replicate rapidly and convert the insect tissues into more bacteria that serve as a food source for the nematodes which may then reproduce. It is around the time of insect death (when the food source will soon be exhausted... and signalling of that fact needed) that the bioluminescence of the insect corpse due to the bacteria can be seen. This will be important. Hereafter a couple of photo from Nick's site: on the left, two insect larvas glowing a little bit before being destroyed by the bacteria. On the left, a larva exploding and ejecting its full load of nematodes. (courtesy of Dr. Nick Waterfield, Bath University)


A load of bacteria in an insect, just below the collagen outside sheat.








2.2 RELATION OF PHOTL AND YERSINIA PESTIS (the black plague microbe): More stuff for nightmares, lateral transfer of genetic material between Photorhabdus and Yersinia has been demonstrated and is probably a result from their common association with insects as bacterial pathogens .

The association with yersinia pestis opens up interesting avenues for my novel. A few centuries ago (in 1720), there was a famous black plague epidemics in Provence, just where I need it. Yersinia and PhotL were there and were associated. Could they have been incorporated as part of the multispecies, underground Provencal bactorg community at that time? Could they then have been kept dormant until now for two centuries and then suddenly reactivated and released outside the cave as an answer to some quorum sensing set of signals from the outside eenvironment having suddenly reached the bactorg after the earthquake?

Remark: However note that the black plague has recently been the subject of alternative theories attributing its origin to other causes like anthrax or a virus like ebola…?

2.3 BIOLUMINESCENCE IN PHOTL:Bioluminescence is the production of visible light by a chemical reaction in a living organism (see the photo above). Bioluminescence is rarely reported in clinical bacteriology laboratories because bacterial bioluminescence is seen primarily in marine species. Some fishes indeed have an organ in which they grow a large colony of resident luminescent bacteria which provide them with a powerful light useful to attract preys or mates. But what could be the usefulness of light in a bacterium living in the gut of a worm inside an insect? Photorhabdus are the only terrestrial bacteria known to exhibit this property.A useful signalling system?

A culture of PhotL growing and swarming on an agar plate. It emits a faint light visible in the dark. Do you remember the fractal shapes of bacterial growth we saw when we discussed Eshel Ben Jacob's work? I think that this might be another example of it. Do these cultures grow in difficult conditions? Can we experiment on them by modulating their growth conditions like Eshel did? Will we observe nice fractals?

WHY DO PHOTL EMIT LIGHT? Energetically speaking, bioluminescence is a costly process, difficult to justify on an evolutionary basis if it has no clear role. Current theories include some unknown biochemical role or even that it is a lure to tempt fresh insect victims into range. I do not very much believe in them.

When the insect resources have been exhausted, the bacteria provide the nematode with an unknown "food signal" which switches them into a developmental state known as an infective juvenile. At this point they re-package the bacteria before bursting from the insect corpse in search of fresh victims. Could light play a role? A remark: Worms with enough food cease to emit light.


2.4 PHOTORHABDUS, AN EMERGING HUMAN PATHOGEN

Photorhabdus has never been isolated as free living in the environment. However, recent cases of human infections due quite plausibly to Photorhabdus have been reported in the US, Australia and Nepal. Many other cases might be misdiagnosed due to the failure of laboratories to recognise this unexpected pathogen.

Let us describe a clinical case (reported by Dr. Gerrard, Gold Coast Hospital, Queensland, Australia).

a 29-year-old woman with an intensely painful and swollen right foot (3). Two days before presentation, she had cleared debris and weeds from her country property while barefoot. She was started on oral amoxicillin-clavulanic acid in the emergency department, but by the next day her foot had become even more swollen, erythematous, and painful. She was admitted to the hospital and started on intravenous antistaphylococcal (flucloxacillin) antibiotics. Abscess before and after treatment with antibiotics... (courtesy of Dr. Gerrard)

Despite treatment, a local abscess formed. This was incised, and pus was sent to the laboratory for culture. Three days later, a gram-negative rod was isolated in pure culture. The Vitek GNI card identified the organism as Flavobacterium sp. It took them a lot of ingenuity to identify Phot L as the culprit, Thanks to them...

Another case (Dr Alice Weisfeld, Microbiology Specialists Incorporated, Houston, Texas )
A 54-year-old male presented to the emergency department of a local Houston hospital during July 2003. He was a ranch hand who believed that he was bitten by a spider on his left
breast. He presented with multiple carbuncles on his left chest wall and multiple pustular nodular lesions over his extremities. The patient, who has a family history of diabetes, had a blood sugar level of 400 on admission. His temperature was 101°F, his blood pressure was 135/70, his respiratory rate was 20, and his pulse was 60. Culture of the left-breast abscess showed moderate numbers of methicillin-resistant Staphylococcus aureus and an unremarkable gram-negative rod identified by a MicroScan Neg Urine Combo Panel Type 34 on the MicroScan WalkAway (Dade Behring, Inc., MicroScan Division, West Sacramento, CA) as Pseudomonas oryzihabitans. An identical gram-negative rod was isolated from four of four blood culture bottles from two separate venipunctures. However, it was identified on the same system as Providencia rustigianii.
Both isolates were sent to a local reference laboratory (Microbiology Specialists Incorporated). Each isolate produced two colony types, which exhibited annular hemolysis and swarming on blood agar (Fig. 1 and 2). Annular hemolysis is unusual in that there is no hemolysis immediately around the colony but there is a thin line (about 2 mm wide) of hemolysis about 12 mm from the edge of the colony. Each isolate was oxidase negative, catalase positive, and motile, with a nondiffusible yellow to dirty-brown pigment. Neither isolate reduced nitrate to nitrite, but both fermented glucose (Table 1). The isolate was finally identified as Photorhabdus asymbiotica (formerly Xenorhabdus luminescens) on the basis of weak bioluminescence when tryptic soy agar slants grown at either 25°C or 35°C were observed in the dark.

