S-STEM Scholar Leilani Boren's Blog

Introduction;     In the previous summer, one of the main projects taken by the lab was to formulate a DNA extraction protocol that could be used for 16 different Deinococcus species in order to sequence them and continue research. Not only did we do these species, but over 20 Deinococcus aquaticus isolates were also done, but with a greater focus on maintaining high molecular weight for the genomic DNA extracted. In doing this, the species were extracted by using different bead beating times depending on what was needed for each species and then the QIAGEN DNeasy kit, and the isolates with a much more intensive protocol, the QIAGEN genomic tip with some minor modifications, predominantly cell lysis by sonication. It was later found to be wit the new chemistries developed for sequencing that samples could not be eluted in anything other than nuclease free water, or else the sequence would be inhibited by a surplus of contaminants. Even the trace amounts of chemicals in elution...

 Introduction: As a continuation of last week's project, research into D. sonorensis' optimal lysing method for DNA extraction was further studied, and usable data was necessary in order to create a poster for the upcoming conferences. With this particular goal in mind, it was crucial to maximize time and resources to produce results that could hopefully be  measured and visualized with a coherent story that would be useful for not only this lab, but other labs that are currently dealing with a bacterial species that forms the signature plaque like structures that D. sonorensis likes to make. These plaques have been described in the one paper it is featured in, where it was originally isolated and scarcely characterized due to the "clumping" formations that it makes (Rainey et al 2005). These structures inhibited the work of these individuals, and have historically been difficult for us as well. This is exactly why it is so important that not only can these cells be h...

 Introduction:     Deinococcus sonorensis is a species from the Deinococcus genus that has a history of being particularly difficult to work with, as seen during DNA extractions for sequencing efforts during last summer. It is a gram positive bacteria with a short rod morphology, as well as forming plaque like structures when its grown on agar plate. These plaque like structures, what may be a biolfim formation with further research, prevent these cells to become homogenous in solution even with maximum vortexing and pipette mixing. This issue is very problematic when doing DNA extractions, taking OD values and trying to normalize multiple samples, or most other protocols for any investigative research. This bacteria has only been studied in one paper so far, which is assumed to be because it is so difficult to work with. Previous DNA extractions with bead beating, lysozyme, and boiling as well as multiple combinations of these three techniques, produced very low yields o...