Life Sciences Commons^™

Identification Of Tandem Repeat Families From Long-Read Sequences Of Humulus Lupulus, Katherine A. Easterling, Nicholi J. Pitra, Taylan B. Morcol, Jenna R. Aquino, Lauren G. Lopes, Kristin C. Bussey, Paul D. Matthews, Hank W. Bass

Publications and Research

Hop (Humulus lupulus L.) is known for its use as a bittering agent in beer and has a rich history of cultivation, beginning in Europe and now spanning the globe. There are five wild varieties worldwide, which may have been introgressed with cultivated varieties. As a dioecious species, its obligate outcrossing, non-Mendelian inheritance, and genomic structural variability have confounded directed breeding efforts. Consequently, understanding the hop genome represents a considerable challenge, requiring additional resources. In order to facilitate investigations into the transmission genetics of hop, we report here a tandem repeat discovery pipeline developed using k-mer filtering and dot plot …

Evaluating Satellite-Based Sea Surface Temperatures, In Situ Observations, And Coral Symbioses In Southwestern Puerto Rico, Andrea Michelle Gomez

Dissertations, Theses, and Capstone Projects

I examined the effects of in situ and satellite-based sea surface temperatures (SST) on the seasonal coral-algae symbiotic relationship in La Parguera, Puerto Rico. Climate change-driven rising sea temperatures are endangering most of the world’s reefs, which are currently in decline. Satellite remote sensing datasets support global-scale characterization and monitoring of risks to reefs associated with increasing temperatures. Corals’ unique symbiotic relationship with unicellular algae in the family Symbiodiniaceae is largely responsible for helping corals cope with increasing ocean temperatures, and some corals are able to adjust their symbiont species in response to temperature disturbances. My research had two components …

Dna Damage Recognition And Uvrb Loading By Uvra Within The Nucleotide Excision Repair Pathway, Silas Hartley

Dissertations, Theses, and Capstone Projects

Maintaining the cellular genome is paramount to survival by any organism. A mutated genome can have detrimental effects on different cellular processes, especially replication and transcription. Cells maintain their genome using different deoxyribonucleic acid (DNA) repair pathways. The nucleotide excision repair (NER) pathway has a unique capability of repairing the genome from several different mutations, deletions, and adducts. In bacteria, the NER pathway accomplishes repair through four important steps: damage recognition by UvrA, damage verification by UvrB, DNA incision by UvrC, and repair synthesis using various cellular machinery.

UvrA forms a head-to-head dimer (UvrA₂) with two ATPase sites …

Development Of Ligand Guided Selection (Ligs) To Identify Specific Dna Aptamers Against Cell Surface Proteins, Hasan Ekrem Zumrut

Dissertations, Theses, and Capstone Projects

Oligonucleotide aptamers (nucleic acid-based affinity reagents) are an emerging class of synthetic molecules that display high affinity and specificity towards their targets. Aptamer molecules for a target of interest are obtained using a combinatorial chemistry-based method termed systematic evolution of ligands by exponential enrichment (SELEX). SELEX is an in vitro selection process in which a random oligonucleotide library is subjected to repeated cycles of target incubation, separation, and amplification until target-specific evolved sequences become prevalent in the library. Typically, SELEX is used against target molecules such as small molecules and proteins, in their purified state. However, aptamers selected against purified …

Gene Regulation And Cell Fate Choice In The Developing Vertebrate Retina, Sruti Patoori

Dissertations, Theses, and Capstone Projects

The diverse neuronal cell types in the vertebrate retina all originate from multipotent retinal progenitor cells (RPCs). These undergo a series of molecular changes driven by developmental gene regulatory networks (GRNs) as they divide to generate RPCs which are more restricted in their potential fates. It is crucial to understand these GRNs and changes to gene expression in order to understand how cell identity is established during retinal development. In particular, the GRN that promotes the development of cone photoreceptors and horizontal cells is not well-defined. This work focuses on two approaches to further elucidate the components of this regulatory …

Probing The Limits Of Singular Gene Expression Through The Activity Of High Representation Odorant Receptor Transgenes, Eugene Lempert

