I have been more absent than usual from this blog, which is something I regret. However, the time constraints of preparing for my upcoming qualifying exam necessitate this. I decided to break my strict “no distractions” policy to bring you this bit of info that was emailed to me by a lab mate.

Scientists have discovered DNA components in a meteorite, and they seem to be fairly certain it was made there! You can read the actual NASA press release here, and check out a cool video of one of the scientists explaining the discovery here. The cliff notes version is that, while claims of meteorites containing DNA components have been made before, they may very well have been terrestrial contamination. This seems to be different, because the meteorite also contains similar molecules that are never found in biological matter, which is what would be expected if the DNA molecules (technically nucleobases) were created chemically on the meteorite. This has implications for the evolution of life on earth, and all those big exciting questions about how the search for alien life.

The actual paper (which I admit, I have not had time to read yet) can be found, freely accessible here, in the most recent issue of PNAS.

I know, this might remind you of another fairly recent NASA press release that seemed to tease us with hints of alien life, but I, personally, am much more optimistic about this one.

Thats all for now, wish me luck studying. I promise all sorts of exciting new microbial knowledge to share after I (hopefully) emerge “Docrotral Candidate” from the other side of this exam.

-Heather

I came across this article recently in a university-wide email newsletter. The article was a bite sized appetizer with hints of science fiction, green energy, history of life, not to mention a pretty picture with green sparkles. I needed more, so I found the paper where the study was formally written up.

I am a sucker for short, elegant, intriguing titles – ones that pull you in rather than make you re-read 3 times before you have any idea what the paper is about. “Towards a Synthetic Chloroplast” (open access: http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0018877) was just such a title. By the end of the abstract I was still engaged and wanting more.

Our results show that it is possible to engineer photosynthetic bacteria to invade the cytoplasm of mammalian cells for further engineering and applications in synthetic biology. Engineered invasive but non-pathogenic or immunogenic photosynthetic bacteria have great potential as synthetic biological devices.

The paper made me think of one of my favorite books, “Oryx and Crake” by Margaret Atwood, which describes a world in which bioengineering has created a group of people with photosynthetic pigments in their skin. Hungry? No problem, just go sit in the sun for a while. So, what did these Harvard Medical School scientists do that seems to poise them somewhere along the path towards futuristic biological engineering?

First they injected individual Zebrafish embryos with up to 10 million Synechococcus elongatus cells before the embryos underwent their first cellular division. The researchers compared this to injections of E. coli (both living and dead) cells, and found that while both types of E. coli cells killed the developing embryos very rapidly, the S. elongatus cells seemed to have no impacts on the embryo’s development. These embryos are clear, so light could penetrate to the photosynthetic bacteria injected into the cell. The bacteria were easy to track because of their red autofluoresence. Scientists saw the bacteria throughout the embryo (even in the brain and eye), but did not see any abnormal morphological changes in the embryos. The bacteria survived for 12 days within the embryos, and at that point the experiment was stopped because the fish began to become opaque, which would block the light that the bacteria would need to survive.

In a second experiment the scientists wanted to see if S. elongatus could invade mammalian cells if they were provided with the genetic machinery to do so. They identified genes in a different bacteria (invasin from Yersinia pestis Yersinia pseudotuberculosis (see comment below) and listeriolysin O from Listeria monocytogenes) that are known to cause invasion of mammalian cells. They then inserted these genes into S. elongatus. After this, 4.8% of the mammalian cells that they exposed these S. elongatus were positively fluoresent, showing that they had been successfully invaded by the engineered version of S. elongatus.

A third experiment involving macrophages showed that, unlike E. coli, the engineered S. elongatus was able to increase its fluoresence within the host cell (for a few days at least). This means that the bacteria were growing and dividing successfully within the cell.

The work described in this paper demonstrates, in a controlled laboratory setting, the first few steps that would be required to establish an intracellular symbiosis such as the one believed to have been responsible for the first chloroplasts (which therefore enabled the evolution of plants, an oxygen atmosphere, animals, and eventually you and I. There are no known mammalian endosymbioses, and work such as this is one way to understand why. The demonstration that it is possible to engineer a bacteria to be able to invade a mammalian cell has implications for synthetic biology in addition to allowing us insight into the evolutionary history of symbioses in general and even photosynthesis specifically.