The organism identifications were subsequently confirmed by the Centers for Disease Control and Prevention (Atlanta, US) using conventional biochemicals (1) and a number of other rapid identification systems.

Source of infection: The source of human infection is not yet known, although an invertebrate vector(why not a spider bite, which would be nice for we SHARE in which spiders play a big role) is suspected. Indeed, cases occur indeed in warm wet months, usually after rain storms, and the victims are often people working in the outdoors. Moreover, the abscesses appear on feet and legs.

REmark that with th eclimate change in Some parts of Provence, the climate there is becoming dryer in summer but winters are warmer and wetter, ideal for PhotL...?

CONCLUSION: PHotL associated with severe soft tissue and systemic infections, and is now considered as “emerging human pathogen”.

ANGEL GLOW: Notice that some people believe that PhotL was the cause of a phenomenon called "angel glow", soldiers wounds glowing in the dark which were observed in people lying on the ground for days during the war of independence in the US. The soldiers with glowing wounds were recovering better, hence the name.
The hypothesis is that PhotL was infecting them by contact with the soil (either due to nematodes or free living bacteria). They were killing other bacteria with their antibiotics, hence the better survival probability. At that time, they were not pathogenic for humans... things change.

All together, I have an ideal scheme for my glowing wounds, I have just to suppose that PhotL is now pathogenic for humans, that it attacks not only the legs but also the eyes and that in its final stage, it infects the brain and kill people... a piece of cake.

A last twist I promised you: Why does the light emission from PHOTL++ pulsate?

Glowing rotting eyes are nice but in addition, in "WE SHARE", the light intensity is always changing.

Admittedly, PhotL does not do that. Why does PHOTL++ do it? The real reason is because it is nice. The second reason is that it allows PhotL to modulate its signal and make it more complex... Advanced signalling... more sophisticated language!

How does it do it? Consider the following reference:

Electromagnetic field effect on luminescent bacteria Berzhanskaya and al. IEEE transactions on Magnetics Vol 31, Issue 6, Nov. 1996 - pp. 4274-4275
Abstract: The effects of electromagnetic fields with frequencies varying from 36 to 55GHZ on the bioluminescent activity of bacteria were investigated. EMFs resulted in a decrease of bioluminescence which depended on frequency. The time of adaptation of cells to the EMF was longer than the intrinsic temporal constants of the bioluminescent signals. The effect was non thermal. Magnetic storms resulted in an increase of bioluminescence.

That's a good start. I'll leave you on this.

A NOTE ON THE USE OF PhotL as a biopesticide (see before), cf the following paper:

Biosafety concerns on the use of Photorhabdus luminescens as biopesticide: experimental evidence of mortality in egg parasitoid Trichogramma spp. Sharad Mohan1,* and Naved Sabir - CURRENT SCIENCE, VOL. 89, NO. 7, 10 OCTOBER 2005

Photorhabdus luminescens exhibit biopesticidal potential against important pests, independent of its host nematode. Indeed, it secretes powerful toxins and large spectrum antibiotics. The question is: can it also attack useful non-targeted organisms? The authors have tested this. They tested the bio-ecological compatibility of PhotL in vitro, against the common biocontrol (and thus useful) agent Trichogramma living as parasites inside the eggs of the rice grain moth, Corcyra cephalonica. Most Corcyra egg-shells became flaccid and there was significant reduction of up to 84% in the emergence of Trichogramma adults. The nematode carrying the bacterium within its gut had no effect on the emergence. This result points to the bio-ecological hazards of indiscriminate use of P. luminescens as a biopesticide. Due to its wide host range, the use of P. luminescens in a pest management programme must be questionned until it is proven safe for non-target organisms

EXTRAPOLATION FOR "WE SHARE": I might decide that PhotL has been used as a pesticide in Provence. Unknown to us, PhotL has been transformed by the insects they invaded which were containing other bacteria transmitted to them by the bactorg (remember what I call enslaving).
They've become PhotL++ and they carry death with them.They are thus there in the soil in large quantities but do not attack humans. Then some signal (probably transmitted by a phage) from the bactorg reaches them and they become active...
PhotL++ uses light as a modulated signal to control it sexpansion. But its light generation mechanism is receptive to EMF influence. In the cave, this was making no harm, EM fields were too weak. But outside, they receive EM radiations from the NSA-like site in the legion camp. It disorganizes them completely and they can't control themselves anymore... a recipe for disaster.

That's it folks?. Have a good night.

BACTERIALLY SPEAKING: BONNIE BASSLER

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1. BONNIE BASSLER AND THE LANGUAGES OF BACTERIA

One of my problems when starting to think about bactorgs was to assess the plausibility of the science basis for that extrapolation. I wanted thus to look at what well respected, first class scientists were thinking about multicellular bacterial colonies and chemical signalling. Then I started reading the works of people like Hellingwerf, Kolter and Ben Jacob. Assessing their ideas the best I could and seeing where they were leading, I soon realized that here was a burgeoning yet important bud of science. The idea of communication and signalling in bacteria was rapidly becoming and is now a new paradigm.Today, you will meet another of these first class scientists studying "bacterial chat"...