Dissertations, Theses, and Capstone Projects

Singular gene expression is a common phenomenon in biology, making its appearance in immunoglobulin selection, protocadherin expression, X chromosome-inactivation, random monoallelic expression, and olfactory receptor choice. Singularity involves an activation and a feedback step. The mechanisms of singular gene choice have some capacity to integrate additional member genes while still maintaining singularity, but will activate an additional member if an earlier choice was incapable of triggering the feedback step. Odorant Receptor (OR) genes are substantially divergent from each other in terms of coding sequence, promoter structure, and genomic locus, all of which plays a role in how many Olfactory Sensory …

A Diverse And Inclusive Academic Membership For All, Victor Puac-Polanco, Alfredo Morabia

Publications and Research

With the growing recognition that diversity and inclusion are essential for the improvement of science and innovation, this commentary provides some perspectives on three findings in the DeVilbiss et al. (2020)'s article and provide points of discussion on factors and strategies to consider when drafting diversity and inclusion programs for the Society for Epidemiologic Research.

Elucidating The Role Of Apl-1, The C. Elegans Ortholog Of The Human Amyloid Precursor Protein, Adanna G. Alexander

Dissertations, Theses, and Capstone Projects

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, impacting approximately 6 million Americans. AD is the leading cause of dementia amongst the aged population. Post mortem analysis of the brains of AD patients shows high quantities of extracellular Aβ peptide deposits, which are derived from cleavage of the amyloid precursor protein (APP). Mutations in APP and proteins responsible for APP cleavage, PSENs, greatly increase the incidence of developing AD at an early age. Despite its strong correlation to the progression of AD, the role of APP remains unclear.

Here we investigate the role of the Caenorhabditis elegans ortholog, APL-1. We …

Molecular Roles Of Small Inner Membrane Proteins In Escherichia Coli Cell Envelope Integrity, Aaron Mychack

Dissertations, Theses, and Capstone Projects

The biological membrane is an essential, defining feature of all cells. Biological membranes comprise phospholipid bilayers as well as a complement of proteins which are unique to a given organism. These proteins play a central role in dictating the biochemical state of the cell’s internal cytoplasm by controlling selective passage of solutes in and out of the cell, transducing signals in response to extracellular stimuli, and controlling the biogenesis of the bilayer itself which is critical towards barrier function. For most bacteria, the periphery of the cell is multi-layered, including both a biological membrane as well as a peptidoglycan cell …

Proactive And Reactive Aggression, Respiratory Sinus Arrhythmia, And Sleep In Adolescents, Allison L. Brasch

Dissertations, Theses, and Capstone Projects

Current research evaluating the relationship between proactive and reactive aggression, sleep, and autonomic dysfunction has shown inconsistencies. The unique etiologies, manifestations, and presentation of these two aggressive subtypes have garnered much speculation, and research has shown mixed, and oftentimes conflicting, results. Generally speaking, insufficient sleep has been linked to increased agitation, cognitive impairment, emotional dysregulation, and poorer physical health. Many studies have provided support for an inverse relationship existing between sleep problems and sympathovagal health, implicating hypo- or hyper-autonomic function with proactive and reactive aggression, respectively. Concurrently and conflictingly, additional research has shown support for the exact opposite relationships between …

The Effects Of Self-Esteem And Motivation On Cognitive Control, Andrea Benavides

Dissertations, Theses, and Capstone Projects

Cognitive control describes a set of mechanisms that guide behavior towards a goal (Cohen, 2017). The successful execution of cognitive control is essential for effective learning, information processing, problem solving, and academic achievement (Visu-Petra et al., 2011). The Expected Value of Control framework (EVC; Shenhav et al., 2013) suggests that control carries an inherent cost, which is weighed against the potential benefits of expending it. This cost-benefit analysis determines the direction and intensity that a goal is pursued. Importantly, motivation plays a role in this cost-benefit analysis and may function as the factor that offsets the cost of control expenditure …

The Impact Of A Single Session Of Mindfulness Meditation On The Attentional Blink In Non-Meditators, Arielle L. Klopsis

Dissertations, Theses, and Capstone Projects

Attentional resources are limited therefore a stimulus can go undetected if it closely follows another target by 200-500ms. This phenomenon is known as the attentional blink. Mindfulness meditation has been shown to be beneficial in target detection and in decreasing the attentional blink. Since there is no standard for the type of meditation or duration of practice that leads to attention benefits, this study compares the two most popular types of meditation in a group of non-meditators: focused attention and open monitoring meditation. This study utilized an attentional blink paradigm to measure if a single session of mindfulness meditation can …

Proton Pumping Mechanism In Cytochrome C Oxidase, Xiuhong Cai

Dissertations, Theses, and Capstone Projects

Cytochrome c Oxidase (CcO), is the terminal electron acceptor in the membrane bound aerobic respiratory chain. It reduces O₂ to water. The energy released by this reaction is stored by pumping protons from the high pH, N-side of the membrane to the low pH, P-side. The generated proton gradient provides the motive force for synthesis of ATP by the ATP synthase.

