Life Sciences Commons^™

Pointing The Zinc Finger On Protein Folding: Energetic Investigation Into The Role Of The Metal-Ion In The Metal-Induced Protein Folding Of Zinc Finger Motifs, Inna Bakman-Sanchez

Dissertations, Theses, and Capstone Projects

Interactions between inorganic metal-ion cofactors and organic protein scaffolds are important for the proper structure and function of metalloproteins. Zinc finger proteins (ZFPs) are an example of proteins with such crucial metal-protein interactions. Incorporation of the Zn(II)-ion into ZFPs allows for their correct folding into structures that can carry out vital biological functions which include gene expression and tumor suppression. In addition, engineered ZFPs have shown to be promising genetic therapeutics in the clinic. And yet, there is still a gap in a quantitative understanding of the energetic contribution of the metal-protein interactions towards the structure and function of these …

The Cognitive Thalamus: Source Analysis Of Scene Working Memory Delay Activity, Bernard A. Gomes

Dissertations, Theses, and Capstone Projects

Working Memory represents a limited-capacity store for maintaining information and manipulating the store's contents over a short period for the guidance of goal-directed behavior. Working Memory is an essential component of executive functions that are intricately associated with the prefrontal cortex (PFC). The PFC has been implicated in maintaining task-related information online for brief periods in the absence of relevant information. This active maintenance phase is called the delay period that occurs between encoding and retrieval of the stimulus. Previous studies have attempted to understand the relationship between working memory and the PFC, especially during the delay or maintenance phase …

Rehabilitative Movement Approaches And Dance Interventions In Parkinson’S Disease, Cecilia Fontanesi

Dissertations, Theses, and Capstone Projects

The scope of this work is to address the functional deficits and symptoms experienced by those living with Parkinson’s Disease through movement interventions.

Chapter 1 offers a brief overview of current pharmacotherapy and rehabilitation approaches in Parkinson’s, focusing on dance in particular as a movement intervention that may be particularly suited to this population.

Chapter 2 focuses on brain plasticity and motor learning in PD, reporting the effects of rTMS applied after the acquisition of a motor skill. In this study, adaptation tested in patients with PD was comparable in the sham and TMS sessions, while retention indices tested on …

Analysis Of Newspaper Coverage Of Psilocybin From January 1, 1989 To December 31, 2019, Dax Oliver

Dissertations, Theses, and Capstone Projects

Psilocybin is a chemical compound that has received a lot of attention from medical researchers in recent years. However, this research is not merely a medical issue but a social and political one as well. In the 1960s, psilocybin and other psychedelic compounds were widely ingested outside of clinical settings. This alarmed some of the American public, resulting in severe legal restrictions on psilocybin use and research.

Today, many psilocybin advocates hope that it will avoid the negative public sentiment of the 1960s. To help gauge public sentiment about other psychoactive compounds, some studies have examined newspaper coverage, but there …

Employing High Probability Gene Choice Elements To Understand Singular Odorant Receptor Expression, Raena Mina

Dissertations, Theses, and Capstone Projects

The ability to detect odorous chemicals in the environment is the oldest of the senses necessary for survival, from escaping danger, finding mates, to locating food. It is said that humans can identify and discriminate up to a trillion different odor mixtures. For chemoreception to have such a high discriminatory power, would require a diverse population of cells dedicated for odor detection. These detector cells are the olfactory sensory neurons (OSNs), which express odorant receptors (ORs) that bind to chemical odors in the environment. In order to increase specificity and sensitivity, an essential property in olfaction is for each OSN …

Dietary Development And Nutritional Ontogeny In Gorilla Beringei : A Multi-Layered, -Omics Approach, Emma C. Cancelliere

Dissertations, Theses, and Capstone Projects

In species who consume folivorous diets, immature individuals must contend with the challenges of extracting nutrients from fibrous foods before dietary adaptations and strategies are fully developed. Additionally, immatures have distinct nutritional needs to support their stage-specific metabolic and biophysiological requirements. To meet these stage-specific needs, while constrained by underdeveloped feeding strategies and digestive capacities, immatures may adopt distinct diets better suited to their specific developmental context. However, where dietary modification is constrained by low dietary diversity or landscape homogeneity, it is unclear how immature individuals compensate through alternative strategies. In turn, little is known about the nutritional and life …

