Tuesday, June 26, 2007

Mutations, gene passing, and the evolution of gut microbes

The gut is a particularly interesting niche for evolution because things change there so rapidly. You eat a undercooked hamburger from a poorly butchered cow and all of a sudden your intestine is full of E. coli O157:H7, you've got the worst stomach ache of your life, and you have bloody diarrhea. But this doesn't just create an difficult life for you, this also causes a great deal of confusion for the bacteria that were happily living in your intestine. Before the O157:H7 invaders arrived, your normal intestine residents (i.e. your normal flora) were grabbing the food you didn't eat and passing on the some of the benefits to you. Now all of a sudden the flow rate through your intestine is much faster. Perhaps the normal flora are having trouble staying attached to your intestinal lining? A new food source, blood, has arrived from the E. coli O157:H7 that so rudely invaded your intestine. And most of your intestines normal residents are probably not optimized to eat blood.

Now let's assume you were misdiagnosed and the doctor gave you antibiotics to get rid of the new E. coli O157:H7 residents in your intestine (unfortunately, the current best treatment for O157:H7 is to wait a week or two for it to go away). Now, the bacteria in your intestine are being bombarded by these antibiotic chemicals that kill off most of them.

So how do bacteria survive, and often thrive, in such a complicated environment?
  1. they are tiny so lots of them can live in a small space; their large number allows for diversity; and diversity is largely why they survive drastic changes in their environment - only a few diverse individuals of a particular species need to survive each in order for the species to remain a resident of the normal flora
  2. the different species trade DNA in the gut; this means that if one type of bacteria in the gut develops resistance to a particular antibiotic, another type of bacteria can develop resistance more easily, because they can just obtain the important piece of DNA from the bacteria that already figured out how to survive
Point 1 above deals with mutations and selective pressure. Point 2, the gene-exchanging idea, deals with a phenomenon called horizontal gene transfer. However, it's not clear how often any of these things happen, or if they occur more often in some situations than others (e.g. is there more horizontal gene transfer when there is a strong selecting force like an antibiotic). Mutations and selective pressure has been studied for quite a while in the lab (see the NY Times article "Fast-Reproducing Microbes Provide a Window on Natural Selection") with pretty interesting results. But I think its time we moved these evolution studies into more complicated environments like the gut. We also need to further explore the extent to which horizontal gene transfer plays a role in these organisms' survival and adaptation, because previous studies (as far as I know) have focused more on the mutations in cultures of a single bacteria put under some sort of selective pressure.

Here's what I propose:

Inoculate a gnotobiotic mouse with N species of bacteria (probably make N = low = 2-4; also make the species diverse: one Firmicute, one Bacteroidetes, and one Archaea). You should probably place things under selective pressure to push the organisms in different directions. For example, give the mouse diets that have few of the nutrients necessary for the gut residents, or add one antibiotic resistant strain of bacteria and give the mouse a weak but constant dose of the antibiotic (to see how long / if the bacteria horizontally pass on the gene).

Now pass on the microbial residents to new mice (either the children of the inoculated mouse or another germ-free mouse; both would be interesting). This passing could be done by mixing a little feces in their food, but it would probably just happen naturally if you put them in the same cage for a few days. Now at set times in each mouse's life take a feces sample to be sequenced at a later date (might as well delay sequencing as long as possible, since the stuff gets so much cheaper with time). Then sequence the frozen samples to see the extent of the mutations and gene transfers over time and in different selective environments and genetic backgrounds of mice. The sequencing will also show how the proportions of the normal flora change over time.

The problem with this experiment is that it would take several years of work, and you'd always need to be careful to pass on the flora before the mouse died. But according to that NYTimes article I linked to above, most of the action in the single-species studies occurred at the beginning, so even the early results might yield some interesting insights into gut ecology and evolution.

Friday, June 15, 2007

why can you feel when you are close to remembering something?

There are plenty of models for how memory works at both a psychological and a physiological level. What I want to talk about now is a curious thing that happens with what is typically referred to as long-term memory. Long-term memory refers to the stuff that we remember for more than a few minutes - things like our phone number, the names of our friends, and where we live. These memories must be stored chemically in the brain. I think the current working model is that memories are somehow encoded in the strength and pattern of synapses, which are junctions between the neurons in our brains.

