Name That Fungus

Now for the much anticipated pictures of the mystery fungus! Please comment or email me (joolya at gmail dot com) if you can identify these beasties.

Some more info about my mycotic friends:

• They grow at 37 degrees C in 10% CO2 or in room air.


• They grow in liquid and in air.


• They grow better in media with 1% bovie serum albumin than they do in media with calf serum.


• On incubator walls, the colonies are white and lacy looking, radiating in spidery fractal arms from a central point.

Put on your thinking caps, microbiologists!

The top pictures were taken using DIC with a 100x objective, the following were boosted to 150x.

Ritualistic Procrastination - Bleb Monsters - Vindication At Last - Incipient Fatal Fungal Infection - A Call To Microbiologists!

In order to effectively write my committee meeting report, I am watching every episode of Mystery Science Theatre 3000 featuring 50s educational films ("A Date With Your Family", "Good Grooming" and "The Home Economics Story").

This is an example of ritualistic procrastination. I will continue to watch MST3K videos on YouTube until I begin to get bored, at which point the sweating panic of not having written my report will kick in. Then I will be spurred on to write, which will take all afternoon and evening. I am not in the lab this morning because the urge to set up just one more experiment would be even more impossible to resist than YouTube.

I think there is a certain amount of ritual procrastination that is an inescapable part of the writing process. Don't you?

Actually, there's a sidebar to the reason I'm not in the lab and it involves filamentous fungi. I would not really be doing experiments because I would be devising strategies to identify and destroy the fucking fungus that is growing in the incubator. I don't even know if I can talk about this yet ...

I did a great experiment the other day but when I went to do the analysis (single cell morphology) the controls were all funkster. Wha??? Shit. Now I don't believe anything!

I set it up again with freshly-thawn cells, this time with even more experimental goodness, extra coverslips just in case. In parallel I set up a big-ass RNAi experiment with brand new siRNAs and cells that I could tell were knocked down even before blotting, that's how much of a phenotype they have. Aw yeah. Two big money experiments right before my committee meeting. I am a rock star.

But oh no. The FSM does not want me to be data gathering when I should be writing this buggering progress report. Yesterday I was looking at my cells under the 20x in the tissue culture room. As one does. Although I am fairly sure I look at my cells about seventy-nine times more often than any of my lab mates. I have probably logged ten thousand hours of looking at cells under 20x. I am like a cell anthropologist. I look at them. I learn their ways. I know what is a happy, healthy cell and what is an unhappy, unhealthy cell. Seriously.

So there I am, looking at my cells prior to doing the experiments; this is several days after the weird controls problem. And then ... uh-oh. Cells are doing things that strike the chord of fear in my soul. They're not popping off the plate or even dying in the normal way. I know what a cell looks like when it's just undergoing random apoptosis. It happens, especially when you start messing about with serum-free medium and different matrix proteins. This is not that. I have seen this before.

Flashback, about two years ago. My cells are looking ... just not quite right. I thaw them out, they do okay for a couple passages, and then I see the Bleb Monsters. The Bleb Monsters are cells who look all spindly, with long retraction fibers that are dotted with phase bright blebs. These are presaged by cells who leave extremely long, thin tails behind them as they migrate around the plate. Eventually, these cells round up and come off the plate, often remaining attached to the substrate by one or more of the thin, blebby fibers for a while before completely detaching .The debris accumulates in the media, which becomes full of phase dark blobs.

A hefty double whammy of fungicide and antibiotics slows the process but doesn't stop it completely. I chuck all my media and make new. Still happening. Can I trust my cell morphology experiments when there are Bleb Monsters in the culture?

I show my lab mates. "What's wrong?" they ask. "Cells look okay to me." My brow furrows - I am seeing a problem no one else seems to see. Hm, I think. Maybe it's nothing. I do my experiments, with a growing sense of unease. How can I confidently study migration and membrane extension if my cells are leaving huge chunks of themselves behind when they migrate and their membranes are weirdly blebby? I start surreptitiously looking at other people's cell cultures. Now I am seeing Bleb Monsters every where I look. Still, no one else seems concerned about this.

Holy shit, I think. I have a tendency toward hypochondria - am I displacing my stress-induced hypochondria onto my cell cultures now??? That takes the psychosomatic cake.

Six months of this. By now I have cleaned and autoclaved the incubators, which really ought to be done every few months but which in my lab only gets done when I insist on it. The problem is less severe but still after a few passages, I see Bleb Monsters accumulate. (In retrospect, I froze down many vials of cells before I identified the problem, which may account for the slow contamination.) No one notices anything funny in their cultures. Is it that they don't look carefully enough at their cells, or am I looking too closely at mine?

