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Role Of Tissue Microenvironment In Recruiting Macrophages During Apoptosis-Induced Proliferation, Neha Diwanji 2020 University of Massachusetts Medical School

Role Of Tissue Microenvironment In Recruiting Macrophages During Apoptosis-Induced Proliferation, Neha Diwanji

GSBS Dissertations and Theses

Apoptosis-induced compensatory proliferation (AiP) is a mechanism that maintains tissue homeostasis after stress-induced cell death. During AiP, apoptotic cells induce proliferation of the neighboring surviving cells to compensate for tissue loss. AiP is important for wound healing and tissue regeneration in several model organisms. Additionally, AiP is an important feature of tumorigenesis and tumor relapse as it contributes to tumor repopulation following radiation or chemotherapy. Using an overgrowth tumor model (“undead tissue”) in Drosophila melanogaster, we determined that the initiator caspase Dronc promotes generation of extracellular Reactive Oxygen Species (ROS), which drive activation of the stress kinase JNK and downstream ...


Use Of Embark Database And An Active Learning Protocol In A High School Classroom, Landon Goodreau 2020 University of Mississippi

Use Of Embark Database And An Active Learning Protocol In A High School Classroom, Landon Goodreau

Honors Theses

With advances in technology, personal genome sequencing has become more affordable than ever before. With this wealth of genetic information come new individualized approaches to medicine and pharmacology, along with moral, legal, and ethical issues to carefully consider. Yet studies suggest that most members of the general public do not have the genetic literacy required to understand the implications of genomic data. It is important that today’s students are able to grasp concepts relating to their own genome to make informed medical decisions in the future. Here I describe an active learning-based activity designed to enhance high school students ...


The Embark® Protocol: Dog Genomics In Genetics Laboratories, Alexandra Kissel 2020 University of Mississippi

The Embark® Protocol: Dog Genomics In Genetics Laboratories, Alexandra Kissel

Honors Theses

In a world of ever-advancing technology, it is imperative that young pre-health professionals are educated according to the most relevant research. One of the most fundamental, foundational concepts of health is genetics. This field is rapidly expanding, and quickly engraining itself into the realm of healthcare. Genetic testing and gene therapies, once subjects of science fiction, have become commonplace. It is more important than ever that health professionals have a concrete knowledge of genetics, and this begins with the proper education of pre-health students.

With this idea in mind, a laboratory protocol was designed for students of the Bisc 336 ...


Population Genetics Of A Recent Range Expansion By The Southern Pine Beetle, Dendroctonus Frontalis, Into The Northeastern United States, Megan Stubbs 2020 University of Mississippi

Population Genetics Of A Recent Range Expansion By The Southern Pine Beetle, Dendroctonus Frontalis, Into The Northeastern United States, Megan Stubbs

Honors Theses

Population genetics as a field of study aims to determine the genetic variation among individuals in a population, and differences among populations. Certain population genetic analyses can provide such information and be used to better understand the biological aspects to a species’ expansion beyond its native range. The southern pine beetle (SPB), Dendroctonus frontalis, has become an invasive pest to pine forests in northeastern United States with its recent range expansion. Nine microsatellite loci were first developed and then used in analyses. To determine what the genetic variation is among individuals in SPB populations across its entire range, including ones ...


Multi-Generational Effects Of ∆9-Tetrahydrocannabinol Exposure On Gene Expression In Liver Tissue, Kayla Lovitt 2020 University of Mississippi

Multi-Generational Effects Of ∆9-Tetrahydrocannabinol Exposure On Gene Expression In Liver Tissue, Kayla Lovitt

Honors Theses

Cannabis is the most commonly used, cultivated, and trafficked illicit drug worldwide. Increased availability and acceptance of cannabis and cannabinoid-containing products provide the necessity for understanding how these substances influence aging. In this study, zebrafish (Danio rerio) were exposed to concentrations of Δ9-tetrahydrocannabinol (THC) (0.08, 0.4, 2 µM) during embryonic-larval development, the effects on aging were measured 30 months later and in the offspring of the exposed fish (F1 generation. We observed results indicating a biphasic and hormetic effect. Treatment with the lowest concentration of THC significantly increased egg production, while higher concentrations resulted in impaired ...


