The transcriptome of an organism is a collection of the various messenger RNAs that the genes of an organism produce. As the level of gene expression is different between different tissues of an organism, understanding the transcriptome serves as a way to better understand the differences between the functions and abilities of tissues and cells in an organism. This understanding of the transcriptome can aid further research in targeted disease treatments and indentifying new biomarkers. This study aims to gather the transcriptome from various tissues of the organism Daphnia pulex. This will be done by using a combination of single cell RNA sequencing (scRNA-seq), which involves the isolation and sequencing of single cells, and single nuclei RNA sequencing (snRNA-seq), which involves the isolation and sequencing of single nuclei. Here we show the viability of isolating single cells and single nuclei from various Daphnia pulex tissues using different techniques and enzymes including trypLE, trypsin EDTA, accutase, etc by using microscopy and automatic cell counting. The results show that each tissue is best isolated using different techniques.

Model organisms like Homo sapiens, Drosophila, and E. coli, while useful to various fields of study, present a problem to the scientific community: many other organisms’ proteins, metabolic processes, and biochemical mechanisms are not as well understood by comparison. Pocillopora damicornis (Pdam), like many other coral organisms, faces environmental stresses and threats to its survival in ocean ecosystems with limited understanding of its biochemical mechanisms, making it difficult to help preserve. However, upon analyzing the symbiotic relationship of Pdam and photosynthetic algae, it was reasoned that the coral organism is capable of detecting light. Following up with results of prior bioinformatics analysis courtesy of Kumar, L., Klein-Seetharaman, J., Et. Al, it was proposed that light sensitive proteins in corals are the following four candidates: 2270, 12246, 629, 19775. If chromophores form and their opsin shifts can be visualized in the case in any of the coral candidate opsin genes, it supports the hypothesis that the proteins are indeed a light sensitive opsin protein. If a light sensitive opsin protein is identified, it provides a direction by which efforts can be directed towards to understand corals at the biochemical level for their preservation in the face of unprecedented threats to sustainability.

Quantifying halogen presence and speciation in particulate matter is crucial given the role atmospheric particulates play in transport and cycling. While some halogens (fluorine and chlorine) are often included in aerosol studies, iodine and bromine have rarely been examined, especially outside of a marine environment. Focus on this environment is, in part, due to the existence of biogenic marine sources for both halogens. However, examining iodine and bromine in an urban environment has the potential to provide key insights into the transport and processing of these species in the atmosphere. As Tempe is set within a desert environment, bromine concentration is expected to be relatively high due to its presence in Earth’s crust, while iodine is expected to exist in higher concentrations near the coast. To detect presence and concentration, ICP-MS analysis was performed on samples taken in Tempe, AZ as well as sites in Bakersfield, CA and Davis, CA, which yielded preliminary results in line with these expectations. A secondary set of samples were taken in Tempe, AZ during dust storms, haboobs, and winter holidays. CIC was used to determine the organic fraction. In doing so, this study aims to identify species present in an urban environment as well as potential transportation pathways.

Lab-grown food products of animal cell origin, now becoming popularly coined as, ‘Cellular Agriculture’ is a revolutionary breakthrough technology that has the potential to penetrate the lives of every American or citizen of the world. It is important to recognize that the impetus for developing this technology is fueled by environmental concerns with climate change, rising geopolitical instability, and population growth projections, where farm-grown food has now become a growing national security issue. Notwithstanding its potential, in addition to the necessary technological innovation and economic scalability, the market success of cellular agriculture will depend greatly on regulatory oversight by multiple government agencies without which it can cause undue harm to individuals, populations, and the environment. Thus, it is critical for those appropriate United States governing bodies to ensure that the technology being developed is both safe and of an acceptable quality for human consumption and has no adverse environmental impact. As such, animal foods, derived from farms, previously regulated almost exclusively by the United States Department of Agriculture (USDA) are now being regulated under a joint formal agreement between the US Food and Drug Administration (US FDA) and the USDA if derived from the lab, i.e., lab-grown animal foods. The main reason for joint oversight between the FDA and the USDA is that the FDA has developed the in-house expertise to oversee primary cell harvesting and cell storage, as well as, cell growth and differentiation for the development of 3D-engineered tissues intended for tissue and organ replacement for the emerging field of regenerative medicine. As such, the FDA has been given the authority to oversee the ‘front end’ of lab-grown food processes which relies on the very same processes utilized in engineered human tissues to produce food-grade engineered tissues. Oversight then transitions to the USDA-FSIS (Food Safety and Inspection Service) during the harvesting stage of the cell culture process. The USDA-FSIS then oversees the further production and labeling of these products. Included in the agreement is the understanding that both bodies are responsible for communicating necessary information to each other and collaboratively developing new regulatory actions as needed. However, there currently lacks clarity on some topics regarding certain legal, ethical, and scientific issues. Lab-grown meat products require more extensive regulation than farm-grown animal food products to ensure that they are safe and nutritious for consumption. To do this, CFSAN can create new classes of lab-grown foods, such as ‘lab-grown USDA foods,’ ‘lab-grown non-USDA foods,’ ‘lab-grown extinct foods,’ ‘lab-grown human food tissues,’ and ‘medically activated lab-grown foods.’

