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Lab Songs

Adeline's Song

In the Hook Equivalence Group 

(To the tune of In the Big Rock Candy Mountain

Well we're pretty sure we know the signals that determine each cell type in the vulval epithelium of the C. elegans hermaphrodite. But when it comes to the male, and the fates in the tail, we're a little out of the loop. That’s when Adeline came, and started to explain, the hook equivalence group. 

Well P9p through 11p play roles in hook formation.
Redundant with the PCS, it helps vulva location.
P11 gets the primary fate and P10 is number two.
P9 might decide that it wants to divide,
but sometimes it's the type to fuse with the hyp,
And that's the hook equivalence group.

Now it seems that the very same signals can make a vulva or hook,
But Adeline found specificity when she took a closer look.
We know P6p responds to lin-3 but not so much to Wnt,
But in lin-17, hook defects were seen, and that gave her a hint…

That these equivalence groups are patterned by slightly different codes,
and the HCG just might reflect the more ancestral mode
You need some Wnt for the primary fate, and Notch for number 2,
And lin-3 RNAi, with Wnt compromised,
showed you need EGF only when you're bereft,
In the hook equivalence group.

This difference in induction might explain these varied fates
But maybe Hox expression puts these groups in different states
We hate to dwell on the history of the cell, I don't think it's a stoop (to say)
it might address why mab-5 is expressed in the hook equivalence group.

And that's not all she did, oh no, her curiosity made her
Examine inductive signaling by TGF-beta
Adeline, you brighten the lab, and nothing seems to phase ya
We'll miss your mood, and your love of good food,
It’s quite a long list, all the things that we’ll miss,
When you go to Southeast Asia.

Ted's Song

You've Got That Law School Feeling

You never close your eyes anymore when you make worm picks
And there's no tenderness when you reach for your pipet tips
You're trying hard not to show it,
but Reerie (Ririe!) You know it!



You've got that law school feeling, whoa that law school feeling
you've got that law school feeling, now you're gone, gone, gone, whoa-oh.



Maybe I don't have the answers but I know it's true
No one will find vulval enhancers like you used to do
You had a gene regulatory network you don't find everyday
But now you're freezing all the worm strains you made along the way

On the LSAT you did so well, and it weren't no fluke,
Now you've run your last DNA gel, and you're off to Duke
And in patent litigation, we know you'll go far
If you can handle cis-regulation, you'll surely pass the bar



You've got that law school feeling, whoa that law school feeling
you've got that law school feeling, now you're gone, gone, gone, whoa-oh.



You found the regions that some transcription factors bind,
And shed light on the roles of lin-11 and -29
Without you cis-reg won't be fun,
So don't you ever forget ZMP-1!



You've got that law school feeling, whoa that law school feeling
you've got that law school feeling, now you're gone, gone, gone, whoa-oh

Jennie's Song

Ground Polarity

video here

If you're going for symmetry, you need a central cue 
So if you're P7.p, you can use mom-2 
But which direction do you pick when you lack Frizzled and Ryk? 
Looks like you face posterior by default 
But that's a model that we take with a grain of salt 
Yeah, what happens if you get rid of all the Wnts? 
You'll find there's ground polarity, it's something you can always see 
When you take away the central cue 
And beneath that ground polarity, it's default stochasticity 
Without a Wnt, they haven't got a clue. 



What's CAM-1's function? Jennie wanted to see 
Could it inhibit induction non-autonomously? 
And the result was quite the same even without the kinase domain- 
It could work in nearby tissues so she started to think 
That CAM-1 might be acting as a Wnt sink! 
So what does the binding constant of CAM-1 need to be in order to 
sequester enough Wnt molecules to inhibit signaling? 
Revealing ground polarity, it's something you can always see 
when you take away the central cue, 
and beneath that ground polarity it's default stochasticity 
that hs:CAM-1 can reveal to you. 



That old model is passe, you need multiple Wnts
With her reverse-binding assay, Jennie caught this glimpse: 
If it's default you wanna score, heat-shock CAM-1 in lin-44 
It shows there's a polarity that must get refined. 
But isn't there another function that we ought to keep in mind? 
Yeah, didn't she show that CAM-1 is more than a Wnt sink? 
It acts in ground polarity, established by egl-20 
and regulating SYS-1 with Van Gogh, 
and in that ground polarity, CAM-1 needs its ICD 
That kinase might not be so dead, you know. 



