my clone in pMAD!!!! about freaking time, i've been trying to put this insert in this tricky shuttle vector for several months now!
sheesh. now all i have to do is the allelic exchange. in staph.
yay me!
Monday, November 23, 2009
Monday, November 16, 2009
imposter syndrome
yeah we all have it at least occasionally and mine is rearing its ugly head. i fear i'm in over my head with my new zippy project proposal. why? cause the topic is new to me and to the literature, cause it's out (waaaaaay out) of my comfort zone, cause i need some results immediately if not sooner and then i have to figure them out and write them up. i'm spending hours a day on learning everything i can think of about New Zippy Topic (NZT) and yet feel like i'm not getting anywhere. seriously, i spent most of the day at lab researching/aligning/predicting and developing stuff for this project that might not fly (because it's based on a prediction and stuff i have a hard time wrapping my mind around). since this is my own idea in a topic that i normally shy away from, it's pretty tough to shake the feeling that i'm somehow missing something, that i'm way off base etc. the only reason i feel this way though is because there's literature on prediction and some verification of regRNAs, but not a lot. certainly not much in anything other than e. coli or salmonella.
the crazy thing is, i think i'm on to something. i think this WILL result in some verification, but i can't be sure (like anyone ever is when embarking on a new project without any preliminary data).
i think i'm mostly really very overwhelmed with the amount of labwork i need to finish, research for my grant i need to assimilate and write up, and good lab luck i need to recover and plant on my bench like a venus flytrap.
the crazy thing is, i think i'm on to something. i think this WILL result in some verification, but i can't be sure (like anyone ever is when embarking on a new project without any preliminary data).
i think i'm mostly really very overwhelmed with the amount of labwork i need to finish, research for my grant i need to assimilate and write up, and good lab luck i need to recover and plant on my bench like a venus flytrap.
Monday, November 9, 2009
happy anniversary
i can remember going thru these gates when there was still an east and a west.
i was born in west germany and lived there as a child for 4 years. i remember the warnings about traveling to berlin. i remember seeing the russian soldiers guarding the wall and the checkpoints. i have been to anne frank's house in the netherlands. i cannot believe its been 20 years since the iron curtain fell. it's my bookmark that democracy will happen and free will will prevail. i remember watching the footage of the wall falling and thinking that it was faked because i was there 2 months earlier with my family. in a small mercedes (the hyundai of german cars) with my parents in the front and the 3 of us in the back squished around my brother's carseat. my sister and i were flirting with the russian soldiers (even though we weren't supposed to) and all of us were terrified of getting detained for hours and loosing our passports.
the brandenburg gate.
i can't wait to go back.
i was born in west germany and lived there as a child for 4 years. i remember the warnings about traveling to berlin. i remember seeing the russian soldiers guarding the wall and the checkpoints. i have been to anne frank's house in the netherlands. i cannot believe its been 20 years since the iron curtain fell. it's my bookmark that democracy will happen and free will will prevail. i remember watching the footage of the wall falling and thinking that it was faked because i was there 2 months earlier with my family. in a small mercedes (the hyundai of german cars) with my parents in the front and the 3 of us in the back squished around my brother's carseat. my sister and i were flirting with the russian soldiers (even though we weren't supposed to) and all of us were terrified of getting detained for hours and loosing our passports.
the brandenburg gate.
i can't wait to go back.
you win some....
it's a good news bad news situation over here in phd-land.
good news (here after, GN): i figured out a way around having to learn code lickity-split and found some noncoding RNA homologs in my sequences (though i still might hit you up for code help toaster!)
bad news (BN): i'm chin deep in background reading to write my grant (and haven't written it yet.)
GN: i've plowed thru a few papers and BLASTs today and have pounded out my specific aims
BN: i was productive because i've been home sick and thus NOT in lab
GN: i'm not infecting co-workers or picking up co-circulating strains of anything
BN: the cats feel obliged to help with my research and i'm no closer to getting a new knockout mutant made
GN: i've gotten my adviser and a biochem prof interested in my topic (ok, biochem prof was already into RNA so it wasn't hard...)
