Thursday, February 22, 2007

i can seeeee you!

as you can see, my big hole arrived today. i know you are jealous that you too cannot have such a marvelous gaping maw in your kitchen,* but they are reserved for special people like me.

in exciting news, they were able to tear everything out while limiting the porthole between the upstairs and my apartment to the kitchen. this means i can continue to shower without having to worry about collecting a cover charge.

in other exciting news, the plumber graciously agreed not to cut the sewer pipe until he is ready to cap it so that i don't have 'sewer vapors' wafting through the apartment for an undisclosed period of time. that this item required serious discussion completely baffles me. but i am weird like that.

*honestly, i am impressed that they managed to make it so tidy. it certainly didn't start out that way.

how happy he will be...

Stripey socks for TraV
Originally uploaded by jacquichris.
tonight i finished TraVy's first pair of handmade socks. they took longer than i would have liked because i kept decreasing needle size until i liked the way the pattern lay in the round. unfortunately, that meant i knit these puppies on US 0s. oy.

i also finished that last preemie set for the Warm Hearts, Warm Babies handoff tomorrow.

next to finish up: mittens for my boss. well, those and my dissertation.

Wednesday, February 21, 2007


my upstairs neighbor was evicted last month. this would be irrelevant to me but my landlady is taking advantage of this opportunity to gut and improve the apartment.

the downsides are:

  • incredibly huge pieces of lumber regularly careen from above to crash into the ground outside my living room. this makes concentration on my writing almost impossible.

  • i have been informed i will soon have an extremely large hole in my kitchen wall that will extend into the ceiling and remain in 'hole' form an extended period of time before being closed.

the upsides are:
  • incredibly huge pieces of lumber regularly careen from above to crash into the ground outside my living room. this creates a certain sense of action movie danger and/or amusement.

  • apparently i will soon have a washer and dryer in my kitchen. well, as soon as the impending hole of doom is closed.

i also have the dubious pleasure of conversations like this:
me: "Just so you know, one of the cats may be in hospital for several days so don't panic if you can't find that one." (me pointing at Mr. Head)

plumber: "Why don't you lock the cats in your bedroom so we don't risk losing them tomorrow."

me: "No problem. I just wanted you to know about Mr. Head in case you need to get in on the weekend since he won't be here."

plumber: "I won't be looking for the cats if I am here. I have no reason to go into your bedroom. When I have no reason to go somewhere, I don't. I find that helps with keeping things simple."

me: "Um, okay. I wasn't going to lock them in the bedroom indefinitely but..."

VERY LOUD CRASH from above and then slightly less loud WHIMPERING

me: "Maybe you better check on Ray?...

I hope he is okay."

[awkward silence]

plumber: "This is why he is missing fingers...

And a vertebrae...

You knew that right?"

me: [blink blink]

plumber: I guess I'd better go look."

chasing the high

yesterday, something wonderful happened. not quite as wonderful as falling in love but close... i got the results back from my protein isolation.

things that are wonderful about my results:

  • even though i did not manage to get all three bands, all three proteins were still present in sufficient quantity in the sample to be sequenced [which really says alot about the specificity of Western blots if you think about it].

  • the proteins identified thus far appear to make sense, not that i want to jinx anything here.

  • antibodies against one of the proteins identified have been associated with multiple immune-mediated diseases in humans, including nephritis. this supports the protein's identity and provides an independent degree of support for my hypothesis that these antibodies are associated with immune-mediated disease in cats.

overall, the results appear to be everything a girl could possibly want. they validate that my research hasn't been total bunk (which i was starting to secretly wonder) and indicate it may in fact be pivotal work. the kind of work that changes things. again, not that i want to jinx anything.

as you can imagine, i felt incredible yesterday. by ten last night though, the high had mostly dissipated. i am recapturing it a bit this morning as i read the human literature on my proteins, but it certainly isn't the same.

i find myself thinking, 'A year of struggle to purify the proteins and the high can't last a bit longer? Sheesh.'

