Molecular Cloaks of Invisibility

Posted on by
Reply

One of the subjects in biology that I find really interesting is how the immune system and micro-organisms interact with one another, and how their respective defense and attack moves have evolved relative to one another. This was the first essay I wrote on the subject, and it’s about how some bacteria can hide from the host immune system by wearing an invisibility cloak.

This essay was originally written for the Biochemical Society Science Communication competition, April 2011. (It was not short-listed.) This is a revised version.

In these modern times one cannot escape knowing that our bodies are colonised by many millions of micro-organisms, those that the media tells us are the ‘good bacteria’. These organisms inhabit our skins, noses, mouths, stomachs, intestines and genitalia, typically the ‘mucosal surfaces’; those areas open to the outside. Such regions are constantly patrolled by guards – the immune cells: macrophages and dendritic cells. Cells making up the mucosal surfaces, the epithelial cells, also sense their boundaries, poised to send out danger signals to the patrolling guards if a breach in their membrane is sensed. The micro-organisms are allowed to live quite happily in these patrolled regions of our bodies, provided they stick to the rules and don’t become too rowdy.

Disease can be considered to be a perturbation in the ‘normal’ or natural environment of the body, and is generally associated with pain, dysfunction and pathology – in terms of infectious disease, this is damage caused by either the invading micro-organism or by the immune system as collateral damage. The discovery of an intruder causes alarm bells to be raised, which mobilises immune cells; those specialised for fighting are activated to do so, others are responsible for co-ordinating the fight. The co-ordinators ensure the right fighters are present by sending out chemokines, and ensuring the environment is locally inflammed to give the fighters an advantage. Molecules called cytokines are sent out to increase blood flow to the area, enabling increased access for the fighters and local swelling to enlarge the fighting arena. (This gives a redness to the skin and increases the heat). Already one can imagine a boiling pot of noise and whistle-blowing; rarely would an intruder want to trigger the alarms to put in motion this sequence of events. Chances are they will be out-numbered in battle and be overcome before being able to achieve very much at all.

There are of course many advantages in penetrating inside the body, where food and shelter is plentiful. Far better than a costly fight is to achieve invasion without being noticed at all. It may be important to note at this point that although the relationship between the immune system defending a human being from an invading micro-organism lends itself very nicely to the analogy of guards defending a castle from attack, a key difference (other than scale) is the concept of ‘seeing’. A cloak of invisibility, or perhaps the ability of an invader to hide in the shadows, enables the person in question to become part of the background as though invisible. In some societies, such as the ninjas in feudal Japan, this ability to move around undetected was considered to be an essential skill – undetected here, within the spectrum of visible light. If one viewed the same ninja using an infra-red camera (forgive the anachronism), the stealthy person becomes a beacon of yellow and red. By contrast, the sentinels of the immune system gather information about their surroundings in terms of chemical or protein shape. The ‘antigen-presenting cells’ (the guards: macrophages and dendritic cells) are constantly sampling the environment, gobbling up proteins and other debris in their surroundings, processing it and presenting snippets on their surface in special carrier molecules. These cells are unaware of the difference between host/human (self) and foreign/microbe (non-self), and so present the processed material to cells that can tell the difference, in this case T lymphocytes (T cells). T cells have a receptor on their surface which has been expertly trained not to recognise self molecules, thereby detecting foreign peptides, and responding by instructing other immune cells to sharpen their swords. A trained ninja, having obtained passwords or other means to enter a castle, would avoid arousing suspicion once inside by hiding in the shadows, walking silently and perhaps obtaining a disguise so if seen would not look unusual, or at least rapidly change identity so the character the guards have been alerted to look for can no longer be found.

Invading pathogens use similar approaches to hide from the immune system and obtain a ‘cloak of invisibility’. Both methods involve making a cloak of host proteins; by one method, the micro-organism gathers actual host proteins to cover its surface, and in the other the invader synthesises its own cloak components to look like host proteins, in a process known as ‘molecular mimicry’. The cloak has several advantages: as well as allowing the invader to blend into its surroundings, it also acts as a shield or armour to protect the micro-organism’s fragile membrane beneath from penetrating weapons should the need arise.

Schistosomes are trematode worms whose adult forms live in the blood of vertebrates. It has been reported that adult schistosomes may survive for years or even decades in the blood, gaining all the nutrients that they require to live. It is only when the worms mate and lay eggs that the immune system is alerted to their presence. The eggs are released into the environment in the human faeces, and if the eggs find freshwater and their intermediate host, freshwater snails, they can develop into their larval form (cercariae), able to infect humans. From freshwater, the free-living cercariae are able to recognise humans and other mammals, and will penetrate through the skin, into the body. Within hours the cercariae lose their outer membrane to avoid recognition by the immune system, and rapidly gather host molecules to cover themselves, perhaps like stealing clothes from a washing line in the castle grounds to facilitate a disguise as a servant. The schistosome is now able to exist unhindered in the blood before mating and laying eggs, thus beginning the schistosome lifecycle once more.

