so happy

Dunno about this blog. I can't say that it is doing much for me. That is why i haven't updated in so long. what do you think blog? should i cancel you?

I guess it just feels kind of funny writing to no one.

but then i don't really care to open it to the public either. I rather just talk to people.

As for the specific purpose of the blog, i don't know...i feel like i am better off just reading things and making notes of them. I don't really feel like I succeeded in making this a science-oriented blog. I don't have the patience to be consistent and write things in layman's language. But then again rewriting something is a really good way of testing one's understanding.

maybe i'll just keep this as an image blog. even then...i'm feeling pretty meh about all this. we'll see.

Newly discovered info on L234

Here is what I read today about L234 in HIV (the book, 2000). L234 is in the NNRTI binding pocket which is in the palm domain of p66 (roughly 10-15 angstroms away from the catalytic site (containing the aspartate residues). The NNRTI binding pocket is lipophilic and consists of three stranded beta sheets (beta 4, 7 and 8). What is of interest to me is the fact that eventhough L234 is indeed part of the wall of the binding pocket, its mutation has not been freqently associated with NNRTI resistance (except for the case of capravi???, which i wrote about awhile ago). Furthermore, it is associated with our inhibitor. But i guess i will learn more about that after the conference in L.A.

earrings

The Fresh Prince of Bel-Air really was an amazing show. we don't have shows like that anymore do we?

i have never been this comfortable with being alone.

this implies that i do not seek some else's comforting. I don't feel that i need it.

And this scares me because it, in turn, implies that no one can help me.

annd that is scary because it brings me to the conclusion that this is a helpless problem.


This is really at the interface of my rationality/reality and the realilty that is in my head and the ties that i can't shake off. but they are not supposed to be shaken off...but i am brainwashed.... i am paralysed here. in limbo.
what i know must be done is a physical impossibility for me.


no it is just too overwhelming. i can't sit down and think about it. If i thought other things were like staring into the sun... this is so much worse. this is paralysis. my brain will not go any further.

I am completely drained. and i will continue to be drained. this has already shaped so much of me. this can never be resolved.

home feel good

aaaaaaaaaaah.

i think i go sleep now.

Grizzly Bear

ok three time is the charm so here we go with the third post of the evening (now i can cross them out on my to do list)

i went to see Grizzly Bear sunday night and....no wait...i can't post about this just so i can cross it off somewhere. Yeah this is not that type of thing. well neither was the picture posting i guess.


well ok. i come back later.


over all it was good though.

that whole MS thing

This is the sequel post to what i was talking about a while ago about MS. Sicne the presentation is over and i am less inspired at the moment and i have other things to do, I will only briefly go into the details of MS vacciantion.

Basically, the IL-17 story boiled down to this: Inject patient with IL-17 and adjuvant, cause immune tolerance to IL-17 to break. Get antibody production. The antibodies neutralize IL-17. Mouse models show a delay in onset of disease and milder symptoms. Not very convincing as far as i am cocnerned because the animals still ended up with EAE and the study was short term. As my prof pointed out, had they continued the study, by day 90, all the mice would've been in the same mess. I guess although I appreciate that IL-17 therapy may be a better target than other interleukin vaccines because of its early inflamatory and downstream role (I.e. its function is not as broad as oh say IL-2, and so its inhibition may have fewere side effects), I still think the same questions of safety (whether it be infection/cancer risk or some other physiological issue) and efficacy still apply here. So i guess in hindsight, I am not too impressed.

