Amateur arachnology (and why I fear I may no longer be fit to have a normal job)

You know you’re a biologist when:

(in increasing order of severity–some of these pertain to myself and others to my labmate, whose desk recently became the next-door neighbor to a sparrow’s nest, and who has just left to take a shower)

-you are happy to have a bird’s nest outside your window

-you think the half-plucked-looking naked baby birds inside are adorable

Baby sparrows outside my labmate’s window

-you are not unduly distressed when the bird’s nest becomes fairly obviously infested with some sort of tiny bug

-you are only mildly distressed when it becomes clear that the bugs have made it inside the window.  You carry on writing your dissertation.

Ookaay. Once the bugs make it inside the window things are less cool. 12 point “G” included for scale.

-you relent and decide to head home only when the bugs start actually crawling on your person.  You notify the lab manager, who calls pest control (see–we’re totally normal and responsible), and your lab mate down the hall (me) who…

-does not avoid your bench like a normal person.

-captures some of the bugs to look at under a microscope

-shares the view with her labmate, who would rather look at them than go home and wash up right away, and her baymate, a former arthropod specialist who declares they’re “kinda pretty.”

-then browses the internet with her baymate and labmate to identify that they’re some kind of bird mites (duh).  Labmate, still totally calm but succumbing to common sense, goes home to shower and continue writing, while I…

-use the break offered by an hour-long incubation period to take better-quality microscope photographs and browse the internet for another half an hour or so to try to find out their species name.

I think they must be some kind of Ornithonyssus, possibly Ornithonyssus bursa, but if there are any arachnologists who know more I’d really love a stronger ID.

Bird mite, Ornithonyssus bursa (possibly). 20x, inside a 12-point font G.

As I write this, I’m wondering to myself if “arachnologist” is a real thing.  Certainly bird mites are arachnids (subclass Acari, order Mesostigmata), so entomologist seems inappropriate.

Lest you think we’re unusually bonkers, I think Haeckel made a decent case that arachnids were kinda pretty, in one of my favorite books, “Forms of Art in Nature.”  You can get id’s to the various creatures here on Wikipedia.

“Arachnida” from Forms of Art in Nature, Ernst Haeckel, 1904

At the MBL

I’m in Woods Hole MA for the next 10 days, TA’ing for the Marine Biological Laboratory’s summer Embryology course.  Since lecture starts at 9am and lab finishes around 2-3am, I’ll probably be an irresponsible blogger.  I am hoping to get a chance to mill around the libraries and peek at all the old botanical illustrations, so hopefully I’ll have some old-school paintings and lithographs to share at the end of it all.

In the meantime, here’s some of the preposterously bright blue hydrangeas I always look forward to out here:

…and an equally preposterously adorable rabbit.  We saw at least a dozen of these on our walk yesterday evening; they were extremely casual about having us walk right up to them.

Sure I’m a wild animal. Why do you ask? Hey, do you by chance have a carrot I could nibble on in a charmingly tame fashion? Or should I just curl up in your lap?


Alliums: giving the immune system a smelly leg up

By February I am generally fed up with the cold and flu season, and this year is no exception.  Our household has been hit hard by a cold/bronchitis 1-2 punch, and we’ve been single-handedly keeping the makers of Ricola and our local Pho (Vietnamese chicken soup) shop financially solvent for the last few weeks.

It’s about this time that I start musing about zinc, antivirals, ICAM-1 inhibitors, VP4 protein based vaccines…in short, why the heck haven’t we found a way to beat the common cold?  Continue reading

Prettiest Plant in the Lab: Foxgloves, Digoxin, and Digoxigenin

A while ago I posted about oleander and the structural similarities between the oleander cardiac glycoside oleandrin and the foxglove cardiac glycoside digoxin.   But foxgloves express enough biologically useful (and harmful) molecules that they’re worth showcasing.  Plus they’re such nice eye-candy!

Gloves that pack a punch

The various members of the Digitalis genus, which include the gardener’s favorite foxglove Digitalis purpurea and a range of other Digitalis species, are favored ornamental plants for their tall showy flower spikes and bright colors.  A disputed but appealing origin for the name was advanced by William Henry Fox Talbot, who proposed that the whimsical ye Olde English people imagined fairies wearing the deep cone-shaped flowers for gloves, and called them folks’ gloves.  Very cute.  But given that fairies were famous not only for being adorable but also for other light-hearted mischiefs like stealing babies and poisoning livestock, it’s perhaps fitting that their pleasing-to-look-at gloves come barbed with a heavy dose of serious poison.

Enough folk's gloves for a children's book full of fairies. Digitalis purpurea, by Ferdinand Bauer.

Foxgloves are poisonous because they contain two cardiac glycosides, digoxin and digitoxin, which are found in all parts of the foxglove plant but are most concentrated in the leaves.  There are a few ways to poison yourself with foxgloves by mistake: the flowers have some appealing similarities to honeysuckle, which might lead the unwary to try to suck nectar from them.  Because the plant is still poisonous when dry, a hapless gardener might inadvertently inhale foxglove plant matter when digging or replanting near an old foxglove bed.  The leaves of foxglove (especially before it flowers) resemble and have sometimes been mistaken for comfrey, which is benign and a common basis for tea (here’s an article about several people poisoned this way).  Never fear though, ehow has a handy how-to on distinguishing comfrey from foxglove leaves; the clearest difference might be that foxglove leaves are finely toothed while comfrey’s are smooth.

