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.