S-STEM Scholar Josiah Kaiser's Blog

This week I will once again be using the UCSC Genome Browser ( http://genome.ucsc.edu ), this time to gather data on how PIR expresses the pirin protein (Kent, Sugnet, Furey, et al., 2002). One of the traditional methods of gene expression analysis is through the use of DNA microarray assays, a process in which a sample of mRNA is essentially reversed engineered into DNA through a Reverse Transcriptase Polymerase Chain Reaction (RT-PCR). RT-PCR synthesizes DNA by taking the mRNA sample and utilizing an enzyme known as reverse-transcriptase as well as a polythymine primer (mRNA has a polyadenine tail) to create a single stranded complementary DNA molecule to the mRNA sample by deducing the proper nitrogenous bases for the DNA strand given the nitrogenous bases of the mRNA. This single stranded complementary DNA (cDNA) can then be dyed and placed into the microarray with any number of single stranded genes and DNA polymerase, thereby allowing the gene DNA to bind to the cDNA (Unbound cDN...

  This week I will be using the UCSC Genome Browser ( http://genome.ucsc.edu ) to  investigate the qualities and mechanisms of PIR, the gene that encodes the protein pirin. The database was created by the Genome Bioinformatics Group for the purpose of compiling  genomics information such as gene modifications, transcription factors, expression patterns, and more. The strictly moderated database is capable of linking to genetic information  available on other databases, but also directly cataloging scientist-submitted data (Kent,  Sugnet,  Furey, et al., 2002).  The UCSC Genome Browser contains an absurd amount of data; it is truly a monumental feat of modern science. From the loci of every gene in a chromosome to the individual nucleotides in a specific modification of a specific gene, the UCSC Genome Browser is capable of generating imagery of it all. The database feels like the apotheosis of The Human Genome Project placed at the fingertips of anyo...

     The databases I will be utilizing in my research this week are the Integrated Microbial Genomes and Microbiomes (IMG/M) database and the CollecTF database. IMG/M is a microbial genomics database created by the United States’ Department of Energy for the purpose of cataloguing microbial genomic datasets (Chen, Chu, Palaniappan, et al., 2021) (Mukherjee, Stamatis, Bertsch, et al., 2021), while CollecTF indexes transcription factor binding sites in bacteria ( Kiliç, White, Sagitova, et al.,2014). A transcription factor is a protein that binds to a specific domain of DNA, thus enabling RNA polymerase to  catalyze the transcription of that portion of DNA into RNA.  The IMG/M website contains an absolutely baffling amount of information; the breadth and thoroughness of the project is admirable and impressive, if not difficult for someone inexperienced with the website, such as myself, to navigate. After a little trial and error I managed to navigate to a...

        Last week I utilized EBI’s database to research the pathologies associated with pirin in the human body. This week I will continue to use EBI’s database, specifically VarSite, a portion of the EBI database concerned with cataloging disease-associated variants in humans (Laskowski, Stephenson, Sillitoe, et al., 2020). I will be using this database to further research pirin-associated pathologies as well as its catalytic activity and tissue specificity.  When searching for pirin on the VarSite database I was immediately given pirin’s ID number ( O0065 ), its VarSite ID number ( PIR_Human ), as well as a brief description of pirin’s tissue specificity and tissue related pathology that reads as follows “[Pirin is] highly expressed in a subset of melanomas. Detected at very low levels in most tissues (at protein level). Expressed in all tissues, with highest level [ sic ] of expres sion in heart and liver.” This description fits with my research...