S-STEM Scholar Josiah Kaiser's Blog

Throughout the course of the last several months I have utilized several biology databases and much scientific literature to investigate the novel protein pirin and the PIR gene that encodes it. This week will be the apotheosis of my efforts, in which I will design a research project to conduct upon pirin that will, hopefully, help us to develop a better understanding of the protein. The question as to what type of experiment to design for pirin is an extremely broad one; over the course of this blog I have discussed pirin’s role as a transcriptional cofactor, its correlation with the maturation of myeloid hematopoietic cells and thereby its possible role in the development of leukemia, the potential for pirin to play a role in programmed cell death, and many other aspects of the protein that warrant further research ( The UniProt Consortium, 2021) . However, the research I wish to engage in revolves around pirin's potential to contribute to melanoma when decentralized from the cel...

This week I will continue to utilize the UCSC Genome Browser ( http://genome.ucsc.edu/ ), this time using the Repeat Masker track to research the repeat elements of the PIR gene (Kent, Sugnet, Furey, et al., 2002). Repeat elements are sections of the genome that repeat themselves within the genome. The Screen Masker track is capable of displaying 10 separate classes of repeats: SINE, LINE, LTR, DNA, Simple, Low Complexity, Satellite, RNA, Others, and Unknown. Within each of these classes, areas of the PIR gene are shaded from a light grey to a very dark grey to indicate how many “Base mismatches, base deletions, and base insertions [are] associated with a repeat element,” with a higher number of these being indicated by light shading, while a lower number is indicated by darker shading.  Utilizing this knowledge we can see that classes such as LINE and LTR have relatively high concentrations of repeats and classes such as LINE and DNA contain longer repeats. Understan...

This week I will continue to utilize the UCSC Genome Browser ( http://genome.ucsc.edu ) to investigate the PIR gene; particularly, I will be using the ORegAnno track within the database (Kent, Sugnet, Furey, et al., 2002). ORegAnno, short for Open Regulatory Annotation, seeks to document curated information concerning the regulatory factors of genes (Operators and operands, silencers, repressor proteins, transcription factors and cofactors, etc.). Previously in this blog I discussed the redox-sensitive nature of pirin, and how said redox-sensitivity may contribute to pirin acting as a transcriptional cofactor by allowing pirin to interact allosterically with transcription factors in redox-specific environments. Conversely, this week I will be focusing on the regulatory factors involved in the expression of the PIR (Pirin encoding) gene, rather than what regulations PIR expression may itself contribute towards.  Navigating to the ORegAnno track for PIR on the Genome Browser retu...