Sciency Stuff-HIV

I read a very interesting article that had James Robinson as acoauthor. Oct 2005 Journal of Virology p12311-12320. Kinetic Rates ofAntibody binding correlate with neutralization sensitivity of variant simian immunodeficiency virus strains.

One thing that it pointed out was that temperature of runs was done at37 degrees C versus 25 degrees C. Since interactions occur in vivo at37 degrees C. They did studies at both temperatures and saw there wasa direct effect of temperature increase on rate constant. Increasingthe temperature to 37 degree C did not alter the KD, but did increasethe ka and kd of all three mAbs tested (3.8E, 3.11H, 1.10A)

How do you do global fits to a 1:1 langmuir model? The article impliedit designed the experiment so that there would be a good fit. I thinkI'm missing some important information.

I think it would be most interesting to determine if differences inHIV env binding proteins to mAbs( perhaps 2F5, 4E10, and otherneutralizing antibodies ) that are neutralizing and ones that are nonneutralizing using the biacore. It would be neat if we could find a correlary between neutralization sensitivity.

New Goal inspired by Nike + and Apple ipod: Run/walk 100 miles.

I've been really wanting to try out the new nike shoes with their "pebble" inside the shoe that connects to an ipod nano. Well I've been an Apple ipod hold out since 2001. I simply thought it was ridiculous to not be able to play itunes songs on any other mp3 player. Well now I've been sucked in. I not only have itunes songs...I actually have more than 100. Which is getting to the point of awful. I can't play those songs on any other mp3 player. So my deal with myself is: if I run/walk 100 miles in a month ( by Sept 1) then I can buy myself an ipod. Nike + system would be the next 100 miles.

Bribing myself; I love it!

On another note,

I really hate university red tape. grumble-grumble

siRNA, RNAi words I understand but can't verbally define...therfore:

siRNA-small interfering RNA or short interfering RNA
Short (or small) interfering RNA; this is a short 21-23 nt RNA duplex involved in eliciting the RNAi response in mammalian cells.
www.invitrogen.com/content.cfm

Small strands of RNA that interfere with the translation of messenger RNA. Double stranded SiRNA works better than single stranded SiRNA. They are usually 21 to 23 nucteotides long. They bind to the complementary portion of the target messenger RNA and tag it for degradation. siRNA's effect of inhibiting gene expression is commonly known as gene "silencing".
www.alumni.ca/~blan4a0/glossary.html

Small interfering RNAs, which target (in a sequence-specific manner) endogenous RNAs for degradation, thereby reducing the function of a gene.
www.nature.com/nrg/journal/v5/n9/glossary/nrg1427_glossary.html

Small interfering RNA (first found in 1999 Science. 1999 Oct 29;286(5441):950-2. ) Related terms RNAi, Post-Transcriptional Gene Silencing PTGS (found in 1999)

RNAi – RNA inhibitor
RNA interference. A natural cellular mechanism by which RNA is recognized as “foreign” due to its existence in a double-stranded form. This results in the degradation of the double-stranded RNA, along with single-stranded RNA having the same sequence.www.sirna.com/glossary.html

RNA interference is a recently discovered functional tool. This is a phenomenon where an RNA introduced to a cell ultimately causes the degradation of the complementary cellular mRNA, and leads to the knockdown of gene activity.www.invitrogen.com/content.cfm

The use of long double stranded chains of ribonucleic acids to interfere and thus silence the expression of target geneswww.vastox.com/research/glossary.html

In molecular biology, RNA interference (RNAi) is a mechanism in which the presence of small fragments of double-stranded RNA (dsRNA) whose sequence matches a given gene interferes with the expression of that gene. en.wikipedia.org/wiki/RNAi

RNA interference: A gene silencing phenomenon whereby double-stranded RNAs trigger the specific degradation of a homologous mRNA. The specific dsRNAs are processed into small interfering RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA- induced silencing complex (RISC). Useful as an application for specific suppression of an individual gene.www.uark.edu/ua/ricecap/ricecapgloss.htm

Focal Infectivity Assay

Lately in lab I've been doing a lot of focal infectivity assays or FIAs. Focal Infectivity Assays can be used to quantitatively determine the production of virus by infected cells.

To the right is a very clear example of this. You just count the blue dots. When a lot of them are touching and aggregated together they form what is called a syncitia. The official definition of a syncitia is goes something like "HIV-infected patients, macrophages fuse into multinucleated giant cells that produce copious amounts of virus. T-tropic isolates, or syncitia-inducing (SI) strains replicate in primary CD4+ T-cells as well as in macrophages and use the alpha-chemokine receptor, CXCR4, for entry." Thank you wikipedia.

Syncytia formation refers to the observation that HIV infected monocytes and macrophages can fuse together in a rather large conglomeration of cells. This syncitium may occur in lymphoid tissues, bone marrow, and brain. The bad news about syncytia formation is that it enables an HIV-infected macrophage to bring dozens of previously uninfected macrophages into the fold (so to speak) and render them useless. This syncitium of immune cells does not participate in further general immune function and probably represents an attempt to neutralize the HIV-infected macrophage that started the process. The capacity for syncitia formation is not universal in HIV infection. Syncitia forming virus tends to emerge later in the course of infection and is associated with a more rapid decline in CD4 cells.

HIV can be divided into two general categories CCR5 tropic virus and CXCR4 tropic virus. This distinction is based on the predominant type of co-receptors. HIV attaches to cells via a CD4 receptor and requires one of these two co-receptors to get in. Studies have clearly demonstrated that the CXCR4 tropic virus is capable of syncytia formation, but CCR5 tropic virus is not. Patients with low CD4 counts are more likely to have both CXCR4 and CCR5 (dual tropic) virus. CCR5 inhibitors are now in large scale clinical trials and we are now routinely testing patients in these trials to see which type of virus they harbor. It is likely that this testing will become available for clinical care if these agents live up to their promise.


Counting these by eye under a microscope is so tedious I feel that my eyes will burn out and bleed. It's really quite awful. You start seeing dots everywhere. Yes, we have a plate reader. But it's not calibrated correctly and the camera lens is dirty. So clean the camera lens right? Wrong. You need a metric screwdriver set and the company has told me it's in the mail. I sent them a strong email. Let me see how good that'll do me.

In the meantime I suppose I'll just continue counting and trying to do comparisons with the plate reader which is actually called an AID virureader.

I'm coming across so many more new words daily. Hopefully to keep up with them I'll post them here and that will help me memorize and further understand.

P* Lab

So I'm very excited. I have been accepted into the lab of my choice for completion of my senior thesis in biomedical engineering which may or may not turn into my M.S or Ph.D. Eventually I'd love to do an M.D-Ph.D. The implication of that is many years of study. Not sure if I can handle greater than 7 more years of academia.

In my new lab I get to play with the Biacore and do flow cytometry measurements with a laser. All beautiful things that Tulane doesn't have because they can't afford and/or doens't have anyone to run them. At least in the BME labs. I 'm sure some physics guy has lasers but more than likely isn't looking at specific cell surfaces using it.

What interesting to me is that I get to apply the knowledge I have from BME to immunology. Which is amazing to me to say the least.

I'll be looking at mouse IgG, HIV antibodies, and Ricin antibodies. I'm thrilled.

So my blog will have the dust brushed off of it (with a lint free non static kimwipe of course).

I'll include some journal reviews to get me in the habit of writing more, which after 3 years of engineering I'm in dire need of. Also I'll throw in some wine tasting notes because...well I love wine. I still am Brandy afterall.