Blog Archive: June 2003
June 30, 2003 - restriction
enzyme digest plasmid analysis; refreezing the HeLa cells
-4:23 pm: Today we did the final analysis of our Qiagen Maxi
isolated plasmid DNA by doing a double digest with HindIII and Not1 endonucleases.
We haven't presented the results to the professor yet, but our own rudimentary
understanding of the gel seems to indicate that we did get some useful plasmids
and that the DNA itself was decently pure! In any case, that work took about
4 hours to do.... After that i decided to put my HeLa cell line back into
cold storage, just for practice.
-tomorrow we are going to begin anew with plasmid isolation... this time
using M9 (aka minimal) media to shock the bacteria into making lots of plasmid..
Hopefully we get a better yield than with LB
June 29, 2003
- the weather reverts to ideal
-4:26 pm: Yes! The weather has returned to just about normal,
with highs in the 70s. The extended forecast predicts similar weather for
at least two weeks. So happy!
-got up today at 7am... i suppose body used to getting up in time for
8am class... how unfortunate. Went to RSF for mini-workout (bike and b-ball).
Decent shooting day... although my lay-up skills were on the shitty side.
I returned home to eat brunch... then took a nap until just about an hour
-promising news: three militant Palestinians groups (Hamas, Islamic Jihad
and Fatah/Al Aqsa Matyr Brigades) agreed today to halt attacks on Israel
today for three months, in exchange for Israeli military withdrawal from
the Gaza Stip. Such news comes as a surprise to me, but it is a very pleasant
surprise. At least now both sides seem willing to try peace. I really hope
that neither side decides to ruin this by launching attacks, but i have
some strong feelings that one side may falter.
June 28, 2003
- almost 7 straight hours of Halo
-11:07 pm: Weeeeeee.. i went over to Yeh's to play some co-op
Halo... Some fear involved since i'm don't play FPS, but it was fun anyway.
The controls take some getting used to, especially if you're used to Metroid
Prime controls (and vice versa, many ppl also complain that Metroid Prime's
controls suck and take getting used to)... The only thing i really didn't
like was jumping control. Control misgivings aside, the game itself is
very fun, especially controlling various vehicles. As the title says, we
played co-op mode for almost 7 hours, getting through about 60% of the
game. By the end of the 6th level if was feeling way too dizzy to continue..
i would have gone on, but alas damn dizziness. I hope to play through to
the end, mainly because the storyline is particularly interesting and i
wanna know what happens.
-The heat wasn't too bad today, in fact walking home from Yeh's around
9, it was actually kinda cold and i shivered a bit. Hopefully the weather
stabilizes into a nice constant temperature in the low 70s.
June 27, 2003
- Analysis of plasmid DNA
-9:00 pm: Today was a relatively short day in lab, probably
because we knew exactly what we were going to do... and we didn't have to
wait around for someone to tell us. Basically we analyzed the samples we
got from yesterday. Mainly some spectrophotometry and agarose gel electrophoresis.
The results? Spectrophotometry says that we got some DNA with some protein
contamination. Electrophoresis confirms the isolation of DNA. Yay! we got
DNA... BUT we will not know if it is the correct DNA, until we run some more
electrophoresis with restriction enzyme digested samples..
-Even though we did get some DNA, the prof. wasn't satisfied with the
amount. She suspects that the wrong media was used mass-propagate the bacteria
(or actually the plasmid). Next week we are going to repeat the whole process,
using M9 media instead of LB... At times the process is boring, but
this process is the foundation of molecular biology!
June 26, 2003
- plasmid isolation
-9:12 pm: We spent a long time today watching stuff drip
in the attempt to isolate plasmid DNA from our cultures. Basically spent
the entire day doing that.. hopefully tomorrow we will find out if we actually
got any DNA... and whether or not those pellets we saw were actually DNA.
-What a drastic change in the weather!! It was really cold last week...
and now it's blazing hot. Freakin last week we had temperatures in the
high 60s... today's high was 95! VERY uncomfortable outside...
June 25, 2003
- a long, productive day
-11:26 pm: the first week of IB131 (human anatomy) is over.
The class has been so far, as much as expected... long lists of things
to memorize. Prof. Gilson also likes the lecture at a very fast pace, perhaps
on par with Prof Schekman's pace... Wow... at least human anatomy is as
terribly complicated as vesicle trafficking or whatever.
