Science Buddies: "Ask an Expert"

Hello, I'm doing the project, Creating a Kidney: How Stem Cells Might Be Used to Bioengineer a Vital Organ. I'm in the section, Using the Extracellular Matrix to Drive Kidney Cell Differentiation, Step 7, and I'm not sure how to progress. I need to use the AmaZonia microarray atlas to find out which of my ECM proteins are highly expressed during kidney cell development, but I have been unable to find any of the proteins I'm using on the AmaZonia atlas. Also, I need to be able to find each of the proteins' subunits, but I don't know where I can find what the alpha, beta, and gamma subunits for some laminins are, and the table included with this part of the project doesn't include the abbreviation for fibrinogen, either. Can anybody please help me get some of this cleared up? Thank you!

Hi,

I am looking at the Amazonia microarray search page and I typed in 'fibrinogen' and found an abbreviation for the gene of FG and also FIB: http://amazonia.transcriptome.eu/search ... ield=alias

Which laminins were you unable to find? Here's the search results for lam%
http://amazonia.transcriptome.eu/search ... ield=alias

What other proteins are you trying to find microarray data for? How did you search for them in Amazonia? If they don't appear in any list maybe there's no data set for them. You could try doing a search for the protein on Google Scholar or NCBI and see what information you can get that way.

Good luck.

Sybee

Since I'm not that observant, I missed the part that told me EXACTLY how to find the proteins on the Amazonia microarray. I'm so sorry for causing this inconvenience on your part. Please accept my deepest apologies.

No apology necessary. I'm just glad your question was easily answered. Good luck putting together the growth factors for a working kidney. It would really be interesting if you could try it in the lab.

Do a search of the scientific lit to find those papers that mention the protein types you selected and try to estimate the odds of success based on what has been published. This is not an easy thing to do so if you have any questions about the jargon or methods, don't hesitate to ask us. We're here to try and make science understandable for everyone.

Sybee

Thank you. Unfortunately, I will not be able to test my hypothesis in a lab, but I do have an experimental plan that may be a starting place for someone else to try this sort of thing in a lab someday. Based on the research I've done, the soluble factors Transforming Growth Factor Alpha, Transforming Growth Factor Beta, Insulin-like Growth Factor, and Platelet-derived Growth Factor are necessary for general kidney cell development. If I understand correctly, this means that the proper concentrations of these soluble factors will tell a stem cell to become an unspecified kidney cell. Next, to either create Renal Corpuscle cells or Renal Tubule cells, you would need to expose the general kidney cells to more soluble factors that can differentiate the general kidney cell into a more specialized type of kidney cell. Retinoic Acid Receptor A could possibly be used to differentiate general kidney cells into Renal Corpuscle cells, and Wnt4, Hepatocyte Growth Factor, and Activin A could possibly be used to differentiate general kidney cells into Renal Tubule cells. When more of these specialized kidney cells are put together, they should be able to secrete proteins to form the extracellular matrix that will bind the cells together and start to form a kidney's nephron. I'm not sure how realistic this is, so any feedback would be much appreciated. Thank you again.

You are most welcome. It looks like you have nailed down all the factors to grow specific kidney cells. Now if you could just try it in the lab...

There is one more thing you might think about and that is how the cells can be turned into a functioning organ, which I suppose is the reason researchers are trying to grow such cells. If a person needs a kidney transplant and there's not one available, then presumably these stem cells could be converted to renal cells and put into the body to substitute for the failed kidney. But how do you go from cells to organ? Also, how do you insure that they stop growing and don't turn into a tumor?

Good luck with your project, let us know how you make out and I hope you may decide to take up science as a major and become a researcher yourself. It is a highly interesting, satisfying and useful career.

Best wishes,

Sybee