The bristlenose pleco (Ancistrus cirrhosus) is a species of armored catfish in the Loricariidae family that breathes air facultatively when the aquatic environment becomes hypoxic. The bristlenose pleco uses its highly vascularized stomach as an air breathing organ. The two main goals of this developmental study were to determine the size of onset of air breathing and to determine the frequency of air breathing behavior in bristlenose plecos from juveniles to adults. Developing juveniles reach functional maturity within four to six months of hatching and grow to an adult size of eight to ten cm in length. To examine the developmental timing for the onset of air breathing, we tested different sized juveniles beginning at one cm up until 8 cm in length. The developmental timing for the onset of air breathing was measured by exposing each fish to a slowly decreasing aquatic oxygen content from 100% air saturation down to 8% air saturation. Fish were first able to breathe air at just over 2 cm and 1 gram in mass. There was a weak negative correlation between fish length and % air saturation at which air breathing began. When exposed to 15% air saturation, frequency of air breathing was …

The anti-S2 peptides, the stabilizer and destabilizer, were designed to target myosin sub-fragment 2 (S2) in muscle. When the peptides are coupled to a heart-targeting molecule, they can reach the cardiomyocytes and interfere with cardiac muscle contraction. Monoclonal antibodies, MF20 and MF30, are also known to interact with light meromyosin and S2 respectively. The MF30 antibody compared to anti-S2 peptides and the MF20 antibody is used as a control to test the central hypothesis that: Both the anti-S2 peptides and antibodies bind to myosin S2 with high affinity, compete with MyBPC, and possibly interact with titin, in which case the anti-S2 peptides have further impact on myosin helicity and reach the heart with the aid of tannic acid to modulate cardiomyocytes' contraction in live mice. In this research, the effects of anti-S2 peptides and antibodies on myosin S2 were studied at the molecular and tissue levels. The anti-myosin binding mechanism to whole myosin was determined based on total internal reflectance fluorescence spectroscopy (TIRFS), and a modified cuvette was utilized to accommodate this experiment. The binding graphs indicated the cooperative binding of the peptides and antibodies with high affinity to myosin. Anti-myosin peptides and antibodies competition with Myosin Binding Protein C …

Here, we show that training with multiple noncommunicable diseases (NCDs) is both feasible and beneficial to modeling this class of diseases. We first use data from the Cancer Genome Atlas (TCGA) to train a pan cancer model, and then characterize the information the model has learned about the cancers. In doing this we show that the model has learned concepts that are relevant to the task of cancer classification. We also test the model on datasets derived independently of the TCGA cohort and show that the model is robust to data outside of its training distribution such as precancerous legions and metastatic samples. We then utilize the cancer model as the basis of a transfer learning study where we retrain it on other, non-cancer NCDs. In doing so we show that NCDs with very differing underlying biology contain extractible information relevant to each other allowing for a broader model of NCDs to be developed with existing datasets. We then test the importance of the samples source tissue in the model and find that the NCD class and tissue source may not be independent in our model. To address this, we use the tissue encodings to create augmented samples. We test …

PCBs are synthetic organic compounds known for their toxicity to many organisms and are notorious for having large discrepancies between measured and nominal concentrations. Historically thought to be less toxic, non-dioxin-like (NDL) PCBs represent the majority of congeners and are capable of eliciting neurotoxic effects. NDL-PCBs remain understudied, including their effects on aquatic organisms. In the first study, I collected extensive chemistry data and data on neurobehavioral and cardiac endpoints to test the acute effects of exposure to an NDL-PCB mixture on early life stage zebrafish. Neurobehavioral effects observed in the first study indicated a potential for longer term behavioral effects in these fish. In the second study, I collected data on feeding, social, and memory behavior of zebrafish at time points beyond the acute exposure from the first study. Acute and longer-term behavioral endpoints in the first and second studies demonstrated effects from PCB exposure but did not indicate mechanisms. In the third study, I collected untargeted and targeted metabolomic data on amino acid, sugar, anionic compound, and neurotransmitter profiles to determine the specific pathways affected by exposure to an NDL-PCB mixture. These combined data from these studies provide a unique insight into the chemical profile of an NDL-PCB …

Hypoxia as a stressor has physiological implications that have been a focal point for many physiological studies in recent years. In some studies, hypoxia had large effects on the organ tissue degeneration, which ultimately effects multiple ecological processes. These organ tissue studies played a part in the development of new fields like neurocardiology, a specialty that studied the relationship between the brain and the heart. This thesis focuses on how hypoxia-induced cardiac arrest alters the amounts of GLYT2, a glycine reuptake transporter, in the central nervous system of zebrafish, Danio rerio. At 7 days post-fertilization (dpf), zebrafish were exposed to acute, severe hypoxia until they lost equilibrium, and minutes later, subsequent cardiac arrest occurred. Zebrafish were then placed into recovery groups to measure the GLYT2 levels at multiple points in zebrafish recovery. Fish were then sacrificed, and their brains dissected. Using immunofluorescence, the outer left optic tectum of the zebrafish was imaged, and mean image pixel fluorescent intensity was taken. There were significant changes (one-way ANOVA) in the levels of GLYT2 compared to that of the control groups during the course of recovery. GLYT2 levels continued to rise through the 24-hour recovery mark but did not show significant difference after …

