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Symmetry-Inspired Analysis Of Biological Networks, Ian Leifer 2022 The Graduate Center, City University of New York

Symmetry-Inspired Analysis Of Biological Networks, Ian Leifer

Dissertations, Theses, and Capstone Projects

The description of a complex system like gene regulation of a cell or a brain of an animal in terms of the dynamics of each individual element is an insurmountable task due to the complexity of interactions and the scores of associated parameters. Recent decades brought about the description of these systems that employs network models. In such models the entire system is represented by a graph encapsulating a set of independently functioning objects and their interactions. This creates a level of abstraction that makes the analysis of such large scale system possible. Common practice is to draw conclusions about …


Cdc6 Is Sequentially Regulated By Pp2a-Cdc55, Cdc14, And Sic1 For Origin Licensing In S. Cerevisiae, Jasmin Philip 2022 The Graduate Center, City University of New York

Cdc6 Is Sequentially Regulated By Pp2a-Cdc55, Cdc14, And Sic1 For Origin Licensing In S. Cerevisiae, Jasmin Philip

Dissertations, Theses, and Capstone Projects

Control of DNA replication is critical for progression of the cell cycle and genomic stability. Cyclin-dependent kinases (CDKs) coordinate numerous phosphorylation events to accomplish two biological tasks for all living organisms: DNA replication and cell division. One CDK, Cyclin-Cdc28, is responsible for cell cycle progression in budding yeast. DNA replication requires a stepwise assembly of the pre-replicative complex on DNA, including Orc1-6, Cdc6, Cdt1 and Mcm2-7, during M-G1 phase. Cdc6 contains eight Cdc28 consensus sites, SP or TP motifs. Clb5-Cdc28 phosphorylates Cdc6-T7 to recruit Cks1, the Cdc28 phospho-adaptor, for subsequent multisite phosphorylation during S phase. There are two phospho-degrons at …


Young Forests And Fire: Using Lidar–Imagery Fusion To Explore Fuels And Burn Severity In A Subalpine Forest Reburn, Kristin H. Braziunas, Diane C. Abendroth, Monica G. Turner 2022 University of Wisconsin-Madison

Young Forests And Fire: Using Lidar–Imagery Fusion To Explore Fuels And Burn Severity In A Subalpine Forest Reburn, Kristin H. Braziunas, Diane C. Abendroth, Monica G. Turner

Aspen Bibliography

Anticipating fire behavior as climate change and fire activity accelerate is an increasingly pressing management challenge in fire-prone landscapes. In subalpine forests adapted to infrequent, stand-replacing fire, self-limitation of burn severity in short-interval fire is incompletely understood. Spatially explicit fuels data can support assessments of landscape-scale fire risk and fuel feedbacks on burn severity. For a ~1450-km2 largely forested landscape in the US Northern Rocky Mountains, we used airborne lidar and imagery to predict and map canopy and surface fuels. In a fire that burned mature (>125-year-old) and also reburned young (~30-year-old) subalpine forest, we then asked: (1) …


Low Site-Specific Genomic Variability Is Consistent With The History(S) Of Fragmentation Of The Riparian Biota Of The Arid Southwest, Manuela Londono-Gaviria 2022 University of New Mexico

Low Site-Specific Genomic Variability Is Consistent With The History(S) Of Fragmentation Of The Riparian Biota Of The Arid Southwest, Manuela Londono-Gaviria

Biology ETDs

Persistently low population sizes, when coupled with reduced interpopulation connectivity, can impede the long-term viability of species in fragmented landscapes. Riparian-associated species in the arid American Southwest now face a series of threats due to fragmented populations and changing environmental conditions. During the last century, riparian habitats have deteriorated due to the synergistic effects of livestock grazing, increasing incidence of fire, and other anthropogenic impacts potentially have made local populations smaller, less demographically stable, and susceptible to the negative impacts of genetic drift and stochastic events. We evaluated genomic variation within and across geographic areas (i.e., mountain ranges and river …


Using Pooled Data For Genomic Prediction In A Bivariate Framework With Missing Data, Johnna L. Baller, Stephen D. Kachman, Larry A. Kuehn, Matthew L. Spangler 2022 University of Nebraska-Lincoln

