Environmental Studies – Page 3 – UROP Spring Symposium 2021

Environmental Studies

Investigating the Identity of an Ancient Fish Fossil Using CT Scanning

This research project examines Wardichthys cyclosoma, an extinct species of fish that lived during the Carboniferous period (around 350 million years ago) from Scotland. In the past, Wardichthys cyclosoma has been classified as a platysomid, a type of Paleozoic (540-252 million years ago) fish known for their deep, flat bodies. However, this classification is based on limited evidence since there is little detail visible on the fossil. This project applies X-ray computed tomography to examine the anatomy of a fossil of Wardichthys that is still enclosed in rock. Using past scientific literature, we found several points of similarity between Wardichthys cyclosoma and confirmed members of platysomid group. Major observations that are consistent with this placement within this platysomid group include the shape and arragement of the postclethrium, clavicle, cleithrum, and sclerotic ossicle. By corroborating past hypotheses, this research project helps refine the understanding of the early evolution of these ancient fishes.

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Detroit Contractor Ecosystem

Bridging Neighborhoods (BN) was formed to support the optional relocation or retrofitting of houses for the residents of the Del Ray neighborhood due to the construction of an international bridge between Canada and the United States. To conduct activities, BN relies upon attracting local contractors and subcontractors to the program so the residents can opt into the relocation or retrofitting process with confidence. My role is to research contractor programs and outreach strategies in thirty cities nationwide and assist in reaching out to contractors and subcontractors in Detroit. These tasks were achieved through internet research and calling 150+ potential contractors for the 2021 Construction Conference. The purpose of this research is to highlight contractor programs or outreach strategies that the City of Detroit can implement in the future, and the outreach calls have increased the number of contractor connections BN possesses.

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The relationship between Ninia’s responses to predation threats and age

Animals perceive and react to different predation signs based on the severity of the threat; the age of the animal often affects the aggressive and defensive reactions towards the predation signals. My study tests how exposing Ninia (a nocturnal snake) of different age classes to varying stimuli could elicit different aggressive and defensive responses. Data was collected by capturing and filming snakes in the neotropics, and then those videos were analyzed for specific behaviors. I predict that if Ninia are exposed to aggressive stimuli, they will engage in defensive behavior, regardless of age. If Ninia are exposed to non-aggressive stimuli, they will engage in aggressive behaviors if they are an adult but will engage in defensive behaviors if they are younger. The potential influence of age in Ninia’s response to non-aggressive stimuli may indicate that the size of the snake (which correlates with age) is an important predictor for understanding behavioral reactions to threats. If age has no influence on Ninia’s response to aggressive stimuli and their responses are more defensive; this may mean that in a life-or-death situation, it is more advantageous to respond defensively in order to increase the chances of survival. Overall, this study provides the opportunity to shed light on general defensive behaviors of animals, and how age and perceived aggression levels of a predator influence their responses to threats.

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The Application of Genomic Tools for Monitoring Aquatic Endangered, Invasive, and Economically Important Species

Environmental DNA (eDNA) is genetic material from urine, waste, mucus, or sloughed cells collected from aquatic habitats that can be analyzed for species detection without ever seeing the actual organism. It is an emerging management tool that is useful for monitoring invasive, native, and endangered species. Traditional methods of data collection tend to harm or kill species so that they can be preserved for laboratory identification. Sampling done using eDNA methods, on the other hand, is a low-cost alternative that does not harm any species. It can be done in harsher conditions and is able to detect species that tend to be missed using traditional methods. While this technology has been shown to be extremely beneficial, there have been issues concerning a communication and knowledge gap between researchers and conservationists. Our research project aims to bridge this gap by creating a database that is publicly accessible, and user-friendly for both conservationists and other scientific researchers. We have compiled important information from approximately 300 research articles and organized it in a uniform format, within a centralized database. This database focuses on allowing the end-user to search through pre-designed assays for a variety of target species, with generalized information about quantitative real-time PCR (e.g. chemistry (SYBR green, Probe) and primer efficiency). We believe this database will greatly benefit conservationists and other potential non-geneticist eDNA end-users as an efficient tool to search through pre-designed assays, and to understand key concepts for implementing qPCR based eDNA monitoring.