Aside from stealing a disguise once inside the castle walls, numerous micro-organisms have evolved coat components that look like host proteins – like a true ninja they have done their homework in advance and brought with them an appropriate disguise. For example, Neisseria meningitidis (a causative agent of meningitis) expresses proteins comparable to those expressed in the embryonic brain, Mycoplasma pneumoniae (causing a form of pneumonia) expresses proteins similar to those on the surface of red blood cells, and Trypanosoma cruzi (American trypanosomiasis, Chagas disease), has a coat of proteins resembling those of the heart and nerves.

An alternative approach to wearing a single disguise is to frequently change appearance to confuse the immune system. If a member of the castle staff by chance comes across a ninja prowling the corridors, he or she would then raise the alarm and give a description of the intruder to the attending guards. The ninja, having succeeded in getting away from this civilian, then changes his identity so that he is no longer looks like the wanted person. In time the search party would give up looking, allowing the ninja to proceed unhindered until he is discovered once more.

In a similar way many bacteria, viruses and protozoa have developed methods to change their appearance to avoid capture, a mechanism termed ‘antigenic variation’. This may be achieved either by a high rate of mutation of a single protein (‘antigenic drift’), such that the form of the capsule protein changes sufficiently for it to no longer be recognised as belonging to the invader. This is one strategy employed by the human immunodeficiency virus (HIV), explaining why it is so difficult for the immune system to control infection caused by this virus. Micro-organisms also achieve this feat by ‘gene switching’, whereby the micro-organism actually changes the whole protein expressed on its surface. The best example of this is seen for Trypanosoma brucei (the causative agent of African trypanosomiasis, sleeping sickness). These protozoa carry genes for more than one thousand distinct surface molecules called variant-specific glycoproteins, which cover the entire surface of the trypanosome. The trypanosome can switch from the use of one coat protein to another, enabling it to persist whilst the immune system is constantly trying locate an invader that appears to have vanished. This results in a sequence of unrelated infections – occasions upon which the immune system is poised to fight the intruder – at approximately one-week intervals.

The relationship between the human body and invading micro-organisms is a continual battle between the defending castle guards and the intruder. Although the immune system has developed many ways to protect the body from invasion, micro-organisms constantly surprise us with counter mechanisms; development of a molecular cloak of invisibility is just one way that micro-organisms are able to out-smart the detection systems in place.

You can’t eat a scientific experiment

Posted on by
Reply

I discovered baking recently. It began with Journal Club. At UCL we didn’t have a group big enough to warrant organised lab meetings, let alone Journal Club, but I recently carried out some research at the University of Bristol, and with a few groups with common interests combined, there was enough people to each present a paper once a week for a whole term. Also new to me was the concept that the person doing the presenting brought cake. Journal Club was scheduled for 9.15 am, a time unknown to academics I had worked with at UCL, but there was cake! The split of presenters buying vs making cakes was approximately 50:50 and, never one to shy away from a creative challenge, I began planning my cake when my turn for Journal Club appeared on the horizon.

One morning in the cell culture room I was avidly talking about the cake I planned to make, and a woman confided in me that you can always tell the quality of a Journal Club by the quality of the cake: if the cake’s good, it’s to make up for a poor paper. Alternatively, as in my case, the cake was good because I’d put more effort into planning it than I had preparing my Powerpoint slides (a lemon drizzle cake recipe by Hugh F-W, modified to include blueberries and poppy seeds, courtesy of my brother-in-law) – don’t get me wrong, the paper was good, but the cake was really good. The cake, or perhaps a combination of the cake and the paper, secured me a sought-after job interview, but that’s another story.

I came to cooking itself (in life) relatively late. A neurotic mother who seemed to permanently occupy the kitchen, and scream and slam the door when anyone came near, will do that to a kid. On rare occasions I might be allowed to chop carrots, or peel potatoes, but invariably I was told I was too slow and would be sent away to lay the table. Consequently, my own experiences in cooking for other people frequently ended in tears, with my husband having to peel me off of the floor and salvage something edible from what I had started.

A few years ago, my husband began to spend one, and then two, evenings a week at the local indoor climbing wall, rock climbing. For the first few weeks I would starve myself, or perhaps try to survive on various things-on-toast (as I must have done for 3 yrs at Art School), waiting for him to come home. I even followed him climbing for a few months, until my PhD became so intense that I could barely make it out of the lab in time. Eventually I realised that the next best thing I could do would be to treat cooking like a scientific experiment: lots of planning in advance, stringently follow recipes until I was clear in my mind what each component did and its limits in terms of concentration, conditions for cooking (temperature, time, distance from heat source), and so on. I ensured that I’d had something small to eat before I begun so I wouldn’t get too flaky, and allowed myself as much time as possible to complete cooking the meal. When I carry out an experiment for the first time I like to deduce where the exit points are, as it were, at what point can I pause or freeze the whole experiment and go home, go to the toilet, have coffee, etc, and I found one mechanism for coping with cooking was to treat a recipe the same way. As with my scientific experiments, a lot came from experience, how much pasta is too much, how much chopping can you actually get done whilst sauteing an onion, and so on.

