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Articles 61 - 90 of 233

Full-Text Articles in Biology

The Role Of Subclonal Gene Mutations During Progression From Myelodysplastic Syndrome To Secondary Acute Myeloid Leukemia, Andrew John Menssen May 2021

The Role Of Subclonal Gene Mutations During Progression From Myelodysplastic Syndrome To Secondary Acute Myeloid Leukemia, Andrew John Menssen

Arts & Sciences Graduate Student Theses and Dissertations

Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal bone marrow disorders characterized by ineffective hematopoiesis. Approximately 30% of MDS patients progress to secondary acute myeloid leukemia (AML). MDS is caused by somatic mutations in hematopoietic stem/progenitor cells and progression to secondary AML is associated with the acquisition and/or expansion of at least one subclone. We hypothesized that specific gene mutations would be enriched in subclones compared to founding clones, and that the order of mutation acquisition would be critical for clonal evolution and progression from MDS to secondary AML. Sequencing of paired MDS and secondary AML samples from 44 …

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Changes In Gene Sequence That Cause Discordances Involving Disease In Monozygotic Twins, Kacie Jacques Apr 2021

Changes In Gene Sequence That Cause Discordances Involving Disease In Monozygotic Twins, Kacie Jacques

Thinking Matters Symposium

Identical twins or, monozygotic twins, occur when the egg in a mother is fertilized, but one zygote divides into two separate embryos. Monozygotic twins are considered to be genetically identical, but most twins often display discordances, some involving diseases or disorders. Some of these differences are due to environmental factors. For example, one twin may have diabetes due to diet. Recent literature has shown that some differences in monozygotic twins may be due to changes in gene sequence, as opposed to random, environmental or epigenetic factors. Identical twins from pedigrees with familial disease often show discordances. When looking at schizophrenia …

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The Evolution Of Mimicry; The Doublesex Gene, Aisha Hill Apr 2021

The Evolution Of Mimicry; The Doublesex Gene, Aisha Hill

Thinking Matters Symposium

Many butterfly species use mimicry in order to increase their chance of survival. In Batesian mimicry, non toxic butterflies mimic the wing patterns, colors, and shapes of another species that is toxic to predators. Swallowtail butterflies (Papilio polytes) are well-known Batesian mimics, and also display sexual dimorphism with distinct differences between the sexes. Sex limited mimicry is common. The female butterfly may mimic an inedible red-bodied swallowtail, such as the common rose (Pachliopta aristolochiae), or she may be non-mimetic. The male butterfly is non-mimetic. This is a review of recent research into the origin and evolution …

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Compoundhetvip: Compound Heterozygous Variant Identification Pipeline, Dustin B. Miller, Stephen R. Picollo Feb 2021

Compoundhetvip: Compound Heterozygous Variant Identification Pipeline, Dustin B. Miller, Stephen R. Picollo

Faculty Publications

Compound Heterozygous ( CH) variant identification requires distinguishing maternally from paternally derived nucleotides, a process that requires numerous computational tools. Using such tools often introduces unforeseen challenges such as installation procedures that are operating-system specific, software dependencies that must be installed, and formatting requirements for input files. To overcome these challenges, we developed Compound Heterozygous Variant Identification Pipeline (CompoundHetVIP), which uses a single Docker image to encapsulate commonly used software tools for file aggregation ( BCFtools or GATK4), VCF liftover ( Picard Tools), joint-genotyping ( GATK4), file conversion ( Plink2), phasing ( SHAPEIT2, Beagle …

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Genetics Of Pediatric Musculoskeletal Disorders, Lilian Antunes Jan 2021

Genetics Of Pediatric Musculoskeletal Disorders, Lilian Antunes

Arts & Sciences Graduate Student Theses and Dissertations

Pediatric musculoskeletal disorders are an extremely broad category of diseases that are often inherited. While individually rare, collectively these disorders are common, affecting around 3% of live births in the US. Despite the mounting clinical and molecular evidence for a genetic etiology, the cause for many patients with pediatric musculoskeletal disorders remain largely unknown. Major challenges in rare pediatric diseases include recruiting large numbers of patients and determining the significance and functional impacts of variants associated with disease within individuals or families. Whole exome sequencing (WES) is a powerful tool to identify coding variants that are associated with rare pediatric …