With a paper in Development, and another in Cell 
There's more than a little hint, that she'll do well 
It's true that Jennie is no wuss, she's off to postdoc with Roel Nusse. 
I can't believe she's leaving, I'm really quite sad 
But at least she won't be here to make the rest of us look bad! 
And we'll always have something to remember her by... 
We'll think of ground polarity, established by egl-20 
and regulating SYS-1 with Van Gogh, 
and in that ground polarity, CAM-1 needs its ICD 
That kinase might not be so dead, you know. 



Look for the ground polarity, it's something you can always see 
when you take away the central cue, 
and beneath that ground polarity it's default stochasticity 
that hs:CAM-1 can reveal to you 
Those VPCs they don't know what to do 
Without a WNT, they haven't got a clue. 

To the tune of "Bare Necessities" 

chorus 
C-C- F- F- C-C-G-G7 
C-C-F-F-C-G-C (strum down...) 
verse 
G-G-C-C-G-G-C-C7 
F-G7-C-D7 
talking 
(strum up...)

Alok's Song


(blues chord progression: A/A, A/A7, D7/A, E/A; last short verse: D7/A, E/A)
bold=talking, strumming A chord 



He came down from Stanford, this guy with the crazy hair
Feeding yeast diets is what he'd been doing there.
He visualized his microarrays with something new
He'd created his own software, he called it JavaTreeView.


"What, is this guys a biologist or a computer geek?"
"I dunno, I guess he could be both"


In the Sternberg lab he used his program to define
The cuticle collagens making up group nine.
He was searching through promoters to find a common motif,
But trying to find a consensus, well it can bring a lot of grief


"Yeah, how do you know a real motif, anyway?"
"Beats me, I think you have to have a background model or something."


But Alok, with his computer skills and a lot of ambition
He tried find a way to automate intuition
His program can help you find the shortest sequence with a function
by using a method called Maximum Clique Motif Reduction


"What's a clique, anyway? Does it have to do with those circles connected by lines?"
"Dude, don't ask me; I have no idea. I had to get these lyrics from Paul."


Cross a programmer and a biologist, what do you get?
Someone who's right at home with a computer or pipet?
But he does more than just science, as we can confirm
By the creation of M&M Elvis, and Blingy the Worm.


"Yeah, that thing was so cool!"
"We should enter it in the elegans meeting art show under OUR names!"


MIT, Stanford, Caltech, you've clearly made the grade,
So where do you go from here? How 'bout somewhere you get PAID!
He won a contest called Bid Tac Toe and he bought us all some beer
And now he's off to Ellington to be a software engineer.


"So do we have any parting advice for our friend?"
"Yeah, but we might have to put it in video game terms, so he can relate."


Well, Connecticut's where the money's at, but California is warmer, 
So stop hoarding all of that gold, and upgrade your armor.

Paul's Song

Paul's Birthday Song 

(The chords: verses: CC/GC/CC/GC; choruses (bold): FC/GC/FC/GC) 



In the Horvitz lab, he showed what lineage could tell us 
By working out the cell divisions in Panagrellus 
Then with Iva, he started to delve 
Into the gain and loss of function phenotypes of lin-12 

That's a thesis there; to keep on going might seem dopey, 
But he was thinking 'bout some genes that showed pleiotropy 
How to explain the effects of lin-4 and lin-14? 
It's in the timing, that's right, heterochronic genes. 



Well happy birthday Paul, we just wanted to sing, 
You deserve all the good things that life can bring. 
And from everybody here and everyone you've helped along the way, 
We want to wish you a happy birthday. 



At the end of his PhD, things were going well, 
As Paul devoted himself to seven cells. 
The anchor cell signals the VPCs to change their fate; 
Without a signal they stay in the default state. 

Things were going fine but he thought the time was ripe 
To move on to a postdoc in yeast mating type. 
But in the end who can resist the seduction 
Of studying C. elegans vulval induction? 



Well happy birthday Paul, we wanted to proclaim 
That without you, C. elegans just wouldn't be the same. 
And from everybody here and everyone you've helped along the way, 
We want to wish you a happy birthday. 


In the Sternberg lab, you could say things have gone alright, 
and if I tried to list the papers, we'd be here all night. 
On the EGF receptor, we know he wrote the book, 
But he's studied everything from lin-3 to the hook. 

There's Ras and Raf, Sli-1 and Sos, just to name a few. 
Trp channels, Wnt and lin-15, lin-11 and Gq. 
Wormbase, textpresso and genome-wide interactions, 
Evolution, pathogenesis and mating attractions. 


From circuit design and the tracking of worms, 
to spicule protraction and the transfer of sperm. 
From kidney disease to P7.p orientation, 
To IP3 signaling in ovulation. 