The curious thing about memory that I'd like to discuss now is (as you probably have inferred from the title) why can you feel when you are close to remembering something? In case you aren't with me, let me give an example. Let's say you're watching a movie; you see an actor that you've seen in many movies before, and your friend next to you says, "who's that actor?". If you know the actor extremely well, the name will flow off your tongue like a reflex. If you don't know the actor's name instantly, you will almost immediately get a feeling inside, like a gut instinct, that you can use to estimate if you'll probably come up with the actor's name if you think harder about it.

It's odd right? Somehow we can feel if further searching of our brain is likely to reveal that actor's name. And the feeling is relatively accurate. For example, I don't watch that many movies, but like many people I remember faces pretty well. So it's pretty common I'll recognize an actor's face in a movie, but I'll know that I have no idea what their name is. However, if I had previously learned the actor's name and the name was still at least weakly burned into my memory, I would get a sorta gut feeling for how likely I'd be able to dig that name out of my brain.

Ok, let's say we had a good feeling that we'd be able to find the actor's name if we think harder. What happens next?

We would start to search our brains around the areas of our brains where the actor is. Somehow we go to the memories we have for the actor, and we dig around and look through them. We'll see what other movies we can remember the actor in and what other actors we've seen him with. We can often even think of friends we know who would be able to help us answer the question. And then to move towards the actor's name, we might toss around names in our heads that feel right, so that we can listen to them and see if they sound right too. It is all a sorta fuzzy process that seems to move by intuition, but the intuition has a definite sense of direction. We can feel when we've made progress towards the name in our head even if we still do not know the name yet (e.g. we say, "I've almost got it, just give me a second"). When we do find the right name, it's like BAMM - after all that searching you've found the name, said it to yourself, and you get a sorta feeling of satisfaction that instantly lets you know that - yes that is the right name.

Why does this happen?

How does this work?

Tuesday, June 12, 2007

the brain isn't multithreaded

It is impossible to have more than one thought at a time.

Try it.

Try to use your brain to have two unrelated thoughts at the same time. For example think about your kids and listen to a song on the radio - being careful to listen closely and understand all of the words. You can either listen to the words or think about your kids. You may be able to swap back and forth really fast to create the illusion that you are doing both. The two may even get mixed up so that you think about how the words you're listening to relate to your kids. But if you really pay close attention, you'll notice you are either listening to the words or thinking about the kids and never doing both at exactly the same time.

I've asked lots of my friends to try the same thing - none could have two simultaneous thoughts.

So in some ways our minds must function a little like a single-processor computer (up until about 2005 almost all personal computers only had one processing core). Single-processor computers that are sufficiently fast create the illusion of multiple simultaneous computation. Although you can play your itunes and type an email at the same time, the computer is actually going back and forth between the two so fast that you don't notice it. The computer does this swapping by using memory and different buffers. It puts all the information for your email and for your itunes in a short-term memory, and then it simply goes back and forth between the two and computes the next things that need to be computing. Similarly I imagine our brains are just sticking the things we are currently multitasking into a short-term memory, and it just swaps them in and out to think about them. This process creates the illusion of thinking about multiple things simultaneously.

Our inability to have simultaneous thoughts does not preclude us from simultaneously doing multiple things. We must use the spinal cord or other neuronal cells throughout our body as the buffers to keep us running smoothly. So we can think about our next tennis shot while our arm is busy hitting the current one.

Microarrays: scientific indulgences

Let me first admit that the analogy isn't perfect, but then let's move on (if you're curious) to see how the two are more similar than they appear at first glance. I also assume you know a little about religion and a bit about microarrays, otherwise, why are you here?


I'm not much of a Roman Catholic aficionado, so I only know the bad side of indulgences (was/is there a good side?). Pope Leo X, true to his Medici lineage, needed lots of cash to build nice pieces of art (in this case primarily St. Peter's Basilica in Rome) to dazzle the public and to make him look like a powerful badass. When the cash flow got low, he decided to sell piles of indulgences (which were little pieces of paper offering forgiveness). This method worked well for a while. Unfortunately for Leo, the U.S.A. did not exist at this time, as this product would have been a hit in the land known for its people that throw money at quick fixes for all of their problems. More unfortunately for Leo, a German dude, Martin Luther, had the crazy idea to read the Bible and the even more preposterous idea to write the whole book out in a language that people could actually read (we'll kinda; actually few people were literate back then, but more read German than Latin I'd assume). So when people started reading the Bible (particularly Luther), they soon realized that selling forgiveness was a load of crap. Many took this as an excuse to rebel, loot, etc... The Catholic Church was in shambles, the world was at war, and it was our first big step towards creating the more intellectually free society we (sorta) have today in modern science.