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Examining A Functional Interaction Between Chromatin Remodeler Chd1 And Histone H1 In D. Melanogaster, Breanna Kim Jan 2021

Examining A Functional Interaction Between Chromatin Remodeler Chd1 And Histone H1 In D. Melanogaster, Breanna Kim

Scripps Senior Theses

Chromodomain-helicase-DNA-binding-protein-1 (CHD1) is a highly conserved ATP- dependent remodeling protein. It is localized to active genes and directs nucleosome spacing, while its loss has been linked to various human diseases, such as human prostate cancer. In Drosophila, CHD1 is important for fertility and wing development, and overexpression of CHD1 leads to severe wing vein defect phenotypes. The Linker Histone H1, which is known for maintaining heterochromatin and is associated with inactive genes, had been previously identified as a possible functional partner of CHD1, though the exact nature of their interaction is unclear. I undertook a genetic approach to examining the …

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Exploring The Genetic Variability Of Zebra Mussels Dreisenna Polymoprha, Maxwell Carr Jan 2021

Exploring The Genetic Variability Of Zebra Mussels Dreisenna Polymoprha, Maxwell Carr

Journal of Earth and Life Science

Zebra Mussels Dreisenna polymorpha are one of the most well-known invasive species here in the United States. This species can take over watersheds very quickly, causing damage to both the ecosystem and man-made structures. The basic physical behavior of this species has been well documented, but the invasive North American Zebra Mussel is much more aggressive and therefore causes more damage in the Great Lakes region compared to its native waters. Genetic variation may be playing a very large role in how and why D. polymorpha is causing such large problems for stakeholders in the United States. This review cites …

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Composition And Homology In The Taxonomic Classification Of Escherichia Coli, Tanya Irani Jan 2021

Composition And Homology In The Taxonomic Classification Of Escherichia Coli, Tanya Irani

Theses and Dissertations (Comprehensive)

As new techniques have been introduced, specifically the possibility of complete genome sequencing, better methods of defining bacterial species have also been proposed. One of the most recently proposed methods, using bioinformatic techniques, is to calculate the average nucleotide identity (ANI) between the homologous genome segments of different isolates. Another method for species discrimination that has been tested successfully is the similarity of DNA compositional signatures. However, in a recent update, DNA signatures split the available Escherichia coli complete genomes into three groups. To check if this result was consistent with such genomes belonging to different species, we tested methods …

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A Cophylogenetic Analysis Of Fungus Gardening Ants And Their Symbiotic Fungi, Katherine Beigel Dec 2020

A Cophylogenetic Analysis Of Fungus Gardening Ants And Their Symbiotic Fungi, Katherine Beigel

Biology Theses

Fungus-growing ants (Tribe Attini) and their fungal cultivars share a 50-million-year coevolutionary history. Large scale phylogenetic analyses depict a strong co-phyletic signal among ants and their farmed fungi yet fungus sharing among unrelated ant lineages is somewhat widespread. An overview of sharing has been hampered by a lack of genetic markers that exhibit intraspecific variation and surveys across geographic regions. For example, previous studies have shown similar sequences of the internal transcribed spacer (ITS) region of fungus in different species of Trachymyrmex, suggesting that these ant species are farming the same fungal clone. To examine whether this was a …

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The Genetic Influence On Subjective Well-Being: A Review Of The Current Knowledge On The Role Of Genetics On Our Sense Of Subjective Well-Being And The Implications It Has For Future Research In Improving Well-Being At Both A Population And Individual Level., Abhishek Gupta Dec 2020

The Genetic Influence On Subjective Well-Being: A Review Of The Current Knowledge On The Role Of Genetics On Our Sense Of Subjective Well-Being And The Implications It Has For Future Research In Improving Well-Being At Both A Population And Individual Level., Abhishek Gupta

