Mutations in myosin may lead to severe muscle disorders that greatly reduce the quality of life. For example, the embryonic skeletal myosin (MYH3) mutation R672C leads to Freeman Sheldon Syndrome (FSS), a rare inherited disorder that causes severe contractures at birth. A comprehensive understanding of the relationship between protein structure and function is urgently needed to treat diseases such as FSS. Computational methods, such as molecular dynamics simulations, can be used to examine the effects of mutations on protein structure and function. However, the Protein Data Bank (PDB) is missing most human skeletal myosin heavy chain structures. We employed homology modelling to construct structures of human MYH3. To inform homology modeling, I generated a multiple sequence alignment of 7 human myosin genes. The extent of sequence identity was used to identify the optimum myosin isoforms to use as templates for model generation. For example, MYH3 and MYH7 were the most distinct at 78.93% similarity, which was expected as they are embryonic skeletal and adult cardiac myosin respectively. Specific sequence consensus at each position in the sequence was used to determine the most and least conserved regions of myosin. The cleft region was the most conserved; the N-terminal Domain was the least conserved. I used MYH7, adult cardiac myosin, as a template structure to derive a homology model of the ATP state of MYH3. A structure of MYH3 R672C was generated via in silico mutation of the wild type structure. Molecular dynamics of the resulting structures will be used to explore how R672C, which is located near myosin’s converter domain, alters myosin structure and function. This computational platform will model all phases of the cross-bridge cycle, potentially reveal new drug binding pockets, guide and be validated by in vitro experiments using human induced pluripotent stem cell derived myocytes (hiPSC-Ms).

The goal of the Kaeberlein lab is to understand the underlying molecular mechanisms of aging and how they can be perturbed in order to beneficially alter the aging process. To do so, we use the unicellular model S. cerevisiae or brewers yeast. In order to expedite the process of studying aging in large numbers of cells, the Kaeberlein lab has been using microfluidic devices that immobilize yeast cells throughout their lives so that visual data can be collected without manual interference of the cells. The question being investigated here is whether a neural network can be trained to automate the scoring tasks required for processing the image data generated by these microfluidic devices. Using python and the Yolov3 neural network architecture, I have created an AI-based screening tool to quickly analyze data generated with these microfluidic devices, such that the pipeline as a whole produces lifespan data for about 120 cells at a time, using stacks of image files as raw data. This work is significant as it provides insights into the issues of training a neural network on similar objects, and more importantly, insights into how these issues can be mitigated. In addition to increasing the speed with which data can be scored, this system will also increase the capacity for scoring experiments with large numbers of experimental groups. The system itself can also be used in order to expedite biology research.

A survey in the existing literary sources says that there are three main diet-related patterns in Blue Zone communities that contribute to their longevity. After I cross-referenced the micronutrients in Blue Zone diets with the average American diet, I found that the Blue Zone diets are all enriched for some common vitamins and nutrients, specifically: retinol, thiamin, pyridoxine, ascorbic acid, vitamin E, vitamin K, magnesium, and potassium. All of these vitamins and minerals are known to affect cellular metabolism through a wide array of factors, potentially linking them to bettering health and increasing lifespan. I initialially will confirm that these compounds indeed play a vital role in extending the functionality of the biomechanical systems in C elegans. I will then further pursue whether combinations of the nutrients increase effectiveness, and which specific areas in the body they individually impact for promoting longevity. My first step in investigating the biomechanical effects of these micronutrients will be to incorporate each one individually into the C elegans’ diet. My long-term goal, once I test the wild type model, is to focus on how these micronutrients combat age related diseases. To do this I will use my results for optimal micronutrients to test the effectiveness of the specific micronutrients in the Alzheimer’s degenerative pathway. Specifically, I will use the GMC-101 transgenic worm, (genetically modified strain to exhibit the degenerating effects of Alzheimer's disease), which expresses human amyloid- beta - a protein implicated in the progression of human Alzheimer’s Disease - in the body wall muscle and becomes increasingly paralyzed with age. I will use a similar experimental set up, looking for a delayed onset of paralysis. I hope this research will be able to shed light on how micronutrients interact and affect degenerating biochemical pathways in aging C elegans; specifically, in a strain that models Alzheimer’s disease.