Population Structure And Reproductive Biology Of Monilinia Vaccinii-Corymbosi (Reade) Honey In Lowbush Blueberry In Maine, Katherine A. Ashley 2020 University of Maine

Population Structure And Reproductive Biology Of Monilinia Vaccinii-Corymbosi (Reade) Honey In Lowbush Blueberry In Maine, Katherine A. Ashley

Electronic Theses and Dissertations

Lowbush blueberry, Vaccinium angustifolium Aiton, is both an economically and culturally important crop in Maine, being one of the few endemic crops to North America. The fungus Monilinia vaccinii-corymbosi (Mvc) causes mummy berry disease and is a significant pathogen of both highbush (Vaccinium corymbosum) and lowbush blueberries. While impacts of this disease are not regularly documented, it is estimated that 30-50% of the yield in an unmanaged field can be lost because of Mvc. This disease is typically managed with fungicides or burning of the field during years when the field is pruned, however, the impacts to the population structure ...


Control Of Adipocyte Thermogenesis And Lipogenesis Through Beta3-Adrenergic And Thyroid Hormone Signal Integration, Adilson L. Guilherme, Batuhan Yenilmez, Alexander H. Bedard, Felipe Henriques, Dianxin Liu, Alexandra Lee, Lauren Goldstein, Mark Kelly, Sarah M. Nicoloro, Min Chen, Lee Weinstein, Sheila Collins, Michael P. Czech 2020 University of Massachusetts Medical School

Control Of Adipocyte Thermogenesis And Lipogenesis Through Beta3-Adrenergic And Thyroid Hormone Signal Integration, Adilson L. Guilherme, Batuhan Yenilmez, Alexander H. Bedard, Felipe Henriques, Dianxin Liu, Alexandra Lee, Lauren Goldstein, Mark Kelly, Sarah M. Nicoloro, Min Chen, Lee Weinstein, Sheila Collins, Michael P. Czech

Open Access Articles

Here, we show that beta adrenergic signaling coordinately upregulates de novo lipogenesis (DNL) and thermogenesis in subcutaneous white adipose tissue (sWAT), and both effects are blocked in mice lacking the cAMP-generating G protein-coupled receptor Gs (Adipo-GsalphaKO) in adipocytes. However, UCP1 expression but not DNL activation requires rapamycin-sensitive mTORC1. Furthermore, beta3-adrenergic agonist CL316243 readily upregulates thermogenic but not lipogenic genes in cultured adipocytes, indicating that additional regulators must operate on DNL in sWAT in vivo. We identify one such factor as thyroid hormone T3, which is elevated locally by adrenergic signaling. T3 administration to wild-type mice enhances both thermogenesis and DNL ...


Effect Of Low Dose Irradiation On Expression Of Genes Involved In Ethylene Biosynthesis Of 'Granny Smith' Apples, Brian Nyakundi 2020 Chapman University

Effect Of Low Dose Irradiation On Expression Of Genes Involved In Ethylene Biosynthesis Of 'Granny Smith' Apples, Brian Nyakundi

Food Science (MS) Theses

Superficial scald is a physiological disorder characterized by skin browning that appears during or after storage of ‘Granny Smith’ apples. The mechanism for scald development is not fully understood, but it is hypothesized that scald formation is related to increased ethylene production. In apples, low dose irradiation induced ethylene reduction appears to be directly related to prevention of superficial scald. However, the molecular basis of such an irradiation induced effect is not known. In this study, effort was made to better understand the molecular basis of the decrease in ethylene production in apple fruit after treatment with x-ray irradiation. ‘Granny ...


Smrt Sequencing Of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability In Adenines Targeted By Restriction Modification Systems, Samantha R. Coy, Eric R. Gann, Spiridon E. Papoulis, Michael E. Holder, Nadim J. Ajami, Joseph F. Petrosino, Erik R. Zinser, James L. Van Etten, Steven W. Wilhelm 2020 University of Tennessee, Knoxville & Rice University

Smrt Sequencing Of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability In Adenines Targeted By Restriction Modification Systems, Samantha R. Coy, Eric R. Gann, Spiridon E. Papoulis, Michael E. Holder, Nadim J. Ajami, Joseph F. Petrosino, Erik R. Zinser, James L. Van Etten, Steven W. Wilhelm

James Van Etten Publications

Chloroviruses (family Phycodnaviridae) infect eukaryotic, freshwater, unicellular green algae. A unique feature of these viruses is an abundance of DNA methyltransferases, with isolates dedicating up to 4.5% of their protein coding potential to these genes. This diversity highlights just one of the long-standing values of the chlorovirus model system; where group-wide epigenomic characterization might begin to elucidate the function(s) of DNA methylation in large dsDNA viruses. We characterized DNA modifications in the prototype chlorovirus, PBCV-1, using single-molecule real time (SMRT) sequencing (aka PacBio). Results were compared to total available sites predicted in silico based on DNA sequence alone ...


