Don't Shake the Flask

Because you don't know if it'll explode

Month: August, 2006

The Thursday Threesome: Name that Tune

Onesome: Name– Ah, what about names? How did your blog name come to be? Is there a story there?

There’s nothing particularly weird about how I came up with this blog’s title. I named my blog after my pseudonym. Perhaps it would have made more sense if I named it “Syaffolee’s Blog” instead, but I don’t particularly like the word “blog” in the title.

Twosome: that– and this. We’ve all thought about a change of locations from time to time: is there any place you’d like to try living for a while? (You can go back home when you’re done with the tryout.)

I just moved about 2000 miles a little over a month ago. I don’t think I’m going anywhere else soon.

As for somewhere other than my current location–I’ve always wondered what it would be like to live in northern England.

Threesome: Tune– us into what you’re listening to lately. …anything on your radar we should be aware of?

Er…I’ve been listening to some random flamenco music.

An Addendum

Frangled Tank: Extra Servings. (via Pharyngula) This is an addendum to last week’s Tangled Bank that didn’t get posted on time. Interesting stuff.

Although I also have to note, I submitted something to them last Tuesday and they still haven’t put it up. I guess I got rejected again. I’ll submit again for next week. If I get rejected–well, my track record is going to look like the pile of rejection slips I have for my fiction submissions.

The Clean-Up Pro

As of this writing, there are already 367 bacterial genomes completely sequenced in the NCBI Genome Project. More sequences get completed every week. The sheer amount of information accumulated is enough to make one boggle. Many of the sequenced organism are of pathogenic importance–some cause diseases in humans others in plants, etc. And then, there are those of ecological importance. Take for instance, ecological disasters. The damage to the marine wildlife by oil spills (such as the Exxon Valdez in 1989 and the Gulf War in 1991) extends way beyond the initial accident as heavier toxic petroleum products persist in the environment for long periods of time.

A variety of methods are used to clean up oil spills. Setting the oil on fire could burn it away. The spill can be contained by booms and collected by skimmers. Or dispersants can be added to break up the oil into small droplets so it can be easily dispersed in water. Yet another method is to introduce microbes to speed up the biodegradation of the spill. For eukaryotes, petroleum products are toxic to life. Not only can these chemicals attack the membranes of cells, but they also have adverse effects oxidative stress reduction, the cell cycle, and DNA damage repair. Benzene, for example, is strongly associated with leukemia in humans. But luckily for us, there are microorganisms with the ability to metabolize hydrocarbons in petroleum. Pseudomonas, Rhodocccous, Psychrobacter, and Bacillus species all have the ability to munch on oil for lunch.

Alcanivorax borkumensisIn this month’s issue of Nature Biotechnology, Schneiker et al. have published the sequence to Alcanivorax borkumensis, an oil-eating marine bacterium. In fact, not only is the Alcanivorax genus a group of bacteria that can metabolize petroleum-based products, but they prefer doing so. A. borkumensis is so picky that it doesn’t even use sugars and amino acids–the staple diet of so many other known bacteria. In 1991, A. borkumensis was isolated from sea sediment at the Isle of Borkum (off the northwest coast of Germany in the North Sea) by Passeri et al. while they were screening for biosurfactants. Compared to other oil-eating bacteria from the soil or fresh water, A. borkumensis did not have toxic effects on other organisms.

With the A. borkumensis genome at our fingertips, what characteristics can we determine that make this organism so good at degrading petroleum products? The bacterium’s ability to degrade alkane is encoded in a genomic island that has similarity with other unrelated oil-eating bacteria–hinting that A. borkumensis acquired the ability from some horizontal gene transfer in the past. Another important ability is emulsifying oil with water which are usually mediated by proteins called glycosyltransferases–this organism has several genes for this as well. Other important genes include those that are involved in biofilm formation (to separate oil into droplets to be easily digested) and DNA repair (since petroleum products can damage DNA).

So with this blueprint available, not only can we begin to understand how the microbial milieu in the oceans keep the waters from clogging up with oil spilled from natural processes–such as natural seeps in the sea floor–but also possibly engineering a “super bug” to help clean up human-made messes.

The Human Side of Science (via A Blog Around The Clock) Finally, a site dedicated to the fact that science and fiction aren’t mutually exclusive. But I especially like the essays.

Stress and the Scientist. Stereotypes of scientists in the lab! You know there’s always someone who’s hoarding the reagents or being anal about the cleanliness of the equipment. I am most definitely not #2 (a schmoozer) or #6 (party person).


