Blogging for Bacteriophages

Throwing the Clutch (not the Brake) on a Bacterial Flagella

noreply@blogger.com (Tim Sampson) — Fri, 15 May 2009 19:16:00 +0000

For most my of readers, it is common knowledge that bacteria are more than just singled celled entities; and instead bacteria are complex organisms capable of undergoing large-scale, multicellular activities. Of particular interest to many current microbiologists, is the development of biofilms.

These multicellular structures are likely how many bacteria exist in the environment, and are implemented in a variety of diseases. Taken alone, biofilms are fascinating, but I have a keen interest in understanding exactly how a bacterial cell decides it is time to create a biofilm. (In reality, I have a keen interest in how a bacterial cell decides it is time to do anything, but that is beside the point)

While studying the switch between motility and biofilm development in Bacillus subtilis, Daniel Kearns of Indiana University, wanted to know the status of the flagella during the switch.

Mutants of the biofilm regulator sinR are constitutively in a biofilm state and are nonmotile. However, flagellar genes are still expressed and flagella are still produced. The question then became what is preventing the flagella from moving while in a biofilm.

The first idea would be that the extracellular matrix is physically inhibiting the movement of the flagella. By knocking out a gene required for matrix production (epsH), Kearns saw that the flagella became free, but were unpowered.

Then, as any good geneticist, he screened for mutants that were able to suppress the non-motility phenotype of a sinR, epsH double mutant. All of these mutants mapped to a putative glycosyltransferase (epsE) within the matrix operon. Furthermore, expression of epsE alone was sufficient to inhibit flagellar motion, and known conserved glycosyltransferase residues were not required for inhibition.

This brings up the questions: Where is epsE acting? and Is it a brake (completely stopping all flagellar movement) or a clutch (preventing active rotation)?

By selecting for supressors of redundant epsE, the group found that all suppressors mapped to the fliG gene; a gene known to encode the transduction motor between the proton pump (motAB) and flagellar basal body. So, somehow epsE acts to inhibit the motor.

Furthermore, upon examining flagellar motion (in some awesome movies available here) Kearns showed that the flagella were not braked, that is, the flagella were still capable to rotate freely (and in fact did), however all rotation was due to Brownian motion. This implies that the flagella were disconnected from the motor, rather than stopped completely.

So, epsE is acting as a clutch to disconnect the flagellar basal body from the motor. This actually makes quite a bit of sense. If the cell no longer requires flagellar motion as it went into biofilms, it could do a variety of techniques. One is that it could shut off gene expression for the flagella. However, it would take many generations before its progeny were non-motile and the flagellar apparatus was diluted out. Another is that it could put a brake into the flagella and prevent motion entirely. But, this would cause lots of cell envelope stress while in a biofilm. Brownian motion alone could potentially tear the cell apart.

This leaves the cell with the clutch option. Capable of stopping flagellar motion quickly while keeping the cell envelope intact. Due to its high homology to glycosyltransferases, epsE likely represents an example of a duplicative evolution; whereby a duplication of an enzyme leads to the capability to take one copy of said enzyme and "play with it" to create new functions. In this case a sugar-acting enzyme has become a structural protein in the flagellar apparatus.

Source:
Blair, K., Turner, L., Winkelman, J., Berg, H., & Kearns, D. (2008). A Molecular Clutch Disables Flagella in the Bacillus subtilis Biofilm Science, 320 (5883), 1636-1638 DOI: 10.1126/science.1157877

Other Articles of Interst:
Extracellular Membrane Vesicles in Bacteria: Taking Quorum Sensing in New Directions
Altruism in Bacteria: Allowing Yourself to Die for the Good of the Species
Where the Wild Microbes Are: A New Theory in How Pathogens Survive Food Processing

Phage + Metal = Battery?

noreply@blogger.com (Tim Sampson) — Sat, 09 May 2009 16:49:00 +0000

By now, many people have read about Angela Belcher, a professor at MIT, and her lab's recent developments in the use of bacteriophages as a componant of batteries. Having had a very distinct privilage to hear her speak yesterday, I wish to share what I have learned.

In a broad sense, the goal of her lab is to give inorganic compounds (batteries, medical devices, solar cells, etc), "genetic intelligence." That is, to give the power of evolutionary adaptation and self-correction to inanimate objects. Life evolved the ability to perfectly use the ions and metals present in its environment, things like calcium, silica, etc. However, she wants to know what happens when we allow life to evolve in the presence of technologically important compounds, like gold, silver, aluminum, platinum, etc.

One of the original goals was to develop a biological system that could recognize and mark atomic scale cracks in layered materials. She set to do this using a phage library. The phage, M13, is capable of having many of its parts replaced with random gene sequences, allowing us to add in peptides that allow recognition for any particle of our choosing. (A concept referred to as "phage display" and has been used for lots of detection assays)

She selected for attachment proteins that allowed the phage to attach to atomic scale cracks in the alloy used in engine blocks and computer parts. You can then propgate, mutate, and select for phages that have tail fibers with the strongest possible affinity for the substrate of your choosing. This was very succesful, and from my impression, is being scaled up to allow identification of these atomic cracks in engine blocks, airplane wings, and helicopter blades. (She is now figuring out how to mesh the identification of the cracks via phage, to self-healing properties via metal nucleation)

She then found that the proteins in the phage body could be altered as well. Using similar techniques she found that metal ions could be nucleated in both poly crystalline and mono crystalline structures to the phage body. Thus allowing the creation of nanotubes (with a phage inside). By altering ratios of metal ions added, she can create very specificily composed alloys. Importantly, all of this is done at STP, with a rare exception (Ag-Pt tubes for fuel cells) requirein 80C temperatures. She can also rid the system of organic material by heating to >100C, but keep the inorganic structures intact.