Well Paul's a good advisor, and if you're ever in a state, 
You can count on him to tell you everything's 'great, great'. 
And he's pretty funny, but I think that you'll agree, 
That it's not in the joke, it's in the delivery. 

Well, trying to get grants can give you the blues, 
But Paul's pretty good at it, and he's got Howard Hughes. 
And he's a great geneticist so we think it's only fair, 
That now he's sitting in Thomas Hunt Morgan's chair. 


Well happy birthday Paul, we just wanted to show 
That we think you're a great mentor and that you oughtta know 
That from everybody here and everyone you've helped along the way, 
We want to wish you a happy birthday. 

Well happy birthday Paul, we just wanted to sing, 
You deserve all the good things that life can bring. 
From everybody here and everyone you've helped along the way, 
We want to wish you a happy birthday.

Paul's Get-Well Song

video here 

Paul, we bet the last time you were out from lab so long,
Carter was in office and the Bee Gees had hit songs.
We wrote this tune to let you know that we’ve not gone astray
‘cause anarchy’s not fun without you here to lead the way.

Ping found worms are more tempting to fungi that are lean,
Meenakshi had the flu but now she’s labeling protein.
The new virtual worm is really something to behold,
Andrea writes her thesis while her plates are growing mold.

“And it’s great, great, great’; we miss those magic words,
without the ‘great, great, great’, we’re just worm-picking nerds.
So get well soon, then give us a kick-start.
Bring the ‘great, great’ back and the lab won’t fall apart.

The golf course way in Downey finally gave Adler a key;
he and I are working on something you’ve got to see:
Their artificial cricket, which is based on an Arduino,
is a masterpiece, yes something that truly must be seen-o.

They keep curating data down in Church 64
but as fast as its curated, somebody finds some more
I hear that they’ve been working hard on the new OA
they say that when you check it out, it’s gonna make your day.

“It’s just great, great, great’; we miss those magic words,
without the ‘great, great, great’, we’re worm-curating nerds.
So get well soon, then give us a kick-start.
Bring the ‘great, great’ back and WormBase won’t fall apart.

To figure out the circuits that relay ascarosides
I’m lucky that Anusha’s great talents are applied.
She records from CEM when the male can smell a mate
(He thinks he’s meeting girls but it’s only ascr-8).

Mihoko sifts through thousands of genes in the linker cell
While Erich tries to negotiate a position at Cornell
Dan has joined the lab and to Merja we’ve said goodbye;
But the other Finn will be back again & so we’ll drink good wine.

“It’s just great, great, great’; we miss those magic words,
without the ‘great, great, great’, we’re just worm-picking nerds.
So get well soon, then give us a kick-start.
Bring the ‘great, great’ back and the lab won’t fall apart.

For signatures and board meetings, they all ask for Paul,
Mary tells them he’s not gonna make that conference call.
It seems that everybody’s asking for a reference letter
but she tells them no, they’ll just have to wait till he gets better.

So don’t you worry boss; everything’s as usual here -
the worms, the lounge, the chaos, WormBase and wine and beer.
We want you to feel better as we send you cheers and greetings
especially from the ones who were supposed to give lab meetings.

And it’s ‘great, great, great’; we miss those magic words,
without the ‘great, great, great’, we’re just worm-loving nerds.
So get well soon, then give us a kick-start…
Bring the ‘great, great’ back and things won’t fall apart!

Dave's Song

The Anchor Cell Shuffle 

(Goodbye song for Dave Sherwood, 
To the tune of Ben Harper's "Steal my Kisses': C-F-G-C) 



Models of cell invasion weren't so persuasive 
It was hard to study cell behavior that's invasive 
But Dave, he took it in the right direction 
By studying the C. elegans vulval-uterine connection. 



Cell invasion seems like it's a pain 
How you supposed to get across a double basement membrane? 
But with a handful of good markers and some stamina 
He could see the anchor cell breakin' down the basal lamina. 



Are the vulval cells in a permissive state, 
Or is this a process they might regulate? 
Well it turns out there's something that they do, 
They send the anchor cell a navigational cue. 



Now he's headed down to Carolina, 
A job at Duke well nothin' could be finer 
Startin' a lab ain't easy, that's understood, 
But with Nina, Kai and Noa, hey life's pretty good. 



In his lab he's gonna be the boss, 
He can have his students find targets of Fos. 
At first the lab may not be over-sized, 
But you can bet it'll be real organized. 



Choruses: 



Now there ain't nothin' to the anchor cell shuffle, 
No need to get your leading egde in a ruffle. 
First you gotta break that basement membrane down, 
And send your process out till the primary cells are found. 