-IB131 begins at 8am, however i went to lab in LSA at 7:30 am to
take my transformed bacteria LB plates out of the incubator. Succesful
transformation! Actual colonies and the negative control had no colonies,
meaning the plates were properly made. After that i headed off to IB131
to learn about the bones of the skull and the vertebral column
-After IB131 headed promptly back to LSA. Prof. informs us how to
begin a "starter" culture. The starter culture is a mini 5mL culture of
LB to grow up a lot of bacteria from a single colony. We autoclave the appropriate
containers and proceed with the starter culture in the "shake" room. We
complete the work at about 12:45 pm... the culture needed to go for 8 hrs
-Ate lunch from newly opened Quizno's. Pretty good sandwich although
a bit on the pricy side. The toasted aspect was new to me... seems to
deliver what it promises in the commercials.
-at lunches end, i decide to make some more LB broth to help out
another student in the lab. Another 2L of the stinky stuff. 2 hr lag
time before anything else productive happens. At 3:45, we are instructed
about the main bacteria culture, a large 1 L culture used to make 1 g of
plasmid. We were supposed to use the LB we made on Monday, however the
LB became turbid... meaning it was contaminated with bacteria!!! UGH...
Fortunately the other student did not need the LB i made earlier in the
day, and we decide to use that.instead. Some more autoclaving of appropriate
containers. At that point it was 5:00 pm... and 3 hrs, 45 min before the
starter culture would be finished.
-I rush home to change into "RSF" clothes to join my lab partners
for workout. We shoot hoops and play a game of 2on2 for about 1.5
hrs, after which we decide to try our hands at Ping-pong... Ah good old
ping pong from the days in Freeborn Hall. The two years that have elapsed
since then showed.. and i was terrible at it. I did win the HORSE game while
we played basketball... but oh well. After only about 10 minutes of ping-pong we move onto bikes. A pleasant surprise during RSF was running
into three good old friends. Saw Andre and Nam from Hoover High school and
Salman from freshman year Freeborn Hall. I hadn't seen them for so long!
It was definitely nice seeing them again!
-By the time we were all pooped out from the RSF, it was already
7:45, so i decide to head back to LSA to start up the 1L cultures. More
autoclaving... final preparation of LB (injection of appropriate antibiotics)
and finally pouring of the 5mL starter cultures into the main cultures!!
Yay! After some difficulty with the shakers (the damn things weren't set
to the right temperature) i finally finish the day at 9:30 pm.
-Ever since i started working in the lab.. my life has been very,
very busy... Very stark contrast to the boredom i endured the first week
after school ended. Being busy has definitely been much more satisfying
to me though... i can't wait to see if our bacteria cultures turn out correctly
2003 - more LB-agar plates
-6:20 pm: as the title implies... made more LB-agar plates
today. fun, especially popping bubbles with the flame. Also transformed
some bacteria and plated them on our plates from yesterday.... Have to
come into lab at 7:30 am tomorrow to take them out of the incubator. Although
much more happened today, i'm about to step out, so cutting entry short
2003 - the weekend and making LB-Agar plates
-5:54 pm: My brief time in the Los Angeles area was very
fun. Good food, playing basketball, watching/playing videogames, etc..
nothing could be better. Brother got nearly $1700 for graduating from
HS... lucky him! I got back to Berkeley around 4:30 yesterday, left
at 12:00 pm on friday. Damn SF-Oakland baseball game made the Colliseum
BART station extremely crowded yesterday... imagine 10 car BART trains completely
full - standing room only. Ugh.
-Lab on friday was frankly pointless for me.. didn't anything but
received some more literature relevant to projects
-today we began to prepare for bacteria experiments. First we made
2 L of Luria Bertani (LB) broth. Then we made some LB-enriched agar
plates (those pale-yellow plates from Bio1A). Pretty fun making the
plates themselves.. but making the broth was a pretty stinky affair
(damn autolyzed yeast extracts). Tomorrow we are going to grow some bacteria
cuz the lab is out of a particular plasmid.
2003 - the centrifuge of death
-7:37 pm: wow. today was probably the scariest
day of lab ever. We were preparing some delipidated FCS which required
the use of a centrifuge to separate liquid phases. So we set everything
up, made sure the the centrifuge was balanced, and started up the centrifuge.
