Friday, May 30, 2008

Free Hydrogen--Algal Biofuel Production

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

Chlamydomonas: A Hydrogen Factory in Disguise 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" .

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 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.

Wednesday, May 28, 2008

2008 ASM General Meeting, Boston MA

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!

Friday, May 23, 2008

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

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

Thursday, May 22, 2008

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

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

Monday, May 19, 2008

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

ResearchBlogging.orgIn the my last article, I briefly discussed the role of ...specifically the 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 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 (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
2) a portion of mycobacterial (a conclusive example of illegitimate recombination between virus and host)
3) the in mycobacteriophage Bxz1 (a eukaryotic protein implicated in the human disease lupus)
4) Bxz1 also contains a human
5) a portion of in a mycobacteriophages PBI1 and PLot

7) motifs of 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 .....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

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

Friday, May 9, 2008

Got Phage?

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!

Mosaicism: The World of Horizontal Gene Transfer (Part 1)

ResearchBlogging.orgCommonly, gene transfer is thought of as a vertical line from parent to offspring, along which all evolutionary traits are passed. However, as we began delving into genomic sequences, we found that this may not be true and that the lines between "species," especially on the microbial level, are quite fuzzy.

is the transfer of genetic elements between species. The microbial world is filled with examples of this phenomenon. This article is the first in a 3 part series that will explore the ever fluctuating genetic world of our microbial majority.

is perhaps the most well studied and utilized bacterial organism on the planet. This bug also has the capability for a wide range of illness in humans including: non-pathogenic, enterohemorrhagic (such as popular strain ), enterotoxigenic, and uropathogenic. The question is obviously raised--how can the same organism have such pathotypes, and what allows it to be versatile enough to thrive in such different environments as the urinary tract vs. the intestinal tract.

An article coming out of the University of Wisconsin-Madison shows that E. coli consists of a general common backbone that is nearly 100% identical across strains, yet only takes up 75%of the genome. However, they show that within this backbone are regions (islands) that are highly divergent between strains (See figure at left). It is no surprise that within these divergent regions contain the genes which allow for survival in different environments ()

These islands are distinct from each other, the surrounding genome, and the corresponding areas in other strains. However, the striking similarity between islands of different strains is that they all seem to be located in nearly the same locations.

Furthermore, strains of the same pathotype tend to have the same/similar genes located in islands (see figure below)--but not necessarily in the exact location or orientation. These islands tend to occur in areas atregions--commonly utilized by .

Phages are clearly agents of horizontal gene transfer, further examination of these island regions show the presence of cryptic (non-viable) prophages. This indicates that at least 5 phages integrated, but subsequently lost genes required for the creation of viral progeny. It is possible that the other islands are also prophages, but gene loss has occurred to the point where they are no longer recognizable.

What this means as a whole to the definition of species is to me, yet, unclear. Strains of E. coli all share a distinct backbone of metabolic genes, but differ drastically in their specialized regions. How do we decide which belongs in a species?...especially when we differentiate humans from chimpanzees (only ~6% genetic differences).

Welch, R.A. (2002). Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proceedings of the National Academy of Sciences, 99(26), 17020-17024. DOI: 10.1073/pnas.252529799

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