Building a proton gradient across the membrane requires that proton transport must occur along controllable proton pathways to prevent proton leakage to the N-side. It has been suggested that CcO function requires proton transfer channels in both the …

Structural And Dynamic Features Of A Transiently Assembled Complex Between A Bacterial Tyrosine Kinase And Its Cognate Phosphatase, Imane Djemil

Dissertations, Theses, and Capstone Projects

Bacterial tyrosine kinases (BY-kinases) and their cognate Low Molecular Weight Tyrosine Phosphatases (LMW-PTP) work synergistically to regulate diverse physiological processes in both Gram-negative and Gram-positive bacteria. Of these processes, the most widely recognized role of the kinase/phosphatase pair is the biosynthesis and transport of surface polysaccharides. A process that is key in protecting bacterial cell from a variety of environmental stresses through biofilm formation, and the generation of virulence-determining capsules in pathogenic strains. BY-kinases contain a C-terminal tyrosine rich cluster (Y-cluster) located on the catalytic domain that undergoes auto-phosphorylation and is subsequently dephosphorylated by the cognate LMW-PTPs. This phosphorylation/dephosphorylation cycle …

Dictyostelium Discoideum Protein Kinase C-Orthologue Pkca Regulates The Actin Cytoskeleton Through Interaction With Phospholipase D And P21-Activated Kinase, Sean Singh

Dissertations, Theses, and Capstone Projects

Proper regulation of the actin cytoskeleton is crucial to many cellular processes. Many of these processes are regulated by extracellular signaling cues, which direct changes in the actin cytoskeleton, resulting in changes to cellular morphology, and directed motility. The social amoeba, Dictyostelium discoideum, is used as a simple model system to study the translation of extracellular signals to the actin cytoskeleton. When starved, these unicellular amoebae undergo a multicellular developmental process characterized by a tightly regulated sequence of signaling events. This results in chemotaxis and formation of a multicellular aggregate, and ultimately cell differentiation and the formation of a fruiting …

Creating Content For A Healthy New Life, Valeria C. Borja Lopez

Dissertations, Theses, and Capstone Projects

Creating Content for a Healthy New Life is a project consisting of the development of a web page to connect holistic practitioners to people. This page will also allow for the promotion and sale of Ayurvedic Skincare products and services. For the capstone project, I developed a business model for the enterprise. This model offers an educational component by educating our customers to understand the importance of using holistic approaches rather than traditional ones. For this, two videos were developed to educate customers about Ayurveda and the science behind the proposed products and services. I am an experienced Holistic Practitioner, …

Protein Phosphatase 2a Suppresses Spindle Elongation In Saccharomyces Cerevisiae, Shoily P. Khondker

Dissertations, Theses, and Capstone Projects

Eukaryotic cell division is an essential process that is carried out by the cell cycle, a tightly controlled process that has been extensively studied in the budding yeast Saccharomyces cerevisiae. The cell cycle is driven by Cyclin Dependent Kinase (Cdk1) activity. Protein phosphatase 2A-Cdc55 (PP2A^Cdc55) reverses Cdk1 phosphorylation events during late stages of the cell cycle to ensure the correct order of events. This thesis presents evidence that the anaphase inhibitor Pds1 is a PP2A^Cdc55 target. Pds1 binds to and inhibits separase (Esp1). Esp1 triggers sister chromatid segregation by cleaving the cohesin complex that holds the …

Functional Connectivity Of Eeg Is Subject-Specific, Associated With Phenotype, And Different From Fmri, Maximilian Nentwich, Lei Ai, Jens Madsen, Qawi K. Telesford, Stefan Haufe, Michael P. Milham, Lucas C. Parra