Friday, February 16, 2007


as my last few posts have probably already made clear, things are a bit crazy around here. since things always happen all together, that of course means there are many things about which i have not posted. most of these are more of the same but there are two items (of unequal importance) that are not.

Christmas stockings
Originally uploaded by jacquichris.
the lesser item of note is that i finished Hailey's stocking. of course, as i made my way into turning the heel, i suddenly realized that the entire colorwork section was meant to be knit flat. this error partially resulted from the spotty nature of the pattern and partially from my own inability to recognize that the fact that knitting the colorwork in the round while managing the tension was positively hideous just might mean something was awry. Mickey would have chuckled herself silly if she was here to see me. (she helped me map the colorwork on my stocking a few years ago when i first decided to try this.)

the foot was completed at what seemed like lightspeed after the long-suffering misery of the leg Saturday night.

then i sat for awhile and contemplated frogging the entire thing and reknitting it to maximize its perfection. i decided that the story and suffering really better capture the love of a handmade Christmas stocking and put it away from me.

for Hailey and Kylie
Originally uploaded by jacquichris.
being me, i kept returning in my mind to how much faster and more painfree the work should be if knit flat. knowing that i intended to eventually make one this year for Kylie (my other nieceling), i finally caved and decided to do it now. late Saturday night, i cast on and worked most of the name. Sunday i lazed about with TraV and knit. i decided the stockings should not be identical and put children on the top of Kylie's. this decision i regretted almost immediately because the first two versions looked like ghouls and had to be frogged lest they inspire recurrent nightmares.* even with that challenge, i finished the stocking by midday. it took half the time, at most, of Hailey's.

*TraV still thinks they will lead Kylie's imagination into dark alleys given her quick wit and great zest for living. i stoutly maintain they represent a family of vegetarian Quaker snowpeople who would hurt no one.

i am now finishing up TraV's stripey socks, a pair of mittens for my boss, and a preemie set in time for the Thursday drop. oh yeah, and writing my dissertation. superfun!

in other, bigger, shinier news, Monday was TraV's and my first anniversary of dating. of course, we have packed this week full of celebratory goodness in the form of dentist and 'girlie' doctor appointments, exorbitant transmission blow-outs and committee meetings, preparatory blood work for Mr. Head's procedure* and scientific presentations, and planning meetings with the plumber who is going to tear a hole in my kitchen wall and ceiling to fix the upstairs apartment. if only everyone got to have our romantic rock-n-roll lifestyle. still, we are getting by, still adore each other, and have said very little we will regret.

*he 'gets' to have radioactive iodine therapy to ablate an overactive thyroid. wa-hoo! glow, kitty, glow!

Tuesday, February 13, 2007

that clanging from the ocean floor, its me

today in my committee meeting, we set the date for my PhD defense.

as soon as i left the meeting, i started to feel nauseous.

one would think this might have something to do with the two sets of letters... one of my committee members will be attending by teleconference. because the Final Examination Results form has to be turned in basically within a day, i have been instructed to send two sets of forms to Marty. he will then sign one set in the pass column and one set in the fail column and return them for use after the defense has been completed.

Tim, one of my other committee members, said we can celebrate if i pass by burning all the 'Fail' forms. i said, 'Sure. And then we can go scout around in the hallway for my stomach lining.'

realistically, i don't think this is why i feel the walls closing in on me. it is the combination of a ticking clock with outstanding lab results. the committee agreed on a Plan B dissertation structure in case the protein isolation is unrewarding, which is nice. it doesn't change my inability to write up the results and overarching conclusions until i know *something*. [did i mention that the machine used to sequence the protein is currently on the fritz?]

all in all, it is good to have a plan, good to have a framework of expectations...

still, i feel like a naval officer in a top secret nuclear submarine stranded on the ocean floor with 96 hours of oxygen and no one knowing that i am even missing.