Bonnie Bassler is a professor of microbiology in Princeton. She was the recipient of a Mac Arthur "Genius" award and is a member of the US National Academy of Sciences. She is thus a mainstream scientist and, from what I can see on the web, she is also a very energetic and kind person.

Her research is focused on disentangling the mechanisms of signalling and communication in bacteria. She started by looking at quorum sensing as classically defined and now proceeds to more advanced signalling (interspecies, with eukariots..). Clearly she goes a long way to reveal the mechanisms underlying the phospho-neural networks suggested by Hellingwerf. I have read as carefully as I can a few of her papers, She writes superbly. In this post, I will look in detail at one of the papers from her group (for more details, see the web page of Bonnie's lab in Princeton.

The paper I am referring to is by Stephan Schauder and Bonnie Bassler. It has been published in "Genes & Dev. 2001 15: 1468-1480". Download the PDF by clicking here.

Lets start with the title..... provocative but well supported by facts
Bacteria speaking.... a flavor of Bactorgs isn'it? Let's look at it more closely.

2) THE LANGUAGE OF BACTERIA
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Bonnie and Stephan discuss in detail many bacterial behaviors which lead them to believe that bacteria have sophisticated communication abilities. They also go at great lengths to explain the molecular and genetic mechanisms used by the bacteria to implement these communication capabilities.

The mechanisms they describe are very compatible with the ideas of Hellingwerf (see a previous post).. My goal in the current post is to see if we can look at the genetic regulations they describe in bacteria as analogs to neural networks susceptible to learn by evolving (i.e. in evolutionary time, not during the life of a bacterium).

However, Bonnie and Stephan say nothing about learning or adapting. More about that later when we will discuss a recent paper by Saeed Tavazoie and his associates. First let's look if we really have networks. This is the goal of the current post. Later we will see if these networks may adapt and learn.

I am not a cellular biologist nor a chemist. Thus I am not primarily interested in the chemical details of the various mechanisms nor in the exact nature of the various chemicals and genes involved. Moreover, even if I were, I would not understand these details. In what follows, I will just insist on the essentials: what are the behaviors and the general features of the mechanisms involved.

I have not tried to write a summary of Bassler and Schauder's paper. It is so well written that I would have made a abd job of it. Instead, I have collected some of their sentences in a series of excerpts. I have sometimes slightly modified them to suppress technical details and lists of references. I also changed a few words. I believe that I have not destroyed the meaning they intended to convey. I refer you to the original paper for further details.

You will find my modified excerpts in a sequence of blue panels hereafter. I link these panels by a few lines of text to tell you what I infer from them. I have also redrawn and slightly modified their figures. I believe that my panels and figures give to non specialists like myself a nice view of the current state of the art on bactorgs internal mechanisms. Try to imagine what we will know in ten years.

An introduction to quorum sensing:

Bonnie and Stephan start by summarizing what is quorum sensing:

THE LESSONS FOR WE SHARE: coordinated control of genetic expression in a multicellular community, control of many global behaviors, intra and interspecies communication, communication with eukaryotic cells, fight of other species against quorum sensing bacteria. All the basics I need for my Bactorgs are there.

Then Bonnie and Stephan give us a view of the early stages of the research on quorum sensing:


Thus, the evolutionary, functional importance of quorum sensing in V. Fischeri is clearly stated: to avoid the metabolical cost of producing light when it would be ineffective and only produce light it when it brings to the bacteria the clear advantage of protection in the host. It is also important to note that far from being limited to this species, quorum sensing is now known to be widely used by bacteria. It is clear from the beginning that if quorum sensing brings with it a large evolutionry advantage, it must have evolved in many bacterial species.

A network view of the basic mechanism of quorum sensing:

Here is a figure showing you the mechanism of quorum sensing in V fischeri.

LEGEND: The quorum sensing system of Gram negative bacteria. The LuxI protein makes the autoinducers (green pentagons) which then diffuse freely outside. Each bacterium doing the same, the concentration of external autoinducer is a measure of the size of the population(quorum). When the autoinducer concentration is high, it binds to a cognate receptor LuxR (cognate means having the same form and ad hoc characteristics to bind specifically to the molecule it receives). This is quorum sensing.
The complex auto inducer-Lux R then binds at target gene promoters and activate their effect (transcription) which has behavioral consequences.

The Lux-I Lux-R-gene expression pathway indicated here is just an example of the neural network-like pathways we discussed when we saw the work of Hellingwerf. If a bacterium has several quorum sensing pathways like the one above and if they share signals and communicate together, we have an Hellingwerf neural network analogue.

Quorum sensing in Gram positive bacteria

V fischeri is a Gram negative bacteria. As you know, Gram positive and negative bacteria have very different membrane properties (if you don't know this, look in Wikipedia). Hence the mechanism of quorum sensing in gram positive bacteria has to be a little bit different. However, it tells us very much the same story: signal, quorum, high density detection, gene activation. This confirms that quorum sensing gives an important evolutionary advantage to the bacteria using it. Indeed, it exists in almost all bacteria. Each species devised its own way to implement it (convergent evolution). Here is the mechanism in Gram positive bacteria.
Legend: A precursor peptide (the linked red pentagons) is produced by expressing a precursor locus on a gene. It is modified and an ATP-binding cassette (ABC) exporter secretes the end product peptide autoinducer (single red pentagons). It accumulates as a function of the size of the population. At high density (quorum sensing), the autoinducer is detected by a two component S-R system (acronym meaning signal –regulator or signal –response, take your pick).
As the name implies, this signal transduction system has two parts. A sensor protein (the little black bar S) recognizes and autophosphorylates (p) at a specific site (H). The phosphoryl group is transferred to a cognate response or regulator protein R which is then phosphorylated (D). The phosphorylated D binds to specific promoter genes (targets) to modulate the expression of the regulated genes.