Agapakis CM, Niederholtmeyer H, Noche RR, Lieberman TD, Megason SG, Way JC, & Silver PA (2011). Towards a synthetic chloroplast. PloS one, 6 (4) PMID: 21533097

P.S. (5/9/11) I just learned the first author of this paper also blogs here, and wrote her own post about this work. Check it out here!

I was surprised to find this story about scientists exploring the microbial diversity if the Antarctic, which says that they found an unexpected number of heat loving microbes locked in the Antarctic ice. It brings some interesting evolutionary questions to mind, not the least of which is what are those microbes doing there, and how are they adapted to survive such opposite ends of the thermal spectrum? I’ll have to think more about that one and get back to you. I can’t wait to see what the team publishes!

I had a great time moderating Science by The Pint last night! It is always awesome to be reminded how enthusiastic non-scientists often are about science. I find events like this incredibly refreshing when I have been stuck in a science rut or simply less enthusiastic about my work than usual.

I had participated in one of these events last year, when an upper level grad student was speaking. I wandered from table to table talking about how cool hydrothermal vents are, and why we think its important to study them. People asked interesting, important, tough questions, and I was really impressed with the quality of the dialogue. You don’t need a strong, or even any, science background to have a great conversation about science.
This time around I saw it from a different perspective. Being the moderator, I saw it from a few steps back. I tried to make sure every table had a scientist to talk to, and that things were going well with the restaurant (insert plug here for the awesome folks at Tavern by the Square, Porter Square who made sure last night ran smoothly and have been very supportive of Science by the Pint this year). My favorite part of my new role last night was hearing from the speaker and his colleagues afterwards how much they got out of the event. Like me last year, they were pleasantly surprised with the quality of the science discussion, and seemed to enjoy it more than expected.

This type of venue is different from what most scientists are used to. We are used to giving prepared talks and fielding tough nitty gritty questions afterwards that may or may not be trying to poke holes in the research (aka our blood, sweat, tears) that we have just presented. We are not accustomed to (unless we spend a good deal of time teaching) informally discussing our research with a large group of non-scientists who are genuinely curious. It is good practice for us to make sure we can explain our research and why we do it without discipline-specific jargon or over-complicated explanations. It is also good to get very different types of questions than what we are used to answering from our colleagues.

I had a thought last night… that this format would be a great way to talk to students. Not the beer part, obviously – although that certainly would get kids thinking science is cool, but I generally try to stay away from the dark side. Anyhow, I think that rather than a scientist going to a classroom, presenting their research, and answering questions from the students who ask them, I think a scientist going to a classroom with a few colleagues, and breaking into groups and having discussions with the students in smaller groups one on one might be a very effective way to reach these students and get them thinking about the possibility of becoming a scientist themselves.

So, in conclusion, I really like the science café format. I am now re-enthused to go into lab and get my science on!

Cheers!

* Boston, Cambridge, or Somerville, MA

Since microbes are not exactly easy to observe with ones eyes, microbiologists rely heavily on genetic data to tell us about our organisms of interest. For environmental microbiologists, whose organisms can not currently be grown in the lab, knowing what genes our “bugs” contain tells us what processes they might be capable of and can also provide information into their evolutionary history. We can extract the total DNA out of a soil sample and begin to get a picture of what the community living within that soil is capable. However, before we do that we need to take the massive files of As, Cs, Ts, and Gs and figure out how to interpret that.

Imagine a text document of one of Shakespeare’s plays (or even a page of said play) with all of the spaces removed. Imagine each like cut out and shredded into a few random pieces. Imagine that you had 20 copies of that document and each was shredded differently. These multiple copies (or coverage in the bioinformatics world) allow you to attempt to piece together the play by finding pieces that overlap. This can be tricky if there are certain words or phrases that repeat frequently, but given the right computer program you can start to put some of the strips into larger phrases. This is referred to as aligning your sequences.

Once you have aligned sequences there are some tools available to search the alignments for segments that could represent genes. A genome that has been searched for known and recognizable genes is said to be annotated.

There is an interesting paradox here which is that technology keeps improving which means the volume of genetic sequence data we have to analyze is growing faster than the tools and programs we have to do said analyses, however the more bioinformatic data that exists the better our analyses will be because there will be fewer unrecognized genes and more organisms will be discovered. I can’t wait to see how archaic the program that I spent 5 hours struggling with today (ARB for anyone who is familiar… uggh!) will seem in 10 or even 2 years!

