Friday, December 3, 2010

Don't Call It a Comeback

I've been here all month, but finally got motivated to write some stuff down regarding NASA's announcement today: NASA-Funded Research Discovers Life Built With Toxic Chemical. Here is an excerpt:

"NASA-funded astrobiology research has changed the fundamental knowledge about what comprises all known life on Earth.

Researchers conducting tests in the harsh environment of Mono Lake in California have discovered the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic. The microorganism substitutes arsenic for phosphorus in its cell components."

The rest of the writing in the NASA press release is similarly giddy. You might think from skimming the information out there that these researchers found an organism that uses arsenic preferentially, or in the environment, but that is not the case.  The cells were isolated from mud samples collected from Mono Lake, then grown in media with low amounts of phosphorus and high amounts of arsenic. These cells, named strain GFAJ-1, were able to grow in these media despite arsenic's usual toxicity. They do not use arsenic in their natural environment, nor is it accurate to call them an "arsenic-based life form".

Today I read the paper behind this research, published online today in ScienceXpress. (You won't be able to read that unless you have institutional or other access to Science.) I have some questions regarding the results.

  1. Was this testing conducted on other species? NASA is touting this discovery as a whole new type of life. I would be more likely to accept that idea if the researchers had shown that other bacteria did not survive this treatment. According to the phylogenetic tree constructed in the supplementary materials, Escherchia coli is this bacterium's closest relative. More experiments should be conducted to determine E. coli and other common laboratory strains' fitness in this media.
  2. As the cells grow and divide, they should incorporate more and more arsenic into their biomolecules, depleting the phosphorus available in the media and that which was already present in the mother cells. Is there a threshold level of arsenic at which cells can no longer survive? Could they completely replace all phosphorus with arsenic? That hasn't been shown. The data in the paper only shows growth up to 20 days; is there a point at which cells start to die? New Scientist quotes Paul Davies of Arizona State University as saying, "After one year, they are still alive and well"; however, there is no published data to support that, so it could mean anything.
  3. In the paper, cells grown on arsenic-rich medium had a higher dry weight of arsenic that cells grown on phosphorus-rich medium. Similarly, +As/-P cells had a lower dry weight of phosphorus than -As/+P cells; however, even the cells grown on medium with phosphorus had a dry weight of phosphorus (0.54±0.21%) lower than the 1-3% normally needed by bacteria. I can think of two possible explanations: 1) the data is incorrect; 2) this strain typically uses less phosphorus than the average bacteria. I would like to see similar data gathered when the strain is grown on other rich media.
I think that the possibilities created by these findings are fascinating, but as so often happens with science journalism, they have been blown way out of proportion in the media. Far more research is needed before this organism will be accepted as a "parallel form of life".

    Friday, October 22, 2010

    Cholera Has a Vacation Home

    I'm quickly learning how challenging it is to keep up with even a weekly commitment to a blog entry, so this one is last week's entry, a few days late. I'm gonna keep plugging away at it though.

    This week's paper is Kathryn L. Cottingham, Deborah A. Chiavelli, and Ronald K. Taylor. 2003. Environmental microbe and human pathogen: the ecology and microbiology of Vibrio cholerae. Frontiers in Ecology and the Environment 1: 80–86. It is a review of the state of research on Vibrio cholerae in its aqautic environment. I picked it because I got a tip that my advisor may ask me to repeat my current experiment on V. cholerae, and I thought I should start learning more about it. V. cholerae is in the same genus as my current experimental organism, Vibrio vulnificus, and they have a lot in common. They both inhabit two environments (human and aquatic) and they both can enter a Viable But Non-Culturable (VBNC) state. V. cholerae is more interesting to funds-granting organizations since it causes more infections, so it would be beneficial to include it in any papers we generate.

    When in the aquatic environment, V. cholerae can be either free-swimming, or attached to a substrate. In the attached form, it may form a biofilm, an organized aggregation of many thousands of V. cholerae cells. Biofilms provide protection for the cells against predation and antibiotics, but the mechanism of their formation is not well-known. Cells may attach to phytoplankton or zooplankton, which provides a nutrient-rich environment in which V. cholerae can multiply.

    The aim of the paper appears to be not to reveal any new information about V. cholerae, but to point out that very little is known about the aquatic state. The paper raises more questions than it answers, and concludes with a list of areas for new research. These include comparing gene expression between the aquatic both free-swimming and attached) and infectious forms, and determining what, if any, genes are responsible for transition into the VBNC state.