Using phages with affinities for cobalt oxide, lithium, these scientists managed to create a functional battery that is only on the order of nanometers in thickness. Paper thin batteries that have the capacity and power to replace automotive batteries now. The batteries are capable of being charged and recharged numerous times without losing power or capacity. (This was a problem at first). They are very fast to produce (<6hrs)

If you can think of any application for nanowire like phage nucleation of metals, her team is already working on it. This battery concept is definitely going to be an important milestone in development of new energy storage, usage, and production.

Normally when we think of applications of microbial genetic systems, we think of human health and perhaps fermentations. Now, we can truly see the power when genetics are applied to technologically challenging engineering applications.

Source:
Lee, Y., Yi, H., Kim, W., Kang, K., Yun, D., Strano, M., Ceder, G., & Belcher, A. (2009). Fabricating Genetically Engineered High-Power Lithium Ion Batteries Using Multiple Virus Genes Science DOI: 10.1126/science.1171541

Other Articles of Interest:
Utilizing Natural Killers: Phage-Based Antimicrobials
Evolution of Phage Capsid and Genome Size
How Far Do Those Phages Stretch?
Phages with Horns? What's Next?
I Got You Phage

Blogging for Bacteriophages is Back

noreply@blogger.com (Tim Sampson) — Sat, 09 May 2009 16:09:00 +0000

After a rather long sabbatical, Blogging for Bacteriophages is ready to start reporting the exciting and interesting news in the world of microbiology.

The layout is finally optimized. Comments are fully functional. Blogger has also introduced "reaction boxes" to allow you to give feedback with just one click.

Most importantly, I finally have time to devote to publishing again. A realistic goal is 2 articles each month, with a hopeful goal of 4 per month. As always, I would love input from others in the field, especially other graduate students.

I am looking forward to sharing some fun and ground breaking science, as well as interesting experiences I have had over the past few months. I have been privilaged to listen to some fantastic science coming from notable speakers, such as James Watson, Matthew Meselson, Angela Belcher, Pete Greenberg, and many others.

Here's to a new start!

Antibiotic Treatment: Increasing the Rates of Genetic Exchange

noreply@blogger.com (Tim Sampson) — Mon, 15 Dec 2008 23:26:00 +0000

The dangers of single antibiotic treatment are well known and well established. It is common knowledge that improper use of antibiotics can lead to the development of resistant strains in which the antibiotic was created to be used against.

The development of these resistances in a population is most often thought to be due to direct selective pressure. That is, those cells containing mutations that resist the antibiotic, or those that contain a protein to export or degrade the antibiotic, are heavily selected for. Because of this, as bacterial populations grow resistant, treatment includes higher levels of antibiotic or utilizing multiple types of antibiotics.

However, there is a 2006 study, published in Science, which shows that antibiotic treatment does more than "merely" select for resistant strains. Instead, when Streptococcus pneumoniae detects one of a variety of antibiotics, it activates it's competence regulon, thus turning on its ability to be transformed.

To me, this finding is drastic. What this means is that not only do we push direct selection for resitant strains, but we are also stimulating gene aquisition. The ramification of which, means that sensitive strains that detect a low level of antibiotic are now more capable of becoming resistant by aquiring genes via transformation.

This finding stemmed from the hypothesis that since both transformation and DNA repair (sometimes due to antibiotic damage) require similar (the same) recombination enzymes. The authors went on to show that competence was activated in sub-lethal ranges of antibiotics at around 200 minutes post treatment.

The antibiotics that were shown to induce competence, cross many classification boundries. The list includes: mitomycin C, norfloxacin, kanamycin, streptomycin, levofloxacin, moxifloxacin, and norfloxacin. So, mainly the quinolones and the aminoglycosides. (To note: The quorum sensing molecule discussed in the membrane vesicle article, is a quinilone. Perhaps a connection here to competence?)

Those that did not induce competence include: ampicillin, cefotaxime, nalidixic acid, erythromycin, tetracycline, novobiocin, rifampicin, and vancomycin.

The authors propose a few hypotheses on how these are acting to induce the competence regulon, including chromosomal arrest and ppGpp levels, but nothing concrete.

The bottom line is that antibiotic treatment has the ability to increase the rate of gene transfer by activating competence genes (at least in Streptococcus), thus increasing the rate of resistance in a population, compared to direct selective pressures alone.

Source:

Prudhomme, M. (2006). Antibiotic Stress Induces Genetic Transformability in the Human Pathogen Streptococcus pneumoniae Science, 313 (5783), 89-92 DOI: 10.1126/science.1127912

Other Articles of Interest:
Extracellular Membrane Vesicles in Bacteria: Taking Quorum Sensing in New Directions
Utilizing Natural Killers: Phage-Based Antimicrobials
The Origins of Antibiotic Resistance
Wild Bacteria That Eat Our Antibiotics? Of Course!

Update

noreply@blogger.com (Tim Sampson) — Thu, 11 Dec 2008 01:44:00 +0000

Comments are still down....the host site is apparently having trouble with comments across the board. I will have this fixed as soon as I can.

Overall though, I am quite pleased with the new layout. This is looking like how I am going to keep it, for the most part. Small changes may appear over the next few weeks.

I am in the midst of final exams, however I will be back to science posting by the weekend. I have some thoughts itching to be written.

Hope you enjoy the new look and feel. As always, feel free to e-mail me comments, questions, and concerns!

*****Update 13 Dec 08******
I'm fooling around with the site code....so the site may undergo drastic changes in short periods of time. The host site is giving me troubles with comments still and with changing view sizes.