In this dissertation I am using M. truncatula as a model legume that forms indeterminate nodules with rhizobia under limited nitrogen conditions. I take advantage of an M. truncatula Tnt1 mutant population that provides a useful resource to uncover and characterize novel genes. Here, I focused on several objectives. First, I carried out forward and reverse genetic screening of M. truncatula Tnt1 mutant populations to uncover novel genes involved in symbiotic nitrogen fixation. Second, I focused on reverse genetic screening of two genes, identified as encoding blue copper proteins, and characterization of their mutants' potential phenotypes. Third, I further characterized a nodule essential gene, M. truncatula vacuolar iron transporter like 8 (MtVTL8), which encodes a nodule specific iron transporter. I characterized the expression pattern, expression localization and function of MtVTL8. Additionally, I characterized several residues predicted to be essential to function using a model based on the known crystal structure of Eucalyptus grandis vacuolar iron transporter 1 (EgVIT1), a homologous protein to MtVTL8. I identified several potential essential residues of the MtVTL8 protein, mutagenized them, and through complementation experiments in planta and in yeast assessed functionality of the resulting protein. This helped us to better understand the potential mechanism by …

The Nit1C cluster is a conserved gene cluster of seven genes that confers bacterial growth on cyanide as the sole nitrogen source. Bacteria with this ability are referred to as cyanotrophs. To date, the linkage between Nit1C and cyanotrophy has only been demonstrated for environmental isolates but the cluster also exists in certain medically related bacteria. In this study, a nosocomial isolate, Acinetobacter haemolyticus ATCC 19194, carrying Nit1C also displayed the ability to grow on cyanide. Growth on cyanide was accompanied by the induction of the cluster as was the mere exposure of cells to cyanide. Expression of the cluster was determined by measuring the activity of the nitrilase (NitC) coded for by the cluster and by transcriptional analysis (qRT-PCR). However, a disconnect between nitC message and NitC protein was observed depending on the phase of the growth cycle, the disconnect being related to proteolytic digestion of the NitC protein. Ironically, the cluster was also discovered to be upregulated in the absence of cyanide under nitrogen starvation conditions paralleling biofilm formation. The basis of the genetic linkage to cyanotrophy is not understood but taken together with results showing that nitrogen starvation and biofilm formation are also physiologically associated with Nit1C …

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental toxicants found in anthropogenic mixtures such as crude oil, air pollution, vehicle exhaust, and in some natural combustion reactions. Single PAHs such as benzo[a]pyrene (BaP) also impact fish behavior when animals are exposed in early life stages and for short periods of time. Aquatic animals such as fish may encounter BaP through road runoff and oil spills, but few studies have examined the impact of aqueous exposure on adult fish, and fewer have examined the resulting fitness-relevant behavioral consequences of BaP and PAH mixtures and their long-term persistence. This dissertation targets this gap in the literature by examining how aqueous exposure to BaP influences anxiety-like behavior, learning, and memory in adult zebrafish, and how parental exposure to the PAH mixture, crude oil, combined with hypoxia affects social and exploratory behavior in unexposed larval zebrafish. We found that learning and memory were not affected by 24 hour exposure to BaP, that anxiety-like behavior was minimally affected, and that locomotor parameters such as distance moved and times spent in darting and immobile states were significantly altered by exposure to BaP. Additionally, we found that parental exposure to crude oil and hypoxia decreased larval velocity. Additionally, …

The change of land use to include more urban areas is considered one of the main threats to biodiversity worldwide. Urban stormwater retention ponds have been built to collect storm runoff intensified by the increase in impervious surfaces. Although subject to environmental pressures like habitat degradation and pollution, these stormwater retention ponds are diversity hotspots by providing habitat for several aquatic and semi-aquatic species, including dragonflies. Previous research in Denton, Texas, has demonstrated that urban stormwater retention ponds support high taxa richness of adult dragonflies, but not for the aquatic nymphs. The current study builds on what we have seen by focusing on the immature aquatic stage as nymphs using secondary production of dominant dragonfly taxa and community structure to compare ecosystem function in three ponds with differing intensities of land use. Comparing communities and secondary production resulted in specific conductivity, dissolved oxygen, complex vegetation, and abundance explaining the differences between dragonfly communities. Secondary production was dependent on abundance which followed the intensity of urban land use surrounding the pond. This study supports that urban land use does have an effect on the functioning of the ponds and shows the importance of studying the communities over a year to get …