    UPDATE: I started writing this blog entry last night; this morning Haitian officials confirmed that a cholera outbreak is plaguing an area of the country where many refugees headed after the earthquake to escape the conditions in Port-au-Prince. Since V. cholera is shed in the feces and vomit of infected individuals, and can be contracted from drinking contaminated water, outbreaks are common in areas with poor sanitation, such as the temporary housing in Haiti. Read more here:

    Friday, October 8, 2010


    So, I haven't posted in a while. I foolishly thought that I would have oodles of free time once I quit my job and started grad school, but that has not been the case. TAing takes up a lot of time. I don't know how some people manage to get their PhD while teaching the whole time; I'm counting myself lucky that I will probably only have to teach this semester. 3 hours of class time X 2 sections, plus 3 hours of "office hours", 1 1/2 hours of TA meeting . . . and grading and creating quizzes and homework. It easily adds up to the promised 20 hours per week, and is the biggest consumer of my time at the moment. Behind that is my research work and the one class I am taking.

    The work I'm doing in the lab is a short-term project called a rotation; the expectation is that I will have completed it by the end of the semester. Even though I will probably stay in the same lab for my thesis, this is not my thesis work. I've decided to try to work in a bit more literature reading in order to benefit my rotation research and help me decide what I will want to work on for my thesis eventually. So I've set myself a goal of reading one non-required journal article each weekend. "Non-required" meaning I've picked it myself because it seems interesting, not because it is required for a class or my supervisor or advisor told me to read it.

    This week's selection is "Changes in Membrane Fatty Acid Composition during Entry of Vibrio vulnificus into the Viable But Nonculturable State". Day AP, Oliver JD. Journal of Microbiology. 2004 Jun;42(2):69-73.

    Vibrio vulnificus is the organism I am studying for my project. It is a shellfish bacterium related to Vibrio cholerae, which causes cholera. V. vulnificus causes more than 95% of all seafood-related fatalities in the U.S., and it undergoes a transformation in the winter.

    Cold temperatures cause it to become dormant to the point where it cannot be grown in the lab on normal media, yet if it is introduced into animals it still causes infection. My job this semester is to elucidate the molecular mechanism for this change. Interestingly, there are all sorts of papers showing that V. vulnificus does become dormant and what physiological changes it undergoes, but none investigating how to resuscitate it from dormancy (other than warming it back up, which seems a bit obvious), or why it is not culturable in this state.

    The Day and Oliver paper was quite short, and simply showed a a change in the makeup of the fatty acids that comprise the cell membrane while the cells were going into the VBNC state. Their hypothesis is that in order to maintain membrane fluidity at lower temperatures, more unsaturated fatty acids (which have a lower melting point) are needed. In addition to measuring fatty acid ratios during entry into VBNC, they also inhibited fatty acid production by treatment with an antibiotic, cerulenin. The cells that could not produce additional fatty acids due to this treatment died after incubation at 5 degrees Celsius, indicating that this change in membrane composition is required to maintain viability. However, this only addresses one side of the VBNC (Viable But Nonculturable) state--we still don't know why the cells are not culturable if they are still alive. That's what I'm working on.

    Monday, August 16, 2010

    Easy Weeknight Pasta

    This weekend I visited the Boston Cheese Cellar in Roslindale and bought a plethora of cheeses, chocolates, and honey. Now I'm trying to figure out how to use all of my bounty. I made this food for dinner tonight. It was delicious and you should try it.

    One of my purchases was a container of fresh Mozzarella. I love this stuff! If you get the kind packed in water it tastes less salty than the vacuum-packed varieties, but either kind is good. Combining it with some basil from my windowsill pot seemed like the perfect combination. This pasta took about 15 minutes to make. You could add some pre-cooked chicken sausage to the red pepper saute, but I made it vegetarian this time.

    You'll need:
    • Some short pasta like penne or rigatoni. I use half a box, which makes enough for me, B., and leftovers for lunch. Whole wheat or regular, whatever you like.
    • Fresh Mozzarella, duh. Cut it up into little pieces
    • Fresh basil, torn into pieces. You could use dried but the dish comes out pretty different. 
    • Red pepper, cut into 1/2 inch-ish sized chunks
    • Package of frozen peas

    1. Boil up a pot of water and throw the pasta in there once it's ready.
    2. A few minutes before the pasta is done, heat up some olive oil in a skillet. Once it's hot, add the red peppers and stir. Cook for a few minutes, stirring occasionally so they don't get burned.
    3. A minute before the pasta is done, add the peas.
    4. Drain the pasta and peas using a colander, then put them back into their pot.
    5. Add the cooked red peppers to peas and pasta, letting the olive oil drizzle in. Sprinkle with salt and pepper, add basil, and toss.
    6. Add the mozzarella a few pieces at a time. It melts easily, so if you throw it all in at once, it will all glom up together. Stir it in, then add some more.
    7. Nom!

