Wanted: Dead or Alive

It would be very useful for the immune system to be able to discriminate between live and dead bacteria.

Well, that's pretty obvious.

Immunologists have long known that live bacteria induce different, and better, adaptive immune responses than dead bacteria. Again, it may seem obvious, but is hard to reconcile with current thinking about how adaptive, or antigen-specific, immune responses develop. Robust adaptive immune responses need two things: the antigen that makes antigen-specific T and B cells expand, and inflammatory signals, which tell the immune system that something wrong or dangerous is around and that its okay to try and eliminate the sources of the antigens they recognize.

(This is not the whole story, but its a good starting point, and the whole point of this blog is to try and understand the point of immunology and not to get hung up on details.)

Anyway, seminal and beautiful work by many people, primarily Charles Janeway and Ruslan Medzhitov (you'll definitely hear more about him here, I really enjoy reading what he writes), found that those inflammatory signals could be triggered by specific components of microbes, called "patterns". In other words, when the immune system ( the innate immune system, have I mentioned how strange I find these categorizations? I digress) sees a molecule X, which is made by almost all bacteria of a certain kind, it responds because X is a pattern, characteristic of "bad" bacteria. So if you combine foreign antigens and pattern X, you should get nice robust responses to the antigens because you have both antigens and inflammation.

And you do get beautiful, strong responses to antigens this way. The only problem is that dead bacteria usually retain their patterns, like X. So there must be something else that sets live bacteria apart from their dead counterparts, something other than pattern X.

In a simple, elegant study published in Nature, Julie Blander's lab at Mount Sinai found a possible candidate-a pattern that is characteristic of bacterial life, a vita-PAMP they call it ( not my favorite term, but...). They show that ribonucleic acid, or RNA is rapidly lost from bacteria when they are killed, and that if you just add RNA back to dead bacteria, they become as good at inducing strong immune responses as live bacteria. Specifically, they found that messenger RNA (mRNA), so called because they carry the information coded by a gene in a message that is "translated" into a protein, is a vita-PAMP.

What is so strange, and so cool, about their findings is that they found that all bacteria had vita-PAMPs and the ability to induce certain immune responses. Not just pathogenic, or harmful bateria, but al bacteria, including the billions that live in our digestive tracts and at our mucosal surfaces, our commensal families. Why then do we not explode in a mass of inflammation and immune responses-after all we share body space with billions of bacteria? Is it because of strict specialization and compartmentalization: are the cells that recognize vita-PAMPs far away from our natural bacterial buddies, so that their detecting vita-PAMPs is a sign that bacteria are where they have no business being? Or do our immune systems keep responding to vita-PAMPs at a low level, and so get de-sensitized? Or, to get a little fanciful, is it good for us to keep responding to some levels of vita-PAMPs all the time-keep the immune muscles warm and in tone?

Much food for thought. And the nice thing? All this comes from such a simple question and an old observation-someone just asked "But, why?"

(Kind of like-why do ultra-tired babies cry their heads off instead of going to sleep? It's so obvious, you're tired, go to sleep. Don't sit up in bed, throw all your cuddly sleep toys out of your crib and howl to the high heavens. Apparently it is not that obvious. Sigh.)

It's been a while

It's been a long time since I wrote here. I started blogging as a new postdoc, to vent about the frustrations, and to join the community of scientists on the web who describe the vagaries of the scientific life.

I haven't enjoyed being a postdoc very much, and I'm distinctly ambivalent about still having the same job. There are many ups to being a postdoc and many downs, but I' not going to talk about them anymore, there are so many people who say it better. Besides, all that talking blinded me to why I do it in the first place: I think the immune system is pretty damn awesome, and I find something interesting to read about it nearly every day.

A lot has changed since I last wrote here: I have an energetic toddler, I'm far more downbeat about my ambitions to cure disease, I'm tired, I feel guilty most of time, and I'm afraid I'm losing my spark, the zip that makes my mind interesting and unique. All of which said, I find that I'm still jazzed about immunology, and I'm going to just try and focus on that. The ideas, the innovations and the incredible pace with which our understanding of the immune system progresses.

So the next post will be about my new favorite idea. And will be posted in a time period less than three years.

Ending a Statement With a Question Mark?

Have you ever conciliated your way through a scientific discussions by ending negative statements or disagreements with an implied question mark? I do it a lot, and I'm not sure I like the reason why.

As a woman (and maybe as a man too, though I have not had direct personal experience with this, any insight would be welcome), I tend to walk the fine line between directness and conciliation. I am naturally emphatic, and used to state my opinions strongly-maybe too strongly-carried along by the force of my convictions and the absolute determination not to give in to anybody. Some of this crazy certainty faded with age and some wisdom, but I still am pretty definite in what I believe and inclined to be forceful in what I say.