Future Changes

noreply@blogger.com (Tim Sampson) — Thu, 04 Dec 2008 18:57:00 +0000

I hope all of you had an enjoyable Thanksgiving holiday!

Blogging for Bacteriophages has seen a rapid increase in traffic over the last two months. Page views jumped dramatically this fall (Nearly 60% from the summer averages and 130% from the spring)

So thank you! It delights me to no end that there are individuals who take the time to peruse my site. It is funny to think that this started as a study mechanism for me, and turned into a wonderful little hobby that others are benefitting from.

In order to make this site easier to read, explore, and interact with, I am in the process of reformatting the site. Hopefully this will go easily, and may even be finished by the end of today. (Though I can give no promises)

Most importantly, I can not stress this enough, I would greatly enjoy feedback on the articles here. Feedback on everything from the science itself, to how I communicate the science, to new topics, etc. This is ever important to me. So, to facilitate this, I plan on opening up the comments section. I hope that with the great increase in readership, this comments section will be used.

I am also interested in having guest posts, with an interest in hearing from fellow graduate students in the field. I can not offer payment, although free advertising is available. I would also consider sending prints of some of my Phage Artwork in return for articles used.

Thank you!

Extracellular Membrane Vesicles in Bacteria: Taking Quorum Sensing in New Directions

noreply@blogger.com (Tim Sampson) — Mon, 24 Nov 2008 01:46:00 +0000

Bacterial quorum sensing is not a new phenomenon by any means. Although the term has only recently come into the existence, the concept has been around for decades.

In 1964,Tomasz and Hotchkiss, out of Rockefeller, demonstrated the presence of a macromolecule responsible for induction of competence in pneumococcus when the cells reached a specific growth point in mid to late log phase.
This concept has been vastly expanded upon and the ramifications of such diffusible communication molecules are vast. Everything from biofilm formation to stringent responses to bioluminescence have been shown to be controlled by quorum (or diffusion) sensing molecules.

Commonly, quorum sensing molecules are lactones, small peptides, or small lipids. It is thought that these small molecules are secreted by the cell and diffuse through the aqueous environment where they can interact with other cells. This is all well and good, IF the molecule of interest is hydrophillic and freely diffusible. But researchers are finding that many quorum sensing molecules are NOT hydrophillic, and instead very hydrophobic, such as a quinilone with a long chain fatty acid attached. One such example of this, is the Pseudomonas aeruginosa molecule called PQS.

How can a molecule be used as an extracellular signal, if it can not diffuse freely? Dr. Marvin Whitely and colleagues have shown that PQS is able to promote the formation of membrane vesicles off the outer Pseudomonas membrane. Pseudomonas is known to naturally produce these vesicles, however PQS directly induces changes in the lipid membrane to form such vesicles.

Furthermore, these vesicles have the strong potential to be able to capture a variety of macromolecules that are in the vicinity of the membrane bleb. A prime example would be the beta-lactamases that are in the periplasmic space. But we could imagine other molecules being packaged up and delivered.

Molecules that are packaged could be delivered to the same cells in the population, or to foreign cells of different species, perhaps even to humans during pathogenesis. The possibilities are endless as to what these membrane vesicles could be providing instructions for.

One very important piece of data that is missing from this model, is that researchers have yet to observe membrane vesicles of one cell fusing with another cell. This would provide solid evidence that these vesicles could, in fact, deliver signals to other cells.

I had the privilege to have Dr. Whitely as a guest lecturer recently. He has some very interesting work on going in his lab, including the amazing creation of bacterial lobster traps. This work is not yet published, so I should not say anymore than that. However, once it is in the public domain, it has the potential to revolutionize the study of small bacterial populations.

Sources:
1) Tomasz and Hotchkiss. "Regulation of the transformability of Pneumococcal cultures by macromolecular cell products." PNAS (1964). 51, 3. p480

2)Mashburn, L., & Whiteley, M. (2005). Membrane vesicles traffic signals and facilitate group activities in a prokaryote Nature, 437 (7057), 422-425 DOI: 10.1038/nature03925

Utilizing Natural Killers: Phage-Based Antimicrobials

noreply@blogger.com (Tim Sampson) — Fri, 14 Nov 2008 02:30:00 +0000

My last article on the origins of antibiotic resistance perked my interest in the current thinking of how we scientists are planning on overcoming this challange. The two answers that most people will consider are 1) develop new chemical analogs of current antibiotic compounds, and 2) discover novel compounds that act as antimicrobials.

It is this second concept that appeals most to me. However, it raises the question, "Where do we look for novel antimicrobial compounds?"

Some are taking a step back to the days of Felming and looking everywhere: fungal isolates, plant extracts, bacterial products, etc. However, we can not forget the natural-born killers of bacteria. . . thier phages.

Bacteriophages have been coevolving with thier hosts since the dawn of time. As such, I would imagine they know a thing or two about killing a bacterial cell. Phage proteins interact with those of their host to modify and shutdown various functions. By taping into these types of interactions, we could exploit phage proteins to develop ways to attack the host. Furthermore, with the number and diversity of the phage world, there is great potential that each phage attacks the host in a slightly different fashion.

So now the question becomes, how do we find which proteins of the bacteriophage which function as bacteriocidal or bacteriostatic molecules?

The screen is relatively simple. Ask which phage genes, when inducibly expressed in the host, kill the host cell. Researchers have already performed this type of assay in Staphylococcus, and more recently, in the Mycobacteria.

Utilizing an acetimide-inducible promoter system, 3 phage genes (from temperate mycobacteriophage L5) were discovered to have toxic effects on the host, Mycobacterium smegmatis. Further characterization of these genes can find the specific host targets on which they act. Subsequently, small molecules could be developed and screened to act in the same location.