    Thursday, July 29, 2010

    Human Behavior

    I have some tattoos. I don't think about them most of the time, but in the summer, it's hard not to. That's because in the summer, everyone can see them. And although I might not be thinking about them, most people who can see them, are. Here is a list of typical reactions, from best to worst:

    No reaction: exhibited by people my own age, often with their own visible tattoos, but also with none. I look normal to them, so they react to me like they would anyone else.
    Kind curiosity: most often displayed by motherly types over 50. They start off by saying how beautiful my tattoos are, then follow up with either "How much did that hurt?" or "How long did that take?" Sometimes they will take my wrist to get a better look, but I don't mind when it's a round little woman under 5'4". These women are completely nonjudgmental. I may be imagining too much, but it seems to me that they are wistful, knowing that in the time they grew up, women had much less freedom to express themselves than they do now.
    Sidelong glances: expressed by any age or social group. They want to look, but they don't want me to know they want to look. Lately if I catch people staring, I will make eye contact with them and smile, but if I'm not in a good mood, they get an "I know what you're looking at" glare. Frankly, I'm guilty of this myself. I stare at people all the time: other people with tattoos, attractive people, people wearing daishikis or the hijab. So, I try not to get too mad--unless it's in the gym: No staring when I'm not wearing pants, jerks!
    Phony, backslapping camaraderie: universally displayed by men with at least one prison or kitchen tattoo (or similar quality) who have decided that since we both have tattoos, we should be buddies! This still happens when B. is around, but not as often. Typical opening lines include:
      • "I like your work!"
      • "Hey, nice ink!"
      • "Whoa, cool tats."
    Use of the words "ink" or "tats" will immediately qualify an interaction for this category.
    Skeevy curiosity: only displayed by men when B. is not around. Can devolve from the previous category. Asking if I have any other tattoos will be rewarded with a withering glance and an end to the conversation. If you can't see them, they're none of your business!
      Here are some pictures of my tattoos. It's OK to look this time.

      Sunday, July 25, 2010


      Some of you might be surprised to learn that I have a subscription to Glamour. I don't take everything in it seriously, but I miss it when I let my subscription lapse. This month there was an article (sadly not available online) titled "The Cavewoman’s Guide to Good Health". I found that the article mirrored a lot of the observations I have made about the way I achieve happiness (and the Wonder Woman fan in me enjoys imagining herself as a cavewoman). Recently my happiness score has gone up due to changes I've made.

      When I was a little kid, I was not physically active at all, but thanks to the magic of genetics, I was skinny as a twig. I didn't have very many friends either. I would spend all weekend inside reading, with an occasional Saltine break. See that kid, reading during a trip to Walt Disney World? That was me. Fast-forward twenty years, and I have developed a serious gym habit. The changes on the outside have been subtle, but the changes to my mind are more interesting. I used to get angry or sad very easily, but over the last few months, I've become less volatile. There's also a new mental strength that I don't remember having before--a willingness to try something difficult. I think I've gotten tougher.

      Monday, July 19, 2010

      Weekend At Nerdy's

      My husband and I just moved from Salem, Massachusetts, to Medford. We moved to Salem in 2005, because we had just gotten married and wanted to buy a condo. The market in Boston was so overheated that we couldn't have afforded a studio in the town we worked in, so like many people, we adjusted to a long commute. After five years of two hours or more in the car, we decided that our quality of life was more important than owning our own home. We are now closer to work and our friends.We've been in the new apartment just over a week, and I'm very happy with it so far. Because we previously declined so many invitations due to the long trip to get anywhere, I've now been saying "Yes" to everything. This weekend was packed with spontaneous adventures.

      On Friday, I took the T into Boston, where I got a pedicure with some girlfriends. Afterwards, we wandered around in the rain before ending up at Bar Lola, a tapas bar on Commonwealth Avenue. The tapas, sangria, and company were excellent, and hinted at the weekend to come.

      B. and I got up early on Saturday and headed out to Winchester, one town over. He had to withdraw money for a motorcycle purchase, and I wanted to visit Mamadou's Artisan Bakery for some fresh bread. We noticed a farmers' market in on the Winchester town common and stopped in to take a look. Mamadou's had a tent, so I was able to grab some fresh Sesame Semolina before anyone else (and grab it I did). I also acquired a potted basil for my new kitchen window. I'm determined to visit as many farmers' markets as possible this summer, and gorge myself on fresh produce, local honey, and tea. This schedule of markets makes it possible to find one in the area for every day of the week! I explored Il Sogno in Medford for some Provolone and Italian ham to make grilled sandwiches on my amazing Mamadou's bread before heading out to Clinton to get tattooed (more on that later).

      I spent the morning on Sunday making bacon and using the last of the bread for cinnamon French toast. I thought it would be a lazy sort of day around the house, but my friend Stacia called and invited me to the Friendly Toast in Cambridge for brunch. Now, I had already eaten breakfast, but I have a hobbit's love of meals and readily accepted. We lounged there for several hours, sampling cocktails and dining on eggs, beans, and salsa. Finally I headed home to do the grocery shopping and some chores, but I was home just a short while before B. texted me: he was back from picking up his new motorcycle. We met for dinner, then came home and watched A Serious Man. It was one of those difficult movies that probably deserves its own blog entry.

      Phew! I'm tired just remembering all the stuff I did this weekend, but I'm so grateful I again live in a place where I can have a robust social life. Real life > video games, any day.