The amphibian pathogen Ambystoma Tigrinum Virus (ATV) has been an important topic of study within the amphibian community since its discovery. ATV threatens many salamander populations across the US, including those in east-central and southeast Arizona. These populations remain at risk since there are no treatments available. In this thesis, a novel method of inactivation is tested to produce a vaccine with the aim of safely eliciting an immune response within the salamander host. This novel form of inactivation has been tested on several human pathogens but has yet to be used on amphibian pathogens. It has the potential to revolutionize our traditional approach to inactivating viruses. After laser treatment, viral plaque assays suggested that inactivated ATV ceased to grow completely, pointing to the possibility of creating a vaccine. Animal challenge trials were conducted with 60 juvenile Ambystoma tigrinum, but surprisingly there was no protective effect from viral inactivation. Further study is needed to clarify why in vitro and in vivo tests of viral inactivation produced contradictory results.

Infectious disease in wild animals has historically been a challenge that is difficult to overcome, primarily because isolating a disease outbreak to prevent further transmission in these types of populations is nearly impossible. Wild animals are free to roam, and humans often have limited means of tracking infection in populations. Vaccines and treatments can be formulated but are often somewhat impractical for wild populations because it is not feasible to vaccinate or treat every member in a susceptible community. One such pathogen, Batrochochytrium dendrobatidis (Bd) is infecting amphibian populations around the world to the point where many species are already extinct. Even though finding an effective preventative for the fungal pathogen may not mean that I am able to reach every member in a population, it may mean the difference between extinction and eventual release back into the wild for threatened populations.
In this study I hoped to create an attenuated version of Batrochochytrium dendrobatidis, by using a novel laser technology: SEPHODIS. This laser technology disrupts hydrogen bonds between proteins in the lumen of the cell while simultaneously preserving the membrane and associated proteins on the outside of the cell. This process ultimately affects the pathogenicity of the target but leaves identity markers intact so that the host immune system may recognize the pathogen and create antibodies against it. The laser was ultimately effective at killing Bd fungal cells, and I did observe a significant change in the appearance of the cells. However, samples obtained after exposure to the laser were contaminated and more research is needed to determine if SEPHODIS could be a feasible method for vaccine production.

Amphibians around the world are suffering the effects of the chytrid fungus, Batrachochytrium dendrobatidis (Bd). Whenever amphibians are housed in captivity, they must go through a decontamination protocol to ensure they are not infected with diseases such as Bd. Itraconazole is the most commonly used fungicide used in these protocols. This study set out to determine if Bd could develop resistance or tolerance to itraconazole. Two 24 well plates were prepared with different concentrations of itraconazole with Bd zoospores added. Plate 1 had concentrations similar to what animals are currently being treated with in decontamination protocols. Plate 2 had concentrations at and below the published minimum inhibitory concentration values (MIC). Plate 1 displayed the ability of itraconazole to kill Bd sporangia with higher concentrations and Plate 2 showed that even under published MIC values, Bd still struggled to complete its reproductive cycle. I find the evolution of a resistant/tolerant strain of Bd unlikely given the efficacy of this drug, the sensitivity of Bd to itraconazole, and the lack of evidence of the completion of Bd’s reproductive cycle under the conditions used in this study.

Guided by Tinto’s Theory of College Student Departure, I conducted a set of five studies to identify factors that influence students’ social integration in college science active learning classes. These studies were conducted in large-enrollment college science courses and some were specifically conducted in undergraduate active learning biology courses. Using qualitative and quantitative methodologies, I identified how students’ identities, such as their gender and LGBTQIA identity, and students’ perceptions of their own intelligence influence their experience in active learning science classes and consequently their social integration in college. I also determined factors of active learning classrooms and instructor behaviors that can affect whether students experience positive or negative social integration in the context of active learning. I found that students’ hidden identities, such as the LGBTQIA identity, are more relevant in active learning classes where students work together and that the increased relevance of one’s identity can have a positive and negative impact on their social integration. I also found that students’ identities can predict their academic self-concept, or their perception of their intelligence as it compares to others’ intelligence in biology, which in turn predicts their participation in small group-discussion. While many students express a fear of negative evaluation, or dread being evaluated negatively by others when speaking out in active learning classes, I identified that how instructors structure group work can cause students to feel more or less integrated into the college science classroom. Lastly, I identified tools that instructors can use, such as name tents and humor, which can positive affect students’ social integration into the college science classroom. In sum, I highlight inequities in students’ experiences in active learning science classrooms and the mechanisms that underlie some of these inequities. I hope this work can be used to create more inclusive undergraduate active learning science courses.