One big reason why I stopped being loud and emphatic and thumping my metaphorical fist on the table is because I realized I hated being at the receiving end of such treatment. I hate being steamrollered, its uncomfortable and puts me off the discussion. I also found that not thumping table meant I could hear other people, a nice change. So politeness and a genuine curiosity to hear other people's thoughts started me off on my path of less declaiming and more questioning. As an added bonus, people warm to gentle conciliation more than they do to vocal steamrollers.

That there is the rub: within the reasonable demands of courtesy, how much should one conciliate? It's a reflex now, I always take the diplomatic path rather than just say what I think outright. I like to think that I stand by my convictions-I'm just more mellow about them-but is that really true? Have I gone too far down the road of conciliation? In lab meeting particularly, or during seminars, I ask questions and challenge people almost apologetically. In some cases, it makes the questioned feel more comfortable, and in some cases it makes them more dismissive of your question. Is a reputation for being thoughtful and a disinclination to put people on the spot worth being dismissed?

Why so I have this need to instinctively subdue my challenges? The saddest thing is that I think I do it because I am a woman. There are men in my group who are distinctly less indirect, often outright rude and in-your-face with their challenges and it doesn't affect the esteem in which they are held. And in the most bitter of stereotypes, when other women do the same they are called aggressive, bitchy and unpleasant. I used to be against overt feminism because I thought it was loud, exclusionary and exhaustingly unproductive, not to mention bound to get you laughed at. It galls me though that the natural instinct of intelligent ambitious women of my generation is to tone it down, to try and not become one of those women who became PIs in the 1970s and -80s. While I am certainly not a fan of rudeness or putting someone else down out of a sense of your own superiority, I am so tired and fed up of ending every sentence with an implied question mark.


This post is my 50th on this blog(I'm slow), and its also for my mother, the kind of feminist I would like to be.

A Link Between Environemental Toxins and Autoimmunity?

The title of a paper in the advanced online publication section of Nature refers to a possible link between environmental toxins and autoimmune disease: an irresistible hook, and of course I could not resist. So followed some excited perusal of Veldhoen et al (doi:10.1038/nature06881) and another paper on the same subject, Quintana et al (doi:10.1038/nature06880), also in the AOP section.

So is there a link between environmental toxins and autoimmunity? Well, maybe, though I am not entirely convinced of that aspect of things, and here is why. Both papers discuss the effect of triggering the aryl hydrocarbon receptor (AHR) on T cells (description in the sidebar, for those of you are interested). The AHR, to my chemistry-ignorant mind, is a protein that binds hydrocarbon molecules with aromatic rings. The AHR is a type of protein, called a transcription factor, that decides when genes are turned on. In tune with this known ability of the AHR, both studies find that triggering the AHR on a subset of T cells called helper T cells turns on genes that influence the function of these T cells.

Helper T cells can direct the immune response along different paths, towards a more allergic response, one that is better suited to the fighting of infection, or towards a more inflammatory response which can result in the immune system attacking oneself—“auto”immunity. Helper T cells work by producing cytokines, small proteins that zip around the body carrying messages from one cell to another. Helper T cells that produce the cytokine IL-17, called Th17 cells, play a large role in autoimmune diseases: for instance, blocking IL-17 in a mouse model of multiple sclerosis, experimental autoimmune encephalitis (EAE), protects mice from getting the disease. Other helper T cells—regulatory T cells or Tregs—combat autoimmunity by battening down active T cells, and giving mice Tregs can protect them from a variety of autoimmune diseases. So helper T cells can go either way, either promoting or suppressing autoimmune disease.

Veldhoen et al find that triggering the AHR on helper T cells through its ligand FICZ* enhances the generation of both mouse and human Th17 cells. Treating mice with FICZ also accelerates the progress of EAE, suggesting that triggering the AHR enhances autoimmunity. FICZ is generated by UV treatment of tryptophan, an essential amino acid, and the authors suggest that it may be generated by exposure of the skin to UV light, thereby connecting environmental factors to an autoimmune disease. A connection I find a bit tenuous, but the idea is interesting and novel, and I am very curious to know what they find next.

Quintana et al present a more detailed study, with results that suggest something different. They find that triggering the AHR through a more famous ligand, TCDD**, leads to the enhanced development of Tregs, the tranquilizers of the immune response. Now, TCDD is thought to be very toxic, and is found in the environment (most infamously, in Agent Orange), but it seems to actually counteract autoimmunity, because treating mice with TCDD considerably slows down their development of EAE. Qunitana et al also agree that FICZ treatment enhances the generation of Th17 cells, and simultaneously retards Treg formation.