Using Pooled Data For Genomic Prediction In A Bivariate Framework With Missing Data, Johnna L. Baller, Stephen D. Kachman, Larry A. Kuehn, Matthew L. Spangler

Faculty Papers and Publications in Animal Science

Pooling samples to derive group genotypes can enable the economically efficient use of commercial animals within genetic evaluations. To test a multivariate framework for genetic evaluations using pooled data, simulation was used to mimic a beef cattle population including two moderately heritable traits with varying genetic correlations, genotypes and pedigree data. There were 15 generations (n = 32,000; random selection and mating), and the last generation was subjected to genotyping through pooling. Missing records were induced in two ways: (a) sequential culling and (b) random missing records. Gaps in genotyping were also explored whereby genotyping occurred through generation 13 …


Gene Drives And The Consequences Of Over-Suppression, Cole Butler 2022 Virginia Commonwealth University

Gene Drives And The Consequences Of Over-Suppression, Cole Butler

Biology and Medicine Through Mathematics Conference

No abstract provided.


Elevated Substitution Rates Among Wolbachia-Infected Mosquito Species Results In Apparent Phylogenetic Discordance., James E. Russell, Michael Saum, Rebekah Williams 2022 Georgia Gwinnett College

Elevated Substitution Rates Among Wolbachia-Infected Mosquito Species Results In Apparent Phylogenetic Discordance., James E. Russell, Michael Saum, Rebekah Williams

Georgia Journal of Science

As one of the most widely distributed bacterial cytoplasmic symbionts on earth, Wolbachia pipientis Hertig serves as a model organism for the understanding of host-symbiont interactions. Many mosquito species are infected with Wolbachia strains that induce a form of reproductive manipulation called cytoplasmic incompatibility, in which infected females gain a reproductive advantage over uninfected females in mixed infection populations. The selective advantage of cytoplasmic incompatibility often results in a population sweep of Wolbachia and co-transmitted mitochondrial genomes. Mitochondrial evolution and phylogenetic inferences drawn from mitochondrial gene sequences are thus potentially compromised by reproductive manipulating symbionts, like Wolbachia. Our initial …


The Effect Of The Oncometabolite Fumarate In The Response To Dna Damage: An Analysis Of The Role Of Fumarate In The Response Of Cells A2780 To Dna Damage Induced By Cisplatin, Gillian Luczyk, Luisa María Sierra, Enol Álvarez González 2022 University of Denver

The Effect Of The Oncometabolite Fumarate In The Response To Dna Damage: An Analysis Of The Role Of Fumarate In The Response Of Cells A2780 To Dna Damage Induced By Cisplatin, Gillian Luczyk, Luisa María Sierra, Enol Álvarez González

DU Undergraduate Research Journal Archive

Previous research has been conducted on the effect of oncometabolites on DNA damage repair; however, these studies have traditionally focused on the response to damage caused by DNA double-strand breaks, whereas this study involves cisplatin-induced damage that creates DNA cross-links. This study reports on the effect of the oncometabolite fumarate on the response of A2780 cells to DNA damage produced by cisplatin. Three assays were used to complete this study: comet assay, cell cycle assay and apoptosis assay. The comet assay revealed that fumarate influenced the response of cells to DNA damage and, at a lower 1mM concentration, appeared to …


Du Undergraduate Showcase: Research, Scholarship, And Creative Works: Abstracts, Emma Aggeler, Elena Arroway, Daisy T. Booker, Justin Bravo, Kyle Bucholtz, Megan Burnham, Nicole Choi, Spencer Cockerell, Rosie Contino, Jackson Garske, Kaitlyn Glover, Caroline Hamilton, Haley Hartmann, Madalyne Heiken, Colin Holter, Leah Huzjak, Alyssa Jeng, Cole Jernigan, Chad Kashiwa, Adelaide Kerenick, Emily King, Abigail Langeberg, Maddie Leake, Meredith Lemons, Alec MacKay, Greer McKinley, Ori Miller, Guy Milliman, Katherine Miromonti, Audrey Mitchell, Lauren Moak, Megan Morrell, Gelella Nebiyu, Zdenek Otruba, Toni V. Panzera, Kassidy Patarino, Sneha Patil, Alexandra Penney, Kevin Persky, Caitlin Pham, Gabriela Recinos, Mary Ringgenberg, Chase Routt, Olivia Schneider, Roman Shrestha, Arlo Simmerman, Alec Smith, Tessa Smith, Nhi-Lac Thai, Kyle Thurmann, Casey Tindall, Amelia Trembath, Maria Trubetskaya, Zachary Vangelisti, Peter Vo, Abby Walker, David Winter, Grayden Wolfe, Leah York 2022 University of Denver

