S-STEM Scholar Josiah Kaiser's Blog

          Two weeks ago I used the National Center for Biotechnology Information’s protein and  nucleotide databases to investigate the amino sequences in pirin as well as the nucleotide  sequences that allowed the gene PIR to express pirin. This week we will be using a similar  database provided by the European Bioinformatics Institute to investigate what pathological  process pirin is involved in (EBI) (Madeira, Park, Lee, et al., 2019). A search for pirin using EBI’s search tool provides information identical to what I retrieved from the UnitProt and NCBI  databases in past weeks. However, EBI’s database goes much further in depth about pirin’s protein structure and expression than UniProt, compiling information such a R-values and an extensive list of experiments detailing pirin’s baseline and differential expression levels in various conditions. While NCBI’s databases do contain this information it was, at least for pirin, spread ...

        This week I will be using two databases to discover the molecular interactions that pirin is subject to with other proteins in the human body. First is The Human Reference Protein  Interactome Mapping  Project (HuRI), a project by the  Center for Cancer Systems Biology at  Dana-Farber Cancer  Institute  that attempts to better understand how proteins within the human  body interact with  one another (Luck, Kim, Lambourne, et al., 2020). The second database I will  be using is STRING, a broader database that collects and aggregates protein-protein  interactions from  " 24,584,628 proteins in 5,090 organisms" ( Szklarczyk , Gable , Nastou, et al.,  2021).           Or, perhaps, this is would be the case if HuRI's protein database contained data on pirin,  which is, unfortunately, one of the proteins absent from the database. This is a shame, as the...

  The Sequence of Pirin NCBI is a biotechnical database that has amassed a gamut of qualitative and quantitative biological research. I will be using NCBI’s conserved domain and nucleotide databases to conduct the following research on the amino acid sequencing of Pirin as well as the nucleotide sequence of the PIR gene that encodes it.   The NCBI summary for pirin is as follows:  “This family consists of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localized within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures. A tomato homolog of human Pirin has been found to be induced during programmed cell death. Human Pirin interacts with Bcl-3 and NFI and hence is probably involved in th...