Science has a few sins of its own. Not bathing, acting bizarre on purpose so people think you're the out-there smart type, and asking stupid irrelevant questions to show people how clever you are, are all just inconveniences not sins. Science has one mortal sin: knowingly publishing false information; it brings instant fame, but leads to certain excommunication if you're caught. The venial sins are more common. The two most frequent being: not publishing enough papers and not having enough grants. The punishment can be harsh for non-tenured scientists, but the tenured amongst us still must suffer the psychological trauma of being disassociated by your colleagues and being considered a has-been. Thanks to microarrays (which are little pieces of glass with DNA on them that allow you to measure the relative expression of many genes simultaneously) there is help. There is enough information in a microarray result that you're bound to find something interesting to publish, and so far there is no modern day Martin Luther.

Microarray Indulgence Quotes

My current professor doesn't ask me to go to conferences too often, but when I was working at an unnamed famous university, I'd present posters all the time. "Ten chips and a t-test and you got an Abstract". a phD student at the Boston University Pub
There are two major ways people use microarrays: hypothesis testing and hypothesis generation. A lot of labs buy ten chips for hypothesis generation when they need to write a grant. affymetrix field application specialist

Bioinformatics books

Bioinformatics has been around for many years, and there's still only one good book: Biological Sequence Analysis by Durbin et. al., which summed up the state-of-the-art in 1999. It's sad but true that almost everything in bioinformatics is in that book. Since the books writing, the number of bioinformatics publications has sky-rocketed, but the great majority of the publications are variations on a theme of Durbin et.al..

Live imaging of host-microbe interactions

Two photon excitation microscopy allows imaging of living tissue up to a depth of one millimeter. Karel Svoboda has used this to amazing effect to study neurons in mice. I wonder if it would be possible to apply a similar approach to study host-microbe interactions in real time. The idea would be to create a few strains of fluorescently labeled bacteria (or make a fusion protein or U. Alon style fluorescent promoter of a key protein or two) and watch them interact in real time with the gut of a mouse after you feed or inject the mouse with different drugs.

  1. how thick is the intestinal lining (i.e. is it greater than 1mm?)
  2. how easy it is to do surgery on the mouse to get to the intestine?
  3. how easy is it to sew the mouse back up and have sorta a ready-access flap into the intestine like Svoboda does with the mouse neurons?
  4. how much will it alter the physiology of the mouse to have an open wound near the intestine?
2-photon links

Update Dec 2, 2007
Jost Enninga, Philippe Sansonetti and Regis Tournebize wrote an excellent review that covers this idea and much more (as is always the case, this idea has already be worked on to some extent, though never in the context of an intestine as far as I know).

Roundtrip explorations of bacterial infection: from single cells to the entire host and back.
Trends in Microbiology, Nov 2007

Do microbes directly sense host hormones?

Microbes have been living inside vertebrates for a long time now. They and their hosts are constantly interacting. I think it is not clear however on how many scales they interact. For sure the host has things an acidic stomach and bile secretions (which is like a detergent) to keep the microbe populations from growing outta control. The innate immune system also has plenty of peptides that have antimicrobial properties. For every host combatant action, there
must be a subsequent microbe response for the microbe to survive (e.g. E. coli can export detergent-like bile molecules to survive in intestine). But is it known if bacteria can respond to general non-combatant host properties like the presence of hormones circulating about?

For sure if you have a big boast in adrenaline the bacteria populations will be stimulated, but this could occur simply as a side effect to the host's response to the hormone. I want to know if bacteria can directly sense any hormones. What about leptin? Work in Gordon lab at WashU suggests that low leptin might send a signal to the microbiota to become more efficient at extracting calories from food. I'd like to know if this or any other hormonal signals are directly sensed by the microbial community.

Could try running microarrays of microbes in the presence/absence of different hormones.

(see Nature News & Views article "Obesity and gut flora", Bajzer M and Seeley RJ and the two articles from the Gordon lab in the same issue "An obesity-associated gut microbiome with increased capacity for energy harvest" and "Human gut microbes associated with obesity").