the adventures of baymate
apalazzo | February 11, 2009You take out your scissors and start cutting.
(A photo of baymate working on supplemental figure 12 of Ward et al., PNAS 2007.)
To be honest, we didn't know what to make of the final arts & crafts product, a floppy ABC transporter that can be shifted into various conformations, each of which is suppose to represent a different nucleotide-bound state.
(You'll also note that this paper was resubmitted due to an infamous error.)
apalazzo | February 2, 2009Wow, last week was memorable. Not only did I sign my contract with the University of Toronto, but it appears as if my super duper theory that I thought I had killed, might have been resuscitated.
To remind you, the last time I wrote about my trials and tribulations, I thought that I had ruled out my super duper theory because of a simple straight forward experiment. The experiment involved microinjecting a dominant negative protein that blocks a complex from working. What I failed to tell you is that I was waiting for my positive control, a protein whose distribution would be altered if that…
apalazzo | January 19, 2009Hello world.
Once upon a time, I had a laptop. As time went on, its hard drive filled up with pdfs, music files and an enormous (well, relatively enormous) operating system. This pattern of exponential expansion continued for a few years until, the imbalance between data and storage capacity, just like the overpopulation of the Norwegian hills by lemmings with prolific breading capabilities, could no longer be sustainable. A change was needed before the impending threat of mass suicide. And so on January 7th, having realized that my data needed more fertile ground to colonize, I bought a new…
apalazzo | April 19, 2008I'll type something for you quickly as I have a couple of minutes.
This week has been a little crazy. I've been preparing my talk in Montreal and gearing up to perform a major experiment, some old school bucket biochemistry. Baymate performed a similar experiment using dog pancreas, and I need to repeat the protocol with a human cell line. I've already gone through the protocol twice and had to rethink some of the details. Right now the big experiment will start Sunday night continue through "Patriots' Day" and finish some time on Tuesday. So if you are wondering why you won't hear from me…
apalazzo | March 12, 2008Sorry about the paucity of posts. I've been running around lately. Friday right after the Origin of Life Symposia we took off for NYC. After a day of mental stimulation, including stops at the Whitney and the Met to hear Janine Jansen play Bach and an incredible Schnittke String Trio, we raced back to Boston on Sunday to catch a ride up to the White Mountains (that's New Hampshire for you non-east coasters) to attend the almost annual Rapoport Lab retreat. There I participated in the mandatory alcohol toxicity seminar that lasted into the wee hours of the morning. After a quick nap we sprang…
apalazzo | March 5, 2008I'm excited, baymate and I will be off to Radcliffe to attend a symposium entitled, The Origins of Life: The Earth, the Solar System, and Beyond.
In related news I learned from Corie that over the next year, Craig Venter will be a visiting scholar with Harvard's Origins of Life initiative.
apalazzo | January 18, 2008Baymate just freaked-out over that bio-rad PCR clip that's been making the rounds. If you really want to see it, look beneath the fold.
apalazzo | January 10, 2008Forget about all the crazy conspiracy theories about why Hillary won (such as the Deibold theory, the white poor vs black candidate theory, the who is on top of the list theory, the Chris Matthews revulsion theory, the Hillary preconceived teary-eyed pro-sympathy theory) - the real issue is whether reshaven should be counted as a word in Scrabble.
Yesterday we discussed what the Official Scrabble Dictionary had to say on this issue, but as a commenter pointed out:
Also note the irony of letting a book, written by a supposed higher authority, decide your opinion on whether something exists…
apalazzo | January 9, 2008No I'm not going to write about the NH primary. I'll just say that I'm surprised that Hillary won, and I'm glad that the NH and Iowa votes canceled eachother out. In the end the Democratic nomination will be decided by the more populous states (as it should be).
Let's get on to more important issues.
Yesterday afternoon a very serious topic came up in our bay. You see baymate challenged me to a game of Scrabble (or it's facebook equivalent). I then made a big mistake and mentioned the infamous "reshaven incident".
You might be wondering what exactly is the "reshaven incident"? Click on the…
apalazzo | December 5, 2007Yesterday, a postdoc from a neighbouring lab came by to hand over an aliquot of antibodies to baymate. Here's what happened:
me: it looks like Santa came early this year.
friendly neighborhood postdoc: Well actually my PI would be Santa. I'm more of a reindeer.
baymate: Nah, you're an elf. Remember, it's the elves that make all the toys while Santa sits back and relaxes.
I think that baymate was on to something. The elves make all the toys, while Santa goes on a world-wide toy-promotion PR tour. But the only question I have is who are the reindeer?
apalazzo | November 1, 2007So this morning baymate was telling me how she's taking a course called Intro to Maya with Gael McGill, a former gradstudent here at Harvard Med School. Gael co-founded Digizyme and gained quite a bit of attention with his fantastic "cellular movie". You know the one where a kinesin motor protein drags a vesicle along a microtubule.
Gael is teaching gradstudents and postdocs here at Harvard Medical School how to use Maya, a program used to generate animated 3D-movies of the type popularized by Pixar Studios. There are even plans to have a repository of 3D animations of cellular phenomena…
apalazzo | September 7, 2007This morning, baymate and I were debating when would be a suitable time for coffee when we heard a giggle from the next bay. Here's what our neighbor saw on her transformation plate:
And here's a blowup:
As another postdoc said, "you probably don't have to sequence those colonies. They'll have what you're looking for."
apalazzo | August 22, 2007that Sigma-Aldrich advertises on it.
(ht: baymate)
Rout 65 bus info (MBTA).
PS if anyone else sees this send me some photos.
apalazzo | July 20, 2007Warning: the following may not be comprehensible for those not working in a lab.
So the other day, baymate and I were discussing how we use up our pipette tips. Not in terms of experimental procedures or in the types of orifices we jam them in, but in the order we remove our pipette tips from the pipette tip-box.
I tend to start off in one corner and work my way diagonally through to the other end:
In contrast my baymate likes to cut right through the middle of the box to form a horse-shoe pattern. (Quite a bold strategy)
In order to investigate this further we went around the lab and asked…
apalazzo | November 29, 2006OK I finally did that experiment that people asked for ... and more.
If you want to know why I performed this experiment, read this post on RNA treatments for autism. Here I present to you evidence that your body is secreting enzymes, called RNAses, that will chew up your RNA in minutes.
So the experiment:
500ng of RNA was mixed with either
- control buffer (100mM KCl, 10mM Tris buffer pH7.4)
- 1ul of DNAse (1mg/ml), this is what you would call a negative control - no degradation should be seen here
- 1ul of water applied to sweaty skin
(After working a bit with my latex gloves, I puled off…
apalazzo | August 4, 2006My baymate and I started a little discussion about lab fashion. Why? Well I'm a pretty ardent wearer of sandals, I'll wear them until late fall if I have to. I'll wear them with jeans too. But under no circumstances will I wear sandals with socks.
We then listed all the faculty who combine these clothing items on a regular basis (sorry, the list is confidential).
This brings me to my question to all you out there is: why wear sandals with socks? (And why does the sandals with socks phenotype correlate with being in research?)
Now while we were on the topic we asked a deeper, in some sense…