I guess that as a CAFA organizer, I should really contribute to the second page. And I will. But I really don’t mind if someone else jump-starts it.

http://en.wikipedia.org/wiki/Protein_function_prediction

http://en.wikipedia.org/wiki/Critical_Assessment_of_Function_Annotation

Mac OSX: “We only serve ham & cheese on white bread. If you don’t like it, go somewhere else.”

Windows: “Lettuce and lots of Mayo. $400. That will be extra for the ham, extra for the turkey, no, you can’t have cheese with it if you have turkey. Well, you can, but you’ll have to add mustard. You don’t like mustard? Tough. So the sandwich is dripping all over you and falling apart? You can buy a sandwich-handler anti-drip across the street. $40/ year. Sandwich too big for your hands? Get someone else to hold it for you. No you can’t make your own. If you do, I’ll have you arrested.”

Gentoo Linux: “Here’s a sickle. Go to the field outside town, and harvest some wheat. Then you will see a cabin. Go inside, there are five types of grindstones there. Grid the flour you like. Then add water, we can give you mineral water, stream water, or tapwater. We also have different types of yeast. Make your dough. Bake bread (we have fire brick ovens, electric ovens, gas, traditional Bedouin oven, and a new plasma-jet oven). What would you like? Chicken? Go kill one in the back yard, pluck it, gut it, and cook it. You can roast it, fry it, grill it, or boil it. All in all, you can have your sandwich in just under a week if you’re good at what you do.”

Puppy Linux: here is a cracker and a bit of cheese. Enjoy your sandwich.

FreeBSD: Like Gentoo, but we also have a 30-.06 if you want a venison sandwich.

Credit: Joe Shlabotnik, Flickr

As soon as Rabbit was out of sight, Pooh remembered that he had forgotten to ask who Small was, and whether he was the sort of friend-and-relation who settled on one’s nose, or the sort who got trodden on by mistake, and as it was Too Late Now, he thought he would begin the Hunt by looking for Piglet, and asking him what they were looking for before he looked for it.
“And it’s no good looking at the Six Pine Trees for Piglet,” said Pooh to himself, “because he’s been organdized in a special place of his own. So I shall have to look for the Special Place first. I wonder where it is.”
And he wrote it down in his head like this:

ORDER OF LOOKING FOR THINGS

Special Place Piglet Small Rabbit Small again

(To find Piglet) (To find who Small is) (To find Small) (To tell him I’ve found Small) (To tell him I’ve found Rabbit)

“Which makes it look like a bothering sort of day,” thought Pooh as he stumped along.

Of course, it does turn out to be a bothering sort of day, and nothing goes according to plan. Pooh does find Small but that is almost an afterthought considering the other things he discovered that day.

Just like science. You set out looking for something, you find a bunch of other things. You may or may not find what you  to originally set out to look for, but by the time you get to finding Small, finding him may not be the accomplishment you originally thought it may be. Something else has superseded it.

I started writing this post about the search for the smallest organism. Why? Because life in small packages fascinates me. How small can a biological package be, and still be considered living? Or: “The Search for Small(est)”.

But like Pooh, I bumbled along into other things.

So what is the smallest living thing? Starting at the smallest scale, viruses  are considered by most scientists to be replicators, rather than organisms. They do not metabolize, and do not carry a full complement of reproduction machinery. They affect life profoundly, but they are missing a few essential components to actually be living.  This view has been shaken up recently with the discovery of giant viruses that have genomes larger than some bacteria. These genomes are also quite complex, including coding for a large part of the reproductive machinery, having a selective membrane, and other of life’s goodies. Still, even if we consider giant viruses (or mimiviruses, as they are called)  have crossed the border between non-life and life and are considered to be living, they are already not the smallest around. Not in genome size, and not in the particle size. Indeed, mimivirus were, for a long time, mistaken for bacteria due to their size, which is where they go their name: “mimi”  is short for microbial mimic.

So: small bacteria? The bacterium Candidatus carsonella rudii is really small: its genome is just shy of 160,000 base pairs and it codes for about 182 predicted genes. But carsonella is an obligatory endosymbiont: it lives inside the cells of a special organ in the jumping plant louse or psyllid, an insect that feeds on plant phloem. Carsonella cannot survive outside its host and, in fact, its genome has lost so many genes that it is practically an organelle, not much larger than a mitochondrion. (A mitochondrion  has 16,000 base-pairs and 32 genes.) Mitochondria are not living, although they originated from bacteria. Is carsonella there yet? Has it crossed into from life into non-life just as mimiviruses may have crossed from life into life? Buchnera, another insect endosymbiont is not much larger, with about 400 genes.