Caenorhabditis elegans is frequently used as a model organism for testing the effects of various compounds on longevity. A current limitation of running these experiments is the tremendous amount of work needed to collect large sample sizes of data when testing for several compounds in different genetic populations. Fortunately the Kaeberlein lab has developed the WormBot, an image capture robot used to take high resolution images of hundreds of experimental plates each containing ~30 worms. Researchers still have to rely on humans manually annotating tens of thousands of frames to extract valuable metrics for their analysis. I have developed the implementation of a neural network to automatically analyze these images so that the number of experiments and compounds that can be tested is increased exponentially. I utilize a network architecture known as Yolov3 to allow the computer to identify and track individual worms from the images. The results obtained from our new computational method extract data from the images that is equal to or even better than the human method while also requiring a fraction of the time. Using this novel platform, we are analyzing a broad spectrum of natural and synthetic compounds for their effects on longevity and health span in C. elegans.

From the Dakota Access Pipeline demonstrations to increasing popularity around climate-activist-turned-household-names like Greta Thunberg, a resurgence of environmental advocacy has taken the 21st century by storm. The environmental justice movement, a term first coined in the 1980s, was born from the idea that mainstream environmentalism does not examine environmental policy in the intersection of socioeconomic status and race. This literature review explores the history and impacts of environmental racism and the evolution of the environmental movement. It finds that not only have the burdens of environmental degradation been disproportionately distributed across different communities, but that analyses of the ecological impacts of imperialism have created a singular discourse that is paradigmatic of colonial ideologies. It parallels the colonial vision of conservation in North America with the treatment of its Indigenous populations and explores nature as something portrayed as the antithesis of culture. Finally, further examination of the changes from the Trump to Biden administrations is warranted by the construction of a new framework for examining environmental policies, with an emphasis on social equity. The intended outcome of this paper is to create a set of criteria for existing and future environmental legislation.

The Serrasalmidae are a family of Neotropical freshwater fishes that includes carnivorous piranhas as well as their herbivorous relatives, the pacus. Pacu diets consist of leaves, stems, fruits, seeds, and algae, as well as insects, benthic invertebrates, plankton. Likewise, some piranha species are actually more omnivorous than carnivorous, feeding on fruits and seeds in particular and only to a lesser degree the fins and scales of other fishes. These diverse prey materials appear concomitant with diverse jaws and dentitions in both pacus and piranhas, suggesting that some species are ecomorphologically specialized for feeding on certain prey. We investigated how the pattern and tempo of feeding morphological specialization in herbivorous serrasalmids reflects the ecological diversity of their food resources. Pacu and piranha species were first categorized as either algivores, frugivores, folivores, phytophages, planktivores, or omnivores based on a meta-analysis of published gut content data. We used computed tomography (CT) scanning and morphometrics to describe the primary morphological axes of jaw and dental variation and any correlates these phenotypes may have with each species’ primary prey. We found significant differences in the occlusional offset, mechanical advantage, size and shape of the lower jaw among different diet guilds. Phytophages tended to have scissor-like dental occlusion, resembling piranhas more than other pacus. We also found significant differences in the rate of morphological evolution among different diet guilds, notably folivores had morphological rates over 40 times faster than that of planktivores, suggesting different selective regimes acting on each dietary guild.