Honors Scholar Theses

This thesis project explores the genetic underpinnings of one of the most cherished attributes in the world, well-being.1 Specifically, it attempts to understand the influence of the genome on subjective, or experienced, well-being. An investigation was conducted into current literature concerning both the structure of measurement devices of well-being as well as association studies to determine the scope of the correlation that exists between the genome and well-being and identify genetic findings of interest. Ultimately, being able to provide evidence of causality between the genome and sense of well-being at this iteration of well-being and genome research is limited, …

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Introduction To Neutrosophic Genetics, Florentin Smarandache Dec 2020

Introduction To Neutrosophic Genetics, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

Neutrosophic Genetics is the study of genetics using neutrosophic logic, set, probability, statistics, measure and other neutrosophic tools and procedures. In this paper, based on the Neutrosophic Theory of Evolution (that includes degrees of Evolution, Neutrality (or Indeterminacy), and Involution) – as extension of Darwin’s Theory of Evolution, we show the applicability of neutrosophy in genetics, and we present within the frame of neutrosophic genetics the following concepts: neutrosophic mutation, neutrosophic speciation, and neutrosophic coevolution.

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The Design And Validation Of A Qpcr-Based Approach To Cell Quantification Of Fungal-Algal Symbioses, Isabelle Katherine Garlotte Dec 2020

The Design And Validation Of A Qpcr-Based Approach To Cell Quantification Of Fungal-Algal Symbioses, Isabelle Katherine Garlotte

Honors Theses

Symbiotic relationships are extremely common in virtually all species. These relationships between organisms, particularly mutualistic symbioses, can have an incredibly large impact and can greatly affect the evolution of the species involved. Of particular interest is the suspected mutualistic relationship between green algae and fungi that may hold key evidence of how terrestrial plants evolved. In this experiment we established a method of quantifying the cells of each species involved in these symbioses through qPCR analysis to determine if the relationships are truly mutualistic. We developed a system for using DNA copies as a proxy for cell count in co-cultures …

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Identification And Characterization Of Novel Genes And Genetic Interactions That Influence Iba Metabolism, Vanessica Jawahir Oct 2020

Identification And Characterization Of Novel Genes And Genetic Interactions That Influence Iba Metabolism, Vanessica Jawahir

Dissertations

Indole-3-butyric acid (IBA) is an endogenous storage auxin important for maintaining appropriate indole-3-acetic acid (IAA) levels that influences primary root elongation and lateral root development. IBA is metabolized into free IAA in the peroxisome in a multistep process similar to fatty acid β-oxidation. Although many components specific to IBA metabolism and peroxisome function have been identified, our understanding is incomplete. I sought to identify novel components of IBA metabolism or peroxisome function by conducting a forward genetic screen for Arabidopsis thaliana plants with enhanced resistance to IBA. I identified Long chain acyl-CoA synthetase 4 (LACS4) as a novel gene functioning …

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Identifying Positive Selection In Multiple Subspecies Of Xylella Fastidiosa, Daniel Doroteo Flores Aug 2020

Identifying Positive Selection In Multiple Subspecies Of Xylella Fastidiosa, Daniel Doroteo Flores

Theses and Dissertations

For this study, we will be looking to identify positive selection in eight genomes of the bacterial plant pathogen Xylella fastidiosa. A previous study used a branching method that identified 2 genes with positive selection along with a site-specific method identifying 34 genes showing positive selection. This current study focused specifically on the site-specific method, resulting in 28 genes (of 1,039 tested) showing positive selection. Of the 28 genes showing positive selection, 12 of them come from the pathogenicity, virulence and cellular structural categories. The remaining genes are found in the biosynthesis, metabolism, macro metabolism, and cellular process categories. …

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Determining The Genetic Control Of Neural Tube Malformation Through Genetic Interactions With Idgf3, Elli N. Fox May 2020

Determining The Genetic Control Of Neural Tube Malformation Through Genetic Interactions With Idgf3, Elli N. Fox