This method could allow the discovery of new drug targets and the drugs which access them. It is fast assay that uses phages in a clever and indirect way to fight disease.

Sources:

1) Liu et al. (2004). "Antimicrobial drug discovery through bacteriophage genomics". Nat Biotechnol 22, 185-191.

2)Rybniker, J., Plum, G., Robinson, N., Small, P., & Hartmann, P. (2008). Identification of three cytotoxic early proteins of mycobacteriophage L5 leading to growth inhibition in Mycobacterium smegmatis Microbiology, 154 (8), 2304-2314 DOI: 10.1099/mic.0.2008/017004-0p>

Other articles of interest
The Origins of Antibiotic Resistance
I'll Have My Bacteria Extra-CRISPR

It's Gonna Be There (The E. Coli Song)

noreply@blogger.com (Tim Sampson) — Thu, 23 Oct 2008 21:04:00 +0000

I'm back again with a dorky song. Written originally years ago for undergraduate Microbiology Lab, this song was in response to the many outbreaks of E. coli (specifically those occuring in spinach and other produce).

I hope you find this song as enjoyable as I do.
I would love to hear some feedback on this and the other "performances" I have posted under the "Phage Fun" heading. Feel free to e-mail me at the address on the left.

It's Gonna Be There (The E. Coli Song) To the tune of Blessid Union of Souls' "I Wanna Be There"

Lyrics
Don't you let that burger fall
I really hope you washed your hands
Invisible to eyes, that means small
Is that too hard to understand.

You got to clean everything
Or it will be filled with coliforms
And pretty soon, someone may be dead.

Chorus
It's gonna be there when you zip your fly
It's gonna be there when you rub your eyes
It'll cramp your stomach, cause internal pain
It'll make your intestines go insane.
It's gonna be on beef, whether or steak or ground
And in leafy greens it has been found
You better cook your food
You better wash your hands
Cause E. coli's on the lamb

You'd never know that it was there
But it has been there all the time
And if it had its way, it stay in cows on farms
But it loves bad hygeine and your grime

Cause you got dirt on yourself
When you leave the toilet room
Though the sign says, "Employees Wash Your Hands"

Chorus

And if its got blood cells to kill
Well you'd have to take some pills
And with some time, your kidneys may fail

It's gonna be there when you zip your fly
It's gonna be there you don't have to try
Gram negative and anaerobic too
And it lives inside of me and you

It's gonna be there on your burger
It's gonna be there on your knife
It'll cramp your stomach, cause internal pain
It'll make your intestines go insane.

Other Songs to Listen To:
The Brillant Dance of the Starvation Response
The Ballad of the Virus (They're Everywhere)
I've Got You Phage

The Origins of Antibiotic Resistance

noreply@blogger.com (Tim Sampson) — Fri, 17 Oct 2008 21:18:00 +0000

Antibiotic resistance is becoming an increasingly important plight that we face in our treatment against bacterial infections. The acronyms MRSA and XDR-TB have become headlines across the world; and the number of untreatable infections is on the rise. But even as we learn more about the increase in antibiotic resistance and what we must do to overcome this, we must also look into past evolutionary history and try to deduce how these resistance mechanisms arose.

One way to do this is to look for functional antibiotic resistance genes in a bacterial population that has not been exposed to our medical treatment pressures. Researchers from the University of Wisconsin-Madison recently published an article that shows just this. They have demonstrated that antibiotic resistance genes (specifically those which encode beta-lactamases) can be found in soil bacteria from pristine regions of Alaska.

Using soil cores from a region of Bonanza Creek Experimental Forest, the researchers extracted bacterial DNA. This was then cloned into a library and constructs were screened for resistance to beta-lactamase. Those constructs that were positive for resistance were then subjected to transposon mutagenesis to identify the precise region conferring resistance.

Not only does this demonstrate that beta-lactamases were present, but more importantly, it demonstrated that these genes were functional. This is a far leap up from merely metagenomic sequencing. A sequence may be able to tell you if a type of gene is present, but it can not tell you if it is functional. Furthermore, merely sequencing may hide the presence of a beta-lactamase that has no homology to known genes.

Of the nearly 12 Gigabases of DNA that they extracted, they isolated 14 clones that had the ability to grow on clinically significant concentrations of beta-lactam antibiotics. The genes encoded by these clones were found to be distantly related to the current bank of known beta-lactamases. This allows us to have a look back in time to see the functional beta-lactamases that gave rise to the types in our current strains.

(The authors also found the first example of a bifunctional beta-lactamase. That is, a single protein created by the fusion of two different, yet functional, beta-lactamases. Perhaps an example of duplication giving rise to a new subset?)

I am a firm believer in the fact that in order to know where we are going, we must always remember where we came from. On that note, in order to provide better answers to antibiotic resistance, we must first understand how it arose.

Allen, H., Moe, L., Rodbumrer, J., Gaarder, A., & Handelsman, J. (2008). Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil The ISME Journal, 3 (2), 243-251 DOI: 10.1038/ismej.2008.86

Other articles of interest:
Altruism in Bacteria? Allowing Yourself to Die for the Good of the Species
Wild Bacteria That Eat Our Antibiotics?! Of Course!

A MAP to Crohn's Disease; Revisiting Koch's Postulates

noreply@blogger.com (Tim Sampson) — Sun, 05 Oct 2008 22:45:00 +0000

The fundamental principle of infectious disease is Koch'sPostulate. To be brief, he set forth the qualifications that must be fulfilled in order to associate a pathogen with an illness. This includes the isolation of the organism from diseased tissue, the ability to grow the organism in pure culture, and the recreation of the disease in a healthy individual following introduction of the purified organism.