How excited was I to learn that the most recent issue of Nature Geoscience had a special focus on deep sea carbon cycling? I admit it, pretty excited. I was even more excited to learn that one of the 3 papers making up this special focus was about the microbial component of deep sea carbon cycling. This may not be something that you think about every day, but I do… well most days at least. The first two sentences of this paper explain why I find this topic so interesting.

Circulation of hydrothermal fluids in upper oceanic crust may support one of the most extensive, but least understood, of the Earth’s biogeochemical systems. However, little is known about non-living organic matter carried in crustal hydrothermal fluids or its possible impact on the carbon cycle of the overlying ocean.

Organic carbon, that is molecules with carbon-hydrogen bonds that have been created by living organisms (ie carbohydrates, proteins, lipids, nucleic acids…), exists in water in two different pools. Particulate organic carbon (POC) is the fraction of organic C that is physically large enough to be filtered out of the water. POC has a shorter lifespan in water (easier to eat, and more reactive) and therefore can tell us something about the local, recent happenings in the water. Dissolved organic carbon (DOC), on the other hand, has a much longer “lifespan” in water, and therefore contains information about the conditions that water has seen over much longer time scales. In the case of the deep sea DOC can tell us about processes that the water carrying the carbon was exposed to as it traveled through the crust.

One of the main ways scientists “read” the carbon to learn about environmental conditions and processes is by analyzing the carbon isotope rations. Carbon isotopes are atoms of carbon with slightly different masses. Certain processes preferentially use “light” or “heavy” carbon, and therefore the overall pool of carbon compounds created by that process becomes enriched in that particular isotope of carbon. The isotopic signature acts as a fingerprint, allowing scientists to determine the processes that likely created the pool of carbon.

Analyzing the type and source of organic carbon that comes out of the Earth’s crust, and spills into the ocean can help scientists understand the extent to which the deep ocean processes (microbial and purely geological) influence the broader marine, and global, carbon cycles. This, in turn, is important in understanding the climate system of our planet. If the organic carbon present in vented hydrothermal fluids contains organic carbon that was present in the deep ocean waters before they were entrained in the crust and traveled through it, then the microbial communities in that crust are likely heterotrophic – consuming some of the organic carbon as it passes through the crust. However, if it turns out that much of the organic carbon in these fluids is different from the carbon that went in, that is – if it was produced in the crust rather than carried down into it, it is likely that the crustal microbial communities are at least partially chemosynthetic, and this has much greater implications for the role that the subsurface biosphere plays in the global carbon cycle.

OK… enough background.

In a paper entitled “Chemosynthetic origin of 14C-depleted dissolved organic matter in a ridge-flank hydrothermal system” scientists analyzed the isotopic composition of DOC in hydrothermal fluids (both on and off axis) along the Juan de Fuca Ridge (JdFR). Added bonus (!)- JdFR just so happens to be where my research takes place.

Their data suggest that the organic carbon coming out of these vents is different that the carbon that went in, and therefore there are communities of microbes deep in the crust, turning inorganic carbon into organic carbon. This process may represent an important source of organic carbon into the overlying ocean… or it might not. Yes, its frustrating, but the jury is still out on this one.

The areas where hot fluids that come directly out of the vent chimneys are fairly limited in geographic range, but the warmer fluids that percolate through the ridge flanks represent a very large geographic area and fluid volume. This fluid flow is likely greater the combined fluid flux than from all the world’s rivers into the oceans. However, until we know more about how quickly this DOC is degraded, it is difficult to estimate the impact that it has on the chemistry or ecosystems of the deep sea. This study to paints a picture of the deep subsurface as both a DOC scrubber and a DOC producer. According the the author’s the deep ocean carbon that gets sucked into the crust with seawater is removed in the crust, and new, different organic carbon is released in the hydrothermal fluids that leave the crust. At this time it is hard to quantify the extent to which deep subsurface acts as a source or a sink for DOC, and as such the influence of vent and subsurface microbial communities on the ocean carbon cycle remains a mystery. However this study is one step towards figuring that out.

McCarthy, M., Beaupré, S., Walker, B., Voparil, I., Guilderson, T., & Druffel, E. (2010). Chemosynthetic origin of 14C-depleted dissolved organic matter in a ridge-flank hydrothermal system Nature Geoscience, 4 (1), 32-36 DOI: 10.1038/NGEO1015

Readers: I am interested in your feedback on posts like this. Are studies like this of interest, even though they don’t have a clear and obvious punch line and answer? Are you more interested in the scientific process (ie how did the researchers carry out their study), or the conclusions that were reached (forget the boring details, just tell me what they discovered)?