A Glance At The Mirror: Ensemble Perception Of Symmetry, Gene Jerskey

Dissertations, Theses, and Capstone Projects

A growing body of research has demonstrated the ability of subjects to extract representative statistics from visual ensembles, images of similar but distinct groups of objects, without conscious effort or attention focused on individual members of the ensemble. When presented with ensembles, subjects have been able to accurately report the mean, range, and even distribution of various features in the ensemble. Research into ensemble perception, as it has become known, has divided mainly into studies of either low-level features, such as orientation, motion, and color, which are processed in early visual areas, at least for individual objects, or high-level features, …

Small Molecule Synthetic Carbohydrate Receptors, Marcelo F. Bravo Carranco

Dissertations, Theses, and Capstone Projects

Carbohydrate – receptor interactions are often involved in the attachment of viruses to host cells, and this docking is a necessary step in the virus life cycle that precedes infection and, ultimately, replication. Despite the conserved structures of the glycans involved in docking, they are still considered “undruggable”, meaning these glycans are beyond the scope of conventional pharmacological strategies. Recent advances in the development of synthetic carbohydrate receptors (SCRs) – small molecules that bind carbohydrates – could bring carbohydrate-receptor interactions within the purview of druggable targets. Here we discuss the role of carbohydrate-receptor interactions in viral infection, the evolution of …

Sex/Gender Differences In Serial Position Profiles In Patients With Mild Cognitive Impairment And Healthy Controls, Emnet Z. Gammada

Dissertations, Theses, and Capstone Projects

Introduction: Alzheimer’s disease disproportionately affects more women, but paradoxically, men have a higher incidence of Mild Cognitive Impairment (MCI). Researchers have suggested that women’s verbal memory advantage across the lifespan reflects better premorbid skills, which then require more neurodegeneration to manifest early clinical impairment. To date, measurement of sex differences in verbal memory have used total list scores. We proposed that a granular examination of serial position effects (SPE) in list-learning can refine the source of sex/gender differences.

Methods: A cross-sectional analysis of participants with Mild Cognitive Impairment (MCI) and Healthy Controls (HC) was examined from the Alzheimer’s Disease Neuroimaging …

Regulation Of A Messenger: Raising Oskar, It Takes A Village, Livia V. Bayer

Dissertations, Theses, and Capstone Projects

D. melanogaster oogenesis serves as an excellent system to study the life of an mRNA. Tremendous work has been done to understand the numerous complex mechanisms of mRNA regulation, still there is still so much that is yet to be discovered. In this thesis, I present studies I carried out to address several aspects of oskar mRNA post-transcriptional regulation. Leading me to extend our current understanding of the carefully controlled regulation of oskar mRNA life cycle via a myriad of proteins. I found that a specific NPC component, Nup154 is necessary not only for its export from the nucleus, but …

Ecology And Evolution, David J. Lohman

Open Educational Resources

Introduction to the basic principles of ecology and evolutionary biology emphasizing quantitative approaches and hypothesis testing. Scientific reasoning, computer literacy, and writing skills are developed in the laboratory.

Performance Of A Dna And Protein Co-Extraction With Trypsin In Comparison To Two Proteinase K Based Dna Extraction Methods, Dinura A. Gunatilake

Student Theses

Effective DNA extraction methods are important for forensic applications. The main goal of this experiment was to determine if a newly developed trypsin based protein/DNA co-extraction method applied to contact traces would yield comparable results to a commercial Proteinase K method (QIAamp DNA Investigator Kit) and a Chelex extraction method with Tween 20 used in forensic laboratories. This was tested on 20 sets of sebaceous fingerprints on glass slides.

