Life Sciences Commons^™

Methods For Drone Trajectory Analysis Of Bottlenose Dolphins (Tursiops Truncatus), Jillian D. Bliss

Theses and Dissertations

With the increase in the use of UAS (Unmanned Aerial Systems) for marine mammal research, there is a need for the development of methods of analysis to transform UAS high resolution video into quantitative data. This study sought to develop a preliminary method of analysis that would quantify and present a way to visualize the dynamics and relative spatial distribution and changes in distribution of bottlenose dolphins (Tursiops truncatus) in the waters of Turneffe Atoll, Belize. This approach employs a previously developed video tracking program ‘Keypoint Tracking’ that enables manual tracking of individual dolphins and the creation of …

Effectiveness And Safety Of Direct Oral Anticoagulants Among Patients With Non-Valvular Atrial Fibrillation And Multimorbidity, Amol Dhamane, Mauricio Ferri, Allison V. Keshishian, Cristina Russ, Nipun Atreja, Cynthia Gutierrez, Birol Emir, Huseyin Yuce, Manuela Di Fusco

Publications and Research

Introduction

In the USA, there is a steady rise of atrial fibrillation due to the aging population with increased morbidity. This study evaluated the risk of stroke/systemic embolism (S/SE) and major bleeding (MB) among elderly patients with non-valvular atrial fibrillation (NVAF) and multimorbidity prescribed direct oral anticoagulants (DOACs).

Methods

Using the CMS Medicare database, a retrospective observational study of adult patients with NVAF and multimorbidity who initiated apixaban, dabigatran, or rivaroxaban from January 1, 2012 to December 31, 2017 was conducted. High multimorbidity was classified as having ≥ 6 comorbidities. Cox proportional hazard models were used to evaluate the hazard …

Eavesdropping On Animals: Can Bioacoustics Help Save Species?, Zoe Grueskin

Capstones

Around the world, scientists are using sound to study the natural world in a growing field called bioacoustics. Researchers are eavesdropping on frogs and fish, elephants and earthworms, and many hope what they hear can inform and inspire conservation action around the world. From the field’s auspicious beginning with accidentally-recorded whales, to researchers today listening to locations as diverse as the Arctic seafloor and India’s Western Ghats mountain range, this capstone project explores the potential — and limitations — of conservation bioacoustics. Read the story, see photos and listen to audio pieces featuring three bioacousticians and their field recordings here: …

Single-Cell Approach Reveals Intercellular Heterogeneity In Phage-Producing Capacities, Sherin Kannoly, Gabriella Oken, Jonathan Shadan, David Musheyev, Kevin Singh, Abhyudai Singh, John J. Dennehy

Publications and Research

Bacteriophage burst size is the average number of phage virions released from infected bacterial cells, and its magnitude depends on the duration of an intracellular progeny accumulation phase. Burst size is often measured at the population level, not the single-cell level, and consequently, statistical moments are not commonly available. In this study, we estimated the bacteriophage lambda (ƛ) single-cell burst size mean and variance following different intracellular accumulation period durations by employing Escherichia coli lysogens bearing lysis-deficient ƛ prophages. Single lysogens can be isolated and chemically lysed at desired times following prophage induction to quantify progeny intracellular accumulation within individual …

The Impact Of Pharmacogenetics On Oral Fluid Steady State Drug Testing Results, Aliya D. Lewis

Student Theses

Pharmacogenetics refers to the relationship between phenotypic variation in metabolism and response to certain drugs. The interface of pharmacogenetics and forensic toxicology is not well explored. A major component of the opioid metabolic pathway has to do with a family of cytochromes called cytochrome P450 (CYP450). CYP450 refers to a general family of enzymes capable of catalyzing the oxidative biotransformation of lipophilic substances, CYPs are further categorized into families and sub-families (Roller, 2015; Zanger & Schwab, 2013). The gene CYP2D6 belongs to the CYP2 family which is responsible for the biotransformation of xenobiotics. This study looked at the effect of …

Distinct Thalamic And Frontal Neuroanatomical Substrates In Children With Familial Vs. Non-Familial Attention-Deficit/Hyperactivity Disorder (Adhd), Rahman Baboli, Meng Cao, Jeffrey M. Halperin, Xiaobo Li