Mycoplasma genitalium is parasitic,  but at least it codes for (almost) all of its proteins. It is usually heralded as “the smallest organism that can be grown in cell-free culture”. Its genome is  521 genes strong: just 3 times more than that of carsonella. It is not an obligatory endosymbiont, but it is a parasite: we can trick it to live and grow in a nutrient-rich soup, but in nature you will not find it outside a host.

Pelagibacter ubique, a marine bacterium, is, as far as we know, the smallest free-living organism, with approximately 1390 predicted genes.

So in searching for Small, I was asking a question that seemed to become more awkward each time I thought I found him: is this Small I found  living or not?  Each of the Smalls has certain characteristics of life, but where on the scale outlined by pelagibacter, mycoplasma, carsonella and a mitochondrion does life turn into non-life?

When a question you ask makes you feel weird, you may want to consider whether you are asking the right question. So maybe I was asking the wrong question. Maybe the definition of life is not a binary one and we should not think in terms of “living” and “not living”. Life may very well be a quantitative thing.  Life sheds itself into non-life gradually, from free-living to parasitic to endiosymbiont to organelle.  Indeed, self-replicating proteins (prions) and self-replicating RNA (viroids) are the byproduct of much more complex life, which has arisen before those replicators were derived. As they are, they are non-living, but they owe their existence to life.

So there is no single boundary where “life”  crosses over to “non-life”. That’s not the right way to look at it. When journeying  from virus through mimivirus,  through organelle, various endosymbionts, parasites to free-living we are are simply hitting milestones on a continuum. Perhaps not that different from the continuum from which life emerged in the first place.

Understanding this probably beats actually finding Small.

Prepared by daughter. Not to scale. Species not yet identified. Delicious.

Together with obesity, insulin resistance is the harbringer of metabolic syndrome. Insulin resistance is when the body cannot use insulin effectively. Insulin is needed to help control the amount of sugar in the body. As a result, blood sugar and fat levels rise.  Therein lies the path to morbid obesity, diabetes, stroke, and heart problems.

So what’s the connection of metabolic disease to bacteria? Well, for one thing, we know that in obese people the bacterial population in the gut is different, and the different population of bacteria may lead to a vicious cycle contributing to obesity.

Another possible connection has to do with an  important group of molecules in our body called Toll-like receptors, or  TLRs. TLRs are a family of  membrane proteins that sense a wide variety of bacterial populations and activate our innate immune system. TLRs are like a first-defense warning station: they sense the bacterial enemy first, and, if needed, activate the proper defense mechanisms. Researchers studying TLR-2 have created knockout mice lacking TLR-2, and they discovered is that many of TLR-2 knockout mice do not develop insulin resistance when fed with a high-fat diet. Think about it: all the McCrap you can eat, yet your blood sugar level remains normal (although you still grow fat).  So why does that happen? How come these mice lacking a bacterial sensor also seem immune to insulin resistance?

To answer this, we must understand that TLR receptors (quite a few are known so far) are known to serve as a bridge (or “mediate crosstalk”) between the immune system and the body’s metabolism.  Mice without TLR-5 develop eating disorder known as hyperphagia which is characterized by an increased appetite; they also show other pre-diabetic  symptoms: hypertension, high lipids, and insulin resistance. I have posted before about how TLR-5 may control the type of gut bacteria mice have and, in turn, control their propensity for obesity.

TLR-4 deficient mice, on the other hand, seem to be protected from insulin resistance, just like TLR-2 deficient mice. So a connection between these front-line sensors of the immune system and whole body metabolism is well-known.

A group of researchers from Brazil have decided to look further into these “diabetes resistant” mice. The thing about mutant TLR deficient mice, is that they are normally grown in sterile conditions because possible infections and because the uncontrollable gut microbes add uncontrolled variables to any experiment. When scientists cannot precisely control for experimental conditions, they face two choices: One, they can deviate from the model to emulate “real world” better, but sacrifice control of one or more of the variables in an experiment. Or, maintain full control of the experiment and sacrifice a simulation whatever they are trying to model. Most scientists go with the second option: they would prefer to have a well-controlled model, even if it supposedly detracts from its supposed practicality and application to “real life”. That is because a model (in our case, mutant TLR mice), is somewhat removed from the real thing anyway: mutant TLR-deficient are basically a  an artificial construct used to investigate the effect of knocking out a TLR from the mouse, so hopefully we can draw conclusions about humans. So the second type of possible error is the one scientists generally prefer to make.