Publications and Research

A variety of psychiatric, behavioral and cognitive phenotypes have been linked to brain ‘’functional connectivity’’ -- the pattern of correlation observed between different brain regions. Most commonly assessed using functional magnetic resonance imaging (fMRI), here, we investigate the connectivity-phenotype associations with functional connectivity measured with electroencephalography (EEG), using phase-coupling. We analyzed data from the publicly available Healthy Brain Network Biobank. This database compiles a growing sample of children and adolescents, currently encompassing 1657 individuals. Among a variety of assessment instruments we focus on ten phenotypic and additional demographic measures that capture most of the variance in this sample. The largest …

Using Short Chain Fatty Acids To Inactivate Pseudomonas Aeruginosa Biofilms, Stephen Lee

Dissertations and Theses

Abstract

Using Short Chain Fatty Acids to Disinfect Pseudomonas Aeruginosa Biofilms

by

Stephen Lee

Background

The study of bacteria typically focuses on the planktonic or free-living single-cell state that is purely cultured in a laboratory for subsequent growth with appropriate media. Although this traditional way of growing bacteria has been paramount to the understanding of bacterial behavior, physiology, and pathogenesis, bacteria rarely exist as pure cultures of planktonic growth forms in the natural habitat. Bacterial contamination of environmental surfaces, in the form of biofilms, is a prime public health problem and causes numerous infections within the general public. Biofilms are …

Two Nights Of Recovery Sleep Restores Hippocampal Connectivity But Not Episodic Memory After Total Sleep Deprivation, Ya Chai, Zhuo Fang, Fan Nils Yang, Sihua Xu, Yao Deng, Andrew Raine, Jieqiong Wang, Meichen Yu, Mathias Basner, Namni Goel, Junghoon J. Kim, David A. Wolk, John A. Detre, David F. Dinges, Hengyi Rao

Publications and Research

Sleep deprivation significantly impairs a range of cognitive and brain function, particularly episodic memory and the underlying hippocampal function. However, it remains controversial whether one or two nights of recovery sleep following sleep deprivation fully restores brain and cognitive function. In this study, we used functional magnetic resonance imaging (fMRI) and examined the effects of two consecutive nights (20-hour time-in-bed) of recovery sleep on resting-state hippocampal connectivity and episodic memory deficits following one night of total sleep deprivation (TSD) in 39 healthy adults in a controlled in-laboratory protocol. TSD significantly reduced memory performance in a scene recognition task, impaired hippocampal …

An Osteocalcin-Deficient Mouse Strain Without Endocrine Abnormalities, Cassandra R. Diegel, Steven Hann, Ugar M. Ayturk, Jennifer C. W. Hu, Kyungeun Lim, Casey J. Droscha, Zachary B. Madaj, Gabrielle E. Foxa, Isaac Izaguirre, Vai Vivarium And Transgenics Core, Noorulain Paracha, Bohdan Pidhaynyy, Terry L. Dowd, Alexandra G. Robling, Matthew L. Warman, Bart O. Williams

Publications and Research

Osteocalcin (OCN), the most abundant noncollagenous protein in the bone matrix, is reported to be a bone-derived endocrine hormone with wide-ranging effects on many aspects of physiology, including glucose metabolism and male fertility. Many of these observations were made using an OCN-deficient mouse allele (Osc– ) in which the 2 OCN-encoding genes in mice, Bglap and Bglap2, were deleted in ES cells by homologous recombination. Here we describe mice with a new Bglap and Bglap2 double-knockout (dko) allele (Bglap/2p.Pro25fs17Ter) that was generated by CRISPR/Cas9-mediated gene editing. Mice homozygous for this new allele do not express full-length Bglap or Bglap2 mRNA …

16s Rrna Amplicon Sequencing Of Urban Prokaryotic Communities In The South Bronx River Estuary, Eugenia Naro-Maciel, Melissa R. Ingala, Irena E. Werner, Allison M. Fitzgerald

Publications and Research

Biodiversity monitoring is an essential component of restoration efforts. We sequenced 16S rRNA gene amplicons from sediments and waters of Hunts Point Riverside Park and Soundview Park, located in a historically degraded but recovering urban estuary in New York. In total, 16,165 unique amplicon sequence variants were recovered, and Proteobacteria was the dominant phylum.

