Saturday, September 20, 2008

The Brillant Dance of the Starvation Response

Another dorky song that only a microbiologist could love. This one is about the amazing regulation of the starvation response in E. coli during sugar starvation. Some of the details may be skipped through, but the core concept is there.

This is dedicated to undergraduate Microbial Physiology, instructed by Jeffery Lawrence.

The Brillant Dance of the Starvation Response (To the tune of Dashboard Confessional's "Brillant Dance")

So this our
Painful realization
glucose is gone
And there's no
PTS sugars at all
No, there's no PTS sugars at all

So we build up E2A-Phosphate
Which goes to bind
Which creates
Which activates crp

And the lacY channel comes unbound
So if there's
lactose to be found
It diffuses in and is eaten by the cell

So this is strange
Our lactose pools have been used up
And now they are no more
And we have no carbon source at all
No we have no carbon source at all

So our charged
tRNA pools start to fall
RelA has to make the call
And synthesize

oxidation becomes a task
protein synthesis is too much to ask
And you're measuring the minutes with a
protein MCP

Well this is incredible
Starvation's inevitable
Yes we have become more

Well we'd like to think we were invincible yeah
Well weren't we all once
Until we got starved for our sugars

Where are our sugars?
I need some lactose
Or even a Twinkie

I wish that I could become a

Friday, September 19, 2008

How Far Do Those Phages Stretch?

The number of viruses in the biosphere has been estimated to be anywhere from 1030 to 1032. But what does this number really mean? How big is 1031? (The number I see most commonly cited as the number of phages in the biosphere)

Roger Hendrix gives a great list of examples, and one of these is "How far will 1031 phages stretch if laid end to end?" I thought I would do the calculation for myself (and the readers) to see exactly how long 10^31 phages will stretch.

So, we must first begin with two assumptions.

1) The number of phages in the biosphere. 1031 is the number I see most cited, but I have also seen 1030 and 1032. Since 1031 is more familiar too me, and is between the others, we'll use this.

2) The length of a phage virion. The average range of virion size is 25ish to 250ish nm. So, I will use 125nm as a middle average.

The Equations
125nm at 1031 phages, laid end-to-end is 1.25 x 1033 nm.

This converts to 1.25x1024m
Or 1.25x1021 km

But how far is 1021km?

1 km is 1.05702341 × 10-13 light years
So, 1.25x1021km = ~1.3 x 108 light years

108 light years?! THAT'S A LOT!

Here's some scale:

Distance to the Moon: 0.00000004 light years
To the Sun: 0.000016 light years
To Pluto: ~0.0005 light years
Distance from the Sun to the Center of the Milky Way: ~2.6x104 light years
Diameter of the Milky Way: 1 x 105 light years
To Andromeda Galaxy: 2.5x106 light years
To the M81 Local Group: 1.1x107 light years

Phages would stretch a whole order of magnitude further than the next closest galactic local group! Almost 100x farther than the Andromeda Galaxy! And 1000X longer than the diameter of the whole Milky Way!

Mind boggling.

Thursday, September 18, 2008

The Ballad of the Virus (They're Everywhere)

I wrote this on a short bus ride to campus about a year ago, specifically for a Virology Lab course final presentation.
I am taking a study break from biochemistry / molecular biology, and so I decided to try out my new webcam. Hope you enjoy!

Ballad of the Virus (To the tune of "The Storm is Passing Over" cmpsr: Charles Tindley)
They're everywhere
In our food and in our lotion
They're on our skin
And floating in the ocean
They're viruses
And there's more of them than us

They have a protein capsid

And nucleic acid
They replicate themselves

Inside our cells

Attach to the cell
Then inject your DNA
Hijack the host
Make it do what you say
Despite all of this
Some say that your not alive


Where did you come from?
We only have speculation
Escaped DNA
Or reductive evolution
Whatever it is,
We know that you're here to stay.

Other Phun Songs:
I Got You Phage
It's Gonna Be There (The E. Coli Song)
The Brillant Dance of the Starvation Response

Wednesday, September 10, 2008

Altruism in Bacteria? Allowing Yourself to Die for the Good of the Species

ResearchBlogging.orgAltruism in general is an interesting concept from an evolutionary perspective. As defined by, altruism is "the principle or practice of unselfish concern for or devotion to the welfare of others," or more specifically, it is "behavior by an animal that may be to its disadvantage but that benefits others of its kind, such as a warning cry that reveals the location of the caller to a predator. " On the surface, this appears to be in direct opposition to the idea of survival of the fittest. In reality, this is not the case. However, the point of this article is not to delve into such evolutionary relationships.

Rather, I would like to point out that the practice of altruism is not limited to humans, or even animals. Animal behavioralists have described altruistic behavior in such species as chimpanzees, rats, dogs, and many others. A recent study by Ackermann, et al in last month's Nature, shows a form of altruistic behavior being practiced by Salmonella typhimurium.

S. typhimurium utilizes a Type III Secretion System (T3SS) which triggers inflammation when expressed in the gut of the bacteria's host. This inflammation kills off any competative organisms and allows the bacterium to colonize further into the gut tissue. Since the inflammation response is primarily directed at cells within the gut tissueAn example of a Burkolderia Type 3 SS. Image Credit: Chen Kang 2002, rather than the lumen, those bacteria residing within the tissue are at a high risk of death.

These researchers show that within the gut lumen, only 15% of the bacteria are expressing the T3SS (even if genetically clonal). Those that are found within the gut tissue are all expressing the T3SS. In fact, the T3SS is necessary for colonization of the gut tissue. So, in essence, those cells expressing this secretion system are able to enter the gut tissue and stimulate a response which can kill competitors (but also themselves). The 85% not expressing this T3SS in the lumen, can not enter the tissue and so are not at high risk for death, BUT are able to benefit from the death of the competiting organisms. One review of this study called the cells utilizing the T3SS "kamikaze bacteria" destroying themselves to benefit the greater good.

I believe that this observation, from a reductive standpoint, can help to show that complex social behaviors can be seen in "simpler organisms." This experiment also demonstrates how altruistic genes can be kept within a population, despite destruction of the organisms expressing the suicide genes.

From my understanding, how this phenotypic switching (or as the authors refer to as "phenotypic noise") occurs is as of yet unknown, and will be interesting to discover. The behavior of phenotypic switiching (whereby clonal organisms express a variant of their genes set in identical environments) is seen in other circumstances, including bacterial persistance in the face of antibiotics.

Ackermann, M., Stecher, B., Freed, N., Songhet, P., Hardt, W., & Doebeli, M. (2008). Self-destructive cooperation mediated by phenotypic noise Nature, 454 (7207), 987-990 DOI: 10.1038/nature07067