Again, the similarity with Hellingwer's views are striking

Going further than the basic mechanisms: layered networks

Remember what Klaas Hellingwerf told us: in a single bacterium, several mechanisms are linked together to form a complex signal processing network, what he calls by analogy a phospho-neural network... Bassler and Schauder tell us very much the same story. Read the following excerpt:

They describe what is the beginning of a network: sequential steps, response to several signals (here from various species and even eukariots...), behavioral complexity. Bacteria can think in the same primitive sense that simple artificial neural network (Mc Culloch Pitts or PDP) can think (admittedly a rather limited definition of thinking but, as a starting point, it is not bad!). To read more about Mc Culloch and Pitts neuronal networks, click here, to know more about neural networks using Rumelhart's PDP approach, click here).

Remark that, like in Hellingwer's paper, thet do not say a lot about "crosstalk".

Speaking with prokariot and eukariot friends and foes: interspecies communication

One more step: it is nice to speak with your own kind but life is more complex than that. You need to dialog with ennemies and potential friends from other species (bacteria or eukariots). For instance, in a biofilm, many species of bacteria coexist. They cooperate or compete. They have to exchange all sort of signals like "I am a friend, I can give you this.." or "Beware, I can kill you.., look at this toxin". How do our bacteria achieve this?
Remark that they describe an exchange of signals at the community level or even among species. Moreover,their signals are what I called "tagged" a specific signal can only be seen by the bacteria having the proper receptors for it. It is all I required to build a "fluid neural network" or a "collective ant-like brain".

Here is a view of the mechanism, Bonnie and Stephan propose for V. harveyi. We will see the answer to the mystery question (see end of the blue panel) just afterwards.

Legend: The hybrid quorum sensing circuit of V. harveyi. .Elements characteristic of both Gram-negative and Gram-positive bacterial quorum sensing systems are combined.
An acyl-HSL autoinducer (AI-1, green pentagons) is produced by the activity of LuxLM. This is typical of Gram negative circuits. A second autoinducer (AI-2, red pentagons) is synthesized by the enzyme LuxS. AI-2 is proposed to be a furanone. Both autoinducers accumulate as a function of cell density. The sensor for AI-1 is LuxN, and two proteins, LuxP and LuxQ, function together to detect AI-2.
LuxN and LuxQ are regulator proteins that transduce information to a shared integrator protein called LuxU. LuxU sends the signal to the response regulator protein LuxO. The mechanism of signal transduction is a phosphorelay (denoted P). LuxO controls the transcription of a putative repressor protein (denoted X), and a transcriptional activator protein called LuxR is also required for expression of the luciferase structural operon (luxCDABE). The conserved phosphorylation sites on the two-component proteins are indicated as H (histidine) and D (aspartate).

This become more complex. I do not pretend to understand all of this but the message is clear: we see emerging a network associating the red and green messages. The node LuxU has all the connection characteristics of a two input logic processing node in a neural network. The exact nature of the computation done by that circuit is still a bit unclear.

Remember the pathways in Hellingwerf's paper. Some of them were associating several signals at some logical computing non linear nodes. Here they are.

Bonnie has thus found the perfect test system: V. harveyi. Why did this bacterium evolve such a complex network? How do other bacteria do? Here is what Bonnie says: A NOTE: Remark that, for "WE SHARE", another point should be developed: communication in biofilms. I will have to study a paper by Nadell and colleagues entitled "The evolution of quorum sensing in biofilms" (PLOS biology, January 2008, vol 6, Issue 1, p. 171 - 179). This is for another post.

A special case: communication with higher species

And finally, communication with higher species! Remember, bactorgs will infect humans and animals in order to defend themwelves against what they perceive as threats. However, the spectrum of infection will be wide, from lethal (no discussion between species) up to soft attacks, subtle influences on the brain (mainly the temporal lobe) and the reward/penalty system, lethal attacks, compromises and truces. This will need sophisticated two way communication between bacteria and higher species. Am I entitled to extrapolate in that direction?

Another reason for communications with the so-called higher species: I told you that, during their eons of evolution, bactorgs have enslaved many insects and small mammals just like the collective brains of ants and termites enslave some aphids. Bactorgs will use their slaves as messengers, weapons and spies in the outside world. Again, this will need a two way communication system between bacteria and the so-called higher species.

So, what does Bonnie tell us about communication with higher species?

First from higher species to bacteria:

And now from bacteria to their competitors (other bacteria) or to their hosts and preys (higher animals);Here are a few examples of bacterial strategies
What about eukariots
NOTE: I will have to write a post on toxin-antitoxin plasmid addiction systems (they are called "addiction modules", to see a paper on them, click here).

NOTE: One more points to look at: prisonners dilemma in bacteria (they have been documented in viruses...?) and more generally cheaters. I think that this might develop as an important theme in" WE SHARE".