Other proposed vaccine strategies:
TCR vaccination. Brilliant idea. Pretty damn safe. will it work? dunno. Basically, this stategy involves priming and activating Th2 (or not) suppressor cells to suppress cells which harbor TCRs that recognize self antigens (I.e. autoimmune Th1 cells). The idea is that Th2 cells recognize peptide sequence of Th1 TCR and suppress it. I think this is a great idea and there is no risk of activating the "wrong" response. But for this approach to work, you pretty much have to genotype every patient individually to figure out what their self-TCR peptide sequence is. I mean they say 90% of patients have these specific sequences but i dunno, the fact that the efficay isn't great tells me something is up. And what i don't udenrstand is where is the APC help coming from? I mean the Th2 cells need APC help no? And there is things there about HLA and MHCI or II or i dunno. basically genetic stuff that i am not too familiar with. Again, this strategy is a good idea but since i don't know enough about many of the details i'll leave things here.

Altered Peptide Ligand (APL) strategy:
what were they thinking?!??! This is a super risky strategy. Inject the patient with a peptide that resembles the self antigen but has a lower binding??!?! this is scary stuff! I am not surprise they observed adverse effects in the clinical trials. Again though, I didn't read much about this so no further comment. Just that I think this is dangerous stuff. I wonder if this is the same story that i heard about a few years ago where things went terribly wrong in the clinical trials of them MS patients...

Ok Copaxone:
it has passed all phases of clinical trials. 8 year long term study (as far as i know the longest existing trial on MS vaccines) and still all is well. according to the discovering scientist 100000 doses are being administered daily.
The way it works is that they this compound (Aka glutatimer(?) acetate (GA) or Cop 1) works by binding to the TCR /MCH receptors really really really strongly. This strong binding out competes binding of the natural self-ligand and apparently more importantly kick starts the suppressive response because of its high affinity. I have no objections against it. The clinical trials speak for themselves.

There are a couple of other strategies as well. Like using bacterial toxins to boost the immune response etc. but since i don't know much about them, i won't go into the details.


anyway, that was that for MS vaccination. Over all i think prophylactic or therapeutic vaccination against autoimmune diseases are perfectly valid strategies. But i guess if we want to dive into immune modulation as a therapeutic method, first we have to learn a lot more about the immune system as a whole and its complex communication web (with itself and other organs/tissues). But that is exactly what we are doing...so...fight the power you immunologists.

one day my friends...one day.

dunno

it's 3 am and i wanna go to be-he-ed. gotta lady, runnin' through my he-he-head.


well. i am dosing off at my lap top. i think that is a sign that i should leave and go to bed.

i was at a crowded party tonight, where people knew enough people to feel comfortable but at the same time they didn't know enough people so that every one was eager to have a conversation and introduce themselves. I met many people.

yeah sure it was fun over all.

ok it's over now

see? i did absoluetely nothing, 4 hours passed. And now it's over.

It went well by the way. well i mean nothing great but it wasn't a disaster. Most people looked pretty bored though. Oh well, at least they weren't shaking their fists in anger...and they did ask questions.

ok now i am going to clean my place. well i'll lie down for a bit first.

also,

procrastiwhatever

so my presentation is in 2 hours. and did i slack off for its preparation or what? i think this is the most unprepared presentation i have ever given. I'll be up there for an hour and man i predict disaster.

The funny thing is i was just thinking two days ago how i couldn't remmeber the last time i was sick and how awesome and in tune my immune system is...and today i am sick. I have no doubt in my mind that this sickness is teh direct result of the stress (increased glutocorticoids) of this presentation. I was so bitter yesterday. just pure bitterness. the library was up the hill, and it was cold, and my zipper was broken. I just a bundle of hate yesterday.

and today, well i am done worrying about the presentation. I just don't feel like doing it for a whole hour. my bed feels too good. I woke up early to read but after a couple of hours i went back to bed. And my morning has been silent and a back and forth between dreaming and fantasies of the most subtle nature. I also enjoyed staring out of my window. It was snowing.

I just can't wait for time to go 4 hours ahead. i'll clean my appartment again and wash some dishes and revisit my daint corner in the living room under the lamp and my earrings. It's wierd huh? 4 hours, is just nothing, but there is nothing I can do at this point in time. i am absoluetely helpless.

da da da da da da da da the past is a gortesque animal, da da, and in its eyes you can see , da, how completely wrong, , , , you can be.... da da DA DA DA DA DA DA DA DA


i. am. loving. this. i. am. doing. summer.saults.

