Quick notes on the studies in progress


List of studies undertaken or are currently in progress. All studies listed here will have entries in the open lab notebook linked on the front page.

Current major long-term ongoing study centers around phage screening of the East River of New York City, with rotating host bases that include Deinococcus radiophilus and Halobacterium salinarum NRC-1. The river presents an interesting trove of biological specimens, notably around my sampling site at the southern end of Queens, where the tidal wave from the Atlantic and the river water from the north forms an estuary of a rather high salt concentration. The river's proximity to one of the densely populated regions on the East Coast is a bonus as well.

Another major ongoing study had been the sequencing of Deinococcus radiophilus, which did not have a publicly available genome at the beginning of the study. Our goal was to see if we could use a single Nanopore flowcell along with the simplest sequencing kit available (rapid sequencing kit) to generate a genome of radiophilus capable of producing two key insights; confirming the presence of plasmids and gaining evolutionary insight into the history of the radiophilus based on the knowledge of the plasmids. The entire study was a long learning experience that far exceeded our expectations in many different ways, with the rendition of the genome and its analysis methods improving rapidly and drastically with each attempt at the original raw data. We're currently compiling the research into two different articles for publication, the first a study of the possible prophage origin of Deinococcus radiophilus plasmid (as of 2019 September) and the second focusing on the process of learning and refinement that took place for us as amateurs- how a relatively simple sequencing project quickly became an introductory evolutionary biology study across the bacterial and viral kingdoms should prove to be an interesting one for those interested in modern amateur research in general.

We always try to maintain a healthy degree of awareness in scientific publications from a bygone era that remains untranslated and unknown, and I'm particularly interested in the work of early modern microbiology and phage biology from forerunners like Jacques Monod and Felix d'Herelle. My moderate translation projects resulted in some unexpected bits of knowledge, such as the origin of PhiX174 phage. Originally thought of as being named for Paris sewer under arrondissement 10, sample 174 (from the famous recollection written by Sydney Brenner) the phage instead is one of main specimen of researchers Sertic and Boulgakov at Felix d'Herelle's personal phage laboratory, with Phi indicating the host type and X indicating serotype under immune system exposure. I believe we have the first English translation of the particular research paper and the data describing PhiX174 and other phages being treated at Felix d'Herelle's lab. We're hoping to publish the translated data soon, maybe along with a comparison study of PhiX174 described in Sertic and Boulgakov's study versus modern samples available from repositories.

Another classic we're studying in the same vein is Jacques Monod's original graduate thesis describing what is considered the first direct observation of the diauxie in microbes- we're working on translating the thesis itself (a moderate length book of about 300 pages). This process led us down another unexpected path of study in the replication of the diauxie studies. To replicate the study in a finer-grained manner, we designed our own automatic cell culture turbidimeter that is capable of taking constant growth data at an interval of our choice, which showed some unexpected behavior that we hope to share soon in a more extensive study.

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