Conclusion of the Schauder - Bassler paper

Really, I have all I need to say that Bactorgs are a valid hard sci fi extrapolation of what is currently known about bacterial multicellular systems. Considering that this kind of research is about ten years old, I feel entitled to extrapolate quite a bit. In WE SHARE, bactorgs will be alive, fit and kicking, thinking and speaking.

Here is the conclusion of Bonnie and Stephan's paper
Bonnie and one of her colleagues, Richard Losick, have written a more complete review of bacterial languages. It is mind boggling. I invite you to read it(it is in "Cell 125, April 21, 2006", click here to get it). I will certainly come back to it later, for the moment, the above excerpts should give you the essentials of what I think is needed to justify the bactorg idea. Here is a photo of the title of Bassler's and Losick review... You see, bacterial languages are with us to stay. Bactorgs are not unplausible. It is just a matter of knowing where I can place the limit.
A FEW MORE NOTES: I have now to make a list of all the extrapolations I envision for bactorgs in "WE SHARE". I have also to read more about Ben Jacob's work who studies isolated but wild cultures and put forward some highly speculative hypotheses about advanced communication and intelligence in bacteria. I have to make a synthesis of Hellingwerf, Bassler and Ben Jacob's work. What could be the language underlying Ben Jacob's organizations? Do we find fractal organizations in wild colonies and in biofilms? What is the true extent of the meanings conveyed by bacterial languages?

A NOTE ABOUT SIMULATING BACTERIAL COLONIES: Last but not least, at least from my own viewpoint as a researcher: over the last few years, I have developed a graphical modelling language for general kinetic systems at a population level (not at what is called an agent or individual-based level). I call my language "Kinetic Graphs or KG". I have implemented KG in a simulation package called 20 SIM which is a standard in electrical and mechanical engineering. I have adapted the 20-SIM graphical language which is called "bond graphs" to kinetic systems.
When, above, I said "generic" I was meaning that kinetic models are used in fields as diverse as chemistry, biology, ecology and even in resource modelling in management. My language, being generic, covers all these cases and I have developed demonstrators in each. I have taught KG at several universities (Technion Haifa, Ecole Polytechnique Fédérale de Lausanne, University of Lille and Kings College London).
I think that it is a very good language (but I am not neutral), forcing you to be accurate and rigorous while staying very intuitive and simple. Yet, as a generic language, it is not specifically optimised for genetic regulation although it may cover it. I think that, for circuits like those described above, it could be very nice and I intend to publish at some stage a few posts on it.

Just one more point on KG: They may, under some constraints, cover the case of networks which change their connections due to adaptation or learning. This is not easily done by other methods. Considering adaptive evolutionary learning in bacterial communities (Tavazoie, paper), we are led to networks like those described above but more complex and with adaptive connections. It could be a nice feature to have in modeling bacterial communication.

I am going to bed, I wish you a happy time.

Jack

HYPOGENIC CAVES IN PROVENCE: BIGOT

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1) BACTORGS HAVE TO LIVE SOMEWHERE
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In the last post, you learned about the hypogenic caves of Movile and Villa Luz which are home to enormous biofilms containing hundreds of species of exotic bacteria eating rocks and producing sulphuric acid. These caves contain also "out of this world" ecosystems feeding on these bacteria. With their spiders, worms, scorpions and many other, they form a nice set up for my bactorgs.

Now the next question is:
This post tells you all about the reasons underlying that choice.

2) PROVENCE, THE IDEAL LOCATION FOR "WE SHARE"
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My novel will describe events taking place in the part of Provence named "Alps of high Provence", near the towns of Apt and Forcalquier, a transition area between the provençal plain near Marseilles-Aix and the high Alps of the Mont Blanc.

I want to locate the novel there for personal reasons because this is my favorite area in the world, the one I know best, the one in which I have been caving for the last thirty years, the one in which people are so kind to me.

I want my reader to experience its lavender fields, its hills lined with mountain oaks, its quiet, three hundreds years old, small villages perched on top of the hills, its springs and fountains, its serene way of life, the warmth of the day and the coolness of the night when the crickets sing their song. Let's also not forget the cold "rosé" wine, the goat cheese and the olives...

2.1 A few photos of the Apt area

Just to introduce you to the area, you will find hereafter a few photos. To see more, do a Google image search on keywords like "Banon, Oppedette, Forcalquier, Montagne de Lure, Mont Ventoux, Dignes, Gap, Sisteron". Try a Google Earth 3D view. You'll be rewarded by peace, beauty and pleasure.

First a general map: on the map, the area we are discovering is centered in one square centimeter around the town of Apt.Let's see now a view of the nature there. For France, it is a quite unpopulated area but not a wild one,by far. It is a peaceful union of man and nature. You can see a lavender field on the left side, wheat fields, hills, oak forests where boars and deers are roaming. Human life is hard, simple and still far from the unbearable pressures of the consumption society (but perhaps, not for long anymore).

It is time to go underground. Let's do some caving. In this area, we know about two hundred caves, ten of them going to depths of about minus 600 to 700 meters. Local cavers discover new caves and kilometers of passages every year. These are predominantly vertical caves with series of huge pits (the longer one being more than 150 meters deep). Hereafter a photo I took of my son going down one of these pits. It was taken in the Aven ( cave in provençal) of Jean Bernard near Apt and Sault in the summer of 1995. It gives you a feel for what is caving there.

Now, what about "surface life"?

Here is an old village called Saignon, five milles from Apt (look at the map again). it was built in 1500 on top of a hill to protect its inhabitants from the religious wars of that time.