YOU KNOW WHO

autoimmunity, MS, IL-17....no no, it's actually nice.

So.
classical vaccines by definition are these things (live, dead, subunit, viral, bacterial etc. things) that ultimately help the immune system increase its response to an invading entity. And based on what i just said, as our teacher was saying the other day, the word vaccination, until now, belonged to us microbiologists. I say until now because vaccination can now go further than it has gone in the past in that it can (potentially) protect and or cure/treat us against two other types of diseases : cancers and autoimmune diseases. A hypothetical vaccine against a given tumor can serve to prime the immune system and help it attack that specific tumor. But since i want to focus on autoimmunity, that is all that i will say about cancer vaccination.

Autoimmune diseases are pretty nuts...almost kinda literally. They happen when the immune system attacks its own host. I.e. when the immue cells react and attach a specific tissue or organ or cell or cell product within the body. Examples of this include psoriasis, rheumatoid arthiritis, certain types of diabetes, lupus (i think), Mya-something-Gravis, colitis, crohn's and perhaps the most popular one, multiple sclerosis. Asthma and allergies can sometimes be put in the same category in terms of treatment since they also pivot around immune modulation irregularities.

let's focus on MS for now. I still have to read up on MS pathology to refresh my memory and give you the correct terms but the basics of pathogenesis here are as such: The immune system somehow ends up over reacting to a protein in the brain. Despite severe brain access restriction imposed on immune cells by the blood brain barrier, somehow, some of these self-reactive cells (let's not go into who is the main culprit here exactly but let's say it is a Th1 dominated response (i'll explain later)) get in the brain, cause inflamation and all sorts of other damage and hence a disease is born.

Standard therapy against MS is usually the use of immunosuppressants (that's all I know about it. sorry)

So here is where autoimmune vaccination comes into play. Now at a first glance, vaccinating against an autoimmune disease seems completely counter-intuitive right? because as we said vaccination is an immune booster and in an autoimmune disease we have too much of a immune response. so it seems that vaccination would just fuel the fire yes?

I have two scenarios to explain to you which will address the aforementioned concern.
1) The acquired immune response is classicaly divided into two branches: Th1 and Th2. Let's not get into what the role of each branch is right now (too long to explain and too many things that i don't remember exactly and will have to look up). For our purposes, it is sufficient to say that MS is modulated by a Th1 response. So, if MS progression needs Th1, if we find a way to modulate the immune response away from Th1 and towards Th2, well, we might alleviate the disease. That is all i am going to say about that for now.

2) This second scenario is what i just learned about today so i will be more specific. Interleukins are these little molecules that cells send out to communicate with each other and tell each other what to do. There are hundreds of them along with cytokines and chemokines which basically do the same thing. Each of these "messenger particles" have a specific purpose. The amount of their production and release, along with their location, as well as their combination with other messengers will result in variable immune responses ( they controle things like vasodilation (i think), inflammation, Th1 va Th2 favoring, immune tolerance and activation).

It turns out that this interleukin, called IL-17 promotes early inflamation. Remember inflamation, or too much inflamation plays a big role in causing MS. So this IL-17 can potentially play a big role in promoting MS. So hypothetically blocking it may reduce the autoimmune response that causes this disease.

I have to go now. But next time, i'll explain the papers that i read that confirm this last statement. and then we can talk about the risks.




My laptop is getting hot now and it's burning my wrists. Narges is coming over. I predict Tea Time. Yes. I am listening to Cat Power now. I can't find my Karajan festival CD nor the guarantee for my mp3 player which stopped working this week. how can i lose things in a space this small and transparent...and organized?

New deadline= new energy

I just found out that i have to give a presentation next week for my reading and conference class. The topic i chose is the potential to develop vaccines against autoimmune diseases such as MS. This is an interesting topic. I thought i had till march to work on it but now that I only have till next wednesday, you are going to hear alot about it in the next few days.