Honors Projects

Genetic mutations disrupting human neural tube formation can lead to birth defects such as spina bifida and anencephaly. Defects can result in lack of neural tube closure in either the caudal (spina bifida) or cranial (anencephaly) regions. Little is known about the genes that cause these malformations. Researchers have been using the model organism Drosophila melanogaster in an attempt to determine genes responsible for neural tube malformations. Recently, an ortholog of human chitin-like protein, imaginal disc growth factor 3 (Idgf3), has been identified as important in the proper formation of Drosophila egg dorsal appendages. However, the molecular mechanism responsible for …

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Investigating The Role Of Genetic Variants And Environmental Factors In The Trajectory Of Substance Use Disorders, Linda Johnson May 2020

Investigating The Role Of Genetic Variants And Environmental Factors In The Trajectory Of Substance Use Disorders, Linda Johnson

Arts & Sciences Graduate Student Theses and Dissertations

Substance use disorders are a serious threat to public health with devastating social, economic, and health impacts on affected individuals and their families. This dissertation aims to improve understanding of substance use disorders in three parts: first, an epidemiological project examining smoking cessation and e-cigarette use at a population level; second, a genetic project examining the role of genetic variants on tobacco, alcohol, cannabis, and cocaine use; and finally, a review of the utility of polygenic risk scores in predicting risk of substance use behaviors. Cigarette smoking is a leading cause of preventable death, accounting for over 480,000 deaths in …

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

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 …

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Genetic Analysis Of Flower Color Differences Between A Hummingbird-Pollinated And A Self-Pollinated Monkeyflower (Mimulus) Species, Caitlin Foster May 2020

Genetic Analysis Of Flower Color Differences Between A Hummingbird-Pollinated And A Self-Pollinated Monkeyflower (Mimulus) Species, Caitlin Foster

University Scholar Projects

Flower color plays an important role in pollinator discrimination and speciation. Understanding the genetic contributions to flower color differences between two closely related species, Mimulus cardinalis and Mimulus parishii, can improve understanding of how they developed different pollination syndromes and diverged from a recent common ancestor. M. cardinalis is hummingbird-pollinated and has large, bright red flowers while M. parishii is self-pollinated and has small, pale pink flowers. An F2 hybrid population between these two species was created to establish a platform for analysis of the genetic architecture controlling the differences in anthocyanin pigmentation. Statistical analysis of anthocyanin concentration distribution …

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Genetic Intelligence: Myth Busted, Carissa Brand Apr 2020

Genetic Intelligence: Myth Busted, Carissa Brand

Academic Symposium of Undergraduate Scholarship

No abstract provided.

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Analyzing The Effect On Ligand Sensitivity For Xenopus Tropicalis Mc1r, Mc3r, Mc4r, And Mc5r As A Result Of Coexpression With Gallus Gallus Mrap1 In Chinese Hamster Ovary Cells, Avery Niemann, Robert Dores Jan 2020

Analyzing The Effect On Ligand Sensitivity For Xenopus Tropicalis Mc1r, Mc3r, Mc4r, And Mc5r As A Result Of Coexpression With Gallus Gallus Mrap1 In Chinese Hamster Ovary Cells, Avery Niemann, Robert Dores

DU Undergraduate Research Journal Archive

Some melanocortin receptors and the accessory protein MRAP1 have been found to interact in novel ways when co-expressed in the same cells following stimulation with either ACTH (1-24) or αMSH. These interactions have been seen for mammalian, bird, and some bony fish melanocortin receptors. Such analysis has not been done yet on the amphibian melanocortin receptors, MC1R, MC3R, MC4R, and MC5R. To this end, this study was done on the effects regarding ligand sensitivity for ACTH (1-24) and αMSH, when the MC1R, MC3R, MC4R, and MC5R paralogs of the amphibian, Xenopus tropicalis were expressed in Chinese Hamster Ovary cells either …

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Does Preimplantation Genetic Testing Increase The Risk Of Adverse Clinical Outcomes?, Robyn Weiss Jan 2020

Does Preimplantation Genetic Testing Increase The Risk Of Adverse Clinical Outcomes?, Robyn Weiss

