In 1960, Graham Higman postulated that the number of conjugacy classes of the group of Unitriangular Matricies of size n over F_q is polynomial with respect to q. To better understand these groups, we explored the group of Unitriangular Matricies of size n over F_2. In particular, we sought to understand the relationship between such matricies and the set of simple graphs on n verticies. The relationship between these two sets defines a multiplication between the edge sets of simple graphs on n verticies. Hence, we awnser the following question: if G_X=([n],E_X) and G_Y=([n],E_Y) then what is G_XY=([n],E_XY)?

Bottom water hypoxia is a feature of many coastal embayments and fjords in the Salish Sea. Ongoing research in Bellingham Bay (Bellingham, WA USA) has identified a seasonally recurring area of low dissolved oxygen near the center of the Bay. Similar to other regions of the Salish Sea, hypoxia in Bellingham Bay may be a naturally occurring phenomenon, yet the extent of eutrophication and influence of anthropogenic nutrient loading on patterns of regional hypoxia is poorly understood. The present study has continued an established monitoring program documenting the range, duration, and severity of low dissolved oxygen in Bellingham Bay in the summers of 2013-2015, while adding an experimental component investigating factors that regulate respiration in the water column. Results suggest the displacement of an oxygen-depleted layer of bottom water in the bay is strongly correlated with spring-neap tidal cycling. In 2015, anomalously low river discharge and high temperatures may have also contributed to the lowest observed oxygen concentrations in our record (1.2 mg/L O2). In addition, manipulative experiments were conducted to investigate factors regulating oxygen consumption in bottom waters. Organic matter availability appears to be a prominent limiting factor to Bellingham Bay oxygen consumption, and ongoing research is investigating whether shifts in the resident phytoplankton community may affect the quality of carbon available for respiration. The study’s findings broaden our knowledge of factors regulating the consumption of oxygen in bottom waters of the Pacific Northwest and provide insight into the effects of organic carbon delivery and climate change.

As our planet warms, organisms that cannot migrate to more suitable habitats will be forced to adapt to the increasing temperatures or face extinction. An important question to address is how the rate of environmental change affects an organism’s chance to adapt. If an environment changes suddenly, then organisms must also adapt rapidly, whereas slower rates of change allow the organism more time to adapt. Microorganisms, such as the virus phi-6, can be utilized to answer this question because they evolve rapidly, allowing us to watch evolution in real time. We evolved phi-6 over 11 weeks to survive high temperatures. In different treatments, the viruses experienced sudden, moderate, or gradual changes in temperature. Sequencing the evolved lineages at two genes revealed multiple mutations. We added the mutations one by one to the ancestor to determine how each mutation affects thermotolerance. We find that each mutation can increase or decrease thermotolerance by a different amount. Interestingly enough, mutations that give the greatest increase in thermotolerance appeared in viruses that experienced slower temperature change. There is also a trend where viruses that experienced slower temperature change had more mutations per lineage than viruses that experienced sudden change in temperature. My results demonstrate that rate is an important parameter when taking adaptation into consideration. If the temperature increases too rapidly, there may be fewer ways for organisms to adapt, and they are unlikely to survive climate change.

The B-class genes of the ABCE model of floral development are necessary for the initiation of petal and stamen development in Arabidopsis thaliana (a core eudicot). Loss of B-class function results in homeotic conversions of petals to sepals and stamens to carpels, resulting in a female flower. All ABCE genes are activated by LEAFY (LFY), a master regulator of floral development. The F-box protein, UNUSUAL FLORAL ORGAN (UFO) is a co-factor of LFY, necessary for transcriptional initiation of the APETALA3 (AP3) lineage genes; a subset of the B-class. In the model plant Arabidopsis, the UFO mutant phenotype strongly resembles classical B-class mutants confirming UFO’s role as a regulator of AP3 genes. Although the function of the AP3 genes has been investigated in a wide variety of flowering plants, little is known about UFO outside of the core eudicots and rice. In order to gain a deeper understanding of the evolution of AP3 regulation, we are investigating the function of the UFO ortholog in flowers of the early-diverging eudicot Thalictrum thalictroides (in the buttercup family) using Virus Induced Gene Silencing (VIGS). Unlike many core eudicots which only have one AP3 homolog, T. thalictroides has three copies that arose from recent duplication events. We have previously shown that these three paralogs have a partially redundant role in stamen identity and in petaloidy of T. thalictroides sepals. We predict that the down-regulation of ThtUFO will result in a B-class mutant phenotype equivalent to a full ThtAP3 mutant knock-down. By studying ThtUFO and its effect on petal and stamen identity genes in an early diverging eudicot we hope to gain a deeper understanding of the implications of gene regulatory evolution on floral morphology.

Bacterial endocarditis is an infection on the inner lining of the heart. When studying bacterial adhesion, researchers often ignore that blood is pumped through the heart in a pulsatile manner. Because of this, all studies have been done with constant flow. We hypothesize that pulsatile flow conditions play a critical role in this disease. We studied how Streptococcus gordonii, a strain of bacteria that is known to cause bacterial endocarditis, bound in constant and pulsatile flow. The rate of adhesion in both constant and pulsatile flow was measured at different shear stresses. When suspended in buffer, the bacteria bound at the same rate in both flow conditions. The overall trend showed the rate of bacterial adhesion was highest at 10 dyne/cm². At the shear stresses predicted to be present within the heart, 20 – 80 dyne/cm², only about 10% of bacteria bound as compared to the peak value. In a solution with 50% buffer and 50% red blood cells (RBCs), the percentage commonly found in the blood, there was a dramatic change in the trend of bacterial adhesion in constant flow. Instead of having a peak value, the rate of adhesion increased with the level of shear stress, allowing for a much higher rate of binding in the 20 – 80 dyne/cm² range. We were unable to repeat this experiment using pulsatile flow due to limitations in our flow device but this could mean a dramatic change in the trend observed in pulsatile flow as well. We have created a new device to further investigate our hypothesis and better simulate the conditions found in the heart.

Antibodies play a critical role in our health system, adding specificity to diagnostics and therapeutics with their strong binding capabilities. Unfortunately, the binding cannot be controlled over time, introducing contamination of the target and preventing further testing with the bound sample. We propose an alternative to antibodies: a switchable binding protein. This protein has affinity for its binding target which can be modulated by environmental change without directly altering the binding site, otherwise known as allosteric regulation. This presents the potential to later change the binding target to a medically relevant antigen. A binding protein FimH, found on the end of bacteria pili, was used as the scaffold for the design because its binding depends on a significant structural change. I predict that if this protein is locked in place with a cross-linker or covalent bond, which experiences a large structural change under a simple external stimulus, FimH binding could be precisely triggered. Inserting a disulfide bond or a photoswitchable linker are two methods I am investigating with their binding triggers being dithiothreitol (DTT) and ultra-violet (UV) light, respectively. The photoswitchable linker design is ideal because it would induce reversible binding, allowing for reuse of our protein. Using past structural knowledge, multiple mutation designs are being created and their binding tested under external stimulus. The design requires mutation placed far from the binding site in order to create this allosteric switch. Initial results indicate the design with a disulfide bond between residues 112 and 189 does switch binding affinity, triggered to unbind, when DTT is added. This research also has the potential to contribute a novel approach to regulating large proteins and add specificity in diagnostics by concentrating the target.