This procedure was used at the time to demonstrate Mycobacterium tuberculosis as the causative agent of consumption. Although to be sure, Koch's Postulate does run into some trouble with organisms such as M. leprae which can not be grown ex vivo. (More on M. leprae's reductive genome found here)

It is only fitting that a modern day example of pathogen associated disease is that of another mycobacteria, the intracellular pathogen M. avium paratuberculosis (MAP) and its potential to be a causative agent of Crohn's Disease.

Crohn's Disease is a severe inflammatory bowel syndrome, characterized by inflammation in discrete sections of intenstinal tissue seperated by healthy tissue. Affecting over half a million people in our country (CDC 2001), this chronic illness has no known cure. Treatments include anti-inflammatory drugs, and tellingly, the anti-mycobacterial rifampicin.

A recent study from the University of Otago in New Zealand has shown a strong correlation between the presence of MAP and Crohn's Disease. Using a PCR detection method, they amplified a region specific to MAP, the IS900 element, from white bloodcells of both Crohn's patients and non-affected individuals. The PCR screen is sensitive enough to detect 100 cells/mL of blood. Furthermore, this study is currently the largest of it's kind, examining samples from over 350 affected individuals and 200 controls. Past studies have only looked at groups of around 50 individuals.

Owing to the larger number of samples, this study lends itself to a more detailed statistical analysis. Firstly they found that 122 of the 361 individuals (33.8%) affected by Crohn's were postive for MAP. On the otherhand, 43 of the 200 control samples (21.5%) were also MAP positive.

In my humble opinion, this does not seem significant. However, the author's statistical analysis shows otherwise. They show with a 95% confidence interval and a 0.002 p-value, that MAP is closely associated with Crohn's Disease. A handful of other (smaller) studies have confirmed similar results. However, the conclusion remains controversial due to many other studies that have not found a correlation.

A close friend has said that this study reminds him of the Heliobacter pylori and stomach ulcer story (of Nobel Prize winning proportions). However, a fundamental difference between that story and this one, is that we have yet to show that a pure culture of MAP is capable of inducing pathology in an individual. (Although it is the causative agent of a bovine inflammatory bowel syndrome)

***Revision 17 Oct 2008: An astute reader pointed out that Dr. Rod Chiodini has already fulfilled Koch's Postulates for MAP-induced Crohn's Disease. A little digging found the article: Dig Dis Sci. 1986 Dec;31(12):1351-60. MAP from Crohn's patients was isolated and used to induce the bowel disease in goats! ***

It is my belief that we will find that MAP is not the sole agent of Crohn's, but is likely an instigator for many individuals who are genetically pre-disposed to inflammatory disease. We are peeling back more knowledge each day that demonstrates that disease isn't as simple as an invading pathogen. Stochasticity and host response must be taken into account when determining the cause of disease.

Source:
Bentley, R., Keenan, J., Gearry, R., Kennedy, M., Barclay, M., & Roberts, R. (2008). Incidence of Mycobacterium avium Subspecies paratuberculosis in a Population-Based Cohort of Patients With Crohn's Disease and Control Subjects The American Journal of Gastroenterology, 103 (5), 1168-1172 DOI: 10.1111/j.1572-0241.2007.01742.x

Other articles of interest:
Reductive Evolution in Mycobacterium leprae
A Brief Bit More on Reductive Evolution in M. leprae

The Brillant Dance of the Starvation Response

noreply@blogger.com (Tim Sampson) — Sun, 21 Sep 2008 02:36:00 +0000

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")
Lyrics:
So this our
Painful realization
That 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 cya
Which creates cyclic-AMP
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
And RelA has to make the call
And synthesize pppGpp

And oxidation becomes a task
And 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 stringent

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 forespore...

How Far Do Those Phages Stretch?

noreply@blogger.com (Tim Sampson) — Fri, 19 Sep 2008 22:54:00 +0000

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.

Featured in the Fall Harvest of the ASM Blog, "Small Things Considered"

The Ballad of the Virus (They're Everywhere)

noreply@blogger.com (Tim Sampson) — Fri, 19 Sep 2008 00:35:00 +0000

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)
Lyrics:
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

~Chorus~
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

~Chorus~

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

Featured in the Fall Harvest of the ASM Blog, "Small Things Considered"

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

noreply@blogger.com (Tim Sampson) — Wed, 10 Sep 2008 19:20:00 +0000

Altruism in general is an interesting concept from an evolutionary perspective. As defined by Dictionary.com, 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 tissue, 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.

Source:
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

Other Articles of Interest
Mosaicism: The World of Horizontal Gene Transfer (Part 1)
Where the Wild Microbes Are: A New Theory on How Pathogens Survive Food Processing
Wild Bacteria That Eat Our Antibiotics? Of Course!

Apology

noreply@blogger.com (Tim Sampson) — Tue, 19 Aug 2008 23:45:00 +0000

I need to apologize for my lack of activity recently....things got a little out of hand, but now that I have finished a rather large move and am settling in to things, there should be more content in the near future!

Thanks!

Tim

A Brief Bit More on Reductive Evolution in M. leprae

noreply@blogger.com (Tim Sampson) — Fri, 13 Jun 2008 02:53:00 +0000

In a previous post I discussed the evidence for reductive evolution in Mycobacterium leprae, an interesting obligate intracellular parasite.

At the 2008 ASM General Meeting, the Division U keynote lecture was headed by Tom Gillis of the National Hansen's Disease Program. His talk described the same work I cited in the previous article, which showed the immense amount of pseudogenes in the M. leprae genome.