The Science Journal of the Lander College of Arts and Sciences

Before 1990, options were limited for couples who were at risk for transmitting a genetic disease or a structural chromosomal abnormality to their children. Couples traditionally underwent invasive procedures such as amniocentesis and chorionic villus sampling, after which termination was offered if the fetus was found to be affected. Many couples chose not to have children at all. Since then, technological advances have allowed preimplantation genetic testing (PGT) to be offered to these couples. Couples who choose PGT undergo in-vitro fertilization (IVF) with intracytoplasmic sperm injection (ICSI), where the oocyte is injected by a single sperm and is then implanted …

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A Look At Gene Control: Tracking The Ccnd1 Gene, Bryan Anders Jan 2020

A Look At Gene Control: Tracking The Ccnd1 Gene, Bryan Anders

Mahurin Honors College Capstone Experience/Thesis Projects

Cancer occurs when the cell does not properly control its own cell cycle. It then replicates in an out of control fashion leading to the death of various organs and then the demise of the organism as a whole. As it seems to have always been a problem for cell-based life, certain safeguards against cancer have been evolved over time. One such method comes in the form of prevention via cyclin proteins, which are encoded from cyclin genes. The gene that is the focus of this research is the CCND1, or cyclin D1, gene that controls the progression through various …

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Using Crispr-Cas9 As A Restriction Enzyme, Zack Crawley Jan 2020

Using Crispr-Cas9 As A Restriction Enzyme, Zack Crawley

Master's Theses

Restriction digests are a commonly utilized process for cleaving DNA at specific, but relatively common sites. Restriction enzymes have widespread use in DNA manipulation. CRISPR/Cas9 is a recently identified endonuclease which utilizes a customizable guide sequence to recognize and cut specific ~20 bp sites located in a DNA sequence. This preliminary research aimed to exploit the potential benefit of DNA restriction using the CRISPR/Cas9 procedure through alterations of different components involved in that system. We sought to refine existing CRISPR/Cas9 protocols and make a budget friendly, user-selectable CRISPR/Cas9 restriction digest protocol. The motivation for this research was to simplify and …

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Identifying Essential Viral Genes Through Genomic Engineering, Amber Carroll Jan 2020

Identifying Essential Viral Genes Through Genomic Engineering, Amber Carroll

Mahurin Honors College Capstone Experience/Thesis Projects

Bacteria developed resistance to penicillin a mere four years after the groundbreaking antibiotic was first mass produced (Casadevall, 2010). Since then, the development of antibiotic-resistant bacteria has steadily risen, causing millions of difficult to treat infections annually. The challenge is to identify ways to combat these menacing microbes. Bacteriophages are viruses that infect bacteria and can potentially be used to eliminate deadly antibiotic-resistant bacteria. The number of sequenced bacteriophage genomes has increased tremendously over the past 10 years, but little is known about the function of most bacteriophage genes. The purpose of this study was to expand our understanding of …

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Genetic Analysis Of The Endangered Gray Bat Species (Myotis Grisescens), Emma Fitzgerald Jan 2020

Genetic Analysis Of The Endangered Gray Bat Species (Myotis Grisescens), Emma Fitzgerald

Lewis Honors College Capstone Collection

This study attempts to analyze the genetics using specific haplotype sequences of the endangered gray bat to determine genetic events that have happened in the past as well as determining how the species population has changed over time. We were able to conduct a Tajima’s D test to investigate whether a potential bottleneck has occurred. A linear regression of the genetic vs. geographical distance was produced to investigate the patterns of haplotype distribution. The species past distribution was compared to the current distribution using known collected specimens. A map of future predictions was constructed using present and future climate layers …

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Current Dog Breeding Practices Impacts On Health And Preservation Of Purebred Dogs, Bridget E. Baker Jan 2020

Current Dog Breeding Practices Impacts On Health And Preservation Of Purebred Dogs, Bridget E. Baker

Honors Theses and Capstones

No abstract provided.