A little shaking at 800 RPM, some more at 2100 RPM... the centrifuge is
stopped just make sure everything is OK... Stuff seems to check out alright.
We put the solution back in and start up. The same shaking at 800 and 2100...
we decide to go on. No shaking and the centrifuge reaches max at 3500.
All green.... for 5 seconds... a sudden pop noise. We needed to check
what the noise was... As the centrifuge slows down, it begins to violently
shake. I thought it was going to blow.. people in the lab start arguing
over how to best handle the situation... The centrifuge mercifully stops
and we open it up to inspect the damage. The glass containing the liquid
is completely shattered. I mean really shattered, it looked like fine grain
sand. After much talk and clean up... we decide the culprit was probably
leaving the stir bar inside...
-The most interesting thing about the experience with the centrifuge
was that that centrifuge was a low speed one... The professor told us
about how she's see ones that walked around when they were unbalanced.
Yikes! Hopefully we have no centrifuge disasters in the future.
-A NOTE TO MY LOYAL READERS (YOU RULE!!) This blog won't be updated
again until Monday as i'm going home to LA this weekend (it's my bro's
HS graduation party!!)
2003 - another looong day
-9:02 pm: the days in lab are starting to get really
long. I came around 10:15 and didn't leave until 8pm. Wow. Yesterday
i had the impression that we were only going to watch how to do immunostaining...
however we actually did the immunostaining all the way from fixation
to mounting the coverslips onto slides. Probably the most frustrating
part was micropipetting 1 microliter of antibody solution. I became really
frustrated with the P10 micropipetman; the stupid thing didn't seem to
like me. OH well... we didn't get to look at our immuno stains today, but
we will be doing that first thing tomorrow.
-Because we were in lab so long today, we did not get to go play
basketball at the RSF as we had planned yesterday.. BOO!! I'm hoping
we can go tomorrow... it probably won't be a long day, but who knows.
2003 - watching more of the GAG chain assay
-9:19 pm: for mostly just watching the rest of the
GAG chain assay, i spent quite a long time in lab today.. from about
10:45 to 7:15. Most of the time i was either watching someone else do
experiments or chatting away. The GAG chain assay was finished up by
transferring precipitated GAG chains to scintillation vessels. This actually
takes a long time because it involves the filtration of liquid from 64
tubes! I also watched people prepare coverslips for cell binding and
immunostaining. Tomorrow we're going to watch the immunostaining process
as well as see our results from the GAG chain assay. I actually did some
lab work today... but it was simple routine cell culture.
June 17, 2003 - the stupidity of Bush and Sharon
-12:08 am: i'm pretty tired of hearing all about
the Bush and Sharon intentions to rid Israel/Palestine of terrorism
by eliminating Hamas. What utter stupidity. What these idiots do not
understand is that Hamas is much more than a terrorist group. Before
you get me wrong, i do not condone their terrorist acts, but you
must consider what other things that Hamas does. Hamas provides the most
basic of human services to many Palestinians including food, potable
water, economic aid and schools. This is why their support base is so
strong and why the general Palestinian public really likes Hamas. Targetting
Hamas only enrages the Palestinian public; Israel is targetting basic
services. The real culprit is the lack of Palestinian government. Government
should be providing these basic services.. only then can Hamas be safely
"eliminated." So at this point, attacking Hamas only makes things worse...
an enraged Palestinian public can only be more willing to produce more
-There are a few Republican Senators who in recent days have
suggested that the U.S. military actively engage Hamas... I really
hope that this does not happen. Not only would it makes things worse
for both Palestinians and Israelis, but would only serve to further
inflame deeply held Arab hatred for the U.S.