And a close view of the lavender field which you saw above in the general picture.

You can't feel them of course but when I see this picture, I experience the smell, the tiredness of the day spent in the caves, the excitement to get there, the hot sun, the sound of the crickets, the burning hope for a glass of white or rosé whine in the nearest village, I tell you... this is, life at its best!

Now, a medieval passage in a nearby town (Sisteron). By the way such a passage, between houses and covered by stones, is called an "Androne" in Provençal. Does it ring a bell (anything in common with my neuronal cultures)?
From the above pictures, you might get the feeling that life is tough and austere in these high lands,... far from it. Here are a few proofs: goat cheese (the locally famous Banon), wine (the world famous Luberon wines), fruits and little terraces where, in quiet evenings, you can just enjoy life at its best.

2.2 The Apt area, more than just a nice place

Its nice to locate my plot there but I told you before that I wanted my novel to be realistic, I want not only my science to be as exact as possible but also other aspects like geography, ecology, human life and economy. If I want the reader to discover and enjoy the true Provence, I cannot invent an artificial one well suited to my purposes. I have to make my plot to fit naturally in the real Provence.This is a tough order; it means that in an area of about one hundred square kilometers, I must have several very specific features:

° First, I need an area suitable for quite advanced caving.

From what I have told you, you already know that the Apt area fits the bill but let me give some more details.

Look at a map of Southern France. Near Avignon, between Forcalquier, the Montagne de Lure, the valley of the Jabron, the Ventoux mountain, and the towns of Sault and Apt lies an area called the "Pays de Giono" or in English, the "country of Giono" (Giono is one of the main French writers who placed almost all his novels in this area). It is a country of rude living , big skies and green hills. People are friendly but reserved and cautious. Their life has many joys but little comfort.

The city of Apt lies just at the border of the "Pays de Giono". The caving part of the "pays de Giono" has the geologic structure illustrated below. There is a limestone layer (see "massif calcaire karstifié" in the figure). It is 600 to 1000 meters deep. Through it, run many predominantly vertical caves (the black jagged lines). Under this limestone layer, there is a layer of molasse and marne in which water cannot penetrate.

The water from all the caves is thus collected naturally into a series of collector, underground rivers. You can see one of them in the figure. They flow at the boundary between the limestone and marne layers. Cavers have been able to penetrate many of these caves and they have reached a few collector rivers at depth from -600m to -700m. The names of the most impressive caves are the Caladaïre, Jean Nouveau, Autran, Le Souffleur d'Albion.

As you can see, on the right side of the figure, the layer of molasses forces the water to come up and in fact, all the rivers join in a single vertical resurgence which comes out at only one point, the world famous “Fontaine de Vaucluse”, made unforgettable by Petrarque's poems and one of the biggest perennial springs in the world. Many divers (human and robotic) have tried, (currently without success) to reach the bottom of the Fontaine hoping to visit the deepest horizontal parts.

In addition to these caves which have a normal speleogenesis from surface water, the area contains also several sulfur and geothermal springs and, probably, a few fossil hypogenic caves (in what is known as the gorges d’Oppedette (the Oppedette canyon) near the city of Apt and nearby in the cave of Daluy).

Note: a fossil hypogenic cave is a cave of hypogenic origin which, during its evolution has been traversed by an exogenic cave (carved by surface waters). After eons of isolation, the hypogenic cave has thus came in communication with the atmosphere. Oxygen has completely destroyed its hypogenic ecosystem but fossil remains of the wall carving by bacteria and sulphuric acid can still be seen. It is what we have in Provence.

Extrapolations for WE SHARE

Thus the Apt area has all I need to suppose that unknown to everybody, a truly hypogenic cave is developing somewhere in the limestone, at a depth of about -600 meters below the surface, traversed only by a small flow coming from the surface and another one coming from the volcanic depths. The small surface flow allowed some invertebrates and insects to crawl in the cave and a Movile-like ecology developed a million year ago. Its bacterial communities are at least a million year old. During that time, they evolved and became Bactorgs (see previous posts)

I will also suppose that contacts were established by the bactorgs with larger insects and mammals which swam or crawled through some side exits of the flow. Bactorgs will be able to influence the behavior of these larger animals and domesticate some of them. Finally, through the domestication of these insects and rodents, bactorgs will be able to control the release of viruses and well choosen bacteria for which their slaves act as reservoirs.

When the story begins, an earthquake has widened the cracks between the hypogenic cave and a normal cave. The Bactorg ecology is perturbed and the hypogenic ecosystem defends itself by launching bacterial and virus attacks on the outside world. Much of the events described in the beginning of the thriller are just due to this defense reaction. Of course humans will react and organize a caving expedition into the Bactorg domain.

° This, I need a caving area which can plausibly harbor an active hypogenic cave.