Gillis was interested in elucidating the role of these pseudogenes. This included asking whether or not these genes are transcribed and translated. If these pseudogenes are not providing any function, then it stems that the cells will not put energy towards their expression.

The work he discussed showed that ~44% of all M. leprae transcription was due to pseudogene expression. There doesn't appear to be a locational bias for pseudogene transcription either. Looking closely at 10 pseudogenes downstream of full-length genes, only 8 produced full-length transcripts.

More indepth in silico analysis shows that all these pseudogenes are unilogs (no duplicates present in the M. leprae genome), the vast majority lack a strong Shine-Delgarno sequence upstream, ~75% lack a translational start codon, and ~98% have one or more in-frame stop codons inserted.

This indicates that a very small percentage of pseudogene transcripts actually create a full-length translational product. So, although the cells still create the transcript, few (if any) resources are put towards creating a functional (or detrimental) protein product.

I also picked up some interesting epidemiological facts of the M. leprae genome. For one, the global M. leprae population is nearly clonal (1 polymorphism to 20,000bp compared to 1:5000 for M. tb.). However, variation in SNPs can be seen in local populations. In looking at ~60 cases from a town in India, the bug had a higher rate of diversity than compared to 3 cases in the South Eastern US or to 20 wild armadillos. Furthermore, the US cases and the wild armadillo cases were strikingly similar on an SNP scale.

I think an important point to take home from this is that M. leprae is still an evolving organism, and we are only catching a snapshot in time. It is a prime example of a parasite that has come to depend greatly on its host and has lost the ability to function outside said host.

Other articles of mine that may be of interest
Reductive Evolution in Mycobacterium Leprae
Evolution of Phage Capsid and Genome Size (Another 2008 ASM General Meeting Lecture)

Evolution of Phage Capsid and Genome Size

noreply@blogger.com (Tim Sampson) — Sun, 08 Jun 2008 20:32:00 +0000

Viruses come in all shapes and sizes. From the very small, such as the picornaviruses or the parvoviruses, to the very large like mimivirus, or the herpesviruses, and poxviruses. These large viruses are not just large in physical size, but in the size of their genomes as well.

At the recent 2008 ASM General Meeting, Roger Hendrix of the University of Pittsburgh, laid forth a rather interesting hypothesis as to how large genomes, and the capsids that hold them came into existance and how they managed to be competitive in the gene pool.

Using phage P1 as an example, we know that larger capsids can be created "simply" by a single mutation allowing capsid subunits (capsomers) to come together in a quasi-equivilant matrix that is larger than the previous. This matrix follows the mathematical model set by Casper and Klug, and has discrete sizes (triangulation numbers, such as T=1,3,4,7,13). An increase in T number, as in our P1 example, causes a dramatic increase in capsid volume. Hendrix proposes that a mutation causing a such a shift acts as an evolutionary ratchet, and therefore smaller capsid sizers would no longer be available.

Now that we have a larger capsid, the phage now has the ability to package much more DNA. Not only does it have the ability, but in many cases, the phage MUST package DNA until its capsid is filled (headfull-packaging). With a larger capsid, phages who package via headful mechanisms now must package more DNA creating a greater amount of redundancy in its genome.

Hendrix explained that a greater amount of terminal redundancy leads to greater resistance from DNA damaging agents, specifically UV light. Although some in the session contended this, Hendrix described large amounts of genomic redundancy as an evolutionary advantageous trait for phages which live on the surface of the ocean and soil.

Furthermore, the extra space in the genome acts as a virtual genetic laboratory to aquire and mutate genes without disrupting the ability of the phage to survive. Gene aquisitions and subsequent mutations could create genes which provide some sort of marginal (or large) benefit to the phage or the host it infects.

With a simple click of the ratchet and a headfull of DNA, the role that large phages play in novel gene development are only now beginning to become clear.

My posts on similar topics

Mosaicism: Life on a Small, Ever Changing Scale

The Definition of Life; and, Taxonomy as We Know It

Free Hydrogen--Algal Biofuel Production

noreply@blogger.com (Tim Sampson) — Fri, 30 May 2008 23:20:00 +0000

Blogging for Bacteriophages is proud to give you it's first guest post. This article comes from M. McGuirk., a biochemistry student at Chatham University.

Green algae are photosynthetic microorganisms capable of using protons as a reductant and producing molecular hydrogen. As technology advances, these organisms might provide an efficient, cost-effective method to mass produce hydrogen gas to be used as a renewable source of energy. Currently, hydrogen fuel is extracted from natural gas and other non-renewable energy sources, which release particulate matter and greenhouse gases into the atmosphere during their extraction and processing. Algal biosynthesis of hydrogen is particularly promising because it uses two of Earth’s most abundant resources, light and water, to form an "eco-friendly" biofuel.

Hydrogen gas production by green algae is a consequence of anaerobiosis, which forces the cell to rely on molecular hydrogen as a reductant. Green algae are exposed to anaerobic conditions in lake and sea sediments, which can become anoxic with insufficient water turbulence or excessive algal blooms. Historically, hydrogen production by green algae was induced by anaerobic incubation in the dark, which stimulates the expression of a hydrogenase enzyme.

The major roadblock for commercial application of hydrogen biosynthesis by algae is the fact that algal hydrogenases are inhibited by molecular oxygen. This sensitivity to oxygen has motivated extensive work to genetically engineer mutants of Chlamydomonas reinhardtii with more oxygen tolerant hydrogenases. The successful engineering of a more oxygen tolerant hydrogenase would put us one step closer to commercial biosynthesis of molecular hydrogen for fuel. Another approach to the problem of hydrogenase oxygen sensitivity is temporal separation of the water splitting and hydrogen evolving reactions.

