Cdc6 Is Sequentially Regulated By Pp2a-Cdc55, Cdc14, And Sic1 For Origin Licensing In S. Cerevisiae, 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 ...
Genetic Impacts Of Deforestation On Mouse Lemurs, 2022 The Graduate Center, City University of New York
Genetic Impacts Of Deforestation On Mouse Lemurs, Darice Westphal
Dissertations, Theses, and Capstone Projects
The impact of deforestation on the genetic structure of mouse lemurs is poorly understood. In this project, I assess deforestation of Madagascar’s terrestrial protected regions, quantify genomic wide genetic variation in two sympatric mouse lemurs, and evaluate the role of landscape structure in genetic relatedness patterns within two sympatric mouse lemur species. Overall deforestation rates across the 98 terrestrial protected areas in Madagascar are increasing, resulting in an average annual deforestation rate of 0.68% per year, with approximately 10,600 km2 lost between 2000 and 2019. In a comparison of relatedness patterns between the sympatric gray mouse ...
Gene Drives And The Consequences Of Over-Suppression, 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., 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 analyses ...
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 ...
Investigation Of Dna Variability And Phylogenetic Relationships Of Perlesta (Plecoptera: Perlidae) In Mississippi, 2022 University of Southern Mississippi
Investigation Of Dna Variability And Phylogenetic Relationships Of Perlesta (Plecoptera: Perlidae) In Mississippi, James C. Valentine, Mac H. Alford
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 using ...
Characterization Of A Helicobacter Pylori Small Rna By Rt-Pcr, 2022 Eastern Washington University
Characterization Of A Helicobacter Pylori Small Rna By Rt-Pcr, Roxanne Mcpeck, Andrea Castillo
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 pathogen ...
Isolation Of Arabidopsis Thaliana Plants Homozygous For An Insertional Inactivation Mutation Within Atprp4., 2022 Southern Adventist University
Isolation Of Arabidopsis Thaliana Plants Homozygous For An Insertional Inactivation Mutation Within Atprp4., Sydney Raitz, Timothy D. Trott
The AtPRP4 gene in Arabidopsis thaliana has been shown to function in several specific parts of the plant’s cell wall. It is shown to be expressed in the seeds, radicles, roots, leaves, inflorescences, and embryos of Arabidopsis thaliana. These patterns have suggested unique functions for ATPRP4 in determining cell-type-specific wall structure during the development of a plant as well as contributing to defense reactions against physical damage to the plant and pathogen infection within the plant. In this study, a simple DNA prep was performed on the true leaves of Arabidopsis thaliana. Subsequent PCR reactions were performed using AtPRP4F ...
Comparing Two Non-Invasive Methods For Assessing Marine Mammal Genetic Diversity: Environmental Dna Vs. Fecal Dna, 2022 University of Maine - Main
Comparing Two Non-Invasive Methods For Assessing Marine Mammal Genetic Diversity: Environmental Dna Vs. Fecal Dna, Sydney Jackson
As technology and science progresses, the methodology behind observing, monitoring, and sampling marine mammals advances as well. One such technique is environmental DNA or eDNA, which entails extracting organismal DNA from water samples without ever handling or disturbing the organism. It is a cost-efficient and non-invasive method that can be utilized in the sampling of seal haulout sites as is its purpose for this research. Another method, using the DNA analysis of seal fecal samples, is a less invasive method that can also be utilized to monitor and assess marine mammals. Through collecting both fecal and water samples from gray ...
Effects Of Sunrise/Sunset Lighting On Corticosterone Levels In Coturnix Quail (Coturnix Coturnix), 2022 University of Arkansas, Fayetteville
Effects Of Sunrise/Sunset Lighting On Corticosterone Levels In Coturnix Quail (Coturnix Coturnix), Hannah Feuerborn
Poultry Science Undergraduate Honors Theses
Both genetics and environment play an important role in the growth, performance and overall welfare of poultry species. Current commercial production practices typically do not mimic the natural environmental conditions of ancestral poultry species, specifically lighting requirements. In nature, poultry species are subjected to natural day length and the slow rising and setting of the sun. This is compared to commercial conditions in which lights are sudden on/off, not mimicking the natural trajectory of the sun in terms of light intensity and exposure. The current study aimed to evaluate the impact of genetics and the effect of sunrise/sunset ...