Evolution is the foundation of biology, yet it remains controversial even among college biology students. Acceptance of evolution is important for students if we want them to incorporate evolution into their scientific thinking. However, students’ religious beliefs are a consistent barrier to their acceptance of evolution due to a perceived conflict between religion and evolution. Using pre-post instructional surveys of students in introductory college biology, Study 1 establishes instructional strategies that can be effective for reducing students' perceived conflict between religion and evolution. Through interviews and qualitative analyses, Study 2 documents how instructors teaching evolution at public universities may be resistant towards implementing strategies that can reduce students' perceived conflict, perhaps because of their own lack of religious beliefs and lack of training and awareness about students' conflict with evolution. Interviews with religious students in Study 3 reveals that religious college biology students can perceive their instructors as unfriendly towards religion which can negatively impact these students' perceived conflict between religion and evolution. Study 4 explores how instructors at Christian universities, who share the same Christian backgrounds as their students, do not struggle with implementing strategies that reduce students' perceived conflict between religion and evolution. Cumulatively, these studies reveal a need for a new instructional framework for evolution education that takes into account the religious cultural difference between instructors who are teaching evolution and students who are learning evolution. As such, a new instructional framework is then described, Religious Cultural Competence in Evolution Education (ReCCEE), that can help instructors teach evolution in a way that can reduce students' perceived conflict between religion and evolution, increase student acceptance of evolution, and create more inclusive college biology classrooms for religious students.

One way pathogen prevalence is maintained is by persistence within reservoir host species. Reservoir hosts are species that do not show any signs of disease when a pathogen infects them. As a result, the pathogen survives and is able to remain in the host population. Batrachochytrium dendrobatidis (Bd) is a chytrid fungus that has caused extensive amphibian declines. It has been suspected that reservoir hosts are a key to Bd remaining in certain amphibian populations. I studied dragonfly naiads (Anisoptera spp.), the aquatic life cycle stage immediately following hatching and preceding the emergence of wings, as potential reservoir hosts for Bd on the Mogollon Rim in Arizona. On the Mogollon Rim winter temperatures fall below the optimal thermal range for Bd. Boreal chorus frogs (Pseudacris maculata), the most common amphibian species on the Rim, maintain subzero body temperatures to survive the winter. Since the optimal thermal range for Bd is between 4°C and 25°C, it is unlikely that Bd can grow on the skin of these frogs during winter. As a result, it is unknown how Bd prevalence is maintained in the area. Recent studies showed that Bd can grow in non-amphibian hosts. I hypothesized that Bd could grow within the digestive tracts of dragonfly naiads, since they stay in the water and don’t maintain subzero body temperatures during the cold winters on the Rim. Non-native and native naiads were both included in this study; the non-native naiads were purchased from a company in California while the native naiads were captured from ponds on the Mogollon Rim. The digestive tracts of the naiads were then dissected, and the DNA was extracted using an animal tissue spin-column protocol. The extracted DNA was analyzed by qPCR. The qPCR analysis of the native and non-native dragonfly naiads revealed that the samples were either Bd-negative or very weakly Bd-positive, with most being the former. Based on these results, it does not appear that naiads are biologically significant reservoir hosts for Bd.