Characterization Of A Mycoplasma Pneumoniae Cards Toxin Mutant, Nikaash Pasnoori 2020 University of Connecticut

Characterization Of A Mycoplasma Pneumoniae Cards Toxin Mutant, Nikaash Pasnoori

Honors Scholar Theses

Mycoplasma pneumoniae is a high-burden pathogen which causes mild to significant infections of the respiratory system. According to the CDC, an estimated two million cases occur yearly in the United States alone, demonstrating the widespread effect of the pathogen. In addition to being the cause of respiratory infections, M. pneumoniae has also been implicated in exacerbating pre-existing asthma conditions. These morbidities make finding a vaccine candidate a vital part of easing the healthcare burden caused by the pathogen. The current mechanism of infection is unknown, but recent evidence points to the Community Acquired Respiratory Distress Syndrome (CARDS) toxin as being ...


Editing Fusarium Graminearum Using Crispr/Cas9, Grace Marie Sack 2020 University of Northern Iowa

Editing Fusarium Graminearum Using Crispr/Cas9, Grace Marie Sack

Honors Program Theses

Fusarium graminearum is a pathogenic fungus that causes scab or Fusarium head blight disease in barley and wheat. Alternative approaches to protect barley from this devastating disease are badly needed. In recent years, an RNA-guided genome-editing system known as clustered regularly interspaced short palindromic repeat and CRISPR-associated protein 9 (CRISPR/Cas9), has become a popular method for genome modification (Jinek et al., 2012). We applied CRISPR/Cas9 technology in an effort to make F. graminearum less infectious. We used CRISPR/Cas9 plasmids constructed by a former UNI student (Akers, 2019) to mutate three genes in F. graminearum. One of the ...


Investigating The Redox Sensitivity Of Mitf Splice Variants, Rachel Berryman 2020 Linfield College

Investigating The Redox Sensitivity Of Mitf Splice Variants, Rachel Berryman

Senior Theses

Within pigment-producing cells known as melanocytes, the transcription factor MITF is intimately involved in regulating genes associated with cell cycle maintenance and melanocyte differentiation. Research, however, has provided conflicting results on the relationship between the expression levels of MITF and melanocyte cell fate. To complicate matters, two splice variants of MITF exist, differing by only 18 base pairs. These variants have been observed at variable levels of expression in melanocyte and melanoma cells, raising the question as to their functional purpose. Building upon previous research by the Leachman/Cassidy lab that identified the redox sensitivity of MITF while additionally establishing ...


Soybean Aphid Biotype 1 Genome: Insights Into The Invasive Biology And Adaptive Evolution Of A Major Agricultural Pest, Rosanna Giordano, Ravi Kiran Donthu, Jonathan H. Badger, Glen L. Hartman, Arian Avalos, Brad S. Coates, Doris Lagos-Kutz, Matthew E. O'Neal, Sijun Liu, et al. 2020 Puerto Rico Science

Soybean Aphid Biotype 1 Genome: Insights Into The Invasive Biology And Adaptive Evolution Of A Major Agricultural Pest, Rosanna Giordano, Ravi Kiran Donthu, Jonathan H. Badger, Glen L. Hartman, Arian Avalos, Brad S. Coates, Doris Lagos-Kutz, Matthew E. O'Neal, Sijun Liu, Et Al.

Entomology Publications

The soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae) is a serious pest of the soybean plant, Glycine max, a major world-wide agricultural crop. We assembled a de novo genome sequence of Ap. glycines Biotype 1, from a culture established shortly after this species invaded North America. 20.4% of the Ap. glycines proteome is duplicated. These in-paralogs are enriched with Gene Ontology (GO) categories mostly related to apoptosis, a possible adaptation to plant chemistry and other environmental stressors. Approximately one-third of these genes show parallel duplication in other aphids. But Ap. gossypii, its closest related species, has the lowest number ...


Identifying Phenotypic Effects In Sporisorium Reilianum And Ustilago Maydis Lacking The Alternative Oxidase Gene., Caroline D. Culver 2020 University of Louisville

Identifying Phenotypic Effects In Sporisorium Reilianum And Ustilago Maydis Lacking The Alternative Oxidase Gene., Caroline D. Culver

College of Arts & Sciences Senior Honors Theses

Ustilago maydis and Sporisorium reilianum are both dimorphic fungi that cause infection in the host plant, corn (Zea mays). In order for infection to be successful, compatible haploid mating types must form a dikaryon that later leads to the development and dispersal of teliospores. In order to sustain growth, energy is produced via the electron transport chain within the mitochondrion. Host plants often produce harsh reactive oxygen species, resulting in the need to use an alternative respiration pathway such as employing an alternative oxidase. Therefore, this study attempted to investigate the role of the aox gene in pathogenicity for these ...