Finally, I show my Bleb Monsters to Wacky Microscope guy, who says, "Looks like endotoxin. Might be that the media bottles aren't thoroughly sterilized." Endotoxin! At this point I'm just glad someone else sees that my cells aren't normal! Again, I throw everything away and start fresh, with the oldest cells in the liquid nitrogen and all new media. Summer turns into winter. Finally, the Bleb Monsters disappear. (In retrospect, this also coincides with the time that I stopped working with a certain cell line I got from a collaborator - not coincidentally, in retrospect, this was the first culture in which I saw Bleb Monsters.) But, I have spent six months feeling like I am taking crazy pills, possibly winding myself up over an imaginary problem, and never really identifying the problem, which has now, as mysteriously as it arrived, gone away. And no one but me and the Wacky Microscope Guy has even noticed anything amiss, which makes me think I was just seeing Bleb Monsters everywhere I looked because I was so obsessed with them.

Fast forward again to this past week. Weird controls in morphology experiment. Fuck. Then, the Return of the Bleb Monsters. Double triple fuck with whipped cream and a cherry on top. But now I am not an insecure, mentally distressed G3 (third year PhD student) anymore. I am a scientist, dammit! I am, furthermore, the person in the lab who most often takes long, hard looks at her cell cultures - both as part of my research project and during routine cell culture maintenance. (The reason for this is largely that I enjoy looking at my cells, but the focus of my project is identifying subtle differences in cell morphology and behavior so it is actually very important that my cells are happy and healthy looking, or else my experiments will be inconclusive.) If there's anything amiss in cell culture, I am going to be the person who spots it because I am the one who is looking. I didn't trust my own instincts back then. Now I do. If I say a cell is fucked up, it's fucked up. Period.

"Lab mate," I say. "I think there's a problem in this incubator. My cells are looking fucked up." We investigate the incubator.

"Lab mate," I say. "What are these whitish crystaline entities on the ceiling and back wall of the incubator?"

"Oh, we think it's just salts," says my lab mate, who is in most ways one of my favorite people but who right now I want to bludgeon.

"Salt crystals?" I query. "Right. Why would there be salt crystals forming in the incubator? That shit is alive."

To test my hypothesis, I scrape some of the mystery "crystals" into a petri dish with some water and head to the microscope.

"You probably shouldn't scrape them like that," says my otherwise cool lab mate.

"Why?" I ask. "If it's salt, it's harmless, and if it's alive then we have to throw all these plates away anyway."

I image the scrapings at 10x, 20x, 60x, 100x, 150x. Long branched filaments, some with visible internal partitions, surrounded by grape-like clusters of small ovoids, some with visible nuclei. I don't have to be a fucking mycologist to know a filamentous fungus when I see it. Closer inspection of the incubator reveals not just a few but hundreds of enormous white colonies of the stuff all over the ceiling, on the undersides of the shelves, in the corners, on the walls - it's polluted. If this incubator was the Jersey shore there would be big Mister Yuck warning signs all over the beach telling you not to go near the water, and dead three-eyed fish littering the sand.

Jesus H. Christ. This is why I don't have to wait a few passages to see Bleb Monsters. The whole incubator is one big fucking spore spewing mysterious mycotoxins all over the place. I stick my head in and take a sniff. Smells like apple cider vinegar. Later, I regret doing that as the hypochondria asserts itself and I imagine filamentous fungi filling my nasal passages and lungs ...

Then I put the pieces together. About a week ago I plated some of the Cell Line of Death, but then the cells were ugly and I threw them away. Shit shit shit shit shit! Okay, so at least I know what it is, and I am finally vindicated re the six months of being Cassandra at the Incubator Gates two years ago.

Here, too, is where the story gets interesting. The control cells that have been exposed to our mystery mycotoxin are behaving in my morphology assay in a manner similar to the genetic mutant cells I have been studying (which have various cytoskeletal and migration defects).

Whoah, man. Whoah.

So I put it to you, loyal readers. Help a girl out if you can 1) identify fungi based on some photos and written descriptions or 2) advise someone on how to extract potential mycotoxins from media. If you help me, I'll put your name on the paper. No joke.

Haven't told any of this to my advisor, but I will - after my committee meeting. Which reminds me, there's something I really ought to be doing just now ...

The Hierarchy of Toilets

This is hardly a post about An Important Topic, but I was thinking about something the other day when I was sitting at the computer in our "chit-chat room". This is the large outer office between the hallway and my PI's office, which is also pretty big and has two huge windows. It contains three desktop computers and our administrative assistant's cubicle. Next door is the other big-ass office on the floor, which is similar to ours (but not as nice and typically with less snackage). The office area is at the opposite end of the floor from my lab space, the kitchen, conference room, and communal sunny area.

