When two halves equal zero (background)

Fluorescent imaging is all about the contrast between the signal and the background. For imaging to be successful, the signal should be clear above the background. Background fluorescence can come from free/non-specific fluorescent probe, autofluorescence, and out of focus fluorescence.

There are two major strategies to improve signal/background ratio.

The first is to increase the signal. We do that by choosing brighter fluorescent molecules, by increasing the number of fluorescent probes per target, by using more than one color per target, by having photoactivatable probes etc…

The second strategy is to reduce the background. The wash step in IF and FISH protocols is intended to remove excess, non-specific bound, probe. There are even more extensive wash protocols.  We have many type of microscopes that are designed to reduce out-of-focus light (these include confocal, TIRF, multi-photon, and SPIM).  In yeast imaging, we sometimes add an excess of adenine to the culture media, since many strains are defective in adenine biosynthesis, and accumulate a red intermediate molecule. In the field of single molecule live mRNA imaging, we usually add a nuclear localization signal (NLS) to the fluorescently tagged RNA binding protein, in order to reduce its cytoplasmic fluorescence.

Now, my lab-mate Bin Wu develop a system that he calls “Background free imaging of single mRNAs in live cells using split fluorescent proteins”.

The idea is to combine the two most common systems – the MS2 and the PP7 systems, so that the MS2 binding sequence (MBS) and PP7 binding sequence (PBS) will be in tandem. Then the MS2 coat protein (MCP) will be fused to one half of a fluorescent protein (Venus) and PCP will be tagged with the other half. Only when MCP-VenusN and PCP-VenusC are in very close proximity (e.g. bound to the MBS and PBS, respectively) the two halves can bind to form Venus, which fluoresce in bright green-yellow.  Add 12 of these tandem repeats to the mRNA and you have 24 fluorescent proteins on the mRNA in the cytoplasm, with, theoretically, zero unbound fluorescent protein in the cytoplasm, hence “zero background”.

The system has some limitations. For one thing, the protein levels must be low, since the fluorescent protein halves can self-associate at high concentrations independent of interaction with the mRNA. Also, since it takes the fluorescent protein some time to mature, it is not useful to study short-lived mRNAs, or  transcription in live cells, since by the time it matures, the mRNA has already left the nucleus.
Wu B, Chen J, & Singer RH (2014). Background free imaging of single mRNAs in live cells using split fluorescent proteins. Scientific reports, 4 PMID: 24402470

Cells reach out their “hands” to create new limbs

Communication between cells takes many forms. There could be communication by sending out microvesicles with important messages inside, by sending out free molecules (like hormones) or by special structures (e.g. synapses).

Sonic hedgehog (SHH) is a signaling protein that is important for the development of vertebrate limbs. It was thought to be release from a small group of cells at the posterior end of the limb bud, and is recognized by receptors on cells a long distance away.

Not this Sonic Hedgehog… (image taken from http://sonic.wikia.com)

A new paper publish in Nature from Maria Barna’s lab shows that SHH actually remains bound on the external side of the cells that produce it. The cells simply send very long thin protrusions (here named filopodia) that reach all the way to similar filopodia of the receiving cells.

I think that not only the story is very novel and interesting, but the images are very pretty.

Several “technical” issues:

In order to study the SHH signaling in live chick embryos, they designed a custom made live in ovo microscopy system: a temperature controlled plate; on it an egg container chamber, and an objective that is dipping into the yoke.

They show that standard fixation methods (e.g formaldehyde) destroy these filopodia. Also, a volume marker (in this case sfGFP) that just fills the cytoplasm does not give a strong enough signal to detect these filopodia (possibly since they are very thin, and packed with actin filaments  and other proteins, so there’s very little free volume left).

So, they used palmitoylated fluorescent proteins, pmeGFP (green) and pmKate2 (red) that target them to the plasma membrane. This enabled them to visualize these very thin and long filopodia. Here’s a video movie from their paper.

They use a variety of cytoskeletal proteins fused to EGFP or to mKate2 to learn about the structure of these filopodia. Their conclusion is that these structures contain only a specialized form of actin filaments.

They show beautifully that SHH (fused to EGFP) travels to the tip of these filopodia:

They used a split GFP technology to show that SHH is actually found on the outside of the cell membrane.  In split GFP, two fusion proteins are produced, each one is fused to “half” of a GFP protein (its not exactly half but let not go into that now). If the two fused proteins are in close proximity, the two halves associate to produce an GFP that fluoresce irreversibly. The two separate halves do no fluoresce. So one half was fused to SHH and the other was anchored to the extracellular leaflet of the plasma membrane, and when both were expressed, they got green fluorescence.

In total – a very nice and pretty paper.
Sanders TA, Llagostera E, & Barna M (2013). Specialized filopodia direct long-range transport of SHH during vertebrate tissue patterning. Nature, 497 (7451), 628-32 PMID: 23624372