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The application of genomic tools for monitoring aquatic economically important, invasive and endangered species

Environmental DNA (eDNA) is genetic material from urine, waste, mucus, or sloughed cells collected from aquatic habitats that can be analyzed for species detection without ever seeing the actual organism. It is an emerging management tool that is useful for monitoring invasive, native, and endangered species. Traditional methods of data collection tend to harm or kill species so that they can be preserved for laboratory identification. Sampling done using eDNA methods, on the other hand, is a low-cost alternative that does not harm any species. It can be done in harsher conditions and is able to detect species that tend to be missed using traditional methods. While this technology has been shown to be extremely beneficial, there have been issues concerning a communication and knowledge gap between researchers and conservationists. Our research project aims to bridge this gap by creating a database that is publicly accessible, and user-friendly for both conservationists and other scientific researchers. We have compiled important information from approximately 300 research articles and organized it in a uniform format, within a centralized database. This database focuses on allowing the end-user to search through pre-designed assays for a variety of target species, with generalized information about quantitative real-time PCR (e.g. chemistry (SYBR green, Probe) and primer efficiency). We believe this database will greatly benefit conservationists and other potential non-geneticist eDNA end-users as an efficient tool to search through pre-designed assays, and to understand key concepts for implementing qPCR based eDNA monitoring.

The application of genomic tools for monitoring aquatic economically important, invasive and endangered species Read More »

The Application of Genomic Tools for Monitoring Aquatic Endangered, Invasive, and Economically Important Species

Environmental DNA (eDNA) is genetic material from urine, waste, mucus, or sloughed cells collected from aquatic habitats that can be analyzed for species detection without ever seeing the actual organism. It is an emerging management tool that is useful for monitoring invasive, native, and endangered species. Traditional methods of data collection tend to harm or kill species so that they can be preserved for laboratory identification. Sampling done using eDNA methods, on the other hand, is a low-cost alternative that does not harm any species. It can be done in harsher conditions and is able to detect species that tend to be missed using traditional methods. While this technology has been shown to be extremely beneficial, there have been issues concerning a communication and knowledge gap between researchers and conservationists. Our research project aims to bridge this gap by creating a database that is publicly accessible, and user-friendly for both conservationists and other scientific researchers. We have compiled important information from approximately 300 research articles and organized it in a uniform format, within a centralized database. This database focuses on allowing the end-user to search through pre-designed assays for a variety of target species, with generalized information about quantitative real-time PCR (e.g. chemistry (SYBR green, Probe) and primer efficiency). We believe this database will greatly benefit conservationists and other potential non-geneticist eDNA end-users as an efficient tool to search through pre-designed assays, and to understand key concepts for implementing qPCR based eDNA monitoring.

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Comparing Tuberculosis’ and Pneumonia’s Seasonal Dynamics in Thailand from 1980-2020

Infectious disease seasonality is important for informing public health policy and vaccine distribution. Tuberculosis and pneumonia morbidity and mortality in Thailand are high relative to the rest of the world, and to date, these data have not been sufficiently studied. Tuberculosis incidence at the country level in Thailand exhibits a bi-enniel pattern, though the results have not been examined at the province level. Other research suggests that pneumonia seasonality follows influenza’s bi-enniel patterns in Thailand, however the seasonality of pneumonia has not been analyzed on its own. Here, we examine both tuberculosis and pneumonia monthly case reports from Thailand to identify seasonal patterns at the provincial level (71 provinces) for both pneumonia and tuberculosis from 1980-2020. After digitizing and organizing the data using optical character recognition software, we analyzed the data in R Studio. We will use wavelet analyses and general additive models to reveal the seasonal patterns for each pathogen in each province. Annual seasonality with distinct peaks is expected for both tuberculosis and pneumonia at regional levels. Uncovering seasonal patterns would inform public health officials on when to distribute the corresponding vaccines. If similarities between the two pathogens are found, public health professionals in Thailand will be more informed on their relation (such as in what conditions they are spread). Finally, if no seasonality is found in the data, there will be further evidence supporting the hypothesis that the seasons do not affect the incidence of diseases in Thailand.