BN: new topic, so neither one of them can really help much (yet!!)
that's pretty much what's been going on here....lots of reading (about 500 pages of it) which is NOT helped by the lightheaded-fuzzy-cold-meds head i've had since friday. oh well, it's NOT hemorrhagic fever and i'm gonna be better tomorrow. i've told myself that!
as a parting shot, i'd encourage you to hop on over to small things considered to read the new post, the limitations of LB media, which was super enlightening to a neophyte microbiologist like myself...especially one interested in conditions which might increase virulence factors!
(oh for the love of all that is creepy, look at this!!! WANT WANT WANT!!!
good news (here after, GN): i figured out a way around having to learn code lickity-split and found some noncoding RNA homologs in my sequences (though i still might hit you up for code help toaster!)
bad news (BN): i'm chin deep in background reading to write my grant (and haven't written it yet.)
GN: i've plowed thru a few papers and BLASTs today and have pounded out my specific aims
BN: i was productive because i've been home sick and thus NOT in lab
GN: i'm not infecting co-workers or picking up co-circulating strains of anything
BN: the cats feel obliged to help with my research and i'm no closer to getting a new knockout mutant made
GN: i've gotten my adviser and a biochem prof interested in my topic (ok, biochem prof was already into RNA so it wasn't hard...)
BN: new topic, so neither one of them can really help much (yet!!)
that's pretty much what's been going on here....lots of reading (about 500 pages of it) which is NOT helped by the lightheaded-fuzzy-cold-meds head i've had since friday. oh well, it's NOT hemorrhagic fever and i'm gonna be better tomorrow. i've told myself that!
as a parting shot, i'd encourage you to hop on over to small things considered to read the new post, the limitations of LB media, which was super enlightening to a neophyte microbiologist like myself...especially one interested in conditions which might increase virulence factors!
(oh for the love of all that is creepy, look at this!!! WANT WANT WANT!!!
Monday, November 2, 2009
writing
has got me waaay down lately. a bit of background: i'm at that horrible stage known as write a damn grant and take your orals already! (henceforth, WADGATYOA!). now i know i'm gonna be doing this for the rest of my life, but here's the prob. i'm not excited about the topic. BFD you say (and i did too), pick another. i did and it's a bitch to figure out what i'm doing and how i'm gonna "make it work" (insert tim gunn soundbite). i'm oh so slowly learning what i need, but i really freaking want is toaster's (or my friend and uber computing god, larry's) coding knowledge downloaded into my cerebrum straight away.
please.
also, anyone doing RNA prediction work? holla plz and i'll ply you with cookies til i finish picking your grey matter clean.
please.
also, anyone doing RNA prediction work? holla plz and i'll ply you with cookies til i finish picking your grey matter clean.
Wednesday, October 21, 2009
hi! *cue sheepish grin*
well so far i've managed to completely freak myself out about writing a grant and doing my oral comps for over a month now. coping skills? yeah i have some, mostly i've been after the perfect shade of red hair to procrastinate.....you know, red-gold, gorgeous flame colored hair...i digress. amusement should begin.
i actually pounced on someone in journal club, i'm talking intellectual pouncing you dirty minded readers! this 2nd year gets up in front of the class to explain a figure and says something to the tune of, "well part A and B are both westerns and show the same thing so i don't why they included both of them". THREE of us shout NO! at him simultaneously. he then flounders for a minute, admits he read the paper "a few days ago" and i explain that part A is pcr results for multiple strains while B is a western blot for one of the pcr results. he flounders more and i take over explaining the figure.