Modeling Hybrid Novel Traits: A Case Study In Complex Petal Pigment Patterning In Hybrid Mimulus, Xingyu Zheng 2020 William & Mary

Modeling Hybrid Novel Traits: A Case Study In Complex Petal Pigment Patterning In Hybrid Mimulus, Xingyu Zheng

Undergraduate Honors Theses

Hybridization between species, by introducing dramatic trait variation into the population and creating viable, transgressive offsprings with novel phenotypes, can have huge evolutionary implications. Some hybrid traits have been studied in the classical genetics or population genetics context, but most complex traits are determined by multiple causes, e.g. the number of loci involved, the rewiring of the genetic circuitries, and the changes in gene expression pattern. Using the hybrid monkeyflower petal pigment patterning as an example, we present a case study to investigate complex hybrid traits in a systematic manner that includes empirical data analysis and quantitative mathematical modeling ...


A Study Of Matr3 And Its Effects On The Neural Progenitor Cells Of Xenopus Laevis Tadpoles, Kendall Branham 2020 William & Mary

A Study Of Matr3 And Its Effects On The Neural Progenitor Cells Of Xenopus Laevis Tadpoles, Kendall Branham

Undergraduate Honors Theses

Understanding the genes and mechanisms that regulate the highly important process of neurogenesis in the developing nervous system is crucial to uncovering why disease arises when this system is disrupted. Neural progenitor cells and their multipotent nature allow for the growth of a large pool of stem cells in the early stages of development, but the signal that leads these cells to the irreversible fate of becoming a neuron is unclear. The gene matr3 has been implicated in having a role in the maintenance of undifferentiated neural stem cells but its role needs further investigation to fully reveal how its ...


Meta-Analysis Of Biological Research Literature, Evan Suggs 2020 University of Tennessee at Chattanooga

Meta-Analysis Of Biological Research Literature, Evan Suggs

Honors Theses

Comparative studies have been powerful tools in generating a broad understanding about the evolution of animal social systems but they currently rely on the slow, manual process of reading thousands of abstracts and papers from research databases. A web application was created for researchers conducting a comparative survey, in order to speed up their research. This web application automates the retrieval of research papers and their selection process. Using previously obtained data sets on the orders Artiodacytla and Lagomorph, a machine learning application was created to classify the papers. These techniques and tools should greatly increase the speed at which ...


Identification Of Genome-Linked Bacillus Bacteriophage Proteins, Katherine Dyer 2020 University of Northern Iowa

Identification Of Genome-Linked Bacillus Bacteriophage Proteins, Katherine Dyer

Honors Program Theses

Small viruses that can infect bacteria, called bacteriophages, can be found in the soil. These viruses are being examined as a potential treatment against bacterial infections when antibiotics are not available or non-effective. Before viruses can be used as a medical treatment, they must be studied extensively. Previous attempts to sequence the terminal end of the genome of a bacteriophage QCM-11 (Quartz-Crystal-Microbalance-11: Q11) resulted in error. It is thought that a covalently bound protein may be attached to Q11’s DNA, blocking sequencing of the genome from the 5’ end. Proteins bound to the DNA of phages is not unheard ...


Identification And Analysis Of Feather Degrading Bacteria: A Search For Keratinase Genes, Nehal Navali 2020 University of Connecticut

Identification And Analysis Of Feather Degrading Bacteria: A Search For Keratinase Genes, Nehal Navali

Honors Scholar Theses

Over two million tons of feather waste is generated annually by the poultry industry, the majority of which goes into landfills due to the difficulty of degrading its major component keratin. Although a portion of feather waste is eliminated via incineration or chemical treatment, the use of Feather Degrading Bacteria (FDB) has been proposed as a cheap and eco-friendly alternative. FDBs have been consistently isolated from the feather microbiome of birds and contain genes coding for the specialized protein keratinase which is able to degrade feathers. By doing so, feather waste, which is rich in nutrients, can be repurposed as ...


Comparative Analysis Of Metabolic Pathways Of Bacteria Used In Fermented Food, Keanu Hoang, Kiran Bastola 2020 University of Nebraska at Omaha

Comparative Analysis Of Metabolic Pathways Of Bacteria Used In Fermented Food, Keanu Hoang, Kiran Bastola

Theses/Capstones/Creative Projects

This study presents a novel methodology for analyzing metabolic pathways. Utilizing KEGG REST API through a Biopython package and file parser, data about whether or not a bacteria has an enzyme or not was extracted. The results found that differences in metabolic pathway enrichment values follow along the lines of genera and pathway type. In particular, bacteria found in food spoilage and commercial nitrogen fixing products had high values of enrichment.


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