Publications and Research

Attention-deficit/hyperactivity disorder (ADHD) is a highly prevalent, inheritable, and heterogeneous neurodevelopmental disorder. Children with a family history of ADHD are at elevated risk of having ADHD and persisting its symptoms into adulthood. The objective of this study was to investigate the influence of having or not having positive family risk factor in the neuroanatomy of the brain in children with ADHD. Cortical thickness-, surface area-, and volume-based measures were extracted and compared in a total of 606 participants, including 132, 165, and 309 in groups of familial ADHD (ADHD-F), non-familial ADHD (ADHD-NF), and typically developed children, respectively. Compared to controls, …

How Will Climate Change Affect The Future, Ashanti K. Belone, Farrukh Zia

Publications and Research

Climate Change has played a massive role in the habitat of us earth dwellers and the animals that co-exists with us. I believe that essentially climate change plays a massive role because this can dictate whether or not the earth is habitable and if a need for evacuation is necessary. Many might believe that climate change only refers to the rising temperature but that’s just the icing on the cake. Earth is a system that is very much connected, this means that changes in one area will set off a chain reaction allowing these changes to happen in many other …

Females Exhibit Higher Glua2 Levels And Outperform Males In Active Place Avoidance Despite Increased Amyloid Plaques In Tgf344‑Alzheimer’S Rats, Osama Chaudry, Kelechi Ndukwe, Maria Figuiredo-Perira, Peter A. Serrano, Patricia Rockwell

Publications and Research

Alzheimer’s disease (AD) is a progressive neurodegenerative disease that is most prevalent in females. While estrogen provides neuroprotection in females, sex mediated differences in the development of AD pathology are not fully elucidated. Therefore, comparing events between sexes in early-stage AD pathology may reveal more effective therapeutic targets of intervention. To address sex differences, we analyzed early-stage 9-month male and female TgF344-AD (Tg-AD) rats, an AD model carrying the APPswe and Presenilin 1 (PS1ΔE9) mutations that develops progressive age-dependent AD pathology similar to humans. Tg-AD females significantly outperformed Tg-AD males in the active place avoidance (aPAT) test that assesses hippocampal-dependent …

Zebras Of All Stripes Repel Biting Flies At Close Range, Kaia J. Tombak, Andrew S. Gersick, Lily V. Reisinger, Brenda Larison, Daniel I. Rubenstein

Publications and Research

The best-supported hypothesis for why zebras have stripes is that stripes repel biting flies. While this effect is well-established, the mechanism behind it remains elusive. Myriad hypotheses have been suggested, but few experiments have helped narrow the field of possible explanations. In addition, the complex visual features of real zebra pelage and the natural range of stripe widths have been largely left out of experimental designs. In paired-choice field experiments in a Kenyan savannah, we found that hungry Stomoxys flies released in an enclosure strongly preferred to land on uniform tan impala pelts over striped zebra pelts but exhibited no …

Racial/Ethnic Disparities Of Cancer, Metabolic Syndrome, And Lifestyle Behaviors In People Under 50: A Cross-Sectional Study Of Data From The National Health And Nutrition Examination Survey, Lin Zhu, Areebah Rahman, Ming-Chin Yeh, Grace X. Ma

Publications and Research

Introduction: Recent epidemiological studies have suggested a trend of increasing preva- lence of metabolic syndrome (MetS) and certain types of cancer among adults under age 50. How MetS is associated with cancer in adults under the age of 50, however, remains unclear. Furthermore, it remains unknown whether associations between MetS and cancer vary by racial/ethnic group and whether modifiable lifestyle factors influence MetS–cancer relationships. Methods: We used data from the 2011–2018 National Health and Nutrition Examination Survey (NHANES) to define a case-control sample to examine potential racial/ethnic disparities associated with MetS and cancer of any type. We used a chi-square …

Reproductive Traits And Change In Body Shape Of Neonates In The Oak Forest Skink, Plestiodon Lynxe, Manuel Feria-Ortiz, Uri Omar García-Vázquez, Carlos Joaquín Pavón-Vázquez, Adrián Nieto-Montes De Oca