Anchor cell invasion ain't hard to do 
Break that membrane down and send your process through 
If you're extendin' in the right direction, 
You'll make a functional vulval-uterine connection.

 

Shawn's Song

Postdoc Leavin' Blues 

Shawn came to the Sternberg lab to figure out Trp-C, 
so he isolated mutants in TRP 1,2,4 and 3 
Now lack of calcium influx should leave these worms in peril, 
and sure enough trp-4's are unc and trp-3 males are sterile. 



Well he looked closer at trp-3 and much to his surprise, 
those little sperm were motile but they couldn't fertilize. 
Speaking of fertilization, well now Shawn's a dad, 
I guess that tells us one thing- he didn't spend EVERY night in lab. 



Now he's got a job in Michigan, and that's great but you can bet 
that really good Chinese food will be pretty hard to get. 
Moving can be rough, but he's already got his lab together, 
and we know that he'll be fine if he can just handle the weather. 



but now... 



We've got the blues, we've got the postdoc leavin' blues 
Shawn's putting down his pipetman, and puttin'on his walking shoes 
I guess there's nothing we can do but drown ourselves in booze. 



In room 217, things won't be quite the same, 
when we have troubles cloning, we can't just call out your name. 
and late nights in the lab, well they just won't be quite right, 
but then at least we'll get to play our music every night. 



but still,... 



We've got the blues, we've got the postdoc leavin' blues 
Shawn's putting down his worm pick, and puttin'on his walking shoes 
Sure we'll gain some bench space but look at what we lose.

The Ballad of Nadeem

Lab of the Rising Sun 

There once was a man from Ormstown (say what?) 
They called him Deemie or Nad. 
He liked to racewalk, yeah he wiggled his butt, 
and his knowledge of Star Trek wasn't bad. 



In Ben Neel's lab he did his best 
for retinoic acid receptor glory. 
And he wasn't real suave or even well dressed, 
but he managed to win over Lori. 



In the Sternberg lab his screen went great, 
he got sop-1 or was it dpy-22? 
And he found an effect of behavior on cell fate 
that was acting through Gq. 



Now he's got a new job in SLC 
and we're sad he'll be so far, 
But at least we'll have a place to stay when we ski, 
and hey, I get his car. 



Now students, to you I've got something to say- 
while the Moghal lab seems fun, 
he'll have you swim all day and work all night 
in the lab of the rising sun. 
You'll be sore from the pull-ups, too tired to boggle right, 
in the lab of the rising sun.

Martha's Song

Three genes, two species, one PhD 

When Martha started out, she worked on lin-15 
She also looked for suppressors of lin-3 and got a heterochronic gene 
Then she focused on cis-regulation and decided she would strive 
To elucidate the cell-specific elements that drive 
egl-17, zmp-1, and cdh-3: three genes, two species, one PhD. 



Before she came along, it was anybody's guess 
What drove egl-17 in presumptive E and F. 
To identify these sequences, she knew her only hope was to 
Spend all her days and nights at the injection scope 
egl-17, zmp-1, and cdh-3: three genes, two species, one PhD.



Looking for the regions that are driving zmp 
The only cell type that eludes her is VulD 
And for the other cell types, her deletions bring to light that it's 
Not just the nature but the number of the sites 
egl-17, zmp-1, and cdh-3: three genes, two species, one PhD. 



What's driving cdh-3 in the anchor cell, 
Ain't easy to figure out, but Martha she could tell that 
Alpha and beta and/or gamma's whatcha need, 
One's not enough, 'cause you need two out of three 
egl-17, zmp-1, and cdh-3: three genes, two species, one PhD 

egl-17, zmp-1, and cdh-3: three genes, two species, one PhD.

Yen's Song

 
When Yen came to Caltech, she joined the Sternberg lab 
It was just for the summer, but she stayed 'cause it was fab 
She decided the topic of her graduate education 
would be: IP3 signaling in ovulation. 



Well, the IP3 kinase should have an effect, 
but the lfe-2 hermaphrodites, they showed no defect 
and from that moment on she knew she'd spend her days 
workin' on the IPP-5 phosphatase. 



So she looked at ovulation in sy605 
and instead of just one, they squeezed out two oocytes 
Now she's shown that for precise ovulation, 
there's a lot more goin' on than receptor activation. 



As if a PhD from Caltech weren't no big thing, 
now she's headed off to med school, an' she decided this spring 
that while Chicago just might be her kind of town, 
if she left us it would only bring her down. 



So for the Buis and the lab it was a happy day, 
when we learned that she was goin' down to UCLA.