Du Undergraduate Showcase: Research, Scholarship, And Creative Works: Abstracts, Emma Aggeler, Elena Arroway, Daisy T. Booker, Justin Bravo, Kyle Bucholtz, Megan Burnham, Nicole Choi, Spencer Cockerell, Rosie Contino, Jackson Garske, Kaitlyn Glover, Caroline Hamilton, Haley Hartmann, Madalyne Heiken, Colin Holter, Leah Huzjak, Alyssa Jeng, Cole Jernigan, Chad Kashiwa, Adelaide Kerenick, Emily King, Abigail Langeberg, Maddie Leake, Meredith Lemons, Alec Mackay, Greer Mckinley, Ori Miller, Guy Milliman, Katherine Miromonti, Audrey Mitchell, Lauren Moak, Megan Morrell, Gelella Nebiyu, Zdenek Otruba, Toni V. Panzera, Kassidy Patarino, Sneha Patil, Alexandra Penney, Kevin Persky, Caitlin Pham, Gabriela Recinos, Mary Ringgenberg, Chase Routt, Olivia Schneider, Roman Shrestha, Arlo Simmerman, Alec Smith, Tessa Smith, Nhi-Lac Thai, Kyle Thurmann, Casey Tindall, Amelia Trembath, Maria Trubetskaya, Zachary Vangelisti, Peter Vo, Abby Walker, David Winter, Grayden Wolfe, Leah York

DU Undergraduate Research Journal Archive

Abstracts from the DU Undergraduate Showcase.


Investigation Into The Genetic Basis Of Capsaicin Production In Peppers Using Next Generation Rna Sequencing And Synthetic Biology Approaches, Ryan Patrick Calhoun 2022 Rowan University

Investigation Into The Genetic Basis Of Capsaicin Production In Peppers Using Next Generation Rna Sequencing And Synthetic Biology Approaches, Ryan Patrick Calhoun

Theses and Dissertations

Capsaicin, a molecule synthesized by plants in the Capsicum genus, is popular for its ability to produce a sensation of burning in any tissue it encounters. The synthesis of capsaicin molecules is achieved through the capsaicin biosynthesis pathway. In this dual study, our goal was to insert two crucial genes, pun1 and pAMT, into a strain of Saccharomyces cerevisiae to allow capsaicin synthesis and perform Illumina RNA sequencing on seven pepper species of increasing pungency to identify other key or novel genes needed or related to capsaicin synthesis. We implemented a golden gate cloning strategy to insert our genes of …


Defining The Role Of Rare Genetic Variants That Drive Risk And Pathogenesis Of Alzheimer’S Disease, Matthew James Rosene 2022 Washington University in St. Louis

Defining The Role Of Rare Genetic Variants That Drive Risk And Pathogenesis Of Alzheimer’S Disease, Matthew James Rosene

Arts & Sciences Electronic Theses and Dissertations

Alzheimer’s disease (AD) is the leading cause of dementia and is pathologically defined by the aggregation of extracellular amyloid plaques and intracellular neurofibrillary tangles. Rare heritable mutations within the genes for amyloid precursor protein (APP) and presenilin 1 (PSEN1), and presenilin 2 (PSEN2) cause early onset AD and account for approximately 1% of AD cases. While the majority of AD cases are late-onset (LOAD), which is defined by a markedly more complex genetic architecture that is comprised of many genetic risk factors that influence AD through multiple cellular pathways. The advent of deep sequencing analyses have allowed for the identification …


Understanding The Role Of Involucrin In Skin Inflammation, Alina Schmidt 2022 Washington University in St. Louis