Publications and Research

Reproductive traits are critically important for understanding how organisms adapt to their respective environments. In this study, we provide information on relative litter mass (RLM) and other litter and neonate related characters of nine female Plestiodon lynxe captured in the field. We also recorded seven body dimensions in 16 neonates and 15 two-month juveniles, and on the basis of these dimensions we compared the body shape of these two age classes to detect changes in the proportions of body parts. The average litter size (4.55) is larger than that found in other viviparous species of Plestiodon, but smaller than …

Rescue Of Deficits By Brwd1 Copy Number Restoration In The Ts65dn Mouse Model Of Down Syndrome, Sasha L. Fulton, Wendy Wenderski, Ashley E. Lepack, Andrew L. Eagle, Tomas Fanutza, Ryan M. Bastle, Aarthi Ramakrishnan, Emma C. Hays, Arianna Neal, Jaroslav Bendl, Lorna A. Farrelly, Amni Al-Kachak, Yang Lyu, Bulent Cetin, Jennifer C. Chan, Tina N. Tran, Rachael L. Neve, Randall J. Roper, Kristen J. Brennand, Panos Roussos, John C. Schimenti, Allyson K. Friedman, Li Shen, Robert D. Blitzer, Alfred J. Robison, Gerald R. Crabtree, Ian Maze

Publications and Research

With an incidence of ~1 in 800 births, Down syndrome (DS) is the most com- mon chromosomal condition linked to intellectual disability worldwide. While the genetic basis of DS has been identified as a triplication of chromosome 21 (HSA21), the genes encoded from HSA 21 that directly contribute to cognitive de fi cits remain incompletely understood. Here, we found that the HSA21- encoded chromatin effector, BRWD1, was upregulated in neurons derived from iPS cells from an individual with Down syndrome and brain of trisomic mice. We showed that selective copy number restoration of Brwd1 in trisomic animals rescued de fi …

Inhibiting Glutamine Utilization Creates A Synthetic Lethality For Suppression Of Atp Citrate Lyase In Kras-Driven Cancer Cells, Ahmet Hatipoglu, Deepak Menon, Talia Levy, Maria A. Frias, David A. Foster

Publications and Research

Metabolic reprogramming is now considered a hallmark of cancer cells. KRas-driven cancer cells use glutaminolysis to generate the tricarboxylic acid cycle intermediate α -ketoglutarate via a transamination reaction between glutamate and oxaloacetate. We reported previously that exogenously supplied unsaturated fatty acids could be used to synthesize phosphatidic acid–a lipid second messenger that activates both mammalian target of rapamycin (mTOR) complex 1 (mTORC1) and mTOR complex 2 (mTORC2). A key target of mTORC2 is Akt–a kinase that promotes survival and regulates cell metabolism. We report here that mono- unsaturated oleic acid stimulates the phosphoryla tion of ATP citrate lyase (ACLY) at …

Forest Cover And Geographic Distance Influence Fine-Scale Genetic Structure Of Leaf-Toed Geckos In The Tropical Dry Forests Of Western Mexico, Connor M. French, Casey-Tyler Berezin, Isaac Overcast, Fausto R. Méndez De La Cruz, Saptarsi Basu, Roberto Lhemish Martínez Bernal, Robert W. Murphy, Michael J. Hickerson, Christopher Blair

Publications and Research

The biodiversity within tropical dry forests (TDFs) is astounding and yet poorly catalogued due to inadequate sampling and the presence of cryptic species. In the Mexican TDF, endemic species are common, and the landscape has been continually altered by geological and anthropogenic changes. To understand how landscape and environmental variables have shaped the population structure of endemic species, we studied the recently described species of leaf-toed gecko, Phyllodactylus benedettii, in coastal western Mexico. Using double-digest restriction site-associated DNA sequencing data, we first explore population structure and estimate the number of ancestral populations. The results indicate a high degree of …

Mutant C. Elegans P53 Together With Gain-Of-Function Glp-1/Notch Decreases Uvc-Damage-Induced Germline Cell Death But Increases Parp Inhibitor-Induced Germline Cell Death, Jorge Canar, Prima Manandhar-Sasaki, Jill Bargonetti