So far my focus is on MS, and the Th17 T cell subset, and hopefully DNA vaccines. We'll see how things develop...

right now, i go do yoga before i start my work. yesterday I did the half moon stretch which is pretty hard...it made me giggle.

ok.

i think this was Arthur's Seat. Edinburgh 2006.

Big Word Diarrhea

The problem is that I don't feel like reading and i don't feel like writing. Stating it this way is only perpetuating the problem and making it worse. But I can't help it. I can't shake it off. I want to avoid all stages, a pre-emtive strike on all fronts.
I just want to sleep. alot. Or be busy with something that is so pre-occupying that it is like sleeping. like TV, or an experiment, or a social gathering.

...

But you see, i am ok. it is not that big of a deal. It is not an active part of my concious mind. It is just the low drone that everything gets immerced in for the moment.

I just gotta wait it out.

Motivation

This blog should be my boyfriend

wikipedia them.

HIV= human immunodeficeincy virus
RT = Reverse transcriptase
NRTI= Nucleoside-analogue reverse transcriptase inhibitor
NNRTI=non-nucleoside-analogue reverse transcriptase inhibitor
chain-terminator=NRTI=ddNTP
nucleic acid, nucleotide, nucleoside, dNTP, ddNTP all relate to DNA
Primer= DNA
Template=DNA or RNA
DNA synthesis=chain elongation
in vitro
enzyme kinetics, Kd, Km, Kpol, etc.
amino acids
aactive site
phoshodiester bonds, salt bridges, hydrogen bonds
mutations
crystal structures

Music that made me feel (good)

Three Albums that were very special to me this past year were (in no particular order)

The Greatest- Cat Power (has a strong solidifying effect)
The Theater Fire-Everybody has a dark side (makes me giggle to myself quietly)
Ys-Joanna Newsom (i can't say...)

Time for a personal post

yes i would like to make a personal post. ....

well, i have more or less kept quite active. I feel very distant from my body. As if it has become somewhat untouchable...

um, well i really don't have much to say.

Dinucleoside tetraphosphates...continued

So last time we (rather hastily) established what excision is and what TAMs do.

So in this paper (Meyer et al. 2006) instead of chainterminating the DNA chain with a regular chain-terminator, they used a dinucleoside tetraphosphate. This compound basically consists of two nucleotides (which could be chain-terminators) and 4 phospahtes in between them. Or, if you look at it in a more relevant way, these compounds basically represent the intermediate product that is formed at the instant of excision. So imagine if you had a ddTMP as the chain-terminator sitting at the 3' terminus of the primer, and ATP came in as a PPi donor, then as ATP donates its two phosphates, the intermediate product there would be AppppddC. And of course immediately after that, we have the release of the ddC (in the form of ddCTP) and AMP (the old ATP which has now lost two phosphates).

Ok so now that we have established what the dinucleoside tetraphosphate is, we can ask what would be the advantage of its use? Basically, they show that this compound can pretty much inhibit DNA synthesis by RT as well as a regular chain-terminator. More importantly, they show that this compound binds TAMs RT better than WT RT. Mechanistically, this is relevant because it supports the model in which TAMs promotes the binding of the incoming PPi donor better as compared to WT (WildType) RT.

But what makes this compound clinically relevant is the fact that they can selectively bind a group of mutants better than WT. So hypothetically, let's say you administer AZT to a patient. That selects for TAMs which are AZT resistant. Well you can then administer NppppddNs which inihibits what you just selected for! So the two families of drugs can work synergistically in that regard.

One problem however is delivery. How is it going to get into the cell? The paper addresses this point in their discussion.

But I am getting tired of this stuff now.

The paper also discusses how they synthesize the compounds and the mechanism of ddNMP transfer to the DNA chain.