Characterizing The Expression Pattern And Function Of Tartan During Drosophila Development, 2022 University of Arkansas, Fayetteville
Characterizing The Expression Pattern And Function Of Tartan During Drosophila Development, Alaina Baggett
Biomedical Engineering Undergraduate Honors Theses
The development of complex structures and organs by multicellular organisms relies on the ability of epithelial cells to self-organize. Epithelia are sheets of connected cells, and compartment boundaries are formed between certain epithelial cells to create distinct tissue compartments. Compartment boundaries are specialized cell-cell interfaces that are enriched for the cytoskeletal proteins actin and myosin, leading to straight cell edges under relatively high tension that act as fences keep cells from moving between compartments. In the model organism Drosophila melanogaster (fruit fly), compartment boundaries in the early embryo are established in response to the non-uniform striped expression of the cell-surface ...
Root Phenotyping Of Peptide-Treated Glycine Max, 2022 University of Arkansas, Fayetteville
Root Phenotyping Of Peptide-Treated Glycine Max, Salem Jackson
Biological Sciences Undergraduate Honors Theses
Plant elicitor peptides (Peps) – endogenous chains of amino acids involved in natural plant defense – have been shown to decrease damage from herbivores and pathogens by inducing an immune response, increasing the emission of volatile organic compounds (VOCS), transcripts, and metabolites. Exogenous treatment of soybean seeds with plant elicitor peptide GmPep3 has been shown to induce these broad-spectrum defenses and offers a new method for increasing crop yield. However, the effects of GmPep3 on indicators of soybean health – root characteristics, growth stages, etc. – have not been fully realized.
Using the root-phenotyping platform RhizoVision Explorer, several root traits of soybean plants treated ...
The Effects Of Deletion Of The Cytoplasmic Domain Of Robo3 On Drosophila, 2022 University of Arkansas, Fayetteville
The Effects Of Deletion Of The Cytoplasmic Domain Of Robo3 On Drosophila, Jessie Agcaoili
Biological Sciences Undergraduate Honors Theses
My research project examines how the deletion of the cytoplasmic domain affects the function of Robo3. If Robo3 is signaling repulsion in response to SLIT this activity should require the cytoplasmic domain. I investigated the functional importance of Robo3 by deleting the cytoplasmic domain of Robo3 using a CRISPR-based technique. This modified gene was then injected into Drosophila embryos where it replaced the normal copy of the gene. Embryos expressing the modified version of robo3 in place of normal robo3 were dissected and examined.
Comparative Analyses Of De Novo Transcriptome Assembly Pipelines For Diploid Wheat, 2022 University of Nebraska-Lincoln
Comparative Analyses Of De Novo Transcriptome Assembly Pipelines For Diploid Wheat, Natasha Pavlovikj
Computer Science and Engineering: Theses, Dissertations, and Student Research
Gene expression and transcriptome analysis are currently one of the main focuses of research for a great number of scientists. However, the assembly of raw sequence data to obtain a draft transcriptome of an organism is a complex multi-stage process usually composed of pre-processing, assembling, and post-processing. Each of these stages includes multiple steps such as data cleaning, error correction and assembly validation. Different combinations of steps, as well as different computational methods for the same step, generate transcriptome assemblies with different accuracy. Thus, using a combination that generates more accurate assemblies is crucial for any novel biological discoveries. Implementing ...
Investigation Of Microbe And Host Tissue Interactions Contributing To The Pathogenesis Of Colorectal Cancer, 2022 University of Nebraska at Omaha
Investigation Of Microbe And Host Tissue Interactions Contributing To The Pathogenesis Of Colorectal Cancer, Ryan Chapman, Dhundy Bastola
Colorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide. The pathogenesis of this disease can fall under broad categories; however, the specific precursory mechanism of CRC pathogenesis is still unknown. Dysregulations of the gut microbiome have been identified in the CRC tissue environment. Additionally, CRC tissue gene expression has been observed to differ from that of healthy tissue. Despite these noticeable changes, few studies have directly compared the microorganism composition to the gene expression of CRC tissue. Doing so may identify whether the differentially abundant microorganisms influence the changes in gene expression. The goal of this ...