2003 - HeLa cells
-9:49 pm: having nothing to do right while waiting
for the washing machines to finish their cycle, i got a little curious
about the HeLa cells that are used not only in the lab i'm in right
now but all over the entire world. Apparently i was wrong about when
the cell line was established... it was not established in the 1970s
but was actually established in 1951. They were cervical cancer cells
taken from a 31-year-old woman named Henrietta Lacks (hence the name
HeLa) at Johns Hopkins University Hospital. Despite their importance
in cancer research and general cell biology research, they are quite
the controversial little cells. Apparently neither Henrietta Lacks
nor her surviving family ever gave permission for her cells to be used
for research (Henrietta Lacks died 8 months after her cells were taken,
initially only to diagnose them as malignant). Her family found out about
the use of her cells more than twenty years after her death, but by then
the cells had already been distributed worldwide. And to this day, the
family has not received one bit of monetary compensation. The controversy
does not end with the lack of authorization or monetary compensation. After
the establishment of the HeLa cell line, many other cell lines for other
tissue cancers were also supposedly established. People began to do experiments
on the properties of various tissues using the various cell lines. However,
the HeLa cells were apparently too good at proliferating and could easily
overtake a tissue culture contaminated with them. Due to lack of proper
sterile technique, many of the "other" cell lines that had been established
after HeLa, were not actually other cell types but additional HeLa cell
lines. Thus there was much controversy in the 70s and 80s over all experiments
that were done with the supposedly "other" cell lines, but were actually
done with HeLa cells. Research on lung epithelial cells, intestine epithelial
cells, etc. was all rendered fraudulent and the millions of dollars that
were poured into those research experiments were wasted. Some scientists
refused to acknowledge the obviously egregious errors. Journals took no
corrective action, believing that the problem was too widespread (and thus,
as one author i read suggested, could be ignored). I guess there are two
lessons to be learned from the HeLa experience. One lesson was the ethics
involved.. now permission is always sought to use tissue or cells for research.
While that lesson has been learned.. the other lesson is one of sterile/aseptic
techniques... we should all use them! I suppose i should cite where i
got all this info.. since i really only paraphrased what someone else
wrote: Masters, John R. HeLa Cells 50 years on: the good, the bad
and the ugly. Nature Reviews 2: 315-319. Online PDF text available
June 16, 2003 - watching the pulse-chase experiment
-6:45 pm: today wasn't terribly exciting since
all we could do was to watch how the experiments were done. Since
the experiments involve the use of radioactive reagents, we are not
allowed to handle them until we have been trained to do so (that will
be sometime in july). Nevertheless it was interesting to see just how
complex the experiment is, especially with all the controls that were
necessary. When it comes time for us to actually do the experiments
we'll probably have loads of fun incorporating all the techniques we've
learned so far.... It was all there: proper micropipetting, sterile
solution preparation, sterile cell culture.. just about everything except
for gel electrophoresis. Tomorrow the experiments will be finished
up by measuring radioactivity levels and we will see exactly what effect
the level of cholesterol has on constitutive secretion
15, 2003 - the inevitable
-11:18 pm: so the Spurs finally won the NBA championship...
woohoo... it was definitely the ugliest basketball series i've
ever seen in my entire life. i don't think that the Spurs or the
Nets ever broke 100 points and i think the Spurs breached 90 only
once... dang. At least David Robinson gets to finish out his NBA career
on the highest note possible.
-did some rearranging of the left side bar thingie
on this webpage.. added links to other blogs. E-mail me to remove
the link if you don't approve or if you want yours linked there
June 15, 2003 - why are Sundays always
-3:43 pm: Sundays seem to always be a complete
waste of time for me... i never get anything done, although technically
right now i really don't have anything to do (perhaps though i
should be reviewing for that lovely GRE in september). So yeah after
that Simpsons marathon last night, i proceeded to surf the web for
a few more hours. Then Star Wars Episode II came up on HBO, and even
though the movie is terrible (OMG that acting) i couldn't help but
watch it... so i ended up going to sleep at 4 am. Fun. Subsequently
i didn't get up until about 12:30 pm today... Woohoo... so a fansub of
Gundam Seed episode 36 was released during my beauty sleep so i proceed
to start the d/l. I eat the leftovers from last night (leftovers are
always nasty...) while waiting for the d/l to finish. Impressively the
download takes only an hour and a half (impressive in the sense that
the file is almost 200 MB) and proceed to watch! Interesting episode about
how one character catches up to the events of the last episode, although
i didn't have any fun mecha action.
-The experiments we were going to do in lab today
were moved to tomorrow (i guess ppl didn't want to come in on
the weekend which is understandable), so nothing to report about
June 15, 2003 - 6 hrs of The Simpsons
-12:04 am: Wow.. just finished watching 6 consecutive
hours of The Simpsons. I think i don't want to hear that theme
song for at least a week now. Besides that unproductivity, the rest
of the day was pretty much the same.. doing jack shit... It'll end
by next week though, as summer school starts up.