Amphibians have been experiencing a worldwide decline that is in part caused by an infectious disease, chytridiomycosis, specific to frogs and salamanders. Globally many species have declined or gone extinct because of the pathogenic fungus Batrachochytrium dendrobatidis, also known as the amphibian chytrid or Bd. By the time Bd was discovered it was too late to stop the spread and it has now been found on almost every continent. The trade of captive amphibians, used as pets, bait, and educational animals provides an opportunity to spread Bd. Because some amphibians can carry Bd without experiencing symptoms, it is possible for even healthy looking amphibians to spread the amphibian chytrid if they are moved from one location to another. Recently, a new species Batrachochytrium salamandrivorans (Bsal) was found on salamanders. Bsal was identified before it reached the United States, prompting concern regarding its spread and a call for regulation regarding the trade of captive amphibians. There are some regulations in place controlling the trade of amphibians, but they are insufficient to stop the spread of amphibian chytrid in captive populations. A 2016 law prohibits the importation of 201 salamander species. However, there is no central organization to sample or certify if amphibians are free from Bd or Bsal. Although some stores say they test for these pathogens the tests are unregulated and not reported to any central body. If the captive amphibian trade is to go disease free, there would need to be a significant push to coordinate testing efforts. To estimate Bd's prevalence in Arizona captive amphibian populations, I contacted pet stores, bait stores, and sanctuary or educational organizations to ask if I could sample their amphibian collections. My research built on the 2008 work of Angela Picco, who sampled for the amphibian chytrid in Arizona bait shops. I found that amphibian owners were often hesitant and unwilling to participate in this research opportunity. There are multiple reasons for this hesitancy including a fear of increased regulation, the potential for reporting to a government agency (USDA), or the eventual cessation of amphibian trade. The lack of willing participants suggests there may be difficulties in coordinating future sampling efforts for Bd and Bsal.

Batrachochytrium dendrobatidis (Bd), the amphibian chytrid fungus causing chytridiomycosis, is the cause of massive amphibian die-offs. As with any host-pathogen relationship, it is paramount to understand the growth and reproduction of the pathogen that causes an infectious disease outbreak. The life-cycle of the pathogen, Bd, is strongly influenced by temperature; however, previous research has focused on Bd isolated from limited geographic ranges, and may not be representative of Bd on a global scale. My research examines the relationship between Bd and temperature on the global level to determine the actual thermal maximum of Bd. Six isolates of Bd, from three continents, were incubated at a temperature within the thermal range (21°C) and a temperature higher than the optimal thermal range (27°C). Temperature affected the growth and zoosporangium size of all six isolates of Bd. All six isolates had proliferative growth at 21°C, but at 27°C the amount and quality of growth varied per isolate. My results demonstrate that each Bd isolate has a different response to temperature, and the thermal maximum for growth varies with each isolate. Further understanding of the difference in isolate response to temperature can lead to a better understanding of Bd pathogen dynamics, as well as allow us the ability to identify susceptible hosts and environments before an outbreak.

Conservation is a complicated entity consisting of a multitude of professional fields including social issues, cultural issues, and physical science. This thesis evaluates the positive and negative aspects of two broad types of conservation: top down fortress conservation and bottom up community-based conservation. Fortress conservation has many negative aspects, such as displacing human communities and preventing utilization of resources. However, it also has positive aspects, such as preventing the destruction of delicate ecosystems and slowing down extinctions. Community-based conservation is more inclusive and focuses on including the indigenous populations located within the proposed conservation site in the decision-making process. Its negatives include having an anthropocentric goal instead of valuing nature's intrinsic values. Understanding the differences inherent in these two methods is necessary in order to implement a conservation network with the highest chance for success.

Using a simple $SI$ infection model, I uncover the

overall dynamics of the system and how they depend on the incidence

function. I consider both an epidemic and endemic perspective of the

model, but in both cases, three classes of incidence

functions are identified.

In the epidemic form,

power incidences, where the infective portion $I^p$ has $p\in(0,1)$,

cause unconditional host extinction,

homogeneous incidences have host extinction for certain parameter constellations and

host survival for others, and upper density-dependent incidences

never cause host extinction. The case of non-extinction in upper

density-dependent

incidences extends to the case where a latent period is included.

Using data from experiments with rhanavirus and salamanders,

maximum likelihood estimates are applied to the data.

With these estimates,

I generate the corrected Akaike information criteria, which

reward a low likelihood and punish the use of more parameters.

This generates the Akaike weight, which is used to fit

parameters to the data, and determine which incidence functions

fit the data the best.

From an endemic perspective, I observe

that power incidences cause initial condition dependent host extinction for

some parameter constellations and global stability for others,

homogeneous incidences have host extinction for certain parameter constellations and

host survival for others, and upper density-dependent incidences

never cause host extinction.

The dynamics when the incidence function is homogeneous are deeply explored.

I expand the endemic considerations in the homogeneous case

by adding a predator into the model.

Using persistence theory, I show the conditions for the persistence of each of the

predator, prey, and parasite species. Potential dynamics of the system include parasite mediated

persistence of the predator, survival of the ecosystem at high initial predator levels and

ecosystem collapse at low initial predator levels, persistence of all three species, and much more.