Understanding The Role Of Involucrin In Skin Inflammation, Alina Schmidt

Arts & Sciences Electronic Theses and Dissertations

Terminally differentiated keratinocytes are essential for skin barrier function and are surrounded by an involucrin (IVL)-rich cornified envelope. Increased IVL expression in the epidermis is associated with recent positive selection in European populations, yet the functional significance of this finding is unclear. An upstream enhancer of IVL, the 923 enhancer, regulates IVL expression, and the impact of IVL enhancer variants on involucrin expression in modifying the penetrance of filaggrin (FLG) loss-of-function variants associated with atopic dermatitis (AD) has not been explored. I hypothesize involucrin to modulate the environmentally sensitive Vitamin D receptor (Vdr) activity in the epidermis and involucrin enhancer …


The Nature Of Phenotypes: Provoking And Measuring The Dynamic Processes Of Swarm Expansion, Predation, And Antibiotic Resistance In Myxococcus Xanthus, Linnea Judith Ritchie 2022 Syracuse University

The Nature Of Phenotypes: Provoking And Measuring The Dynamic Processes Of Swarm Expansion, Predation, And Antibiotic Resistance In Myxococcus Xanthus, Linnea Judith Ritchie

Dissertations - ALL

The question of how genotype affects phenotype has fascinated and puzzled scientists for generations. Regardless of organism, the correlation between observation and underlying condition is necessary for scientists to understand the world around us. Myxococcus xanthus, a fascinating organism with a large genome (7,314 genes), is known for complex social behaviors and is an excellent model system for the study of this relationship. Upon starvation, M. xanthus cells condense into large multicellular aggregates to await renewed nutrient availability. M. xanthus cells swarm together on surfaces as a predatory biofilm, lysing and killing prey as a singular unit. During predation, swarms …


Evaluating Threats To The Water Quality Of Little Buffalo Creek And Sarver Run Through Water Quality Analysis And Backpack Electrofishing Surveys, Riley Williams 2022 Duquesne University

Evaluating Threats To The Water Quality Of Little Buffalo Creek And Sarver Run Through Water Quality Analysis And Backpack Electrofishing Surveys, Riley Williams

Electronic Theses and Dissertations

Currently, 64.8% and 52.2% of Little Buffalo Creek and Sarver Run stream kilometers are impaired, respectively. Impairment sources to Little Buffalo Creek include agriculture, riparian deforestation, on-site wastewater, and urban runoff. Impairment sources to Sarver Run are unknown. Our goal was to understand sources of impairment through water quality analysis and fish surveys. Water samples were collected monthly and analyzed for cation and anion concentrations. Mass ratio analysis comparing Br/SO4 and Mg/Li, Ca/Mg and Ca/Sr, Mg/Na and SO4/Cl, and SO4/Cl and Mg/Li suggests that mine drainage and conventional oil and gas may be impacting water …


Analysis Of Water Quality And Fish Communities Of Crooked Creek, Tributary To The Allegheny River In Southwestern Pennsylvania, Katherine Stupar 2022 Duquesne University

Analysis Of Water Quality And Fish Communities Of Crooked Creek, Tributary To The Allegheny River In Southwestern Pennsylvania, Katherine Stupar

Electronic Theses and Dissertations

Crooked Creek is a tributary of the Allegheny River with a drainage area of 292 square miles. It has been historically affected by mine drainage pollution. Extensive cleanup and monitoring efforts by the Commonwealth of Pennsylvania and the U.S. Army Corps of Engineers (USACE) have taken place over the last four decades. Unconventional oil extraction, or fracking, presents an emerging threat to the water quality of this stream and the health of its fish communities. Here we perform an analysis of the Crooked Creek watershed utilizing backpack electrofishing, eDNA metabarcoding, and various methods of water quality analysis. Seven sites on …


Identification Of Pneumococcal Membrane Proteins Involved In Colonization/Biofilm Formation And Cognate Host Cellular Receptors, Yoonsung Hu 2022 Mississippi State University

Identification Of Pneumococcal Membrane Proteins Involved In Colonization/Biofilm Formation And Cognate Host Cellular Receptors, Yoonsung Hu