Leaf of comfrey, Symphytum sps. Good for tea, beloved by herbalists, and pretty easy to confuse with foxglove leaves, pictured in the illustration above. Photo courtesy of Heather at, which is also a pretty nifty blog.

Finally, one of the side effects of digitalis poisoning is strong hallucinations, so there may be a handful of people out there ingesting it deliberately…but I doubt the visuals are worth the heart arrhythmias, severe nausea, fainting, coma and possible death that come with them.

Extra nitty-gritty: Digoxin as heart medicine

Cardiac glycosides like digoxin and oleandrin work as sodium-potassium ATPase inhibitors, which means that they interfere with the balance of ions inside cells. The muscle cells of the heart are particularly vulnerable to changes in sodium concentration, because sodium concentration is coupled to calcium export, and the calcium concentration inside the muscle cell is what regulates how strongly or quickly the muscle cell can contract.  When there’s too much sodium, the cell can’t efficiently export calcium, and the cell contracts too strongly as a result.  Erratic muscle contractions are certainly bad news for a healthy heart.

Digoxin: sometimes a help and sometimes a hindrance to heart function.

Unlike oleandrin however, digoxin has considerable utility as a medicine: the same calcium ion hoarding effect that’s so dangerous in a healthy person can be used to combat heart failure by promoting stronger contractions in a damaged heart, and digoxin gained FDA approval as a treatment for chronic heart failure and some kinds of heart arrythmias in 1998.

The initial use of digoxin came before beta-blockers were used to manage heart failure (HF), and there is ongoing study as to whether digoxin remains valuable as an HF management strategy in concert with other therapies. A recent article in the International Journal of Cardiology has undertaken a multivariable regression approach to attempt to classify which categories of patients are more likely to suffer higher mortality or further hospitalizations for heart failure following digoxin use.  Their meta-study combined cases of over 7000 patients, and found that higher mortality and hospitalizations for heart failure were correlated with groups of patients that were female and had high blood pressure.  Studies like this one may help identify which groups of patients can still benefit from digoxin and which groups should avoid it.

Extra nitty-gritty II: Digoxigenin as molecular label

Apart from its cardiac glycosides, Digitalis also harbors a supremely handy steroid, Digoxigenin (DIG), which I use routinely to label RNA molecules.  Digoxigenin is a fairly small little molecule that can be coupled to the nucleotides that make up DNA or RNA (nucleotides=letters: A,G,T/U, and C), and there are specific antibodies for DIG that can be used to detect it anywhere it’s bound in a cell.

DIG-UTP. This labeled "U" is incorporated into RNA molecules just like regular UTP.

So when I want to find which cells in my tissue sample are making a certain RNA, I can make a probe with a complementary sequence and some of the U’s labeled with DIG.  Then I can use anti-DIG antibodies (conjugated to an enzyme that makes a purple color under the right conditions) to look for the probe, with a technique called in situ hybridization.

A little how-to for using DIG-labeled UTP to find a target RNA by in situ hybridization.

Want more details?  Here are references for the articles mentioned:

Ather S, Peterson LE, Divakaran VG, Deswal A, Ramasubbu K, Giorgberidze I, Blaustein A, Wehrens XH, Mann DL, & Bozkurt B (2011). Digoxin treatment in heart failure – unveiling risk by cluster analysis of DIG data. International journal of cardiology, 150 (3), 264-9 PMID: 20471706
Lin, C., Yang, C., Phua, D., Deng, J., & Lu, L. (2010). An Outbreak of Foxglove Leaf Poisoning Journal of the Chinese Medical Association, 73 (2), 97-100 DOI: 10.1016/S1726-4901(10)70009-5

Mung Beans: From Dinner Table to Lab Bench

So today I was doing an experiment, and realized the tube I was pipetting from was a perfect plant topic: mung bean nuclease!

You know mung beans.  You’ve probably eaten them recently, especially if you like Asian food or if you’re on a strict diet.  Mung bean sprouts are the popular white bean sprouts found in every grocery store, and their crisp crunch is a familiar texture in stir-fries, spring rolls and salads. Although they’re native to India, their use is widespread across Asian cuisine.  The beans’ starch is used to make bean thread noodles, and the beans themselves are used to make the paste that fills Chinese mooncakes, or for some kinds of the Indian dish dal (although I’m used to the lentil variety.  Has anyone had mung bean dal—does it taste similar?).

Mung bean sprouts. Fresh, crisp, tasty, and chock-full of nuclease. (Open source photo by Kwantonge).

But mung beans are also a surprising component of every molecular biologist’s toolkit, because they produce a useful enzyme (mung bean nuclease).  There are quite a lot of applications for which this handy tool can be used, but I generally use it for cutting away dangling single-stranded tails of DNA.  A huge, huge part of practical molecular biology is playing cut-and-paste with DNA: I have a piece of DNA over here, and I want to put it into a different piece of DNA over there.  This requires the molecular equivalent of scissors and glue—something that will cut DNA apart, and something else that will glue it back together.  Mung bean nuclease is a very specialized pair of molecular scissors.

Any other favorite uses from the biologists out there?

On my bench: a few precious drops of molecular scissors.

Continue reading