Both compounds bind to the AHR with different affinities, and possibly in different ways, which might explain their opposing actions. In any case, aromatic hydrocarbons are capable of modulating the immune response and shaping its eventual outcome, an exciting and novel set of findings. That they have such strong effects (reversing or accelerating EAE is pretty strong) certainly suggests that they bear further study, and back up the idea that things in the environment can have an effect on our immune systems. After all, having too many Tregs because you were exposed to TCDD may save you form some autoimmunity, but too-tranquil T cells are not very good at fighting off infections. Similarly, too much sun can turn tryptophan—which we absolutely need—into FICZ, which can then diffuse off into our bodies and do something to exacerbate autoimmunity somewhere. Food for thought.

*6-Formylindolo[3,2-b]carbazole (FICZ)
**2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD, dioxin)

The aryl hydrocarbon receptor links TH17-cell-mediated autoimmunity to environmental toxins
Marc Veldhoen, Keiji Hirota, Astrid M. Westendorf, Jan Buer, Laure Dumoutier, Jean-Christophe Renauld & Brigitta Stockinger
doi:10.1038/nature06881

Control of Treg and TH17 cell differentiation by the aryl hydrocarbon receptor
Francisco J. Quintana, Alexandre S. Basso, Antonio H. Iglesias, Thomas Korn, Mauricio F. Farez, Estelle Bettelli, Mario Caccamo, Mohamed Oukka & Howard L. Weiner
doi:10.1038/nature06880

Multi-tasking Madness

"I hate running PCRs to type mice, because I could have been doing X experiment instead."

No I could not have done X experiment instead. I have two hands and one head and unless I can master the usage of my toes, its one thing at a time. The typing of mice (or testing of serum for tissue culture, restocking of boxes, running of FACS samples) is as essential as anything else, despite being boring as hell. This feeling of "I could have been doing something else, obviously more useful or constructive" is a fallacy, and a stressful one at that.

I feel such a strong impulse to multi-task all the time, but often its the multi-tasking that slows me down. I am naturally a quick mover and I tend to dart around doing things, keeping myself busy. This tendency goes to the extreme in lab, where I don't feel occupied unless I have three threads running. And guess what? I make mistakes and have to repeat things, which adds to my not-inconsiderable work load (I have a particular PCR jinx).

There is this drive today to get things done, faster and better, now instead of soon. Lab work is easier and research is more competitive, so it's easy to see how this has come about. Is it constructive though? If something takes a certain amount of time to do, what is the point of rushing it or wishing it along faster? Or, inserting other tasks into the gaps? One does get more done eventually, but at more cost to oneself. And is that really efficient in the end?

I have discovered that I do not like operating at full stretch all the time. Sometimes I really enjoy it, I am in the zone and buzzing. But the rest of the time, I think my research would be better served by my working with more discipline. Unfortunately, when one can work in the zone, one starts to expect it of oneself always, and that is just not realistic. So I am going to run PCRs and DNA gels, and only those, this Saturday and look out of my window at the sunny trees.

(I might reshuffle my papers, read a few, trackback a few references, no matter.)
(And yes, its Saturday, I know)

Postdoc as Domestic Goddess (or God)

Skill 1: Combines ingredients with precision, follows instructions to the letter, but adds the occasional touch of improvisational flair with interesting outcomes. Occasionally works with the reagents at hand instead of what may be ideal, with perfectly acceptable results. Not afraid to use alcohol as necessary.

Skill 2: At the end of a process, puts everything away in its allotted space, wipes down all work surfaces, neatly collects trash. Surveys area, spots missed spots with the eagle eye trained by years of experience. Has no patience with others' sloppy work areas, is disgusted by ill-maintained and unclean surfaces. Is zealous about the weekly wipedown. Again alcohol accompanies as needed.

Skill 3: Monitors the health, diet and breeding habits of several small dependent creatures. Always has a mental map of which little creature is where.

Skill 4: Plans menus and processes days ahead. Has activities allotted to each day, to be carried out according to a strict schedule. Adheres to said schedule with admirable focus.

Skill 5: Does the shopping for supplies as needed. Prefers to do so on a regular schedule (schedule is important), but is willing to pop down to the shop when running short. Combines trips to shop with transport of laundry.

An alternative career maps itself out...

Blog List

Oh I am so stoked by this new feature on blogger (Draft blogger for now), it imports blogs from my google reader and posts them in my blog list! That is so good because I could not figure out blogroll and have been feeling bad about being a lazy one who hasn't manually entered everyone yet.
Love it. Because you are all awesome bloggers, and I am so glad to have found you.