This is not a small point: after all, we know only about ten of them in the world. For weeks, I did not dare to check on that point but finally I did it. A Google search on "hypogenic caves and Provence" got me absolutely flabbergasted. Here they were...! Just where I needed them. Of course, they were not active or alive like Movile, I would have known about them. They were hidden, fossil caves; hypogenic bubbles in the karst opened to the surface many thousand years ago but still showing remains of their hypogenic stages. To read a paper in English about hypogenic caves in Provence, click here (paper by Audra, Bigot and Mocochain in "Speleogenesis and evolution of karst aquifers")

For the last twenty years, my absolutely favourite village in the world has been Oppedette. It has only fifty inhabitants and the nearest town, Apt, is half an hour away. For a densely populated country like France it is quite isolated. For twenty years, I have each year spent months in Oppedette, living, sharing and speaking with the village people. Three hundred meters from the village there is a nice gorge, not like the Verdon or the Grand Canyon of course but still..., very impressive and at a more human scale (200 meters deep, six kilometers long). I have spent hundredths of hours exploring it and abseiling down all its rocks and cliffs. Will I tell you one day about Max Fayet, a retired flutist and now the greatest expert on the Oppedette's gorges. At 80, Max is walking everyday more than seven miles in its nooks and crannies to rescue lost hikers?

Here is a view of the village (about thirty houses) at the entrance of the gorges. Sure, it is not the Verdon or the Grand Canyon, but try to go down and visit every part to find hidden caves and passages. It took me many months..

The village:

The gorge: it starts just thirty meters after the village and runs like that for five millesThere, smack in the middle of the gorges, it exists a natural excavation called the "Chaire à Prêcher"). Jean Yves Bigot, a local geologist, studied it closely and found many traces of hypogenesis. Right where I wanted them to be.

He published his findings on the web (click here to see a map of hydrothermal caves in France). I got in touch with him and he told me that sulfur springs were quite common in the area. He told me also that some geothermal springs were not far apart (in a village called Greoux)... The Area near Oppedette had thus everything I wanted. A few post before, I gave you the address of a site he has developed on hypogenic caves. Here is another one, be sure to look at it (Daluis, grotte du chat).

° One more thing and not a small one: For the novel, I need a large underground laboratory...

At some stage, my bactorgs (underground Movile-like bacterial biofilms) will have to meet andrones (real in vivo cultured neuronal networks) living in a high security laboratory. These two guys do thus live far apart. A plausible way for them to meet is in a large, underground laboratory, nearby thehypogenic cave, five hundred meters deep and where scientists are conducting almost secret experiments on andrones and on many other subjects (geomagnetism, zero magnetic field biology...).

You will not believe me but such a lab exists: five milles miles down the road from Oppedette. It is called the "Laboratoire souterrain à bas bruit", or in English, the "Low noise underground laboratory". Years ago, the French army had its main launching site for nuclear missiles right near Oppedette. They had something like thirty underground silos with a missile in each. All the silos were linked to an underground command post, at seven hundred meters below the surface of the hills, wiht kilometers of passages in which electric trains linked the many command and logistic rooms.

When the French dismantled their nuclear force, the underground headquarter was taken over by the CNRS (French center for Scientific research) and transformed into a large underground laboratory which provides one of the most noise free environment all over the earth (no vibrations, no sound, no electromagnetic perturbations). It is where my andrones will live and be infected by the bactorgs messengers living just outside in the caves.

Do a Google search on "LSBB "laboratoire souterrain à bas bruit - Rustrel"(click here to visit the site of the lab). Here are a couple of images from the site of the primary school at Rustrel who, astonishingly went in to visit... (see their site by clicking here)

First a photo of the entrance of the lab; from there a two miles long passage goes deep into the mountain. The deepest part is seven hundred meters below the top of the mountain. In the vicinity, there are no industries, no towns, no large roads, no electronic installations. Almost no noise of every kind. Hence the name.Now, a photo of the main gallery going down to the labs. You can see the small electric train transporting the researchers.

A third picture: down the gallery shown above, the train lead to several rooms isolated from the outside by an armored door, a concrete wall two meters thick and a wall of steel several centimeters thick. Remember, they were part of the command and control post for the nuclear force, built to stand a nuclear bomb. Now they are laboratories in which you are almost vibration, noise and radiation free and ... secret work can be done there. Here is where my andrones will live. Cross the wall of the lab and you have limestone cracks communicating directly with the caves of the area, the ones in which bactorgs live...Two more pictures from a not so distant past... the nuclear cold war. The missiles were placed underground also but near the surface and all around the control center within about a ten miles radius. Each missile was in a silo and the nuclear heads were regularly transported from silos to silos on specially built roads. Everybody could see them. Goats were just liking it.

First the top of a missile silo a bit scary isn' it. No problem, these silos have all been destroyed in 1999.

Then a picture showing a nuclear head lowered down in a silo where the missile is already awaiting for it. Can you believe that such photos can be found on the web?

And finally, the one I find really nightmarish, a nuclear head transported on an army truck going openly on a public road, between the lavender fields. You could see it and hear your heart missed a beat or two. This leads us far from goat cheese and Rosé wine.

° One more thing I need: a trigger event for a bactorg-driven epidemic.

First and foremost, I need an earthquake. Fine: Provence is one of the most seismic areas of France. They don't have big quakes but lot of small ones. That's OK for me. I prefer small ones. They go unnoticed by humans but may cause large changes in the underground. They will open new cracks and perturb the bactorgs without humans noticing it. A large quake would not fit my bill.

Here is the distribution of small seismic events in Provence (Richter scale below 4.5) over the last twenty years. The region we are interested in is below Sisteron (see the blue oval).

One consequence of the earthquake will be the opening of a crack between a normal cave and the hypogenic cave which, for a million year, has adjusted to a strong level of isolation. Oxygen will flood in. The atmosphere and equilibrium of the bactorgs will be changed.. They will feel attacked and thay will have to react.