The results of this study demonstrate the trypsin co-extraction method yielded the highest amount of DNA. In the first comparison, the mean total DNA yields for the trypsin-co extraction method and …

Defining The Relationship Between Maternal Care Behavior And Sensory Development In Wistar Rats: Auditory Periphery Development, Eye Opening And Brain Gene Expression, Jingyun Qiu, Preethi Singh, Geng Pan, Annalisa De Paolis, Frances A. Champagne, Jia Liu, Luis Cardoso, Adrián Rodríguez-Contreras

Advanced Science Research Center

Defining the relationship between maternal care, sensory development and brain gene expression in neonates is important to understand the impact of environmental challenges during sensitive periods in early life. In this study, we used a selection approach to test the hypothesis that variation in maternal licking and grooming (LG) during the first week of life influences sensory development in Wistar rat pups. We tracked the onset of the auditory brainstem response (ABR), the timing of eye opening (EO), middle ear development with micro-CT X-ray tomography, and used qRT-PCR to monitor changes in gene expression of the hypoxia-sensitive pathway and neurotrophin …

Ionophoric Polyphenols Are Permeable To The Blood Brain Barrier, Interact With Human Serum Albumin And Calf Thymus Dna, And Inhibit Ache Enzymatic Activity, Alberto Martinez, Mai Zahran, Miguel Gomez, Johnny Guevara, Rosemary Pichardo-Bueno, Junaid Asim, Gabriel Ortiz, Yaa Andoh, Sinji Shibutani, Baljit Kaur

Publications and Research

Alzheimer’s disease (AD) is the most common form of dementia that affects more than 40 million people around the world. The incidence is expected to rapidly increase due to the lack of any effective treatment. In previous work we synthesized a family of five ionophoric polyphenols (compounds 1–5) that targeted important aspects related to AD, such as the toxic aggregation of amyloid-β peptides, the production of reactive oxygen species, or the excessive presence of Cu²⁺ ions. Here, in order to gain insights into their potential therapeutic value, we have tested the ability of compounds 1– …

Further Evaluation Of A Dry Vacuuming Technique For Recovery Of Dna From Handwritten Documents, Christian Hopkins

Student Theses

A previously developed, non-destructive, homemade vacuum method for collecting biological material from handwritten documents had promising DNA results for white copy paper, preserved indented writing, and latent prints. Prior to casework implementation, additional validation experiments are warranted and here the method was tested for different paper substrates. This work describes testing of notebook paper, bank deposit slips, magazine pages, and manila envelopes. The quantity of recovered DNA varied from donor to donor, but the mean quantities showed a trend that can be explained by the different sizes and surface properties of the tested paper types. The rougher paper type, like …

Tracing The Human-Avian Relationship In Iceland, Melanie Sua

Theses and Dissertations

An in-depth investigation explores the history of birds in Iceland and the interaction between birds and humans from the 9th through the 19th century, with the help of archaeological evidence, traditional and historical materials.

The Law Of Black Mirror - Syllabus, Yafit Lev-Aretz, Nizan Packin

Open Educational Resources

Using episodes from the show Black Mirror as a study tool - a show that features tales that explore techno-paranoia - the course analyzes legal and policy considerations of futuristic or hypothetical case studies. The case studies tap into the collective unease about the modern world and bring up a variety of fascinating key philosophical, legal, and economic-based questions.

Sensory Perception, Adrian Rodriguez-Contreras

Open Educational Resources

Different types of sensory systems with their functional modalities will be presented. The biological bases for how these functions are generated and modified will then be described. Scientific information will be integrated into the lectures, such that students use critical skills in interpreting data, proposing hypotheses and designing experiments.

Snow-Albedo Feedback In Northern Alaska: How Vegetation Influences Snowmelt, Lucas C. Reckhaus

Theses and Dissertations

This paper investigates how the snow-albedo feedback mechanism of the arctic is changing in response to rising climate temperatures. Specifically, the interplay of vegetation and snowmelt, and how these two variables can be correlated. This has the potential to refine climate modelling of the spring transition season. Research was conducted at the ecoregion scale in northern Alaska from 2000 to 2020. Each ecoregion is defined by distinct topographic and ecological conditions, allowing for meaningful contrast between the patterns of spring albedo transition across surface conditions and vegetation types. The five most northerly ecoregions of Alaska are chosen as they encompass …

Analysis Of Olfactory Mrna Cap Modifications Using Rnaseh And Lc-Ms, Ilinca M. Giosan

Theses and Dissertations

In the olfactory system, olfactory sensory neurons (OSNs) express odorant receptors (ORs) in a singular fashion through unknown mechanisms. Published data supports the notion that singularity is achieved, in part, through a modification the mRNA strand, perhaps in its 5’cap region. This theoretical study aims to test this 5’cap hypothesis.