Down at the pleb end of the floor, where I work, there are two single-person bathrooms. One has got a shower, which is useful if you happen to stay over night and want to not smell before group meeting. These are just marked "Restroom".

But over here at the posh end of the floor, where the big tenured dudes live, the two single-person bathrooms are labeled "Men" and "Women". What, I have always wondered, is the point of designating as male or female a bathroom which is only intended for use by one human at a time? There are no urinals or mysterious feminie hygeine product disposal units in any of these facilities. The only explanation I can think of for the bathroom segregation is this:

So that the naked ass cheeks of the (male) tenured professors do not have to rub against the same plastic toilet seats as the naked ass cheeks of the (female) administrative assistants.

Think about it, though. How can we expect to maintain professional distinctions if we're all pissing in, literally, the same pot?

Even my gut reaction is blanche at the notion of our den-mother administrator's private bits sharing the same urine-scented air as my PI's. But if our PI were a person of the peeing seated variety, it might not even occur to me ...

There are several junior faculty women in the smaller offices down the hall. So I was thinking, isn't it a problem that the smooth PhD tuchases of the lady faculty members must make proximal contact with hienies of the secretarial class? Sex trumps snobbery, I guess.

Of course, this wanton comingling of butt-sweat obviously isn't an issue for the impoverished grunts at the benches down my end. We're not cool enough to have the Sex-Selected Hierarchy of Toilets. In the pecking order of the floor, the low-status, officeless males are equivalent to females of any rank.

I'm not sure what about this toilet situation is the most creepy.

In any case, I'll be damned if I go all the way around the hallway to the "Ladies'" toilet when I'm sitting about ten steps away from the "Mens'".

God, I'm such a freakin' iconoclast, aren't I? Not so much. The other day I actually did slink around the corner to the pissoir de les femmes when I saw the dude PIs standing nearby. So embrassing . . .

Never again. Liberte, egalite, fraternite! Toilets of the world, unite! Take that! Ha ha! Sit in my ass sweat, tenured folks!

Anyway. That is all.

Mammals In My House

Mouse body count: 2

Yes, two little dead mousies have been found in our little snappy mousetraps. Take that, interlopers!

I feel bad for them, but I am sure it was a quick and mostly painless death. Maybe they even got to have a little taste of peanut butter during their last moments on Earth.

Springy put a mouse-proofing strip over the bottom of the door to keep the little buggers out. Why didn't I do that three years ago?!?

Poor little cute little mouses.

Still. Stay the fuck out of my kitchen if you know what's good for you.

Who Needs Sleep? Or Reproductive Freedom?

Did you ever wake up at 2 a.m. from a dream about your research project and then you can't stop thinking about it? You're designing constructs and plotting out the most perfect experiments ever, or maybe just mulling over how to salvage the experiment you started the previous day in which in one of the conditions the cells didn't adhere. And then you kind of wish you had the power of teleportation so you could pop over to the lab to just check on things since you're not sleeping anyway. Or maybe if you lived really close to the lab and you could ride your bike over in your jammies. And once you start thinking of PubMed searches you ought to do or new models that really explain everything this time, you may as well just get up for a while.

Science has murdered sleep.

Then you might try to think about other things. Such as the ban on "partial birth abortion", which despite being a term made up by anti-abortion wingnuts has serious implications for every woman of reproductive age in the country.

Or you might distract yourself with thoughts of how many people died in Baghdad today, and how that number is probably higher than the 33 people who were killed at Virginia Tech, and how there are actual reasons why those people were blown to bits but you'd never know what they were if you just listened to fucking Richard Perle.

You might murmer to your bed partner that you can't stop thinking and he, or she, might murmer back, "Think about furniture" and something else incoherent before his, or her, breathing reverts to the rhythm of sleep. You might put your head on his, or her, chest and listen to his, or her, heart beat, now too hot, now too cold, trying to think about Shaker chairs and Antiques Roadshow but fatally distracted from sleepy thoughts by having, just having, to remember the word that means the opposite of "subside".

Then you might remember that you lost the prescription for the Ambien and if you go back to the health center the doctor will totally think you're a drug addict. Or seller of drugs. Not that you would sell your precious Ambien, if you had it.

You'll never be able to concentrate tomorrow if you don't get back to sleep.

You might, at that point, get up for a while and sync up your iPod, and spill two full glasses of water on the carpet before you give up and have a juice glass full of wine. You might even write yourself an email detailing the experiments you can't believe you hadn't even thought of before now.

But at least you have someone nice in your bed, or maybe you don't but at least you can sprawl out, and at least it's not the sound of gunfire keeping you awake. Glass half full, glass half full. The other half is soaking into the carpet.