Researchers have also shown that sulfur deprivation improves hydrogen yield by inhibiting molecular oxygen evolution. In the absence of necessary nutrients, metabolism and growth slow significantly too conserve the remaining substrates. In the case of green algae and other photosynthetic organisms, sulfur depleted environments stimulate the downregulation of photosytem-II and consequently, molecular oxygen evolution. Under these circumstances, electrons are not sufficiently removed by molecular oxygen. Green algae significantly increase hydrogen production under sulfur-deprived conditions because hydrogenase is charged to remove the excess electrons.

Hydrogen fuel offers an efficient, environmentally friendly alternative to gasoline and biodiesel. Hydrogen is a potent, cost-effective fuel because it has the highest energy content per unit of weight of any known fuel. Hydrogen gas production by green algae shows enormous promise, but requires a few manipulations to make the process feasible on a commercial scale. To improve this process, the number of hydrogenase expressed in the cell must be increased (without being toxic) to increase the yield of hydrogen per algal cell. The oxygen sensitivity of the hydrogenase enzyme must also be reduced so that the enzyme can produce hydrogen more efficiently in easily managed environments. It is highly likley that within our lifetimes, we will see algal hydrogen production on a commercial scale.

2008 ASM General Meeting, Boston MA

noreply@blogger.com (Tim Sampson) — Thu, 29 May 2008 01:09:00 +0000

On June 1st through 5th, I have the distinct pleasure of attending my third ASM General Meeting, in as many years. My poster titled "Novel Generalized Transducing Phages of the Mycobacteria" is number M-005. Feel free to come and chat about esoteric microbiology topics.

I plan on writing on a handful of interesting topics presented.

It should be a great time for all!

Winogradsky Column (Day 1)

noreply@blogger.com (Tim Sampson) — Mon, 26 May 2008 15:10:00 +0000

I have decided that my microbiology education would be incomplete without experiencing first hand the creation of a Windogradsky Column.

I must apologize for not having any sort of dissecting/micro scope to closely examine the succession over time.

This column was started yesterday with mud/silt from Panther Hollow "Lake,"and no extra nutrients or minerals were added. It's currently sitting in my living room window.

Currently, there are a bunch of small worms throughout the mix, lots of daphnia, and a small bunch of insect larvae.

I am most interested to see how the anerobes come into play, whether or not any colorful sulfur bacteria can flourish here.

I'll continue to post updates of the Column here regularly. Hopefully, some will find this excersize as enjoyable as I am!

Walking the Line Between Grades and Experience: My Life as an Undergraduate Researcher (Part 2)

noreply@blogger.com (Tim Sampson) — Fri, 23 May 2008 22:52:00 +0000

Continued from Part 1

I finished my sophomore year with a B-average, and went into the summer with my mind set on losing myself in my research again. I was doing some really cool assays with M. tb and M. bovis BCG (I was the only undergraduate in the lab taking advantage of our facilities). This work spring boarded me into a highly competative fellowship from HHMI. Since this was quite a some of money, and it had to be renewed every semester (including summer's), I was dead set on putting out high quality and large quantity data.

So I did. My junior year (filled with Physics and Biochemistry) was spent skipping classes to put out data. And I did, I revised current protocols for a generalized transduction assay, assayed more than 2 dozen phages for this ability, screened over 200 phages for the ability to infect M. tb. (Manuscript in process) My work in the lab from my junior year was, in my opinion the best I had put out.

However, that summer when I went to renew my fellowship for my senior year, I received surprsing news. I would not be accepted into the program that fall because my grades were raising "red flags." It was in the opinion of the comittee that if I was to head to graduate school (like I planned) I would need to get my grades up. I was startled.

I had heard that experience was the primary factor in determining eligibility to PhD programs. I guess Cs in two semesters each of Physics and Biochemistry didn't look so good, not to mention that O. Chem 1 was repeated, along with its lab.

So, they cut off my funding so that I would spend more time studying, to lower the red flags.

Now, I am not a stupid person. Although, some may say that my grades don't demonstrate the intelligence required for higher learning. I took a step back from my research senior year, and concentrated on bringing my grades up. Each semester this past year (which were both heavy on senior-level biology courses) I earned a GPA of 3.8. Somehow, my final cumulative GPA was ~3.4, despite some very low semesters in the past.

I had to do this to show that I had learned the foundational knowledge of biology. I had already proved I knew my way around the lab, I had to show that I was doing more than going through the motions.

I brought my grades up to a point where there are no longer any red flags that shadow my lab accomplishments. I still managed to put out great work in the lab (soon-to-be first author on two papers), although I will concede that I did not finish as much research as I would have liked.

However, I'm now heading to my top choice of the graduate schools I applied to (Emory University, PhD Program in Microbiology and Molecular Genetics). My words of advice are to gain as much experience as possible, nothing is held in higher regard. But, to do so at the expense of grades...not such a good idea.

Although it worked out better than I could have imagined, there was a strong possibility that it would not have worked out this way. But now, I am onward to a place where building experience is the primary focus, and so I am quite excited to continue on my science career.

The End

Revisit Part 1 Here

Walking the Line Between Grades and Experience: My Life as an Undergraduate Researcher (Part 1)

noreply@blogger.com (Tim Sampson) — Fri, 23 May 2008 01:20:00 +0000

From the moment I began looking for a university to attend after high school, I knew I wanted to do biology research. "Experience is key" I was told, in order to do anything after receiving a 4yr degree. So although I was unsure what it was I truly wanted to pursue after getting my BS in Microbiology, I KNEW that I would need research experience to succeed.