13, 2003 - Short Day
-3:02 pm: Yay! my culture did not have any
bacterial contamination! We had a really short day in lab today
as all we did was to split the culture into two dishes for experiments
later on. I'm coming into lab on Sunday to begin the work on the cholesterol
experiments. As lab was short today... such will be the length
of this entry.... :P
12, 2003 - Sterile Tissue Culture and Reviving Long Dormant Cells
-4:34 pm: After learning about all the techniques
dealing with dead stuff (gels and the like) we moved on today
to handling live cells!! We primarily learned how to properly
thaw frozen cells and how to transfer them to appropriate growth
medium all under sterile conditions. After observing the veteran
student prepare a cell culture we each had to perform the same procedure.
We will see tomorrow if we were successful in preventing microbial
contamination. The type of cells we transferred from cryopreservation
to growth medium were HeLa cells, a cancer cell line that has been
in existence since the 1970s. The cells were cryopreserved at -196
degrees C (77 K, the boiling point of liquid nitrogen) in 10% DMSO
(dimethyl sulfoxide). The cells that we used have been frozen for almost
8 years! After quickly thawing them, the cells were transferred to
DMEM (Delbecco's modified Eagle's Medium) containing 4.5% glucose.
Being sterile about it the whole time proved very interesting... nothing
was allowed to touch anything else etc etc. I was pretty nervous about
being sterile because one mistake meant the entire hood would be contiminated
at great inconvenience to the lab. I don't think i contaminated anything...
but we'll see tomorrow.
11, 2003 - Finishing the western; Cholesterol
-3:59 pm: We began today rather late (around
12). We finished off the western by staining our nitrocellulose
papers with a red dye, revealing the transferred BSA. After discussing
the results we moved on to learning about what experiments we
are going to do to learn tissue culture. We are specifically going
to be studying whether or not cholesterol levels play a role in vesicle
formation from the trans golgi. It's a very cool experiment to run
because it will teach us many techniques including sterile procedures
and some pulse chase. The pulse chase portion is actually something called
the GAG chain assay and it involves measuring the radioactivity from
radiolabeled GAGs (glycosaminoglycans). Basically GAGs are produced
in the trans-golgi. We can created GAG enriched trans-golgi and vesicles
by adding a membrane-permeant xylose analog which initiates synthesis.
If we pulse radioactive sulfate into the cells, a pulse of radioactive
GAGs is produced. You can move the pulse along the pathway by adding
non-radioactive sulfate (the chase). So using this GAG chain assay
and varying the cholesterol levels we can determine just how much of
a role that cholesterol plays in vesicle formation. Today we were told
all about this and the ideas behind it, and we get our official start
-The weather here has been disturbingly
cold. I've not seen the sun in a long time and wondering when
the heck actual summer weather is going to arrive. It feels
like January outside; although at least it is not raining. hmm weather.com
projects mid 70s for the weekend... but they also projected that
for the past few days.... damn you weather, damn you!
10, 2003 - Western Blot
-3:47 pm: They tend to describe many experiments
in MCB classes and a very common one is Western blotting.
They make it sound so simple... it's always "so you just do a
Western blot of this" and blah blah... etc. What they don't say
is that the blotting itself is actually done eletrically (so it's
not actually blotting per se).. and it involves the construction
of a weird sandwich of filter paper, polyacrylamide gel, nitrocellulose
paper, and more filter paper. Nothing terribly tricky about actually
constructing the sandwich, although my freakin gel ripped (a small
unimportant corner of it). I'm also wondering if i cut out a big enough
piece of nitrocellulose paper... we will find out tomorrow when we
see the results and stain the paper. So yeah since we're not actually
doing any experiments yet; we can't probe our paper with antibodies
for a few reasons: 1) the blot was mainly practice, 2) antibodies
are expensive, and 3) BSA is too uninteresting.
-Finished watching the first two seasons
of Gundam Seed (Episodes 1-26). It's a very interesting anime
with some seriously screwed up characters who all seem to like
to use each other for their own means. It's definitely better
than my first Gundam series (which also had some really messed up
characters and one really annoying Relena Peacecraft... erggg),
Gundam Wing, and i look forward to watching the third season and
on. Miss Relena does have a counter-part in Gundam Seed (in the extremely
annoying sense), the revenge-obsessed Frey Alstar.
