Oceanic life is facing the deleterious aftermath of coral bleaching. To reverse the damages introduced by anthropological means, it is imperative to study fundamental properties of corals. One way to do so is to understand the metabolic pathways and protein functions of corals that contribute to the resilience of coral reefs. Although genomic sequencing and structural modeling has yielded significant insights for well-studied organisms, more investigation must be conducted for corals. Better yet, quantifiable experiments are far more crucial to the understanding of corals. The objective is to clone, purify, and assess coral proteins from the cauliflower coral species known as Pocillopora damicornis. Presented here is the pipeline for how 3-D structural modeling can help support the experimental data from studying soluble proteins in corals. Using a multi-step selection approach, 25 coral genes were selected and retrieved from the genomic database. Using Escherischia coli and Homo sapiens homologues for sequence alignment, functional properties of each protein were predicted to aid in the production of structural models. Using D-SCRIPT, potential pairwise protein-protein interactions (PPI) were predicted amongst these 25 proteins, and further studied for identifying putative interfaces using the ClusPro server. 10 binding pockets were inferred for each pair of proteins. Standard cloning strategies were applied to express 4 coral proteins for purification and functional assays. 2 of the 4 proteins had visible bands on the Coomassie stained gel and were able to advance to the purification step. Both proteins exhibited a faint band at the expected migration distance for at least one of the elutions. Finally, PPI was carried out by mixing protein samples and running in a native gel, resulting in one potential pair of PPI.

The incidence of childhood obesity has become increasingly prevalent in the United States in recent years. The development of obesity at any age, but especially in adolescence, can have lasting negative effects in the form of cardiometabolic disease, increased incurred healthcare costs, and potential negative effects on quality of life. In recent years, a rising trend of obesity, in both adults and adolescents, has been observed in lower income and ethnic groups. Increased adiposity can be influenced by modifiable factors -(physical activity, caloric intake, or sleep) or by non-modifiable factors (ethnicity, genetic predispositions, and socioeconomic status). The influence of these factors can be observed in individuals of all ages, including infants. A common indicator of the development of childhood obesity is rapid weight gain (RWG) within an infant’s first year of life. The composition of the gut microbiome can act as a predictor for RWG and the development of childhood obesity. Infants are exposed to an immense microbial load when they are born and their gut microbiome is continually diversified through their method of feeding and the subsequent introduction to solid foods. While currently understudied, it is understood that cultural and socioeconomic factors influence the development of the gut microbiome, which is further explored in this analysis. The DNA from 51 fecal samples from infants ranging from 3 weeks to 12 months in age was extracted and sequenced using next-generation sequencing, and the resulting sequences were analyzed using QIIME 2. Results from alpha-diversity and beta-diversity metrics showed significant differences in the gut microbiome of infants when comparing groups based on baby race/ethnicity, household income, and mom’s education. These findings suggest the importance of sociodemographic characteristics in shaping the gut microbiome and suggest the importance of future studies including diverse populations in gut microbiome work.

The objective of this study is to create a spectrophotometric assay that can measure quinone reduction in the HbRC. The key techniques used in the project consisted of a PCR, a pseudo golden gate, a transformation into E. coli, a conjugation into Heliomicrobium modesticaldum, a growth study, a HbRC prep, and absorbance spectroscopy. PCR was crucial for amplifying the Cyt c553-PshX gene for the pseudo golden gate. The pseudo golden gate ligated Cyt c553-PshX into the plasmid pMTL86251 in order to transform the plasmid with the desired gene into the E. coli strain S17-1. This E. coli strain allows for conjugation into H. modesticaldum. H. modesticaldum cannot uptake DNA by itself, so the E. coli creates a pilus to transfer the desired plasmid to H. modesticaldum. The growth study was crucial for determining if H. modesitcaldum could be induced using xylose without killing the cells or inhibiting the growth in such a way that the project could not be continued. The HbRC prep was used to isolate and purify the Cyt c553-PshX protein. Absorbance spectroscopy and JTS kinetic assay was used to characterize and confirm that the protein eluted from the affinity column was Cyt c553-PshX. The results of the absorbance spectra and JTS kinetic assay confirmed that Cyt c553-PshX was not made. The study is currently being continued using a new system that utilizes SpyCatcher SpyTag covalent linkages in order to attach cytochrome to reduce P800 to the HbRC.

Hybrid metalloproteins incorporating synthetic organometallic active sites within a protein scaffold are being researched as viable catalysts for the production of hydrogen fuel. Our group and others have shown that the incorporation of cobalt protoporphyrin IX in cytochrome b₅₆₂ yields artificial enzymes that reduce protons to molecular hydrogen in the presence of photoinductive light and photosensitizers. Using random mutagenesis via error-prone PCR we have created a library of mutants to use in directed evolution to optimize hydrogen catalysis, though a challenge in this project is that testing individual variants by gas chromatography is not feasible on a large scale. For this reason, we are developing a gasochromic, hydrogen assay that is based on the interaction of molecular hydrogen with tungsten trioxide with a palladium catalyst. Initially, results show this assay to be qualitatively accurate between trials; however, its application in screening remains a challenge.

This thesis is about how Fe catalysts can be degraded using photocatalysis and how Fe catalysts can degrade small molecules in conjunction with light. The goal of this paper is to look further into more sustainable methods of organic chemistry. Many current organic chemistry practices involve the use of precious metals. Iron is a more sustainable catalyst because it is abundant and inexpensive which is important for preserving the earth and making the organic chemistry more accessible. Along the same lines, light is a renewable energy source and has demonstrated its ability to aid in reactions. Overall, the goal of this paper is to explore the more sustainable alternatives to harsh and toxic organic chemistry practices through the use of Iron and light.