And so, I sent out my first requests to volunteer in research labs in October of my freshman year. No one would take a 1st year with no foundational knowledge....except one lab. The following semester, a post-doc in Graham Hatfull's lab, by the name of Marisa Pedulla, took me on board with a group of other students, although I was the youngest, to give us our first taste of research. We set out to perform bioinformatic analysis on a group of 6 Bacillus phage genomes that the Pittsburgh Bacteriophage Institute had recently finished sequencing. I was given the tools to uncover the patterns within the genetic code to find the most likely genes, hypothesize their function, and deduce evolutionary relationships.

I was hooked. It fascinated me to be able to unlock the secrets that patterns of four simple letters could hold.

I spent way to much time in front of a computer screen that semester, engrossed in sequence, running a million BLAST searches or ClustalW alignments at once. Suffice to say, my grades dropped. I had started my 1st year with a B average (not bad for an incoming freshman acclimating to a life 5hrs from childhood friends and family), and ended it with a C average. I dropped the ball. But I thought, "This experience will make up for a loss in grades." Little did I know....

I was asked to continue working on bacteriophage genetics in the Hatfull Lab that summer. So as an 18yr old just finished with one year of college, I began life as an adult. I rented out my own place--while all my friends had packed up to move back home with parents for the summer, I was packing boxes to take to a one-bedroom place a few blocks from the lab.

That summer I again engrossed myself in my work and work for the Hatfull Lab. (I should mention that some of this work is in the process of being published...). Summer went by quite fast, I visited my friends and family from home only twice because I was so over my head in what I was doing at the lab. Too soon, the summer ended and my second year began.

I was still working in the lab--only now I was required to work 10hrs a week. This soon became 20-30hrs a week because I became excited when things went well on some sequencing projects I was doing. Little did I know that I would be smacked over the head by two little words. Organic Chemistry. The bane of many undergraduate biology major's existances. I did not spend as much time studying for that course as I should have, and it showed in my grades. D+ in O. Chem 1--meaning I would have to retake the course. Suffice to say, I got an A in our honors genetics class (mainly because it was so applicable to what I was doing in the lab). But again, I my grades really did not accuratly portay my potential and what I knew. Again I thought, "It's my experience that will count, not my grades."

Again, I knew so little.

Continue Reading Part 2 Here

Mosaicism: Life on a Small, Ever-Changing Scale (Part 2)

noreply@blogger.com (Tim Sampson) — Mon, 19 May 2008 23:50:00 +0000

In the my last article, I briefly discussed the role of horizontal gene transfer in bacteria...specifically the development of mosaic pathogenicity islands in Escherichia coli. However, the formation of mosaics are not just limited to operons within bacterial genomes. In fact, we can see such events in phage and viral genomes. This article is part two in a brief series on genomic mosaicism.

Current research shows that illegitimate recombination events create mosaics of unique genes within the genome. Each gene then acts as an individual unit upon addition, whereby beneficial genes are selected for and remain in the genomes, and non-beneficial genes build up mutations or are dropped. Illegitimate recombination, by definition, occurs within gene boundaries, and as such, highly unique and variable regions within genomes are formed.

Looking within the sequenced genomes of the mycobacteriophages (an obvious interest of mine) we see a large amount of mosaicism. Small sets of genes, individual genes, and parts of genes are constantly being shuffled in, out, and around genomes. There are countless examples of gene insertions and deletions in the phage genomes, adding to the case that genomes are liquid and constantly changing. We see gene swaps not only between phages, but also between hosts.

These events show themselves by the presence of unique genes in genomes. For instance:
1) the presence of photosynthesis genes in many cyanophages
2) a portion of mycobacterial MetE in far right arm of the mycobacteriophage Giles genome (a conclusive example of illegitimate recombination between virus and host)
3) the protein Ro in mycobacteriophage Bxz1 (a eukaryotic protein implicated in the human disease lupus)
4) Bxz1 also contains a human peptide chain release factor
5) a portion of Bacillus VIP toxins in a mycobacteriophages PBI1 and PLot
6)Mycobacteriophage Che8 contains a human prion-like protien
7) motifs of resuscitation promoting factors in a wide variety of of mycobacteriophage tape measure proteins
8)not to mention the countless (30-50%) number of open reading frames with absolutely no homologs in the current databases or which only match other phage proteins.

(Yes, I did say that phage Bxz1 of the mycobacteria contains a human antigen gene, with significant sequence similarity, see here.....I'll leave this discussion for another day, mainly because as far as I know, no one has looked at such a seemingly odd phenomenon outside of bioinformatic comparison. How did a human gene sneak its way into a bacteriophage?)

What I am trying to drive home here, hopefully with some success, is that life at the small scale is ever fluctuating and massively interconnected. Nothing in biology is genetically isolated. We are the current homes of many genes, where they end up next is up to our viral and phage couriers.

PEDULLA, M. (2003). Origins of Highly Mosaic Mycobacteriophage Genomes. Cell, 113(2), 171-182. DOI: 10.1016/S0092-8674(03)00233-2

My Similar Articles
Mosaicism: The World of Horizontal Gene Transfer (Part 1)
The Definition of Life, and; Taxonomy as We Know It
ReQ's Role in Illegitimate Recombination
I'll Have My Bacteria Extra-CRISPR

Also, visit The Phamerator to explore the sequenced mycobacteriophage genomes on your own.

Got Phage?

noreply@blogger.com (Tim Sampson) — Fri, 09 May 2008 22:14:00 +0000

A little bacteriophage graphic that I designed, and placed on some merchandise. I thought that some here may find it interesting / entertaining.

The Blogging for Bacteriophages "Got Phage?" store is selling some T-Shirts and some random things. I think the "Ringer T-Shirt" looks really good, and I also recommend the clock, stickers, and pillow.

Feel free to check it out and enjoy!