Man, i just got very impatient with this stuff all of a sudden. Next time i'll try to write more consisely with a clear structure rather than a rant. That way i'll make my point without getting bored.

ok back to the lab now.

Dinucleoside triphosphates may be more effective against TAMs than regular chain-terminators

The latest paper I have read was published by the W. Scott group in 2006 (Meyer et al. AAC) ( yeah i know that is not proper refrencing. i get better eventually...ma~nana, ma~nana). Here is a little background scoop before we get into the paper. So Regular chain-terminators (i.e. NRTIs) bind wildtype RT and get incorporated into the elongating DNA chain. But! what is special about RT is that even though the forward reaction (i.e. DNA elongation) is favored, the back reaction (e.i. excision; the removal of an incorporated nucleotide) can happen as well. Now obviously under normal conditions this reaction is significantly unfavored. But! if the forward reaction happens to be slowed down (in this case let's say because of the incorporation of a certain chain-terminator), then the excision reaction becomes more relevant.
Now a number of NRTI-resistance associated mutations function by promoting this reaction. Very popular example of this is TAMs (Thymidine-analogue associated mutations).
So then the next question is...well...how? How are these mutations favoring excision?
To answer that question, we have to have a quick review of teh excision reaction itself. Now when a nucleotide is being incorporated, it has three phosphates right? and two of those get released (hydrolysis) and the nucleic acid and one phosphate (5') remain in the growing DNA chain. The excision reaction is exactly the opposite of that. It is when two phosphates come in and bind to the remaining phosphate on the nucleic acid and hence a nucleotide is released. So relevant to what we are saying here is, where are those two phosphates coming from? in vitro, this can be a simple pyrophophate (PPi, i.e. a molecule consisiting of two phosphates). But it seems that a much more relevant in vivo PPi donor is ATP (Adenosine triphosphate). So the way I like to think about it is that ATP basically backs up the driveway from where PPi normally leaves.

So! to make the story short, if somehow a mutation caused ATP to bind more favorably as a PPi donor, then that mutation could theoretically promote excision. And we thikn this is what is happening with TAMs.

ok so this is the background info necessary for getting into the paper. why don't i continue with the actual paper at our next session.

p.s. i will try to reference the statements that i make. Because 1) it will be better for you 2) it will help me with remmebering who said what where and why.

time well wasted...no regrets!

I was going to post the follow-up to the L234F business tonight and talk about another article that I am reading. But...instead...i watched 19 episodes of The Office (US version).

L234F: what is your deal?

Ok so my research for L234F has been futile thus far. I have only found one article on it. It is about capravirine, a novel NNRTI which has failed in clinical trials. Sato et al. (antiviral reseach, 2006) report that this NNRTI selects for the usual NNRTI resistant mutations. But in addition it also selects for L234I. this mutation has not been associated with any other NNRTIs. Interestingly, the presence of this mutation, along with a few other NNRTI mutations, has an antagonistinc effect on T215Y (AZT resistance) and vice versa. This point is of interest to me. It is also important to note that this is the only mutation that relates to my research which is not an NRTI associated mutation.

I also know from conversations that L234 is in the linking area between p66 and p51.

So what remains to be addressed:
1. where is L234F in RT exactly?
2. is it an NRTI associated mutation as well?
3. Leucine is converted to phenylalanine. what's the difference between these amino acids?

ok today was ok to be the day that i write here about that L234F article that i have been reading for the past...month. But i didn't get a chance to do it because i did other fun things instead. But tomorrow....tomorrow...i promise you science. I promise you. I promise you so bad.

My appartment has been feeling rediculously good this past week. I don't want to leave it. well i only want to leave it for short periods of time.

but tomorrow...oh you watch out. I'll L234F this place up so bad. it's not even going to be funny.


m

how do you fix the time? the time is off. It's 2:54 now. Not 11:49. i am rarely sleepy at 11:49.

i am sleepy now. i'll be back later.

test test this is a test.