S-Stem Scholar Kathleen Corfman's Blog

 Hello! This week we used a really cool tool for genome browsing. I typed in my protein name "acidic mammalian chitinase" into the search bar, and was able to see the chromosome my protein is on, the number of base pairs, and its position. My protein is on Chromosome 1, is 29,713 bp, and stretches between 111,290,851-111,320,563. I then hid all the stuff that the genome browser had displayed, and just looked at the NCBI RefSeq option. I chose to look at the full display. When I clicked on the heading at the top of the display, it shrunk it down to show a condensed version. Here is a nice picture of the full display of the NCBI RefSeq track. When I hovered over my protein's name on the side, it highlights the whole top or bottom section. I clicked on the name, and it took me to a page that showed a brief description about the protein. Clicking on the body seemed to take me to the corresponding CHIA's page as well. At first I thought that there was only one single page ...

 Hello! This week we watched a video on transcription factors, which are "proteins that bind to DNA and encourages RNA polymerase to bind to start transcription." Some transcription factors also prevent binding. I also used JGI/IGM to pick 3 random bacteria species. The names are in bold-face, and I also have each of their ecosystem details... Which are all exactly the same!  Neisseria meningitidis:  Host-associated;  Human ; Digestive system; Large intestine; Fecal Helicobacter pylori :  Host-associated;  Human ; Digestive system; Large intestine; Fecal Streptococcus pneumoniae : Host-associated; Human; Digestive system; Large intestine; Fecal Afterwards, I also looked up transcription factors: The above picture shows that this transcription factor is involved in negative gene regulation. Negative regulation is when a gene is prevented from being expressed. Here's additional details on this transcription factor: Motif structure: Inverted repeat ...

Hello! Sorry for the late blog post.  My protein is Q9BZP6 CHIA, AKA acidic mammalian chitinase. For this week, we searched for associated diseases, catalytic activity, tissue specificity, and cofactors. This weeks blog is a bit ramble-y, because I'm just getting my thought process out there. For everyone's sake who is reading this, I'm listing the important stuff first, hahh! Associated Diseases: None.  Catalytic Activity: reaction = random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins. Tissue Specificity: detected in lung epithelial cells from asthma patients (at protein level). Highly expressed in stomach. Detected at lower levels in lung. Cofactors: I didn't see anything about cofactors on the page. According to VarSite, my protein does NOT have any associated diseases. I found this interesting, because my research from last week said that my protein is associated with allergic rhinitis, and otitis media (the f...

  Hello! Protein: Q9BZP6 CHIA This week I am researching my protein on EBI, which is Europe’s version of NCBI. I am using this database to cross-reference information on my protein. This information is on the” Gene & Protein Summary for Q9BZP6.” I’m going to start with the “Gene” tab. Gene When I was researching on NCBI, I had searched CHIA (my protein’s gene) since NCBI was not allowing me to do a nucleotide search for Q9BZP6. The single RefSeq sequence I found was for the chromosome that contains my protein: Chromosome 1. EBI says the same. The cool thing about EBI, is it also says the CHIA gene spans 29716 bps, and even gives the range it spans. Expression This is the CHIA expression summary provided by EBI. UniProt did not get super detailed about expression, but said it is detected in the lungs at lower levels, and in high levels in the stomach. I’m not 100% on how to read this chart, so I don’t want to make any assumptions, but these seem to be CHIA express...