Friedreich's ataxia (FRDA) is an extremely destructive neurodegenerative mitochondrial disease with no cure to date. The disease is characterized by mutations in the FXN gene, resulting in a deficiency of functional frataxin protein. These reduced levels of frataxin protein cause multitudes of metabolic problems, including oxidative stress, disruption in iron-sulfur cluster synthesis, and iron overload in mitochondria. Recently, it has been discovered that hypoxia can rescue frataxin deficiency in various types of model organisms, including yeast, cultured human cells, nematodes, and mice. However, despite frataxin and oxygen’s integral relationship in mitochondrial function, the exact genetic pathways by which they interact remain elusive. I aim to bridge this gap by using yeast homolog and studying its oxygen dependence. YFH1 is the yeast frataxin homolog that can mimic FRDA pathology. I first created a yeast model of ∆yfh1. I am currently in the process of creating synthetic lethals and rescues of ∆yfh1 by mating it with previously identified yeast knockout strains that are known to show hypoxic resistance. After I obtain these double mutants, I plan to screen them for oxygen dependence by subjecting them under hypoxia, normoxia, and hyperoxia. Finally, I will replica plate my experiments in order to confirm the double mutants. Because ∆yfh1 is known to grow better in hypoxia, genes that create synthetic lethals in hypoxia with ∆yfh1 will most likely be the genes involved in genetic pathways of hypoxic rescue of frataxin deficiency. This will not only streamline the process of searching for the genetic basis of the disease but also serve as a platform for novel therapy to treat FRDA at its biochemical basis.

Various fatal and debilitating genetic diseases are caused by mitochondrial dysfunction. To study mitochondrial diseases in humans, the Kaeberlein Lab uses NDUFS4-KO mice as a model of the human mitochondrial disease Leigh Syndrome. These mice have a non-functioning protein in their energy-producing oxidative phosphorylation process. We previously observed an increase in total iron in livers of NDUFS4-KO mice, which can damage cells by producing reactive oxygen species. Thus, we hypothesized a low-iron diet may alleviate the effects of the mitochondrial disease. My project aimed to study the molecular consequences of a low-iron diet in NDUFS4-KO mice by quantifying mRNA transcript levels and protein expression of genes involved in iron uptake, storage, or efflux, and comparing these levels between wild-type (WT) and NDUFS4-KO mice fed a normal or low-iron diet. First, I purified mRNA through cell lysis from 35-day old mice liver samples and used the mRNA to perform a one-step Quantitative Reverse-Transcriptase Polymerase Chain Reaction (qRT-PCR). Next, to quantify protein levels, I performed western blot analysis in collected protein extracts. I observed an increase protein expression and mRNA transcript levels of iron-uptake proteins such as TfR1 in both WT and NDUFS4-KO low-iron diet mice compared both control groups. This suggests iron levels were reduced to safer levels, supporting my hypothesis. Furthermore, when analyzing the expression of genes which respond to iron overload, such as ferritin, I observed a decrease in the low-iron diet NDUFS4-KO mice compared to control diet NDUFS4-KO mice. This observation shows that low iron diet contributes to a reduction in excess iron. My data may illuminate the involvement of iron in mitochondrial diseases as well as support further research into the consumption of low-iron containing foods, and eventually lead to the development of therapeutic drugs to treat humans who suffer from such ailments.

Polymers are commonly seen in our daily lives. Proteins and plastics are both familiar classes of polymeric materials whose utility is heavily relied upon. There are different architectures of polymers, for instance, linear and cyclic, each of which has unique properties. For example, cyclic polymers have a lower viscosity, smaller hydrodynamic volume, and a unique topology as an endless circle. In this project, we are investigating and improving a privileged method to approach cyclic polymers, Ring Expansion-Metathesis Polymerization (REMP), which grows the polymer chain while cyclizing it, using a Ruthenium-based (Ru) system. The goal of the research is to solve the recent major challenge of synthesizing cyclic polymers in a controlled fashion, through systematically modifying the structure of Ru-based initiators. My goal in the research project is to synthesize a precursor ligand, the subsequent initiator, and the monomers(commonly strained alkenes, norbornene). Eventually using the monomers to conduct polymerization reactions and analyze their properties and characteristics with spectroscopic instruments. Preliminary results of this research suggest we can make cyclic polymers that are more evenly distributed in size and weight. Since polymers have played an important role in people’s everyday life, improving the methodology through having better control on making cyclic polymers can make a big contribution to applications in the aspects of biomedicine and energy for our society. For example, cyclic polymers could generate biotherapeutics for the field of medicine; they could also serve as well-behaved and new types of conducting materials for the field of semiconductor.