Escherichia coli can contaminate food, such as beef and spinach, causing illnesses ranging from recurring diarrhea to death in susceptible individuals. They may produce a toxin typically associated with another harmful bacterium known as Shigella spp. This toxin is referred to as “Shiga-toxin”, and E. coli that produce this toxin are known as STECs. While E. coli O157 remains the most common STEC in the United States there are over 100 STECs that can be just as harmful. My project, conducted in collaboration with individuals at CSUEB and the USFDA, involves identifying chemical indicators that would help detect different strains of non-O157 E. coli in contaminated foods, and determining if these STECS are vulnerable to a coliphage and a Bdellovibrio sp. invasion. Specifically, nine different STECs were chosen to be screened for their ability to produce catecholate siderophores (phenolates), such as enterobactin, chelating compounds important for some pathogenic bacteria in the acquisition of iron. The same STECs were screened for the presence of acyl homoserine lactones, chemicals involved in bacterial communication, also known as quorum sensing, and expression of virulence factors. Assays were conducted to determine if a coliphage and a Bdellovibrio sp. can infect these STECs. Detection and identification of non-O157 STECS is not easy, which hinders determination of their origin and, subsequently, how to eliminate them. If new tools, such as the use of predators or chemical indicators were developed to facilitate detection of these bacteria, then determination of the source of contamination (e.g., packing plants and fields) may occur, and quicken measures that prevent or, at least, decrease further infection, disease and/or death.

Infection depends on the successful colonization of a host by a pathogen. For a virus to infect its host, it must come into contact with the host, gain entry into target cells, and replicate. There are a variety of factors that could influence the likelihood of a host becoming infected. For example, a higher concentration of virions in the environment will increase the probability that a host will come into contact with one. The relationship between viral concentration and the number of hosts infected could exhibit various forms, such as linear, logarithmic, or exponential. Viral genetic differences could also influence infectivity if certain genotypes are more effective at initiating infections. In this study we examined the relationship between dose size and the proportion of hosts infected by the fish rhabdovirus Infectious hematopoietic necrosis virus (IHNV), and whether this relationship differed between virus genotypes. We compared the minimum infectious dose of two genotypes, one with higher virulence (HV) and one with lower virulence (LV), to determine how infectivity is associated with virulence. Previous studies indicate that at 100% infection levels, HV reaches higher viral loads than LV, in addition to having a host entry advantage, but to our knowledge the minimum infectious dose of either genotype has not been investigated. We hypothesized that the more virulent genotype would have a lower minimum infectious dose. We infected groups of fish with 10¹, 10², 10³, 10⁴, and 2x10⁵ pfu/mL of one of the two genotypes. After allowing the virus three days to initiate an infection, the fish were euthanized and their viral RNA was extracted and counted with quantitative real-time PCR to determine whether each fish was infected. The information gained about infectious dose can be used to produce a more refined understanding of viral fitness, and thus, viral evolution.

Augmenting course material to be relevant and accessible to students is a ubiquitous challenge throughout academia. We aimed to design, develop, and evaluate the effectiveness of activities meant to promote the learning of difficult concepts in Anatomy and Physiology. More specifically, we focused on the neurophysiology chapter of an open access Anatomy and Physiology course sponsored by the Carnegie Mellon Open Learning Initiative (OLI). This course is being created for pre-nursing students attending community colleges. We used the six-level schema of Bloom’s Taxonomy, a module addressing the knowledge and development of intellectual skills, to design learning activities that encouraged students to analyze, synthesize, and evaluate concepts rather than simply recall, explain, and define them. By compelling students to work at higher cognitive levels during the learning process, we hypothesized that there would be a corresponding elevation in critical thinking skills and a deeper understanding of the material. Our curriculum design strategy was informed by cognitive science research that shows increases in learning efficacy when students are motivated to work at higher cognitive levels. Assessments were designed to align with these higher cognitive level learning activities. Our learning activities were tested by Anatomy and Physiology students using Carnegie Mellon’s OLI course. The Carnegie Mellon course uses an innovative digital dashboard platform which allowed us to track individual student’s understanding of concepts before, during, and after using our materials so that we were able to analyze their success and effectiveness. We revised our learning activities based on these results.

Where plankton reside in the water column is affected, among other things, by haloclines. Therefore the salinity stratification of the water can have major effects on the levels of plankton present. Our study focused on Possession Sound zooplanktons’ response to varying levels of salinity in a vertically stratified column. We questioned the preferred salinity level of various zooplankton found in a sample of Possession Sound water. We hypothesized that most zooplankton will prefer waters approximately 24 ppt since that is the average salinity of Possession Sound. We have so far looked at literature surrounding the subject and constructed the necessary apparatuses for the experiment. As part of our spring thesis research, we plan on observing the plankton’s response to the introduction to this environment.

Populations of P. menziesii on islands should exhibit reduced genetic diversity and canopy coverage, lower population age, increased reproductive succession and reduced understory species richness with respect to Mainland populations. Populations sampling within the same region and elavation should exhibit similar patterns. Seedling density as well as distribution of trees in multiple size classes and their diameter to height ratios were presented for each site. Species richness represented plant community structure and constituted of understory plants and percent coverage for each species within the plots. Genetic analysis consisted of laboratory analysis for selected individuals within the sites. Despite the vulnerability of small trees in establishment due to predation and greater sensitivity to environmental factors, high energetic costs to maintain large support structures of older trees create an additional unexpected source of vulnerability within the population. As genetic variation is component of successful reproductive succession and establishment, reduced variation in populations could result in greater sensitivity to more extreme environmental conditions as might be expected with climate change.