Assessment Of Wild Ring-Tailed Lemur (Lemur Catta) Populations In Southwestern Madagascar With Implications For The Illegal Pet Trade, Samantha D. Calkins

Theses and Dissertations

Accurate population estimates are critical to inform conservation management of species. Incomplete sampling can lead to population underestimates and lacking conservation efforts. Population surveys are important for assessing human and animal welfare to allow for targeted conservation action. Recent ring-tailed lemur (Lemur catta) surveys have led researchers to conclude that L. catta populations are crashing. This has generated much attention and alarm, but may also be based on incomplete information. To better understand population dynamics, more thorough sampling is needed. Here, we survey five such sites to reassess the presence and abundance of L. catta in these locations. …

Epigenetic Targeting Of Mcl-1 Is Synthetically Lethal With Bcl-Xl/Bcl-2 Inhibition In Model Systems Of Glioblastoma, Enyuan Shang, Trang T. T. Nguyen, Chang Shu, Mike-Andrew Westhoff, Georg Karpel-Massler, Markus D. Siegelin

Publications and Research

Apoptotic resistance remains a hallmark of glioblastoma (GBM), the most common primary brain tumor in adults, and a better understanding of this process may result in more efficient treatments. By utilizing chromatin immunoprecipitation with next-generation sequencing (CHIP-seq), we discovered that GBMs harbor a super enhancer around the Mcl-1 locus, a gene that has been known to confer cell death resistance in GBM.We utilized THZ1, a known super-enhancer blocker, and BH3-mimetics, including ABT263, WEHI-539, and ABT199. Combined treatment with BH3-mimetics and THZ1 led to synergistic growth reduction in GBM models. Reduction in cellular viability was accompanied by significant cell death induction …

Method Development For Identifying Counterfeit Cigarettes Using Environmental Pollen Analysis, Tiffany Chan

Student Theses

Cigarette counterfeiting negatively impacts government revenue and undermines tobacco control policies. Tracking geographical origins and potential trade routes of counterfeit cigarettes is important for investigation illegal trade in tobacco products. Traditional pollen extraction techniques provide clear residues of pollen trapped on tobacco leaves and used for geographical identification; however, such methods are time-consuming and utilize concentrated chemicals. This study developed a simple, fast and environmentally friendly method for extraction of pollen grains used in differentiating genuine and counterfeit cigarettes. Experimental factors that may affect pollen recovery including number of cigarettes, extraction solution, and extraction temperature, were optimized. The optimum parameters …

Evolutionary Algorithms Converge Towards Evolved Biological Photonic Structures, Mamadou Aliou Barry, Vincent Berthier, Bobo D. Wilts, Marie-Claire Cambourieux, Pauline Bennet, Rémi Pollès, Olivier Teytaud, Emmanuel Centeno, Nicolas Biais, Antoine Moreau

Publications and Research

Nature features a plethora of extraordinary photonic architectures that have been optimized through natural evolution in order to more efciently refect, absorb or scatter light. While numerical optimization is increasingly and successfully used in photonics, it has yet to replicate any of these complex naturally occurring structures. Using evolutionary algorithms inspired by natural evolution and performing particular optimizations (maximize refection for a given wavelength, for a broad range of wavelength or maximize the scattering of light), we have retrieved the most stereotypical natural photonic structures. Whether those structures are Bragg mirrors, chirped dielectric mirrors or the gratings on top of …

Spatiotemporal Genetic Diversity Of Lions Reveals The Influence Of Habitat Fragmentation Across Africa, Caitlin J. Curry, Brian W. Davis, Laura D. Bertola, Paula A. White, William J. Murphy, James N. Derr

Publications and Research

Direct comparisons between historical and contemporary populations allow for detecting changes in genetic diversity through time and assessment of the impact of habitat fragmentation. Here, we determined the genetic architecture of both historical and modern lions to document changes in genetic diversity over the last century. We surveyed microsatellite and mitochondrial genome variation from 143 high-quality museum specimens of known provenance, allowing us to directly compare this information with data from several recently published nuclear and mitochondrial studies. Our results provide evidence for male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed …

Olfaction Modulates Inter-Subject Correlation Of Neural Responses, Paul Deguzman, Anshul Jain, Matthias H. Tabert, Lucas C. Parra