Publications and Research

The TP53 gene is mutated in over 50% of human cancers, and the C. elegans p53-1 (cep-1) gene encodes the ortholog CEP-1. CEP-1 is activated by ultraviolet type C (UVC)-induced DNA damage and activates genes that induce germline apoptosis. UVC treatment of gain-of-function glp-1(ar202gf)/Notch tumorous animals reduces germline stem cell numbers (and overall tumor size), while UVC treatment of double-mutant cep-1/p53(gk138);glp-1/Notch(ar202gf) increases DNA damage adducts and stem cell tumor volume. We compared UVC-induced mitotic stem cell death and animal lifespans for the two different C. elegans tumorous strains. C. elegans stem cell compartment death has never been observed, and we …

Small Molecule Modulation Of Microbiota: A Systems Pharmacology Perspective, Qiao Liu, Bohyun Lee, Lei Xie

Publications and Research

Background

Microbes are associated with many human diseases and influence drug efficacy. Small-molecule drugs may revolutionize biomedicine by fine-tuning the microbiota on the basis of individual patient microbiome signatures. However, emerging endeavors in small-molecule microbiome drug discovery continue to follow a conventional “one-drug-one-target-one-disease” process. A systematic pharmacology approach that would suppress multiple interacting pathogenic species in the microbiome, could offer an attractive alternative solution.

Results

We construct a disease-centric signed microbe–microbe interaction network using curated microbe metabolite information and their effects on host. We develop a Signed Random Walk with Restart algorithm for the accurate prediction of effect of microbes …

Novel Technologies To Characterize And Engineer The Microbiome In Inflammatory Bowel Disease, Alba Boix-Amorós, Hilarly Monaco, Elisa Sambataro, Jose C. Clemente

Publications and Research

We present an overview of recent experimental and computational advances in technology used to characterize the microbiome, with a focus on how these developments improve our understanding of inflammatory bowel disease (IBD). Specifically, we present studies that make use of flow cytometry and metabolomics assays to provide a functional characterization of microbial communities. We also describe computational methods for strain-level resolution, temporal series, myco - biome and virome data, co-occurrence networks, and compositional data analysis. In addition, we review novel techniques to therapeutically manipulate the microbiome in IBD. We discuss the benefits and drawbacks of these technologies to increase awareness …

Function Of Atm And Msh2 During Dna Repair And Recombination, Emily Sible

Dissertations, Theses, and Capstone Projects

Class switch recombination (CSR) produces secondary immunoglobulin isotypes and requires AID-dependent DNA deamination of intronic switch (S) regions within the immunoglobulin heavy chain (Igh) gene locus. Non-canonical repair of deaminated DNA by mismatch repair (MMR) or base excision repair (BER) creates DNA breaks that permit recombination between distal S regions. ATM-dependent phosphorylation of AID at serine-38 (pS38-AID) promotes its interaction with APE1, a BER protein, suggesting that ATM regulates CSR through BER. However, pS38-AID may also function in MMR during CSR, although the mechanism remains unknown. To examine whether ATM modulates BER- and/or MMR-dependent CSR, Atm^-/- mice …

Expulsive Greening: A Cross-Sectional Analysis Of Green Gentrification In The Resilience Paradigm, Brooklyn 2010–2020, Rose Jimenez

Dissertations, Theses, and Capstone Projects

Background: This project analyzes the spatial coincidence between gentrification typologies and urban greening in Brooklyn, New York from 2010 to 2020. Assets formed under the NYC Green Infrastructure Program were chosen as a proxy for urban greening to represent the spatial practice specifically within the 21st-century climate change resilience paradigm of development. Methods: First, five indexes measuring variations of economic and demographic conditions related to gentrification were applied to Brooklyn for comparative analysis: NOAA’s Social Vulnerability Indicators of Gentrification Pressure, The NYC Heat Vulnerability Index, The Small Area Index of Gentrification, Typologies of Gentrification and Displacement, and The Housing Risk …