The acid-catalyzed dehydration of 4-methylcyclohexanol yields a mixture of several isomeric methylcyclohexene products. The major product of this elimination reaction, 4-methylcyclohexene, is produced through the E2 mechanism. However, mechanisms for the formation of the minor methylcyclohexene products are not predicted by the traditional textbook explanations of carbocation rearrangements. 1-methylcyclohexene is thought to be produced by means of an E1 mechanism in which rearrangement of a carbocation intermediate takes place. This experiment was designed to classify the hydride shifts by observing the products of this reaction using 1,2-²H-4-methylcyclohexanol. The deuterated starting materials for this reaction were prepared in our lab. Gas chromatography-mass spectroscopy and nuclear magnetic resonance analysis were used in the characterization of the products and for the classification of the pair of 1,2 hydryde shifts in tendem and of the single 1,3 di-axial hydride shift, leading to the formation of the 1-methylcyclohexene product. This is useful to know when trying to predict the products of reactions in which intermolecular rearrangements occur during carbocation intermediates.

Cues from predation can have strong effects on prey behavior and development, but antipredator responses can reduce fitness in other ways. Costly responses to predators should be, and often are, proportional to the level of risk (i.e., threat-sensitive); however, the mechanisms by which prey assess risk are not fully understood. In mesocosm experiments, red-eyed treefrogs (Agalychnis callidryas) show threat-sensitive growth reduction in response to predation cues from giant water bugs (Belostoma) and dragonfly naiads (Anax). We reared A. callidryas tadpoles from hatching in individual 400 ml microcosms in an open-air laboratory in Panama to assess their growth responses to variation in water-borne chemical cues from predation on conspecifics. In an experiment manipulating cue concentration, cues from predation by both Anax and Belostoma elicited a similar, dose-dependent reduction in growth. We then investigated effects of the frequency of chemical cueing by holding the total cue amount constant across treatments, but delivering it in fewer larger doses or more frequent smaller doses. We found a strong negative correlation between tadpole growth and the frequency of cue events. These results suggest that the frequency of predation cue events is more important than the biomass of prey consumed, or amount of cue delivered per event, for assessment of predation risk. This is consistent with results from mesocosm experiments wherein tadpoles responded more strongly to predation on small tadpoles, via multiple predation events, than they did to predation of an equivalent biomass of larger tadpoles.

Interspecific hybridization is common in flowering plants.  Hybrids tend to exhibit characteristics intermediate between both parents, and to grow more vigorously.  A novel specimen of the genus Heuchera (alumroot) found in a garden setting in Seattle is thought to be a hybrid between the commonly cultivated Heuchera sanguinea and the PNW native H. cylindrica.  In nature, H. cylindrica and H. sanguinea have non-overlapping geographic distributions.  Heuchera cylindrica is native to the western United States and Canada, whereas H. sanguinea is native to New Mexico and Arizona and it is not known if interbreeding between the two species is possible.  The unknown specimen in question shows intermediate characteristics of both species, which include flower color, inflorescence architecture and more vigorous growth.  To determine the relationship of the putative hybrid specimen with the two suspected parents, fixed differences in the Internal Transcribed Spacer (ITS) regions of nuclear ribosomal DNA of H. cylindrica and H. sanguinea were compared .  ITS regions were amplified using PCR and were then sequenced.  The results were edited, assembled and aligned to look for differences in the parents' ITS regions.  The differences in the parents' ITS regions are present in combination in the unknown specimen's DNA and shows that it is the hybrid of H. cylindrica and H. sanguinea.  A further test, using the maternally inherited chloroplast genome (cpDNA), was conducted in a similar fashion, with the expectation that the putative hybrid should contain the cpDNA of the species that is the maternal parent.

Routine ingestion of, and contact with, myriad chemical compounds in our environment impacts all aspects of human health, from psychiatric to oncological to acute and chronic toxicities. However, health outcomes resulting from exposure events are strongly influenced by genetic variability present in genes underlying pertinent metabolic pathways. There are four genes that have been identified in the literature as playing crucial roles in multiple and interrelated biochemical pathways, and which may have broad implications for human health. These genes include DRD4, which codes for the dopamine D4 receptor and has been linked to numerous neurological conditions including addictions, schizophrenia, bipolar disorder, and Parkinson’s disease; 5-HTTLPR, the serotonin-transporter-linked region that codes for the serotonin receptor and may be involved in a host of behaviors including affective disorders and addictions; CYP2E1, a member of the cytochrome P450 family involved with the metabolism of many endogenous and exogenous chemicals including ethanol; and GSTT1, which is involved with the metabolism of toxic compounds including many carcinogens. In order to offer an accessible advanced preventative health screening tool to patients addressing numerous potential conditions, we attempted to implement a multiplexed polymerase chain reaction that would allow us to simultaneously assay these four genetic variants. We were able to combine the GSTT1 and CYP2E1 assays into a single reaction, however we were unable to find compatible reaction conditions for 5-HTTLPR and DRD4 either together or with GSTT1 and CYP2E1.