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The Seasonality of Measles Across the Globe

Although the United States has come very close to eliminating measles cases through widespread vaccination, measles outbreaks still occur in many low and middle income (LMIC) countries where vaccine distribution is more complex. The World Health Organization (WHO) has collected historical clinical case report data of measles across the globe for almost a century, but has yet to closely examine these data across time and space to identify the seasonal transmission dynamics of the virus and identify the factors responsible for these patterns. In our study, we analyzed monthly measles cases reported to the WHO from 1948-1977 across the world. This data was found in print documents and scanned into PDF format to be digitized using optical character recognition software. Next, it was assembled and organized into CSV format to be analyzed in R using wavelet analyses and general additive models for visualization purposes. We expect to find seasonal patterns in measles outbreaks for each location studied. Hopefully, we will be able to find correlations between case numbers and risk factors so that action can be taken to reduce further outbreaks. If we know seasonality in each location, we could optimize the timing of vaccination campaigns to maximally reduce potential cases, improving the health of individuals and achieving the goals of health experts.

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Variance in the Evolution of Mimicry Behavior in Atractus Snakes

Variance in the Evolution of Mimicry Behavior in Atractus Snakes: Animals often adapt their behavior and physical characteristics to mimic another species as a method to deter predators. Previous studies have identified snake species that mimic the coloration and behavior of venomous coral snakes as a defensive mechanism. This study aims to examine the variance of mimicry in a single genus. The species Atractus elaps and Atractus flammigerus will exhibit different defensive behaviors due to a difference in the evolution of mimicry between the species. The snakes were caught in Peru, placed into an arena, and introduced to various physical and auditory stimuli, all while being video-recorded. Videos were examined by frame and any observed defensive behavior was recorded. The expected results of this study are that Atractus elaps will react with tail presentations that show the red striped underside of the tail, mimicking defensive tail curling in Coral snakes. Atractus flammigerus will have different reactions to the stimuli that do not involve a tail presentation. A difference in behavior between these two species would show that only Atractus elaps uses defense mechanisms that involve coral snake mimicry. The results of this study will further examine snake mimicry behavior and provide more data about coevolution of color and mimicry in the Atractus genus.

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Age-Dependent Anti-Predator Behavior in Leptodeira Snakes

Most animals display some form of anti-predator behavior, from expelling foul-smelling substances to making deafening noises. Snakes, despite their minimalistic form, have a wide variety of anti-predator behaviors. Previous studies surrounding the behavior of snakes have focused primarily on predatory and defensive behaviors of adult snakes. This study tests for differences in anti-predator behaviors between juvenile and adult snakes of the Leptodeira genus. Leptodeira are in the family Colubridae and are primarily found across Central and South America, living in a multitude of different environments. Snakes were captured and each was subjected to a variety of stimuli, including auditory, visual, and physical contact. The resulting responses were videotaped and analyzed to generate an ethogram for each video. The behaviors were then divided into aggressive and passive displays. The frequency and length of each behavior was compared between adults and juveniles. This study predicts that adult Leptodeira exhibit aggressive behaviors more frequently than juveniles. If this prediction is true, the difference could imply that aggressive behavior provides an advantage to adult Leptodeira due to their larger size, but not juveniles. This would mean passive attempts at hiding fail more frequently for adult snakes than for juvenile snakes. If the opposite trend is found, it could imply that juvenile Leptodeira, which have white heads that fade to grey or black at adulthood, are more visible than adults and therefore are incentivized to be more aggressive. This research will broaden understanding of how behavior can change after maturation in nonhuman animals.

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