9, 2003 - DNA (agarose) gel
-7:26 pm: Today's lab training was fairly
straightforward. First we made our second set of polyacrylamide
gel and it was definitely much easier the second time around.
After we were done with that and our gels stored properly, we
moved onto agarose gels. The method used to make agarose gels is far
simpler than that for polyacrylamide gels; it simply involves microwaving
a solution of agarose containing ethidium bromide and pipetting some
onto a glass plate with the plastic comb. While the gels were setting,
we made our DNA solutions, then we micropipetted the solutions into
the wells created by the comb. Then it was simply putting the gels into
the electrophoresis box and turning the switch on (well not THAT simple..
). While waiting for the gels to run, we were shown how to properly
clean just about everything and anything in the lab. Glass beakers,
plastic cylinder, micropipette tips... etc. We were even taught how
to make what i named "super-clean" water. Tomorrow we will run some more
SDS-PAGE and perform a Western blot.
-Yesterday I journied to the newly opened
Trader Joe's at the El Cerrito Plaza. A $26.86 well spent
on this week's food. I'm fairly happy that they've opened a
store that i can reach without having a car.. although having to
BART there limits the amount i can buy.. oh well.
7, 2003 - Return to old habits
-5:30 pm: After watching 12 episodes
of Mobile Suit Gundam Seed and Scrapped Princess it was inevitable
that i would return to 1st and 2nd year of college habit of
always listening to my small collection of anime themes/J-pop...oh
my... of course the catchy themes from both series have been
added... i tend to like "Invoke" (MS Gundam Seed) more just cuz
it has no English in it unlike "Little Wing" (SP). As for the anime
series themselves it's kind of a toss up which one's better. They're
in totally different genres so it's probably unfair to compare them.
Scrapped Princess's storyline is more original though, as Gundam Seed's
plot tends to be along the lines of older MS Gundam series. Gundam
Seed, being Gundam, definitely has more action and the animation itself
seems to be of higher quality, but i think the characters of Scrapped
Princess are far more interesting (although Kira Yamato from Gundam Seed
is a real head-case).
6, 2003 - Running SDS-PAGE
-6:18 pm: SDS-PAGE is a nice protein
separating technique that is often described in many biology
courses as extremely useful. Today we got to run our samples
of BSA through the gels we made yesterday, and though it was
pretty challenging and fun, it involved quite a bit of waiting.
The first step was to take the gels and assemble the electrophoresis
device. Making a device that did not leak was pretty difficult
and took quite a bit of effort. After the devices were all set-up
and filled with running buffer we loaded the protein samples into
the lanes (also a pretty difficult step). The devices were turned
on and we had to wait two hours before proceeding to the staining
step. After the two hours, (we went out to eat lunch and snooze around
some shops), we came back to disassemble the devices and transfer the
gels to staining dishes. Removing the gels from the glass plates was
fairly nerve-wracking. The gels are extremely thin and so the fear of
ripping them was quite high. After transferring to the dish, the gels were
stained with Coomassie Brilliant Blue (CBB) for 2 hours.(we played Hangman
to kill the time.... sigh). After the two hours were mercifully up,
the CBB was removed and destaining solution added. Tomorrow we are
going to dry our gels and see how our BSA samples turned out. I personally
can't wait to see if my gel turned out correctly! On Monday we are going
to make more gels (practice makes perfect!) and that time we will transfer
protein to nitrocellulose paper instead of staining. I feel so lucky to
be able to learn all of these techniques. We've learned in just one
week what is normally taught in MCB130L in four. And plus we've had to
prepare our own solutions, which is usually not the case in course lab
work. I really wish i had tried all of this much earlier in my college
career, but i suppose it's better late than never...
June 6, 2003 - The past
-12:09 am - my brother 's last days
in high school are zooming by right now. He will officially
graduate on the 18th. I warned him yesterday on AIM
to enjoy these finals moments with his friends, for it is very possible
he may never see some of them again. I look back on the same
days of my high school experience and regret that in those last days
i did not do more with my friends. I did not even say goodbye to
most of them and have not seen a single one for almost three years.