16s Rrna Amplicon Sequencing Of Urban Prokaryotic Communities In The South Bronx River Estuary, Eugenia Naro-Maciel, Melissa R. Ingala, Irena E. Werner, Allison M. Fitzgerald

Publications and Research

Biodiversity monitoring is an essential component of restoration efforts. We sequenced 16S rRNA gene amplicons from sediments and waters of Hunts Point Riverside Park and Soundview Park, located in a historically degraded but recovering urban estuary in New York. In total, 16,165 unique amplicon sequence variants were recovered, and Proteobacteria was the dominant phylum.

Can Transcranial Electrical Stimulation Motor Threshold Estimate Individualized Tdcs Doses Over The Prefrontal Cortex? Evidence From Reverse-Calculation Electric Field Modeling, Kevin A. Caulfield, Bashar W. Badran, Xingbao Li, Marom Bikson, Mark S. George

Publications and Research

No abstract provided.

Effect Of Non-Muscle Myosin Ii Inhibition On Epigenetics During Oligodendrocyte Development, Amr Almaktari

Theses and Dissertations

Non-Muscle Myosin II (NMII) is a mechanosensitive motor protein implicated in oligodendrocyte (OL) development. The inhibition of NMII is known to promote OL development and maturation. This project found that NMII inhibition does not affect oligodendrocyte development by altering their epigenetic profile.

Pvt1 Exon 9 A Regulator Of Claudin Expression In Triple Negative Breast Cancer, Fayola Levine

Theses and Dissertations

Claudin low triple negative breast cancer (TNBC) has the worst clinical outcomes in comparison to other breast cancer subtypes. The underlying molecular mechanisms associated with the aberrant expression of claudins are not well understood. The transcript from PVT1 exon 9 is a regulator of claudin expression, and migration, in TNBC.

Cytotoxic Analysis Of Old Drugs: New Drugs For Alzheimer’S Disease, Sebastian Yumiseba

Theses and Dissertations

Microglia are the resident immune cells of the CNS and constitute about 10% of all cells in the CNS. They have a vital role in Alzheimer’s pathogenesis as either cytotoxic or neuroprotective. Recent efforts are being put into repurposing drugs to target the microglia to treat Alzheimer’s disease.

Snapshots Of Human Anatomy, Locomotion, And Behavior From Late Pleistocene Footprints At Engare Sero, Tanzania, Kevin Hatala, William E. H. Harcourt-Smith, Adam D. Gordon, Brian W. Zimmer, Brian G. Richmond, Briana L. Pobiner, David J. Green, Adam Metallo, Vince Rossi, Cynthia M. Liutkus-Pierce

Publications and Research

Fossil hominin footprints preserve data on a remarkably short time scale compared to most other fossil evidence, offering snapshots of organisms in their immediate ecological and behavioral contexts. Here, we report on our excavations and analyses of more than 400 Late Pleistocene human footprints from Engare Sero, Tanzania. The site represents the largest assemblage of footprints currently known from the human fossil record in Africa. Speed estimates show that the trackways reflect both walking and running behaviors. Estimates of group composition suggest that these footprints were made by a mixed-sex and mixed-age group, but one that consisted of mostly adult …

Expression Analyses Of Hippocampal And Cortical Proteins In A Rat Model For Alzheimer’S Disease, Rangon Islam

Theses and Dissertations

Currently, Alzheimer’s disease (AD) has no cure. Using a rat AD model, we identified aberrantly expressed proteins during pre-pathology as potential biomarkers. The expression of certain biomarkers was reversed by diazoxide, a repurposed hypertension drug. These results suggest that drug repurposing at an early stage of AD has therapeutic potential.

Presence Of Electron Donor/Acceptor Radiographic Contrast Media In Unusual Photosynthesis Environment Of Fresh Plant Cells: Near-Infrared And X-Ray Characterization, Tetiana Soloviova, Subhendra Sarkar, Amina Shahbaz, Aldona Gjoni

Publications and Research

Photosynthesis is a chemical process through which light energy is used to convert inorganic material (water and carbon dioxide) into organic molecules. Anaerobic photosynthesis, also known as anoxygenic photosynthesis, is the process by which certain bacteria use light energy to create organic compounds but do not adequately involve oxygen. In this experiment we are trying to influence photosynthesis (light and dark reactions: PS-I and PS-II by electron rich gadolinium/iodine complexes like Eovist and Isovue. We also performed X-ray and NIR reflection spectroscopy (NIRS) to measure Gd difusivity and PS-I/II infrared response. The results for X-ray (45kvp and 5 Mas ) …