Up to Friday 16th

Sabrina has brought to my attention, the fact that I need to update!!!

After the japanese pub, it was three days having to do with my lab work...

For those of you who actually don't give a crap about the scientist stuff you can skip until you see the next series of "*"

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I'm supposed to be working on determining the synthetic lethals in the glycolysis pathway. Mainly looking at the pathways leading to the creation of each one of the enzymes in this pathway.

Ah, so maybe I forgot to say that what Dr. Mori's lab does. This is a link to the Pubmed article that has a 'Review' or summary of what the lab does : http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=14761306&query_hl=2&itool=pubmed_DocSum

basically he's trying to do a large-scale E. coli K-12 tools and data generation/compilation. One of the projects is to create a library of knock outs of every single one of the 4,400 genes in E. coli (that one is finished). The other that is being completed is a library of clones with His-tags, GFP, and KanR on each, complete with incorporated restriction sites so you can customize the clone once you have it. They're also in the process of gaining microarray chip -on-chip technology to apply that to all the genes. As well as biochemical analysis on the remaining genes whose protein functions have not been confirmed or elucidated. All these preparations would leave the entire world with a wonderful sea full of tools for all sorts of molecular genetics and biochemical experiments in E. coli and other organisms (duh e.coli is used as a tool for everything)

Along with all of that, Dr. Mori's lab is working with other E.coli labs (like Dr. Hu's at A&M) and other bioinformatics labs (like Dr. Tsai's at A&M) to compile all bioinformatic and experimental data ever created regarding E. coli (it's going to be called EcoliHub I think). They'll even have links to everything. So say you're looking for the gene in E.coli that encodes for an OMP, links to the sequence, papers, protein structure, protein-protein interactions, flux measurements, etc... will all pop up. Not only that, but registered ppl will be able to comment on data and papers that is available on the server, that way allowing for a more global way of editing content and a better way to assure that everything is being done well. Ah, also, part of EcoliHub's idea is to have a single user-friendly format for each type of data - so, so soooo useful.

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Other than the technical stuff, well i have to find two genes I can use as my positive control for the experiment. So, instead of just using the ones that my overseeing gradstudent suggested, Dr. Mori said I should look through all the literature available on synthetic lethals to find all possible combinations to use..... which, if you search "synthetic lethal K-12 coli" you get 4 papers only one of which seems useful.. so if you cut back to "synthetic lethal coli" you get 165 papers... bah!!! I'm on #90...

also, I had to brush up on localized transduction via P1 phage and conjugation via Hfr strains. Which is necessary, but a little confusing... The theoretical part is easy enough to follow.. but trying to read the actual lab directions it's hard to focus on what should go where... anyways..

ah, and i have to read another 6 or so papers pertaining to lab work.. so I've already read the one that I linked above and one other one... heh.. kind of have been putting it off... iknow bad bad

i've no excuse except that sometimes i just get so damned sleepy trying to deal with this jetlag thing.. and other times i've gotten real kind of scared/unsure about whether or not i can do this whole scientist thing... (but then today i totally picked up a molecular genetic book and read 30 pages and thought it was a great read.. heh)

During this whole figuring out what's going on time, I met Natsuko - which as I might have said before, is the grad student that will be guiding me through this stuff. She's very nice. In Japan, everyone is very polite and most always careful of not disturbing anyone else's privacy/work/harmony etc... Natsuko is definitely one of those ppl where even her manner of being reflects taht she's very polite and respectful... it doesn't mean she's dull or fussy or annoying, in fact she's rather funny, works very hard, has a great style of dress and seems well grounded. She accompanied me to Kyoto the two times that I've been there and each time we've had great conversations that include a lot of laughter over my japanese and her english. I asked her once what religion she belonged to when we were on that subject, and she said she didn't know, that she didn't practice it often (I was explaining the word religious) but she shrugged and said she guessed she'll find out when she dies.

Some of what I will have to do, will require making Knock outs.. which.. means that i'll be
'knocking out' genes from a bacteria's genome (in simplified terms) . This I will have to learn from Tomoko-san. She is also very cool, I dont' get to talk to her much though.... mainly because she doesn't speak english. But she's very relaxed, wears tomboyish clothes, is very funny (even if i don't understand the jokes) and always seems to be happy - also a hard worker - and she has a little girl (hopefully i'll get the picture posted - i just accidentally took it on uber high resolution and might not load b/c it's humongous). She says that she thinks she was American in a former life because she loves to hear ppl speak English. I'm invited to spend a night or so at her house one of these days, it's apparently pretty large and is in farming area. :) I hope my japanese gets better by then.

During my first few days I also got to know Akemi-san well, which I think i mentioned, she's Dr. Mori's secretary. She recently told me she'd only been with the lab for about two years. And that she was hired mostly due to her English skills. She lived in the US from when she was 13-23 years old and still retains a lot of her English. She's incredibly nice, also very polite, but lots of fun. She's like a Japanese version of my mother, except for that she doesn't like all seafood just some. :) She's been extremely helpful with everything and always asks me to call her after I get back from going touristing alone.

In general everyone treats me wonderfully well. i feel like the younger sister/ daughter and I only hope i'm not butchering the politeness part - sometimes i forget you're supposed to keep bowing to the person until they're out of sight if it's someone you deeply respect (which is usu the older ppl.. which is everyone in the lab haha)

Even though at first i forced myself to be on my tiptoes for all the social parts, like eating and walking and talking and greeting/goodbying type things.. I've realized i've integrated it a lot more into my lifestyle than i thought.

I've also started integrating halted English... lol.. I tend to pick up accents wherever I go.. and since most ppl here speak accented or halted english, I think i might go back with similar speech... it's kind of cute (when other ppl do it)

Some of the phrases most often used around here is "Sou desu ka?" and "Sou desu" pronounced ::so-dess-kah:: which means "is that so?" and "yes"/"that's true"
also "Wakarimashita" and "wakarimasu" and "wakarimasen" and "wakatta"
::wah-kah-ree-mash-ta:: ::wah-kah-ree-mass:: ::....mass-en:: ::wah-kah-ta::
all conjugations of the same verb i think...
the first is in past tense and means "oh I see"
the second in present tense "i get it now/i understand"
the next in negative " i didn't catch that/ don't understand"
and the last one.. i haven't asked anyone to explain it to me but i think it's a less formal version of "i understand"

sigh.. ok i'll stop here, next is Nara, my first attempt at laundry and my kyoto days