[so that you can play along at home, i have installed a countdown timer in the right sidebar.]

a break in my lab luck?

as some of you may know, i have basically spent the last year trying to purify 1-3 proteins so they can be identified. this is the last lingering torment of my PhD. to date, i have tried 3 completely different methodologies and something like 20 combinations of reagents, incubation conditions and antibody preps each. early in the fall i got one methodology to yield one of the bands, but that particular technique yielded a huge overweighting of immunoglobulin. this became my back-up, my Plan B.

when all other options were exhausted, i conceded defeat and decided to harvest the one band from Plan B. my world was completely rocked when i discovered that the protein was not present in great enough density to visualize using the less sensitive stain necessary for protein isolation. efforts to concentrate the solution further actually caused the band to disappear.

these results left me teetering in shock, wondering whether perhaps i am not PhD material.

with no other ideas and nowhere to turn, i decided to call the woman to whom i would be submitting a successful sample to see if perhaps she had any ideas. Jessica is fabulous and, after validating that this is hard to do and that many people don't succeed, came up with several great ideas. since one involved learning a fourth methodology entirely and one might compromise the sample quality, i decided to start with the easy option. i reduced my antibody concentration to 3% of the original recommendations. (note: this was not a scientific level of decrease but instead reflected the most i could decrease the antibody concentration without having to make a separate stock dilution. basically, i was disheartened and lazy.]

A protein road map
Originally uploaded by jacquichris.
this magically led to a 1:1 ratio of antibody to protein, which is ideal but makes no sense given the initial starting concentrations and initial band densities. after magic autosubstraction using Photoshop, we are left with this clear illustration of three bands in the right lane. the top is a bit of a mystery band, the middle is the antibody band and the bottom band is my proteinaceous holy grail.

of course the concentration of protein in my sample was far too minute to show up using the cursed (pronounced cur-sed in the style of movie villains) Coomassie stain.

so i spent three days running the column over and over and over and over and over and over and over and over and over again...

...on the same lysate sample since i knew there was plenty of protein in the sample, just a persnickety recalcitrance on the part of the antibody to bind it. yesterday afternoon, knowing i was headed to a committee meeting today and uncertain of how hard to campaign for a failed experiment chapter in my dissertation, i decided to run what i had. before i started, i instructed Jen (my patient, supportive and awesome labmate/friend) to remind me i expected it not to work when it ended up failing. by the time Jen left for the night, i had 20 minutes destaining to go and it was a pretty obvious failure, so she consoled me and i took it well.

twenty minutes later, this is what i slid out onto the glass in preparation to through it in the trash.

A break in my lab luck
Originally uploaded by jacquichris.
and there it was. my sweet, sexy, playful, perfect friend - the ~40 kD band.

you are looking at the blob of slimy goo and thinking, 'She is truly unhinged. There is nothing there.'

but it was obvious when held at an angle with the light shining through it. i dragged my advisor down to witness the glory of the band before i cut it out to save for Jessica. unfortunately, to avoid potential keratin contamination (read failed experiment), i could not risk taking it to the image capture system for a photo. so i did the best i could with my camera through the plexiglass hood and without a mount.

if you squint your eyes up till you feel a headache coming on and use the membrane at the top of the post as a guide, you can almost believe what you are seeing on this photo, annotated for your viewing pleasure...

i could cry. i could laugh. i could laugh until i cry.

Jen and i are going for margaritas at the Rio on Saturday to to celebrate. you are welcome to join us.

Monday, February 05, 2007

today is my birthday.

the last few years, bad things have happened on my birthday and although the rational me understands that that does not mean all birthdays will suck, the human part of me was fearful. after a long yesterday spent reflecting on what has been lost and what has been gained these past few years, i was able to approach sleep with some equanimity.

the day broke with a call from my Mom wishing me the best of days, proceeded with joy and laughter and the company of friends, and has ended quite uneventfully. my emotions swing from halting disbelief to a giddy feeling that the dark, dark chapter has finally closed.

i have been quiet of late for so many reasons and know there is much to share, but for tonight i would rather just leave you with this shot of my cake. enjoy!