Did you ever have that kind of night?

If so, I know how you are feeling.

Bloody Biochemistry

I hate Western blots.

I hate them, hate them, HATE THEM!!!!!!!

Amazing

I had other stuff to say but, eh, buggerit. Watch this instead. You'll thank me.

A Moment of Silence

For Kurt Vonnegut.
And thank you, Mr. Vonnegut, for everything.

Asking For Help

So, one of my problems is that I always feel like if I haven't done everything myself it "doesn't count". Another is that I am often uncomfortable about asking for help as this would a) be imposing on other people's time, b) prove that I am a big dumb idiot who is also incompetent, and c) expose my beloved baby project to the scrutiny and possible mockery and contempt of others.

Clearly these are issues that are hindering my progress.

With that in mind I have sent long emails to several of my most trusted colleagues outlining exactly what I have found, think is going on, and need suggestions about in my project.

It was actually less hard than I thought it would be, and writing it out was helpful for crystalizing the situation and the model in my own mind.

Fingers crossed that laughing and finger pointing do not ensue.

Fascinated Horror

Good God, who are these people?

Springy Is Too Cute

Springy [untangling and winding up multiple computer, printer, and microphone power cords]:

"Joolya, why are cables so keen on one another?"

On Moral Order (shamelessly cut and pasted)

MORAL ORDER

The metaphor of Moral Order fits naturally with the metaphor of Moral Authority, as well as with the literal parental authority central to the Strict Father family. This metaphor is based on a folk theory of the natural order: The natural order is the order of dominance that occurs in the world. Examples of the natural order are as follows:

God is naturally more powerful than people.
People are naturally more powerful than animals and plants and natural objects.
Adults are naturally more powerful than children.
Men are naturally more powerful than women.

The metaphor of Moral Order sees this natural hierarchy of power as moral. The metaphor can be stated simply as: The Moral Order Is the Natural Order.

This metaphor transforms the folk hierarchy of "natural" power relations into a hierarchy of moral authority:

God has moral authority over people.
People have moral authority over nature (animals, plants, and natural objects).
Adults have moral authority over children.
Men have moral authority over women.

The Moral Order metaphor plays a crucial role in an important interpretation of the Judeo-Christian religious tradition. It is an entailment of this metaphor that God cares about human beings in the same way as parents care about their children or shepherds care about their flocks or farmers care about their crops. Logically, after all, there is no reason that a supreme being should care about lesser beings. But if the order of dominance is a moral order, then God does care about mere mortals; setting the rules and enforcing them is how he shows he cares, and in return for his care, we owe him obedience. The consequences of the metaphor of Moral Order are enormous, even outside religion. It legitimates a certain class of existing power relations as being natural and therefore moral, and thus makes social movements like feminism appear unnatural and therefore counter to the moral order. It legitimates certain views of nature, e.g., nature as a resource for human use and, correspondingly, man as steward over nature. Accordingly, it delegitimizes other views of nature, e.g., those in which nature has inherent value.

George Lakoff Moral Politics 1996

A Proposition of a Different Kind

Perhaps atheism is an inevitable stage of the journey towards a higher conception of transcendent truth.

What do you think?

Sexy Stephanie

Hello, loyal readers, if in fact any of you are still checking in!

Ordinarily I am a knowledge junkie. If given a choice between knowing and not knowing something, I'll almost always eat the proverbial fruit. However, I have become privy to a piece of knowledge that I wish I didn't have. This is the fact that:

There is an enormous number of dyslexic and/or visually impaired men in the Boston area who, at all hours of the day, seek to engage the services of a prostitute. Sorry, "escort".

I know this because one such Lady of the Night (and of the morning, and lunch-time, too) has got a phone number one digit different from mine, and as a result I've been fielding calls from the more stupid or careless of her would-be clients.

Estimates of the percentage of Sexy Stephanie's clientele who get her number wrong and call me instead vary (5%? 15%? 1%?) but I've gotten more than a dozen calls in the last couple of weeks "about my ad in the Phoenix". Yuck!!!

I've just been saying "Sorry, wrong number" when the punters proposition, but then I got a text message from "Jim in Quincy" and Springy texted back, "Better check the number carefully next time you want to call a hooker." Needless to say, Jim didn't text back.

I wish I did not have any idea about how many dudes who can't reliably dial a number are calling hookers. I wish I were completely ignorant about the scope of the adult services industry. But now that I'm not, I kind of want to know: Who the hell are these men? Are they just super gross or should I feel a little sorry for them? Are they deformed? Or do they have weird kinks that they don't feel comfortable sharing with non-professional women? Or are they just lazy and horny?

I guess I could ask them - I mean, I have their phone numbers.