Role Of Nuclear Lamins In Oligodendrocyte Lineage Cells, Camila Yattah

Dissertations, Theses, and Capstone Projects

Differentiation of oligodendrocytes from progenitor cells is a highly regulated process characterized by a series of molecular changes, resulting in nuclear and morphological features unique to the mature oligodendrocyte state. Heterochromatin formation starting at the nuclear periphery, as well as increased nuclear rigidity are characteristically observed. The nuclear periphery is characterized by the presence of the nuclear lamina and it has been implicated in higher-order genome organization in cells. Lamins are the protein components of the nuclear lamina, and their expression is dependent upon the cell differentiation stage of the cells. While Lamin B1 (LMNB1) expression is high in progenitors …

Unexpected Arousal Suppresses Memory And Metamemory Predictions During Associative Face-Name Recognition Task, Sameer Sabharwal-Siddiqi

Dissertations, Theses, and Capstone Projects

Successful recognition often depends on probabilistic estimation of memory-signal. Arousal has been shown to offset the influence of heuristic evidence on memory prediction. We conducted three experiments that tested whether arousal also suppresses predictions relevant to memory confidence. Experiments employed associative face-name memory tasks that included retrospective (Experiments 1 and 2) or concurrent (Experiment 3) judgements of confidence. During test, subjects were presented with a masked-affective face on a subset of trials. By timing the masked-affective face to precede a recognition judgement (Experiment 1), we replicated the finding that unexpected arousal offsets the influence of heuristic evidence on expectations of …

Clustered Protocadherins Ubiquitination And Phosphorylation Regulates Surface Expression, Albert Ptashnik

Dissertations, Theses, and Capstone Projects

Clustered protocadherins (Pcdhs) are a family of 60 adhesion-like molecules forming a neural barcode. In vertebrate neurons, 60 Pcdhs are coded by a large gene cluster. Numerous axons in the cluster are coding for the different extracellular, transmembrane, variable portion of the cytoplasmic and constant cytoplasmic domains where their expression is controlled epigenetically. These proteins mediate interactions between axons, dendrites, and glial cells during neural development. Yet, Pcdhs are not strictly adhesion molecules. In the amacrine cells of the retina, Pcdhs promote avoidance of the same cell dendrites, where in the cortex Pcdhs promote interactions between dendrites and astrocytes. In …

The Effects Of False Heartbeat Feedback On Moral Judgment, Scott Koenig

Dissertations, Theses, and Capstone Projects

Research on human morality is at a crossroads, with one side claiming that moral judgment is the result of rational inference and the other side claiming that it is the result of emotion-laden intuition. This study investigated whether emotion drives moral judgment by manipulating a core component of the experience of emotion: physiological arousal. The sample consisted of 77 undergraduate students at Brooklyn College (57% women, 43% men; mean age = 20.1). One group of participants was led to believe their heart was beating quickly, and another group slowly, while they read and evaluated a series of text vignettes depicting …

Novel Therapeutic Strategies For Alzheimer’S Disease: Prostaglandin D2 Signaling And Its Human Polymorphisms As Well As A Polypharmacological Approach, Charles H. Wallace

Dissertations, Theses, and Capstone Projects

Alzheimer’s disease (AD) is an age related neurodegenerative disease with pathology that includes amyloid plaques, neurofibrillary tangles and non-resolving neuroinflammation. Non-resolving neuroinflammation lasts the entire course of the disease and has deleterious effects and is often thought to accelerate AD pathology. Non-Steroidal Anti-inflammatory Drugs (NSAIDs) have commonly been used as therapeutics to treat pain, inflammation and vascular. NSAIDs work by altering the cyclooxygenase (COX) mediated biosynthesis of prostaglandins which are lipid mediators that have many physiological functions, for example nociception, inflammation and vasodilation. Epidemiological studies support the notion that NSAIDs could be used to treat AD. Yet, clinical trials using …

A Polypharmacological Approach To Relapse Prevention In An Animal Model Of Heroin Addiction, Scott T. Ewing