Toll-like receptors: it's complicated.

But Andrea Caricilli and colleagues have decided to look at TLR-2 knockout mice in non-sterile conditions. Rememebr: TLR-2 knockouts seem to have protection from insulin resistance. What Caricilli and her colleagues discovered was quite the opposite of what was known so far: TLR-2 knockout mice were not protected from insulin resistance. Quite the opposite: the mutant mice developed metabolic syndrome. But did  the gut bacteria do it? To check that, the researchers treated the mice with broad-spectrum antibiotics for 20 days. After that, the bacterial species that re-colonized the mice’s guts were quite different in their composition from the bacterial species that originally inhabited them. And they did not have meteabolic disease, or the symptoms were much less severe.

So here it is: changing the mice’s gut microbiota changed them from mice with insulin resistance to mice without insulin resistance. Yes, there are mutant mice, but still: insulin resistance was turned off  by changing the types of microbes in the gut.

They then transplanted the microbiota from TLR-2 mutants which had insulin resistance to regular mice. And what do you know: the regular mice then showed symptoms of insulin resistance and metabolic disease.

There is a lot more to this paper than these two experiments: they have also investigated many other parameters, trying to come up with the chain of events that bacteria trigger when causing metabolic disease. I won’t get into that, the paper is quite long with some 20(!)  figures. A lot of work went into this. But the bottom line again supports what has been shown in other studies: the bacteria that live in our gut are responsible for our metabolism, and it is the interaction between the bacteria and our immune system that not only protects us from pathogens, but also protects us (or not) from metabolic disease.

 Update: this post has been slashdotted. Exercise extreme caution.

Caricilli, A., Picardi, P., de Abreu, L., Ueno, M., Prada, P., Ropelle, E., Hirabara, S., Castoldi, A., Vieira, P., Camara, N., Curi, R., Carvalheira, J., & Saad, M. (2011). Gut Microbiota Is a Key Modulator of Insulin Resistance in TLR 2 Knockout Mice PLoS Biology, 9 (12) DOI: 10.1371/journal.pbio.1001212

EDIT: I got a couple of concerned emails. No, this did not happen to me. Yet.

Once I lived the life of a PI so rich,
Research was going along without a hitch.
Lab manager, four postdocs and grad students eight,
My lab took up the whole floor, and that felt great.

Five years later it all went to hell,
My renewal was declined, because no papers in Cell.
But I just read an RFA that is out,
I’m going to apply, and get it, without a doubt.

Nobody knows you,
when you lose your grant.
In your funding, not one penny,
and as for postdocs, I haven’t any.

If I ever get back on my feet again,
My department chair will not treat me with disdain.
It’s mighty strange, which is why I’m doing this rant,
Nobody knows you when you lose your grant.

Best version of the original, IMHO:

 

Dear  professor  Iddo Friedberg,

    

    First of all, I would like to introduce myself, my name is _____, 30 years old I  occupy a staff position of instructor at the department of pharmaceutical microbiology, faculty of pharmacy, ____ University, _____.

I was graduated in 2003 with an overall grade “excellence with honors” & I was the second among 1000 students.  I have a PhD scholarship totally funded by the ______ Ministry of High Education. The scholarship includes tuition fees, residence, health insurance and everything. Here is the link of the scholarships offered _________. I am interested in doing my PhD study in the field of molecular biology under your supervision. To fulfill the requirements of the scholarship, I should have a research proposal including the following items. I will apply to The University as soon as I receive the proposal.

 

The research proposal includes:

·                   Title Page (including Title, Keywords).

·                   Abstract

·                   General Overview of Research Area and Literature

·                   Key Research Questions and Objectives

·                   Methodology

·                   Tentative Timetable

·                   Selective Research Bibliography

 

I will be so grateful to you if you generously send me  a research proposal few days before the deadline(January 10, 2012)

 

 

N.B. other information is available in the attached C.V.

If you need any additional information or documents, please let me know

I am waiting for your reply as soon as possible in case of either acceptance or refusal.

Kind regards

“We seek to download from the amazing successes of the computer industry two principles: that of open source, and that of crowdsourcing; to quickly, responsibly accelerate the delivery of targeted therapeutics to cancer patients. Our business model involves all of you. This research is funded by the public.”

What a Chevrolet El Camino might look like:

1968 El Camino

Anyhow, the music is great. Here is the first track, Lonely Boy. Enjoy: