Finding new ways of degrading cellulose

Custom LNA™ Detection Probes

Maša Milatovič

Maša Milatovič is a PhD student at the University of Ljubljana in Slovenia. She has been using LNA™ detection probes from Exiqon to detect cellulase mRNA transcripts in P. scaber.

1. What is the current research going on in your lab?

Our group is researching the biology of an isopod crustacean Porcellio scaber, which is used as a model organism for terrestrial ecotoxicological testing as well as for studying biomineralization processes. As P. scaber is an important decomposer of decayed plant material, a part of our research is to investigate its potential ability to produce cellulose degrading enzymes.

2. What made you choose Exiqon?

After successfully cloning two endogenous cellulase genes in P. scaber, and proving their expression with quantitative real-time PC (qPCR), we further wished to analyze their expression in situ. We tried several classic in situ hybridization protocols with both oligoprobes and RNA probes but could not get satisfactory results. Searching for a solution, we read about wonderful ISH results others with similar problems got with the new LNA™ technology. As we knew from our qPCR results that the genes were indeed expressed in P. scaber tissues, we decided to try once more with LNA™ probes before giving up on ISH.

3. How has it worked so far?

As the genome sequence of P. scaber is basically unknown we decided to let Exiqon design specific LNA™ probes based on the sequences of the cellulase gene we cloned. After months of trying every possible ISH protocol we did not expect much when we first tested the new LNA™ probes. But the probes worked!!! We could not believe it at first. But we got beautiful results repeatedly and could even detect the probes fluorescently.

4. What were some specific challenges in your project?

Our qPCR results show the cellulase genes are expressed already in the early developmental stages, therefore we would like to detect the expression of cellulose genes in whole-mounts of P. scaber embryos and larvae.

5. How did you overcome them?

We are still trying to find a suitable protocol for whole-mount ISH which would not damaged the delicate embryos during the hybridization procedure.

6. What would you tell a colleague about why they should work with Exiqon?

If you want good reliable results fast and hassle-free, go for it!

7. Where will your research be showcased next?

Most importantly (for me personally) I can finally finish writing my PhD thesis! The work will also be presented at the 7^th International Crustacean Congress, which will be held in Qingdao, China, in June 2010.