nilthe1st
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How do I do Table 2 in the procedure for Creating a Kidney: How Stem Cells Might Be Used to Bioengineer a Vital Organ?

Postby nilthe1st » Tue Nov 02, 2021 6:40 pm

Hi, I was wondering how to do the table 2 in the procedure for Creating a Kidney: How Stem Cells Might Be Used to Bioengineer a Vital Organ. I was confused as to how to get the information from the databases because I was unable to find them.

Thank you!

brandimiller610
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Re: How do I do Table 2 in the procedure for Creating a Kidney: How Stem Cells Might Be Used to Bioengineer a Vital Orga

Postby brandimiller610 » Sun Nov 07, 2021 9:14 pm

Hi nilthe1st,

Thank you for your questions! For the Creating a Kidney stem cell project, there are three databases that are listed: (1) NCBI Gene Database, (2) Pathway Commons, and (3) Embryonic and Induced Pluripotent Stem Cells & Lineage-specific Markers. These are all hyperlinked in the protocol for this project. Once you click the hyperlink, it will take you to the database, where you can search for any gene -- you will want to search the ones given in Table 2, under the column "Abbreviated Gene Name". From there, the database will generate a lot of information about the gene, which you should use to fill in Table 2.

I hope I have been able to answer your questions about this project. If any more questions come up, please feel free to reply on this forum! Good luck!

--Brandi

nilthe1st
Posts: 2
Joined: Sun Oct 31, 2021 2:18 pm
Occupation: Student

Re: How do I do Table 2 in the procedure for Creating a Kidney: How Stem Cells Might Be Used to Bioengineer a Vital Orga

Postby nilthe1st » Tue Nov 23, 2021 3:43 pm

Thank you for replying back to me. I am trying to fill out Table 2 and I started by putting in the very first gene name into the databases. In the three databases, I searched up INHBA, which is an abbreviation of the Activin A soluble factor, from Table 2. I was unable to find the family it belonged to, whether it regulated proliferation or apoptosis, whether it regulated differentiation, whether it regulated development, and whether it regulated epithelial-to-mesenchymal transition. Please advise me how I would be able to obtain this information from the three databases. If you will be able to show me how to do the Activin A, I will be able to find the information on the other genes and complete the table.

Moderator note: Per Science Buddies policy, I've removed personal contact information. Please use the Ask the Expert forum for all discussions. Thank you. Madeline

brandimiller610
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Re: How do I do Table 2 in the procedure for Creating a Kidney: How Stem Cells Might Be Used to Bioengineer a Vital Orga

Postby brandimiller610 » Fri Dec 03, 2021 9:10 am

Hi nilthe1st,

I hope you are having a great day and I apologize for the delayed reply to your questions.

1. When using NCBI, the functions of the gene can be found in "Summary" as well as under the "General Gene Information" heading. Under the "General Gene Information" heading and "Process" subheading, there is a list of molecular processes that the gene is involved in. For example, INHBA (activin A) is involved in the differentiation of multiple cell types (i.e. GABAergic neurons), negative regulation of proliferation, and development (i.e. hair follicle). The Summary (top of page) says that INHBA is part of the TGF-beta superfamily (likely due to similar functions or structural alignment).

2. For Pathways Common, it is a little bit more complex. You have to look at the other genes and their interaction with the gene of interest. For example, INHBA binds to the ACVR1B receptor and the proteins interact via a signaling cascade. Clicking on the ACVR1B gene gives you a description of the receptor, as well as activins, which you can use to fill in the table. Specifically, it states that activins are growth/differentiation factors that belong to the TGF-beta family of receptors. Pathways Common also provides links to other databases that may give you additional information you can use to fill in your chart. Personally, I like UniProt the best.

3. On the Embryonic and Induced Pluripotent Stem Cell Differentiation Pathways & Lineage-specific Markers database, there are two ways to get the gene information. First, on the homepage, you can click directly on "Activin A" on the schematic. This will take you to a page of Activin A products, with a brief description of the function of the protein. Or, you can search for the abbreviated gene name in the search bar (top of page). Then scroll down to "Background" where additional information can be found about the gene and/or protein.

I hope this helps as you complete your project. Please feel free to let us know if you need any clarification or have additional questions and we will be happy to help!

--Brandi


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