Severe Hypoxia Up-Regulates Gluconeogenesis In Daphnia, 2022 East Tennessee State University
Severe Hypoxia Up-Regulates Gluconeogenesis In Daphnia, Morad C. Malek
Undergraduate Honors Theses
Hypoxia is a significant low oxygen state that has complex and diverse impacts on organisms. In aerobes, hypoxia causes numerous physiological changes and adaptive responses that vary depending on the level of oxygen depletion and on previous adaptation, hence its continued attention as an important abiotic stressor. Adaptive responses to hypoxia are primarily governed by the hypoxia-inducible-factors (HIFs), which activate downstream genetic pathways responsible for metabolic adjustments and homeostasis maintenance. In aquatic organisms, hypoxia is an important ecological constraint, as oxygen availability within waterbodies can vary greatly over time and space. Therefore, adaptation to hypoxia is likely pervasive, especially in ...
Scalable Software Infrastructure For The Lab And A Specific Investigation Of The Yeast Transcription Factor Eds1, 2022 Washington University in St. Louis
Scalable Software Infrastructure For The Lab And A Specific Investigation Of The Yeast Transcription Factor Eds1, Chase Mateusiak
McKelvey School of Engineering Theses & Dissertations
Individual biology labs handle increasingly large data sets. Ensuring accurate data entry, consistent sample metadata, and ease of access to the data once it is stored, are critical for both the integrity of analysis as well as productivity of the lab. Chapter 1 one of this thesis describes three implementations of software meant to facilitate handling data and metadata in the lab as the size of the data and complexity of analysis scale. The first piece of software is a database and entry interface for storing a large and varied amount of data on biological samples. The second is a ...
Temporal And Spatial Comparison Of Pseudo-Nitzschia Species Composition And Domoic Acid In Narragansett Bay, Rhode Island And The Northeast U.S. Shelf, Isabella Church, Bethany D. Jenkins
Senior Honors Projects
Diatoms are unicellular algae that make up a significant portion of phytoplankton biomass at the base of marine food webs. Narragansett Bay (NB), RI is home to several species of the diatom genus Pseudo-nitzschia (P-n), some of which are known to cause harmful algal blooms through the production of the potent neurotoxin domoic acid (DA). This toxin can lead to Amnesic Shellfish Poisoning in humans through the consumption of affected shellfish. Although the presence of P-n has been well established in NB for over 50 years, DA levels have only recently become a problem, with shellfish harvest closures in 2016 ...
Development Of The Ark Assay For Quantitating Dna- Protein Crosslink Accumulation And Fanconi Anemia Pathway Involvement In The Repair Process, 2022 The Texas Medical Center Library
Development Of The Ark Assay For Quantitating Dna- Protein Crosslink Accumulation And Fanconi Anemia Pathway Involvement In The Repair Process, Naeh Klages-Mundt
The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)
DNA-protein crosslinks (DPCs) are a common DNA lesion naturally arising in cells, wherein protein becomes covalently and irreversibly bound to the DNA. Given their excessive size, these adducts present a significant challenge to replication and transcription, thus requiring timely and efficient repair. However, the precise mechanisms involved with processing DPC removal remain unclear. Moreover, current methodologies to quantitate DPC accumulation and removal are restrained by a range of limitations. Here, we describe and discuss a new DPC detection assay – the ARK assay – capable of overcoming the limitations incurred by prior assays. The design, which uses dual chaotropic lysis and anionic ...
Utilizing Pharmacology To Target Transcription Factors Involved With Cancer Onset And Development, 2022 West Virginia University
Utilizing Pharmacology To Target Transcription Factors Involved With Cancer Onset And Development, Tristan D. Sanders
Mountaineer Undergraduate Research Review
Transcription factors (TFs) are a vital part of every living organism on earth, as they allow for the correct genes to be expressed while much of the genome is never used. They can fall victim to mutations or manipulations that lead to the deregulation of many genes within a cell. If specific genes are over/under-expressed, a cell may become cancerous and begin replicating into a tumor. It has been demonstrated that common TFs associated with cancer can be targeted using small molecule drugs, and a popular target of these drugs is the DNA binding site on the TF along ...