ok, it was a bit aggressive. i'll willingly admit that but i won't apologize for it. i wanted to explain that figure (it dealt with toxins produced by staph!!!!!! fave topic= things that will kill you fast!) and this guy rubs me the wrong way. he's a 2nd year grad student who can't be bothered to prep for anything. all his rotation talks (15 min to discuss results from a 6 wk rotation) were ill-prepared, monotone and effing barely barebones. seriously, he works with borrelia and his intros have 1 slide with which to describe the disease, the spirochete AND the vector. WTF? maybe put forth some effort? ok, /rant.
science-y things....i have to write a grant and i need to do it soon. problem? usually you write on the project you've been given when you entered your lab. BUT my adviser already wrote a grant on my project and i've read it. it's such a narrow subject (and a tricky one) that there aren't alternative methods to prove the same (or similar) aims. i can't in good faith write on the same topic. but i just figured out that maybe i'll write on some new regulation stuff i just found (same systems, but it was recently discovered that small regulatory RNAs are encoded and function as regulators)..it's pretty kick-ass stuff....
hmmmm. that's not a bad idea.
lastly, i climbed out my batcave this week long enough to see 2 outstanding shows: social distortion (oh mike ness i heart you) and gaslight anthem (oh fave running soundtrack, i end up sprinting!). love love love the music.
[also, toaster you should check out emilie autumn (ex-classical violinist now doing victorianindustrial and similar to rasputina i feel). that is if you haven't been listening to her for years already :)]
i actually pounced on someone in journal club, i'm talking intellectual pouncing you dirty minded readers! this 2nd year gets up in front of the class to explain a figure and says something to the tune of, "well part A and B are both westerns and show the same thing so i don't why they included both of them". THREE of us shout NO! at him simultaneously. he then flounders for a minute, admits he read the paper "a few days ago" and i explain that part A is pcr results for multiple strains while B is a western blot for one of the pcr results. he flounders more and i take over explaining the figure.
ok, it was a bit aggressive. i'll willingly admit that but i won't apologize for it. i wanted to explain that figure (it dealt with toxins produced by staph!!!!!! fave topic= things that will kill you fast!) and this guy rubs me the wrong way. he's a 2nd year grad student who can't be bothered to prep for anything. all his rotation talks (15 min to discuss results from a 6 wk rotation) were ill-prepared, monotone and effing barely barebones. seriously, he works with borrelia and his intros have 1 slide with which to describe the disease, the spirochete AND the vector. WTF? maybe put forth some effort? ok, /rant.
science-y things....i have to write a grant and i need to do it soon. problem? usually you write on the project you've been given when you entered your lab. BUT my adviser already wrote a grant on my project and i've read it. it's such a narrow subject (and a tricky one) that there aren't alternative methods to prove the same (or similar) aims. i can't in good faith write on the same topic. but i just figured out that maybe i'll write on some new regulation stuff i just found (same systems, but it was recently discovered that small regulatory RNAs are encoded and function as regulators)..it's pretty kick-ass stuff....
hmmmm. that's not a bad idea.
lastly, i climbed out my batcave this week long enough to see 2 outstanding shows: social distortion (oh mike ness i heart you) and gaslight anthem (oh fave running soundtrack, i end up sprinting!). love love love the music.
[also, toaster you should check out emilie autumn (ex-classical violinist now doing victorianindustrial and similar to rasputina i feel). that is if you haven't been listening to her for years already :)]
Friday, August 21, 2009
random weirdness
i think i have a touch of frostbite. wtf? you ask? it's summer in the northern hemisphere, most of the east coast is in the 90s! how is this possible?
i've been frustrated with my lack of experimental progress this week, so i decided to take it out on the freezer. we've been in full defrost mode since 11:45. the freezer is almost completely devoid of ice thanks to my relentless ice scraping, banging and removal.
hence a touch of frostbite.
i've been frustrated with my lack of experimental progress this week, so i decided to take it out on the freezer. we've been in full defrost mode since 11:45. the freezer is almost completely devoid of ice thanks to my relentless ice scraping, banging and removal.
hence a touch of frostbite.
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