Of course there has been the occasional e-mail here and there, but
it's not the same, and can never be the same as talking face to face.
I look back on those fun times in high school and wonder what happened.
I miss the days of sitting in the Lower Quad eating lunch, bashing
our teachers, and talking about TV, sports and the like. I miss our
after school Friday basketball games. I miss going out to the theatre
and movie theatre. Most of all I miss the company. Perhaps one day
in the future we will all see each other again, but it will be very
awkward. Everyone will have changed...
-Looking back on what happened to
my friendships from high school, i can only wonder what
will happen to my friendships here at Cal. Will they suffer
the same fate? To some degree they must suffer inevitably since
we would not be in the same places. It is quite depressing to be
thinking about this, but my brother's upcoming graduation has stirred
up old regrets about my own last days before high school graduation.
"True friendship is like
sound health; the value of it is seldom known until it be
-Charles Caleb Colton
5, 2003 - Making a polyacrylamide gel
-7:02 pm: We did not "do" a Western
blot per se, we simply observed how to "block" (using milk
interestingly enough) the nitrocellulose paper. Blocking
prevents non-specific binding of antibodies (which are very expensive).
After observing the blocking process, we were assigned the task
of making some solutions of BSA which we are going to run through
SDS-PAGE. The most exciting (and long) part about today was actually
making the gels. Back in Bio1a the gel was was already made for us,
but those prefabricated gels do not have enough lanes for our purposes
(we are running 12 lanes at once). Thus we had to make the gels ourselves,
something that proved both interesting and challenging. First a
veteran lab student made the acrylamide solutions, then we had to
form the gels from them. The hardest part was creating the seal
at the bottom of the mold... we used an acrylamide solution that polymerized
really fast, so pipetting the liquid before it solidified proved
pretty difficult. My first attempt failed (the stuff polymerized in
the pipette tip) and even the second time i wasn't sure if i got a good
seal. Fortunately i did get a good seal and making the rest of the gel
was relatively easy. Tomorrow we are going to actually run our gels with
the BSA samples.
-In other news, a post-doc in the
lab got mad at us for using his bench space (we didn't know
it was his.. oops) and started accusing the student who was
helping us of stealing buffer solution. We were also unknowingly
using his micropipettemen.... I now know who to avoid. Everyone
else in the lab is pretty friendly and definitely far more patient
with us than i would ever be hehehe.
4, 2003 - Bradford Protein Assay
-8:22 pm: So the goal of today's
lab lesson was to learn how to properly micropipette.
And boy did we have a LOT of practice. Basically we did something
called the Bradford protein assay. The assay involves a dye
that changes color when it binds protein, and based on the amount
of color change and comparison to standardized concentration-absorbance
curves, one can determine the concentration of protein in solution.
We actually didn't do any protein concentration measurements, instead
we prepared solutions for 3 equivalent standard curves. This involved
making around 50 separate solutions using some insane number of micropipette
tips (of course proper technique is to use a different tip for each
solution)! The idea was to test our micropipetting ability; each
of the standard curves should come out the same. My hand hurts from
depressing the micropipette so much although it was pretty fun. I
used to be pretty bad a micropipetting, but after doing it around
300 times today, i think i can probably micropipette with the best
of them! Yay! I passed the "test" and get ot move onto Western blotting
3, 2003 - Memorable Moments before college
-8:22 pm: i'm currently in the
nostalgic mode, remembering things from before college.
The following is a brief summary of the most memorable things
from school years past (6th through 12th grade)
6th Grade: Space Camp and Washington
D.C. -got carsick on both trips (yikes). Sprained arm
at space camp, but enjoyed "living among the trees." Watched
July 4th fireworks from the National Mall
7th: Renaissance Faire. Dressed
up as monk for school Renaissance Faire, had a disastrous
time making raisin bread
8th: Yosemite Trip: Spent 6 days
in Yosemite Institute program. no shower, Spider Cave,
wet Mist Trail, crossing "lava" in Tuolumne Grove
9th: frequently absent biology
teacher (i think she was high or stoned most of the time),
sue-happy math teacher (sued my high school over asbestos),
overly nice english teacher (she NEVER got mad), fun Spanish
class (Spanish Jeopardy is so fun)
10th: Mr. Crosby's class (a very
terrifying place), first AP class (chem), damn PSATs
11th: Mrs. Lester's vocab lists
(sooooooo looooooong), first exposure to physics (wow),
12th: whacky math class (was
it really a class?), seeing plays ( i miss seeing plays),
sarcastic english teacher (bless his soul)
June 3, 2003 - From paper to AutoClave, Apt. Construction
-4:09 pm: Just got back from research lab.