The structure of this project will open with the dangers posed by inadequate screening techniques to both individuals with Body Dysmorphic Disorder and their plastic surgeons. This discussion will be followed by a summary of the existing mental health screenings implemented in plastic surgery clinics and their limitations. The assessments that will be examined include The Body Dysmorphic Disorder Examination, The Body Dysmorphic Disorder Examination - Self-Report, The Cosmetic Procedure Screening Questionnaire, The Yale-Brown Obsessive-Compulsive Scale Modified for Body Dysmorphic Disorder, and The Body Dysmorphic Disorder Questionnaire. These screening techniques were chosen based on a multitude of factors: frequency of use in psychiatric and cosmetic settings, innovation of screening methodology, and significance of studies that utilize the assessments. After describing the screening techniques, there will be a brief discussion of the limitations of developing a screening method for Body Dysmorphic Disorder, along with suggestions for methodology in future research. This thesis will demonstrate that no existing screening method for Body Dysmorphic Disorder in aesthetic surgery is flawless. Still, future research efforts should investigate combining questionnaires and clinical interviews to screen for the disorder within clinics efficiently and more reliably.

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.

This paper examines the physics behind cancer treatment and more specifically radiation therapy. A phenomenon known as Compton scattering has played a substantial role in the treatment of breast cancer and improvement of lives of women around the world. Through Compton scattering, radiation therapy has been tremendously improved and has allowed for the most accurate and effective treatment in breast cancer patients today.

Bdellovibrio bacteriovorus (B. bacteriovorus) is a predatory bacterium that preys on other gram-negative bacteria. In order to survive and reproduce, B. bacteriovorus invades the periplasm of other bacterial cells creating the potential for it to act as a “living antibiotic”. In this work, a comparison was made between the rates of predation of B. bacteriovorus in vitro and in vivo. In vitro, the behavior of B. bacteriovorus was examined in the presence of prey. In vivo, the behavior of B. bacteriovorus was examined in the presence of prey and a living host, Caenorhabditis elegans (C. elegans). C. elegans were infected with Escherichia coli (E. coli) and treated with B. bacteriovorus. In previous studies that analyzed B. bacteriovorus in vitro, a decrease in concentrations of bacteria has been observed after introduction of B. bacteriovorus. In vivo, B. bacteriovorus were found to not have a net reduction of E. coli but to reproducibly raise the level of fluctuations in E. coli concentrations.

There are limited methods and techniques to quantitatively assess protein content in single cells or small cell populations of tissues. The standard protein insulin was used to understand how potential changes in the preparation or co-crystallization process could improve sensitivity and limit of detection through matrix assisted laser desorption ionization (MALDI) mass spectrometry analysis in Bruker’s Microflex LRF using polydimethylsiloxane (PDMS) reservoirs. In addition, initial imaging tests were performed on Bruker’s RapifleX MALDI Tissuetyper to determine the instrument’s imaging capabilities on proteins of interest through the use of a single layer “Christmas tree” microfluidic device, with the aim of applying a similar approach to future tissue samples. Data on 2µM insulin determined that a 95% laser power in the Microflex corresponded to 12-15% laser power in the RapifleX. Based on the experiments with insulin, the process of mixing insulin and saturated ɑ-Cyano-4-hydroxycinnamic acid (HCCA) matrix solvent in a 1:1 ratio using 10mM sodium phosphate buffer under area analysis is most optimized with a limit of detection value of 110 nM. With this information, the future aim is to apply this method to a double layer Christmas tree device in order to hopefully quantitatively analyze and image protein content in single or small cell populations.