The Mirror: A History by Sabine Melchior-Bonnet. I really wanted to like this book–there’s a lot of potential for the subject of mirrors to be really interesting. Instead, it nearly put me to sleep. I don’t know how the writing style in the original French is like, but the translator’s style is just a zonker.

The book is divided into three parts: how the mirror was invented and spread in society, how the mirror was portrayed in the arts, and the psychological significance of the mirror. I will say that I was interested in the first part of the book–the technological advancements made with the mirror. Making reflective glass just so is no easy matter and mirrors remained fairly expensive until the late 18th and 19th centuries when a series of innovations made mirrors cheaply produced at the factory.

My favorite part was at the beginning of Chapter 2 when Melchior-Bonnet recounts a tale of espionage and murder at the Royal Glass and Mirror Company in 17th century France. At the time, Venice had the monopoly on fine quality mirrors yet every other country wanted a part of the market share. So there was plenty of double-dealing, political maneuverings, mayhem, and underhandedness to satisfy thriller-geeks.

But after that, it was all downhill. The basic question the latter two-thirds of the book wanted to answer was, “What is the meaning of the mirror?” Artists and painters and writers all had different ideas–for some, it was humanity’s narcissism. For others it was morality. And yet others, mortality. I think one can always wring meaning out of a reflection, but when the author tacks on the subtitle A History to a text, she should not go haring off to the po-mo hinterlands trying to explicate every painting in the Louvre that has a mirror.

I will admit, however, that I’m not really the intended audience for this book. I like to find out how things work–this is probably why I liked the first third of the book which was a bit more technically oriented. But when it comes to explaining the symbolism of things–oh, boy–do I shake my head. To me, explaining art is mostly BS. It’s making things up (with citations to other people making things up to make it look legitimate)–and what means one thing to one person may mean something completely different to another.

Getting Beaned

Okay, I didn’t really get beaned. The closest I got to that were flying lollipops parade participants were flinging out to the audience. So what warranted a parade? The National Lentil Festival, that’s what. It’s an example of one of those events of local importance that becomes evidence that a Rockwellian America is still alive and kicking.

I arrived in Pullman at around 10 AM to try one of the festival’s specialties: lentil pancakes. To me, the combination of lentils and almost anything else was a little dubious. Maybe this stemmed from personal experience. I’ve tried cooking lentils before and most of the time, they have never turned out very well. After slathering on the syrup, I sat down at a table where a man was stuffing his mouth and gabbing on his cell phone at the same time, a little boy was complaining about how much he disliked lentils, and his grandmother who was praising the pancakes and wondering where she could get the recipe. The pancakes were…not bad. The lentils are mostly tasteless. I suppose one could imagine that these were walnut pancakes. With really bland walnuts.

Lentil ExpressThe parade started soon afterwards. It was your typical parade–marching bands, cheerleaders with shiny pom-poms, the politicians surrounded by their fan clubs, fire trucks, the local businesses with their mascots (not to mention the lentil mascot for the festival), virginal (or at least I’m assuming) beauty queens sitting on the back of a convertible practicing their Miss America hand waving, the sheriff doing motorcycle tricks. The batteries in my camera died around float #60. The amusing part of the parade was two horse riders followed by a trio of boys lugging a wheelbarrow and shovels for errant manure. (I’m sure these boys were totally mortified, but hey, I feel their embarrassment.) The most head-scratching part were the Asian floats. It just seemed really strange to me to see middle-aged Caucasian women in traditional Chinese clothing and white girls in kimonos.

I was confused as to where the actual festival was taking place, but I had no need to worry. After the parade, I just followed the thousands of migrating people to Reaney Park where various booths (food, arts, kiddy, commercial) were set up. I overheard someone saying that there was nothing there and that they should just leave. I think this is only true if festivals are not your idea of fun. I had a hoot just wandering around. Ever tried chickpea snacks? Or even lentil brownies?

Let’s say you’re a trendy, big city person. And maybe your idea of a good time is bar hopping and clubbing. Then this is not for you. But if you enjoy the slightly quirky, the National Lentil Festival might be something to see if you’re in the area around August. And if you have younger kids, this is definitely an event to go to. It’s extremely kid-friendly–maybe a little overly so at times.

Why People Stop Reading

Yesterday, I encountered a very depressing statistic–very few undergraduates read for pleasure. Less than twenty percent. (I can’t quote the exact statistics to you because I was in one of those brain-glazing TA training seminars where pretty much everything was sort of depressing.) So after reading Tess Garritsen’s post about Legume Literature, I began thinking–maybe part of the reason why people don’t read is because of school. Specifically, English lit requirements.

