S-Stem Scholar Anthony Luna's Blog

 Hello, Today I familiarized myself with iTASSER, which is a platform that uses algorithms to construct models of specific proteins that are being investigated. The protein I requested a model of belonged to Deinococcus Radiodurans, D. rad, and had the following locus tag Ga0133345_1136. Below are four images of the protein rotating through space.  

Hello everyone,  Below you will find some more information I was able to discover about my protein, alpha-amylase 1B. Locus tag : NM_001008218 Size : 1838 bp Accession number : NM_001008218 Version : NM_001008218.1 Comment : REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from CB958705.1, CB957894.1, CB958435.1, and AI627716.1.   Comparing the information from NCBI and the information I used for the first assignment, the only discrepancy I can note is that NCBI gives the length in “base pairs” while the website protein atlas gives the length in “amino acids”. Graphic summary of my BLAST run                                                                            My first two sets of primers

09/09/2020 Anthony Luna Today I finished the first assignment of the bioinformatics project focusing on proteins .  My assigned protein is Q5T084 AMY1B , also known as alpha-amylase 1B polypeptide (Reactome.org). It is found in Homo sapiens and aids in the bodily function of digestion and absorption. Specifically, digestion and absorption of branched starch, amylopectin, and linear starch, amylose (Reactome.org). All of which takes place in the extracellular region of various cells. Moving onto the size, mass, and structure of alpha-amylase 1B. The protein alpha-amylase is folded into three distinct domains, A, B, and C. Yet, my primary focus is on domain B, which has a length of 105 amino acids, aa, and a mass of 12.4 kilo Daltons, kDa (Proteinatlas.org). Alpha-amylase 1B is described as projecting off of domain A in a loop like fashion. However, when a calcium ion binds to domain B, it is then described as relatively rigid (Schutte) . As for diseases involving alpha-amylase 1B, ...

Hi everybody, This past month I have been working with Chad and Trevon on trying to get our experiment up and running involving a flow chamber. With the flow chamber, our goal is to get a biofilm of D . geo growing inside of it so we can then take it to ASU and get some imaging done, specifically confocal microscopy. However, we have had a lot of trouble with getting the experiment going due to contamination along with the lens in the flow chamber breaking causing leakage. Hopefully, next month we can resolve these little errors and gather some images!

Hello everyone, in today's lab, I streaked a TGY plate (my second time ever streaking) with D.geo for Chad to propagate it for the experiment we will be conducting next week. More information on the experiment will be coming soon.

Today, Trevon and I attempted to do yet again another transformation on D. rad. However, with this trail, we are especially hopeful that we will have competent cells on our plates. We changed a couple things this time though. We are now using chloramphenicol and not ampicillin and our plasmid concentrations are now varied. 

Hello everyone, Beginning with Lab on Tuesday this week, Trevon and I looked to see if our transformation on D. rad was a success but unfortunately, it was not... So we then did a transformation on E. coli to see if it was possibly the plasmid that was not any good but E. coli took it up so that hypothesis is longer considered, for now. Although today, Saturday, I replated the E.coli to see if the plasmid will be retained and the transformation did in fact occur. Next week we will have a final answer.