Having learnt cooking backwards, as it were, there are some parts of recipes I find utterly baffling. At the weekend I made a carrot cake and some shortbread, and was met by the following lines at the beginning of, and part-way down, the recipes: “Grease a 23 cm springform cake tin …” and “Line a 15 cm cake or tart tin with baking parchment.” For a while I pondered a single dimension of cake. Could they mean the longest tin measurement? The depth of the tin? The diameter of a round tin? The diagonal measurement across the top of a square or rectangle tin, like for a TV? Perhaps people miss off the ^2 or ^3 for cm-squared or cubed? In the end I looked up the meaning of ‘springform cake tin’, and after finding it to be a tin with a removable base, I used the only one of those I have. Incidentally the one I have has a diameter of 20 cm and a height of 9 cm, which seemed to work just fine – if this was a scientific experiment, that would be the kind of error that would cause my experiment to fail and have me tearing my hair out for weeks, with no clear logic. For the shortbread I used a flat baking tray, 23.5 x 33.5 cm. This was less successful because the shortbread burnt. Alternatively it may have burnt because I left it in the oven too long. I will need to collect some more n numbers before I can come to a firm conclusion on that one.

Systems Biology and Signal Transduction

Posted on by
Reply

I’ve spent much of this week at the University of Nottingham, meeting other scientists and learning about Mathematical Modelling. I feel like I asked, “So what do you do and where do you come from?” a hundred times.

My biological research is concerned with intracellular signal transduction. Also termed cell signalling, this process describes the way that a single cell receives a signal from the extracellular space, perhaps in the form of a hormone or growth factor, and communicates it to the cell nucleus to effect a change in gene transcription, or other appropriate response. Traditionally cell signalling has been investigated using molecular biology to investigate protein amino acid sequence and structure (gene over-expression, silencing and mutagenesis), and using biochemistry to look at protein-protein interactions and enzyme or protein function. Cell biology then contextualises this information, using microscopy to determine the localisation of the protein of interest within a particular cell type. Over many many man hours and large sums of money, this knowledge on individual protein signalling modules can be built up into larger signalling networks. Eventually clues as to the molecular basis of diseases are unravelled, potential drug targets may be identified and the pharmaceutical industry begins to get excited.

In a time in which science funding is scarce (to put it mildly), this activity of painstakingly characterising a single protein and its immediate contacts can seem incredibly futile. For the last three years I’ve been working on a previously uncharacterised lipid transfer protein. After all the late nights and weekends in the lab, I can tell you which phospholipids it likes to bind and two proteins it interacts with. I have little clue as to what the protein actually does or what the interactions mean. Despite this, my progress in three years is considered to be good.

Alongside researchers like myself, toiling away on the mysteries of a single gene, others have used high throughput approaches to produce large datasets on particular aspects of a cell or tissue. A good example is a database of phosphorylations, post-translational protein modifications used to regulate protein function. Such databases can tell you exactly which residue of a protein is modified under particular conditions. It won’t tell you who’s doing the modifying or what activity it’s regulating, but it can tell you which residue to mutate to look at regulation of your single protein.

Enter the mathematician: mathematicians and computer scientists are increasingly finding a place for themselves in the world of biological research as bioinformaticians, mathematical biologists and systems biologists. I place these three terms in order of willingness to dirty their hands with actual biological experiments, with bioinformaticians being the least likely, and systems biologists much more likely to be an experimental biologist learning or collaborating closely with researchers doing mathematics. Earlier this year I attended a Systems Biology conference and encountered a group of Bioinformaticians I have worked with in the past, now re-branding themselves as Systems Biologists and moaning about how long experiments to confirm protein-protein interaction predictions were taking.

But this is good. Finally the field is realising the need to present a united front and use mathematics to begin to combine all the seemingly disparate pieces of information. Which brings me back to my week in Nottingham. I have attended many Systems Biology talks over the last few years and I have to be honest in saying that only one or maybe two have left me feeling excited about what the field can offer. Most usually have been talks by mathematicians who don’t appear to quite understand the signalling pathway they are working on, and are all too quick to show how pretty their differential equations are, quickly excluding the maths-shy biologists in the audience. At the Biochemical Society Signalling conference in Edinburgh in June this year, I finally heard a scientist say (paraphrased), “Using our experimental data as a starting point, we used mathematical modelling to bring together spatial and temporal data, which led us to discover two different pools of signalling molecules.” Finally someone has used maths to tell them something they didn’t already know.

So this is why I went to Nottingham, to a course entitled, ‘Mathematical Modelling for Biologists’. It’s going to take a while for my brain cells to recover from the assault, and even more time to process and fully understand what I have learnt. So I’ll have to let you know how I get on.