Okay, I admit, I have never taken a literature class I didn’t want to. I majored in biology so anything non-science related (aside from two humanities requirements) was completely optional. Perhaps for most people, reading gets associated with school (and yes, for some people, that can be a bad thing).

Then there is Garritsen’s point–when we get older, we’re expected to read literature that is good for us. The key here is “literature”. I think that in today’s culture, there’s this totally bogus expectation that literary fiction is actually good. The only thing that’s true is that literary fiction is good for those who think so. If somebody looks down on your reading taste, they just don’t understand the whole concept of actually reading. Otherwise, why waste your time reading what’s good for you when in reality it’s really to look good for other people?


Animalcules Volume 1, Issue 11 is up at Snail’s Tales. Yep, Animalcules is another blog carnival I’ve discovered, but its about…microbes! Way cool.

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The Thursday Threesome: Free Amazon Prime

Onesome: Free– isn’t always free! What “freebie” have you discovered over the years that really isn’t?

I can’t think of anything–probably because I know there will always be a catch.

Twosome: Amazon– It’s been a bit since we’ve done our Amazon Survey: do you use Amazon? Good? Bad? Indifferent?

I’ve only used Amazon rarely, but I’ve always gotten the things I ordered.

Threesome: Prime–Time! Are there any shows you are looking forward to seeing in the Fall lineup on TV? (okay, football counts).

Um, I do not watch TV.

If You’re Reading This, Go Read…

The latest edition of Tangled Bank, a carnival for science blogging, is up at FrinkTank. I know, I know, it’s been a while since I’ve posted a link to Tangled Bank, but this is no fault of the carnival (one of the very few carnivals I ever read)–rather of my really sporadic posting for about a year and a half.

(Yes, this means I’m regularly posting now. Not that anyone will care–I think everyone stopped reading me around last May.)

Commensal and Pathogen: Not So Black and White Anymore

Move over HPV and EBV, viruses are no longer the only microbes that can mess with your DNA. In a recent Science paper by Nougayrède et al., Escherichia coli was found to induce DNA damage in eukaryotic cells.

E. coli is well-known for being the workhorse of the molecular cell biologist and one of the usual residents of the gut microflora. Some E. coli also cause disease. So far, so good–we know that some strains live in relative harmony in our digestive tract and other strains make us sick. But from the observations of Nougayrède et al., this distinction isn’t so cut and dried. E. coli is a bit of a Jekyll and Hyde–what some strains consider an aid for surviving harmoniously with a host, others use as virulence factors.

When E. coli was added to different mammalian cells, the researchers noticed that the commensal strains and the strains isolated from meningitis and urinary tract infections caused a decidedly different reaction to the cells than laboratory or enteropathogenic/enterohemorrhagic strains. Adding certain E. coli strains caused the host cells to undergo megalocytosis–in other words, the cell became terribly bloated and ceased to divide. This phenomenom was not seen when the mammalian cells were incubated with dead bacteria or when the bacteria were separated from the cells with a 0.2 mm permeable membrane. The cause of megalocytosis, then, was not caused by any toxin that the E. coli was excreting but from something happening during direct bacteria to cell contact.

Nougayrède et al. discovered that E. coli induced megalocytosis required a set of genes which they called the “pks island.” This genomic island contains the instructions needed to make peptide-polyketide hybrid compounds–nonribosomal peptide megasynthases (NRPs) and polyketide megasynthases (PKs). NRPs and PKs are also produced by other bacteria and fungi, some of which are used for therapeutic agents.

At any rate, the compounds made by E.coli aren’t so nice. Here, it wreaks havoc on genomic stability as a genotoxin. The pks island allows the bacterium to deliver its PK-NRP hybrid compound to the eukaryotic cell which causes DNA double-strand breaks. When DNA damage is induced, a cellular signaling pathway is activated to halt the cell cycle. Ultimately, cells enlarge and then die.

Further survey of different E. coli strains revealed that the pks island was only found in the B2 group of E. coli which contains commensal strains as well as strains that cause disease outside of the intestine. Nougayrède et al. speculate that the pks island acts as a fitness factor enabling the bacteria to stop the cell cycle to effectively colonize the host. Because different strains make different amounts of genotoxin this may affect whether a particular strain can live as a harmless commensal or a pathogen as well as being a possible link to intestinal cancer.