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Interactions Between Earliest Linearbandkeramik Farmers And Central European Hunter Gatherers At The Dawn Of European Neolithization, Alexey G. Nikitin, Peter Stadler, Nadezhda Kotova, Maria Teschler-Nicola, T. Douglas Price, Jessica Hoover, Douglas J. Kennett, Losif Lazaridis, Nadin Rohland, Mark Lipson, David Reich Dec 2019

Interactions Between Earliest Linearbandkeramik Farmers And Central European Hunter Gatherers At The Dawn Of European Neolithization, Alexey G. Nikitin, Peter Stadler, Nadezhda Kotova, Maria Teschler-Nicola, T. Douglas Price, Jessica Hoover, Douglas J. Kennett, Losif Lazaridis, Nadin Rohland, Mark Lipson, David Reich

Open Access Publishing Support Funded Articles

Archaeogenetic research over the last decade has demonstrated that European Neolithic farmers (ENFs) were descended primarily from Anatolian Neolithic farmers (ANFs). ENFs, including early Neolithic central European Linearbandkeramik (LBK) farming communities, also harbored ancestry from European Mesolithic hunter gatherers (WHGs) to varying extents, reflecting admixture between ENFs and WHGs. However, the timing and other details of this process are still imperfectly understood. In this report, we provide a bioarchaeological analysis of three individuals interred at the Brunn 2 site of the Brunn am Gebirge-Wolfholz archeological complex, one of the oldest LBK sites in central Europe. Two of the individuals had …

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Genetically Distinct Behavioral Modules Underlie Natural Variation In Thermal Performance Curves, Gregory W. Stegeman, Scott E. Baird, William S. Ryu, Asher D. Cutter Jul 2019

Genetically Distinct Behavioral Modules Underlie Natural Variation In Thermal Performance Curves, Gregory W. Stegeman, Scott E. Baird, William S. Ryu, Asher D. Cutter

Biological Sciences Faculty Publications

Thermal reaction norms pervade organismal traits as stereotyped responses to temperature, a fundamental environmental input into sensory and physiological systems. Locomotory behavior represents an especially plastic read-out of animal response, with its dynamic dependence on environmental stimuli presenting a challenge for analysis and for understanding the genomic architecture of heritable variation. Here we characterize behavioral reaction norms as thermal performance curves for the nematode Caenorhabditis briggsae, using a collection of 23 wild isolate genotypes and 153 recombinant inbred lines to quantify the extent of genetic and plastic variation in locomotory behavior to temperature changes. By reducing the dimensionality of the …

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Surveying Apicomplexan Diversity And Dynamics In Narragansett Bay, Evelyn Spencer May 2019

Surveying Apicomplexan Diversity And Dynamics In Narragansett Bay, Evelyn Spencer

Senior Honors Projects

Parasites play an important role in marine ecosystems and their diversity is generally understudied. Apicomplexans, a group of parasitic protists in the phylum Alveolata, infect a wide variety of animal hosts and are abundant in ecosystems spanning from Polar Regions to Neotropical rainforests. Previous data generated from marine sediments in Antarctica, Naples Bay, and off the coast of Oslo, exhibit high diversity and numbers of apicomplexans. Abundance and diversity of these protists are unknown for Narragansett Bay, despite the fact that they infect many commercially important species. The aim of my study was to obtain abundance data and understand genetic …

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X-Inactivation And Epigenetics, Serena Weston Apr 2019

X-Inactivation And Epigenetics, Serena Weston

Thinking Matters Symposium Archive

To prevent abnormal development caused by expressing both X chromosomes, female mammals inactivate one of their X chromosomes using an epigenetic process called dosage compensation. This literature review examines how X chromosome inactivation (XCI) occurs during the formation and development of an embryo. This condensation of DNA is marked by histone tail modifications, DNA methylation, and the arrival of structural proteins resulting in extraordinarily stable heterochromatin. X-inactivation is regulated in cis by the X-inactivation center (Xic) that contains the Xist gene and its antisense gene, Tsix. On one X chromosome, Xist RNA is expressed and coats the center of the …

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