Another consequence of the quake will be the availability of a new food source to the bactorgs. The earthquake will open another crack through which methane and CO2 will flow in enormous quantities. There will be an exponential growth of some parts of the bactorgs (methane and CO2 eaters). Again perturbation and reaction! Bactorgs will start a war upon the outside world to defend their peace and serenity. They will send many kinds of viruses and harmful bacteria, strange epidemics will develop. Who can blame them?

How can this enormous food income take place? A man made catastrophe obviously!

You will not believe me but it's all there. Sadly enough, Oppedette has all the potential I need for a first class drama. Look again at the pictures I showed you before: peace, serenity, calm and joy... Wrong, totally wrong: you already know that nuclear missiles were there... a recipe for catastrophe. Imagine an underground radioactive leak, thirty years ago, initiating a mutation wave in the bactorgs? Why not? Two such leaks occurred just last week in France (July 2008, Tricastin and Roman, not far from Provence).

More plausibly..., I have spoken with the people in the area and I asked them to show me where sulfurous springs existed. I put them on the map. They were delineating several paths. One of them led me to a village I loved, Saint Maime , where my mother in law lives and where I have spent my holidays for the last thirty years. What was this path pointing at. ... To a catastrophe waiting to happen. Here is a photo showing it.The main picture show an area not far from Oppedette, about ten miles down the road in the direction of Manosque. It is a nice valley in the Luberon and it shows very much the same scenery than those you saw before. But it is disrupted by large clearings. What are they? Not wheat or lavander fields but the outside signs of an important industrial underground activity.

This is a picture of the exploitation site of a company called GEOMETHANE. Twenty years ago, it was called GEOSEL. (SEL = SALT in French). They were injecting water in large, natural underground chambers filled wit salt. The water was dissolving the salt. Then the water was ejected under pressure and was transporting the salt outside. Obviously, after a while, the pockets of salt emptied. GEOSEL found a new use for the remaining large cavities: gas storage. Today, they store methane and they could store CO2 if needed. They just had to rename themselves from GEOSEL to GEOMETHANE.

Obviously it created a big stir in the nearby villages. Not everybody was happy to sit on millions of cubic meters of explosive methane transported from and to Marseilles by a pipe line. Obviously, there are strong security requirements but still, here is a catastrophe waiting to happen (what we, in Europe, call a SEVESO site, click here for informations about SEVESO sites).

Of course; For WE SHARE, I do not need an explosion destroying fifty square kilometers and seven villages. In my novel, I want to be much more subtle, at least in the initial phases of the catastrophe. I'll just imagine an earthquake opening a communication between these methane stores and the bactorgs cave near Rustrel along the line of sulfurous springs I have delineated. An enormous food intake for the bacteria, their explosive growth, their reactions...

The details of one of the storage pits are shown in the inset. In fact, they are much deeper than you might think and are located at depths from 90 to 1300 meters deep, just the right depths for my purposes. To give you the sheer size of the possible catastrophe, let me give you a few numbers taken from the GEOMETHANE site. Am I reading them correctly...300 M Ncubic meters. What the hell is this?
What can be the consequences of such an input of methane on the bactorgs... That's for you to ponder. Let me give you a nice little sentence from their official site...,

"These installations are located in sensitive areas of the "Parc Naturel Régional du Lubéron" and received special attention as regards environmental protection, in close co-operation with the Parc authorities and the local communities. " Nice to know

I might be wrong but to me, it is just a typical piece of marketing nonsense and human hubris. Look their site at GEOSTOCK GROUP.

So the area I love best in the world has all I need for my novel, the best and the worst!

° a geology suitable for hypogenic caves,
° an underground lab,
° earthquakes,
° industrial storage of bacterial food.

° And a final fact: I am not that original, in my plot, like in everyone these days, I need the military (however, I think I found a fresh angle on them). And I have to confess I like some of them, I myself spent five years working with the Belgian army where I had a lot of contact with the French Foreign Legion. I want a Legion battalion in the plot because they are partly belonging to the establishment (which I do not like very much) and partly independent of it (in many aspects of their professional life, they establish and follow their own rules).

In "WE SHARE", the legion will have a security department, in charge of supervising scientific battles against terrorism. They will then be charged by the authorities to conduct the struggle against the epidemics but will make many mistakes and learn from them. They will then cooperate with the civilian scientists who will explore the hypogenic cave.

Obviously, you already know what I am going to tell you. At about six miles from Oppedette, there is a big legion camp with an engineering battalion and a small NSA-like listening center. It is the 2nd Regiment Etranger du Génie (quartier Marechal Koenig). Its people are experts on mountain combat (and thus I may suppose that they are knowledgeable about caving). Close to the quartier Koenig, there is really a site brimming with antennas. They won't tell me what it is but I suppose it is their listening center. This is what I will suppose. I will have a bioterrorist study group residing in the Legion camp. They will be in charge of tackling the "WE SHAR outbreak. Here is the site of the Second Régiment Etranger de Génie

Hereafter, a photo of a legion platoon marching near the entrance of the Koenig camp in St Christol, right in the middle of the plateau d'Albion, eight miles from Oppedette. The security site brimming with antennas is about five hundred meters behind the camp. You can see two antennas on the right.

Bye Bye now, I am a bit tired.. This post is a bit on the longish side, it took me a whole day to write it but I just couldn't stop... There were so many things I wanted to tell you about this place.

By the way, I feel a bit guilty to bring catastrophes, even imaginary ones, to the Pays de Giono. I hope my novel will also convey its peacefulness and soft but wild beauty.

Jack