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Description
Cyanobacteria and its complex photosynthetic systems have been a prime target for synthetic biologists and their molecular engineering tools for the last couple of decades. However, characterizing meaningful carbon dioxide (CO₂) removal performance has always been a struggle within the field. It is proposed that measuring changes in CO₂ gas concentration within a dynamic system can be accomplished with a simple automated Arduino-powered system. The system employs solenoids in parallel (one for each outlet stream) which are then connected to one large manifold which feeds into a single IR-based CO₂ probe. Since CO₂ probes are expensive, this approach allows for sample multiplexing while remaining affordable. The development of such a system allows for high resolution growth experiments between different strains of cyanobacteria. This approach provides continuous data collection over the entire life cycle of each individual culture, allowing differences in total CO₂ fixation between strains to be readily determined. From a culture of PCC 6803, it was found that the peak mg of CO₂ fixed per day is around 92 mg CO₂/day. In the future, the system can be modified to fit other simple dynamic gas systems, as well as testing similar gas utilization/production capabilities of other organisms.
ContributorsInnes, Sean (Author) / Nielsen, David (Thesis advisor) / Jones, Christopher (Committee member) / Varman, Arul Mozhy (Committee member) / Arizona State University (Publisher)
Created2022
Description
This project was completed to understand the evolution of the ability to digest wood in termite symbiotic protists. Lower termites harbor bacterial and protist symbionts which are essential to the termite ability to use wood as a nutritional source, producing glycoside hydrolases to break down the polysaccharides found in lignocellulose. Yet, only a few molecular studies have been done to confirm the protist species responsible for particular enzymes. By mining publicly available and newly generated genomic and transcriptomic data, including three transcriptomes from isolated protist cells, I identify over 200 new glycoside hydrolase sequences and compute the phylogenies of eight glycoside hydrolase families (GHFs) reported to be expressed by termite hindgut protists.
Of those families examined, the results are broadly consistent with Todaka et al. 2010, though none of the GHFs found were expressed in both termite-associated protist and non-termite-associated protist transcriptome data. This suggests that, rather than being inherited from their free-living protist ancestors, GHF genes were acquired by termite protists while within the termite gut, potentially via lateral gene transfer (LGT). For example one family, GHF10, implies a single acquisition of a bacterial xylanase into termite protists. The phylogenies from GHF5 and GHF11 each imply two distinct acquisitions in termite protist ancestors, each from bacteria. In eukaryote-dominated GHFs, GHF7 and GHF45, there are three apparent acquisitions by termite protists. Meanwhile, it appears prior reports of GHF62 in the termite gut may have been misidentified GHF43 sequences. GHF43 was the only GHF found to contain sequences from the protists not found in the termite gut. These findings generally all support the possibility termite-associated protists adapted to a lignocellulosic diet after colonization of the termite hindgut. Nonetheless, the poor resolution of GHF phylogeny and limited termite and protist sampling constrain interpretation.
Of those families examined, the results are broadly consistent with Todaka et al. 2010, though none of the GHFs found were expressed in both termite-associated protist and non-termite-associated protist transcriptome data. This suggests that, rather than being inherited from their free-living protist ancestors, GHF genes were acquired by termite protists while within the termite gut, potentially via lateral gene transfer (LGT). For example one family, GHF10, implies a single acquisition of a bacterial xylanase into termite protists. The phylogenies from GHF5 and GHF11 each imply two distinct acquisitions in termite protist ancestors, each from bacteria. In eukaryote-dominated GHFs, GHF7 and GHF45, there are three apparent acquisitions by termite protists. Meanwhile, it appears prior reports of GHF62 in the termite gut may have been misidentified GHF43 sequences. GHF43 was the only GHF found to contain sequences from the protists not found in the termite gut. These findings generally all support the possibility termite-associated protists adapted to a lignocellulosic diet after colonization of the termite hindgut. Nonetheless, the poor resolution of GHF phylogeny and limited termite and protist sampling constrain interpretation.
ContributorsSanderlin, Viola (Author) / Gile, Gillian H (Thesis advisor) / Wojciechowski, Martin (Committee member) / Weiss, Taylor (Committee member) / Varman, Arul Mozhy (Committee member) / Arizona State University (Publisher)
Created2019