Today we learned the basic of solution preparation, both simple
salt solutions and pH specific buffers, and how to sterilize the
solutions. In old chem and bio labs all of this was done for you;
we didn't have to worry about weighing stuff and mixing with the
magnetic stir bars. And pH-meters? what pH-meter? Seems like silly
stuff to learn, but it's important. We cannot use the classic best-friend
lab report excuse of bad chemicals etc... cuz we've made the chemicals
ourselves. And since this is a lab dealing with mammalian cell
cultures, sterilization is extremely important. Speaking of which,
my favorite part about today was playing with the AutoClave machine.
This machine sterilizes the solutions by heating them up for 20 minutes
to 250 degrees F under 190 PSI pressure (high pressure prevents
the solutions from boiling.... if you remember your thermo!!).
The least fun part today was adjusting the pH of my Tris buffer to
8.0. I had to use 12 M HCl, which is particularly nasty stuff if gets
on anything. I was so afraid of acid burn i had to use two hands on
the Pasteur pipette... i should probably get used to it, overcome
the fear, and come to grips with the fact that i will inevitably burn
myself sometime...weeeeeeee. oh well. Tomorrow i get to re-learn how
to do micropipetting. All this stuff might seem pretty boring to have
to go through and do, but i was thoroughly enjoying all of it (except
for the 12M HCl). Perhaps it was exciting because i hadn't done anything
meaningful for an entire week, but nevertheless it was pretty
fun. I'm looking forward to when we move past the basics and begin
experimenting on cell biology. I'm particularly interested
in experiments on vesicle budding and fusion, as that was one of
my favorite parts from MCB130. w00t... synaptotagmin! (if you know
what that is your either 1) a nerd, 2) an MCB-CDB major, 3)
blog: Aaaaaah... so the pounding of the exterior
walls of the building continues... IT IS SO DAMN ANNOYING.
They sound like they're going to bust through the interior
wall at any moment. The worst is that there is absolutely nothing
i can do about it. the management ppl of this building are unapproachable,
money-loving, unethical and especially bitchy. I really don't
know why we didn't look for another place to live... oh yeah
cuz moving and shit is so damn annoying too. Annoying enough to
tolerate these management ***holes? i'm starting to reconsider.
2, 2003 - First Day of Lab
-10:20 pm: Yay! So I actually
did something other than watch TV today... I officially
began my research position in a protein trafficking lab.
Being totally inexperienced, we began today with the absolute
basics: lab safety and solution preparation. Nothing terribly
interesting about lab safety although I was intrigued by the
Geiger-counter in the lab, since i had never seen one before.
Beep... Beep... ... ... Beep! Beep! Beep! hahah. For those that don't
know, radioactivity is used to study protein trafficking. The
specific process is called pulse-chase; it involves
exposing cells to radioactive amino acids for brief pulses and
tracking the incorporated radioactive amino acids as they move
through the cell's pathways. Solution preparation was all on paper...
we had a series of solutions we had to describe how to make from powder
and stock. Much more difficult and tricky than it seems. Actual preparation
will be tomorrow.
1, 2003 - Watching Panzer Dragoon Orta
-9:57 pm: So the TV in my apartment is
now uber special. It has the privilege of having displayed
games from all three next-gen consoles! Yeh came over with
his brand new Microsoft Xbox to play Sega's Panzer Dragoon
Orta. He only has a small 6" TV at his place, and needless to say
the game probably looks better on a 28" Sony Wega. The game itself
looks pretty fun. It involves shooting enemies with a genetically
engineered dragon in order to protect the genetically engineered
heroin, Orta. I've watched Yeh play through almost the
entire game, the last boss being too uber-difficult to beat.
-In other news, my
boredom should officially end tomorrow as my research
position officially begins at 2pm. I'm very excited,
to say the least, as anything at this point beats watching
TV all day. The last week has definitely been a great waste
of time... i did not do anything even remotely close to