Theses and Dissertations

Colonization is prerequisite for infection and transmission of Streptococcus pneumoniae, or pneumococcus. Currently available pneumococcal conjugate and pneumococcal polysaccharide vaccines can provide protection against a limited number of capsular serotypes. Implementation of vaccines has decreased the frequency of invasive pneumococcal disease and their colonization rates, but only in a serotype-dependent manner. This has led to serotype replacement in pneumococcal ecology and increased invasive disease caused by non-vaccine serotypes. Development of conserved protein-based vaccine that can provide protection against all pneumococcal serotypes is needed. Numerous surface proteins are conserved in all serotypes, and some are known to be involved in …


Investigation Of Dna Variability And Phylogenetic Relationships Of Perlesta (Plecoptera: Perlidae) In Mississippi, James C. Valentine, Mac H. Alford 2022 University of Southern Mississippi

Investigation Of Dna Variability And Phylogenetic Relationships Of Perlesta (Plecoptera: Perlidae) In Mississippi, James C. Valentine, Mac H. Alford

Master's Theses

The genus Perlesta Banks, 1906 (Plecoptera: Perlidae) consists of 35 species, 33 native to the United States and Canada and two native to China. For over a century these small, brown stonefly adults and freckled yellow nymphs have gone by the name of the type species of the genus, Perlesta placida, but taxonomic work in the genus since 1989 has resulted in the recognition of additional species. These species were mostly recognized and described using morphological characteristics, but two areas that are lacking include (1) linking nymphs to adults and (2) phylogenetic analysis of all species occurring in Mississippi …


Characterization Of A Helicobacter Pylori Small Rna By Rt-Pcr, Roxanne McPeck, Andrea Castillo 2022 Eastern Washington University

Characterization Of A Helicobacter Pylori Small Rna By Rt-Pcr, Roxanne Mcpeck, Andrea Castillo

2022 Symposium

Helicobacter pylori, a bacterial gastric pathogen infecting approximately 50% of the human population, produces gastritis, ulcers, and gastric cancers. Colonizing the inhospitable and fluctuating environment in the stomach requires tight genetic control. However, H. pylori lacks many genetic regulatory elements present in other bacteria to control gene expression. Instead, over 200 small RNAs (sRNAs; noncoding RNAs shorter than 300 nucleotides) have been found in this bacterium, but few have been fully characterized. Of those, many are antisense to virulence genes. Characterizing these sRNAs is important in understanding the mechanisms of molecular genetics and potentially supporting medical management of this …


Heterogeneity Of Gene Expression In Peanut-Allergic Cells May Be Related To Differing Cell Subpopulations, Sophia R. Tekorius 2022 Seattle Pacific University

Heterogeneity Of Gene Expression In Peanut-Allergic Cells May Be Related To Differing Cell Subpopulations, Sophia R. Tekorius

Honors Projects

Peanut allergies can have severe and life-threatening complications. By understanding the biology of individuals struggling with this disease, better treatments can be developed. This project explores the possibility of two phenotypically distinct cell types within CD154+ cell types in patients with peanut allergy. Previous studies show that there is a Th2 cell subpopulation associated with allergies, and within effector CD4+ memory populations two distinct phenotypes have been found. This project expands upon this research at the genetic level and through bioinformatic analyses, including the production of heatmaps, the project has found evidence for differing gene expression in two cell subpopulations. …


Developing A Novel Place Preference Assay To Compare Drosophila Species Over Time, Martha M. Brinson 2022 University of Mississippi

Developing A Novel Place Preference Assay To Compare Drosophila Species Over Time, Martha M. Brinson

Honors Theses

Across phylogeny, integration of external factors, memory, and internal states of the organism dictate organismal behavior and mechanisms. The underlying genetic components can affect these behaviors such as in genomic changes arising from speciation. In this thesis, a new place preference assay was evaluated in the analysis and investigation of two species of Drosophila flies (D. melanogaster and D. simulans) to measure similarities and differences and their attraction to two different food substrates. Sleep and circadian measurements were also recorded during experimentation. The Drosophila Activity Monitor 5M (DAM5M) System and Sleep Circadian Analysis MATLAB Program (SCAMP) analysis were …


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