Dissertations, Theses, and Capstone Projects

Chemical compounds that target dopamine (DA) D1 or D3 receptors have shown promise as potential interventions in animal models of cue-induced relapse. However, undesirable side effects or pharmacodynamic profiles have limited the advancement of new compounds in preclinical studies when administered as independent treatments. In this series of experiments, we explored the effects of co-administration of a D1-recepter partial agonist (SKF 77434) and a D3-receptor antagonist (NGB 2904) in heroin-seeking rats within a ‘conflict’ model of abstinence and cue-induced relapse. Rats were first trained to press a lever to self-administer heroin and drug delivery was paired contingently with cues (e.g., …

Role Of The G Protein Beta Gamma Subunits In Serotonin Transporter Dynamics, Nora Awadallah

Dissertations, Theses, and Capstone Projects

Serotonin is a vital neurotransmitter and hormone with significant roles in almost every organ system. In the central nervous system, serotonin mediates physiological functions that in turn guide behavior and mood. Here, serotonin is released from serotonergic neurons and exerts its effects through serotonin receptors. Regulation of serotonin neurotransmission is important for the maintenance of its physiological functions; thus, extracellular serotonin must be sequestered to limit the intensity and duration of serotonin transmission. Disproportionate transmission is strongly linked with neurological and psychiatric ailments.

Extracellular serotonin levels are primarily mediated by the serotonin transporter (SERT), a critically important plasma membrane protein …

Prenatal Choline Supplementation During Maternal Obesity Alters Offspring Response To Western Diets, Hunter W. Korsmo

Dissertations, Theses, and Capstone Projects

Maternal obesity has led to an increase in adverse offspring developmental outcomes and a greater risk for long-term metabolic diseases. Choline, a semi-essential nutrient, can be incorporated into phosphatidylcholine (PC) as well as sphingomyelin (SM) and donate its labile methyl group for the remethylation of homocysteine after choline is oxidized to betaine. Prenatal choline insufficiency has been related to maternal obesity and metabolic diseases, such as metabolic associated fatty liver disease (MAFLD). Choline may interact with maternal obesity to influence the programming offspring.

Chapter 1 presents an introduction of choline and the various clinical outcomes associated with choline supplementation during …

Determining The Roles Of The Oligomerization And C-Terminal Domains In Mutant P53 Gain-Of-Function Activities, George K. Annor

Dissertations, Theses, and Capstone Projects

The tumor suppressor p53 (TP53) gene is often mutated in cancer, with missense mutations found in the central DNA binding domain, and less often in the oligomerization domain (OD) and C-terminal domain (CTD). The OD and CTD have been found to be critical for the tumor suppressor functionality of wild-type p53 (wtp53). Specific missense mutations in the DNA binding domain have been found to confer new gain-of-function (GOF) activities. Mutations that destabilize tetramer formation, or deletion of key lysine residues within the CTD, downregulate the ability of wtp53 to transactivate (increase the rate of transcription of) its target …

Mechanism Of Activation And Regulation Of By-Kinases, A Unique Family Of P-Loop Enzymes, Fatlum Hajredini

Dissertations, Theses, and Capstone Projects

The bacterial tyrosine kinases (BY-kinase) represent a class of membrane-bound enzymes that utilize a cycle of auto-phosphorylation and de-phosphorylation to drive the synthesis and export of exopolysaccharides in both Gram-positive and Gram-negative bacteria. The catalytic domain of BY-kinases utilizes a P-loop nucleoside triphosphatase (NTPase) fold that is commonly used by NTPases and small molecule kinases, being the only protein kinase to do so. In the work presented in this thesis, we aimed to obtain an understanding of the mechanisms of the BY-kinases’ unconventional deployment of P-loop scaffold to phosphorylate on tyrosine. We used the BY-kinase of Escherichia coli (K12) as …

Nutrient Dynamics And Ecosystem Development Of Urban Forests, Gisselle A. Mejía

Dissertations, Theses, and Capstone Projects

Urban growth and expansion are a major component of global environmental change, with impacts on climate, air and water quality, biodiversity, and human well-being. Forests embedded in urban landscapes are critical in mitigating these impacts at local, regional, and continental scales. However, assessing urban forests is difficult because cities are heterogenous in physical, chemical, biological, and social dimensions. This heterogeneity has constrained how urban forests are defined, and therefore, how they are studied. The objective of this dissertation is to determine how these biophysical and social factors drive ecological processes in urban forests and will address three outstanding challenges in …