Publications and Research

Odors can be powerful stimulants. It is well-established that odors provide strong cues for recall of locations, people and events. The effects of specific scents on other cognitive functions are less well-established. We hypothesized that scents with different odor qualities will have a different effect on attention. To assess attention, we used Inter-Subject Correlation of the EEG because this metric is strongly modulated by attentional engagement with natural audiovisual stimuli.We predicted that scents known to be “energizing” would increase Inter-Subject Correlation during watching of videos as compared to “calming” scents. In a first experiment, we confirmed this for eucalyptol and …

Inhibition Of Hdac1/2 Along With Trap1 Causes Synthetic Lethality In Glioblastoma Model Systems, Trang T. T. Nguyen, Yiru Zhang, Enyuan Shang, Chang Shu, Catarina M. Quinzii, Mike-Andrew Westhoff, Georg Karpel-Massler, Markus D. Siegelin

Publications and Research

The heterogeneity of glioblastomas, the most common primary malignant brain tumor, remains a significant challenge for the treatment of these devastating tumors. Therefore, novel combination treatments are warranted. Here, we showed that the combined inhibition of TRAP1 by gamitrinib and histone deacetylases (HDAC1/HDAC2) through romidepsin or panobinostat caused synergistic growth reduction of established and patient-derived xenograft (PDX) glioblastoma cells. This was accompanied by enhanced cell death with features of apoptosis and activation of caspases. The combination treatment modulated the levels of pro- and anti-apoptotic Bcl-2 family members, including BIM and Noxa, Mcl-1, Bcl-2 and Bcl-xL. Silencing of Noxa, BAK and …

Morphological And Molecular Characterizationof A New Species Of Black Coral From Elvers Bank, North-Western Gulf Of Mexico (Cnidaria:Anthozoa: Hexacorallia: Antipatharia:Aphanipathidae: Distichopathes), Dennis M. Opresko, Samantha L. Goldman, Raven Johnson, Katherine Parra, Marissa Nuttall, G.P. Schmahl, Mercer R. Brugler

Publications and Research

The continental shelf edge of the NW Gulf of Mexico supports dozens of reefs and banks, including the West and East Flower Garden Banks (FGB) and Stetson Bank that comprise the Flower Garden Banks National Marine Sanctuary (FGBNMS). Discovered by fishermen in the early 1900s, the FGBs are named after the colourful corals, sponges and algae that dominate the region. The reefs and banks are the surface expression of underlying salt domes and provide important habitat for mesophotic coral ecosystems (MCE) and deep coral communities to 300 m depth. Since 2001, FGBNMS research teams have utilized remotely operated vehicles (e.g. …

Circuits With Broken Fibration Symmetries Perform Core Logic Computations In Biological Networks, Ian Leifer, Flaviano Morone, Saulo D. S. Reis, José S. Andrade Jr., Mariano Sigman, Hernán A. Makse

Publications and Research

We show that logic computational circuits in gene regulatory networks arise from a fibration symmetry breaking in the network structure. From this idea we implement a constructive procedure that reveals a hierarchy of genetic circuits, ubiquitous across species, that are surprising analogues to the emblematic circuits of solid-state electronics: starting from the transistor and progressing to ring oscillators, current-mirror circuits to toggle switches and flip-flops. These canonical variants serve fundamental operations of synchronization and clocks (in their symmetric states) and memory storage (in their broken symmetry states). These conclusions introduce a theoretically principled strategy to search for computational building blocks …

Metabolomic Differences Between Invasive Alien Plants From Native And Invaded Habitats, Sarah A. Skubel, Xiaoyang Su, Alexander Poulev, Llewellyn C. Foxcroft, Vyacheslav Dushenkov, Ilya Raskin

Publications and Research

Globalization facilitated the spread of invasive alien species (IAS), undermining the stability of the world’s ecosystems. We investigated the metabolomic profiles of three IAS species: Chromolaena odorata (Asteraceae) Datura stramonium (Solanaceae), and Xanthium strumarium (Asteraceae), comparing metabolites of individual plants in their native habitats (USA), to their invasive counterparts growing in and around Kruger National Park (South Africa, ZA). Metabolomic samples were collected using RApid Metabolome Extraction and Storage (RAMES) technology, which immobilizes phytochemicals on glass fiber disks, reducing compound degradation, allowing long-term, storage and simplifying biochemical analysis. Metabolomic differences were analyzed using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) of samples …