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Model-Based Analysis Of Chromatin Interactions From Dcas9-Based Capture-3c-Seq., Yong Chen, Yunfei Wang, Xin Liu, Jian Xu, Michael Q Zhang 2020 Rowan University

Model-Based Analysis Of Chromatin Interactions From Dcas9-Based Capture-3c-Seq., Yong Chen, Yunfei Wang, Xin Liu, Jian Xu, Michael Q Zhang

Faculty Scholarship for the College of Science & Mathematics

Deciphering long-range chromatin interactions is critical for understanding temporal and tissue-specific gene expression regulated by cis- and trans-acting factors. By combining the chromosome conformation capture (3C) and biotinylated dCas9 system, we previously established a method CAPTURE-3C-seq to unbiasedly identify high-resolution and locus-specific long-range DNA interactions. Here we present the statistical model and a flexible pipeline, C3S, for analysing CAPTURE-3C-seq or similar experimental data from raw sequencing reads to significantly interacting chromatin loci. C3S provides all steps for data processing, quality control and result illustration. It can automatically define the bin size based on the binding peak of the dCas9-targeted regions ...


Status Of The Blackstripe (Fundulus Notatus) And Blackspotted (F. Olivaceus) Topminnows In The Ozark Uplands Of Central Missouri, Nathaniel Steffensmeier, Naznin Sultana Remex, Robert Hrabik, David D. Duvernell 2020 The Ohio State University

Status Of The Blackstripe (Fundulus Notatus) And Blackspotted (F. Olivaceus) Topminnows In The Ozark Uplands Of Central Missouri, Nathaniel Steffensmeier, Naznin Sultana Remex, Robert Hrabik, David D. Duvernell

Southeastern Fishes Council Proceedings

The topminnow species Fundulus notatus and F. olivaceus have broadly overlapping geographic distributions that extend throughout much of the central and southern United States. In the northern portion of their respective ranges, in Missouri, the regional distributions of the two species coincide largely with recognized ecoregions. In the unglaciated southern half of Missouri, F. olivaceus is distributed throughout Ozark upland habitats while F. notatus is abundant in marginal large river and prairie habitats along the Ozark borders. An exception to this partitioning is the historical report of abundant F. notatus in the Bourbeuse and upper Meramec River drainages within the ...


Identification Of Clinically-Relevant Sequence Variants Within The Human Reference Genome, Lisa A. Lansdon 2020 Children's Mercy Kansas City

Identification Of Clinically-Relevant Sequence Variants Within The Human Reference Genome, Lisa A. Lansdon

Research Days

No abstract provided.


Sines: Structural Characteristics That Aid In The Mobilization From The Nucleus To The Ribosome, Madison Baltzly 2020 Bowling Green State University

Sines: Structural Characteristics That Aid In The Mobilization From The Nucleus To The Ribosome, Madison Baltzly

Honors Projects

From DNA that researchers once believed to be useless to being influential in evolutionary variation and cellular process, Short and Long Interspersed Nuclear elements (SINEs and LINEs respectively) have helped shape the genetic makeup of most mammals by essentially hijacking host cellular processes to amplify their existence within the genome. To be a genomic parasite, these SINEs and LINEs must be able to amplify enough within the genome without destroying the DNA and furthermore the mammal that carries them. In turn, the DNA must actively attempt to suppress the parasitic DNA. This arms race between genomic parasites and genomic DNA ...


Optimization Of Rt-Qpcr Protocols To Quantify Chua Gene Expression In Campylobacter Jejuni Mutants Under Iron-Limited Conditions, Jacob D. Wilbert 2020 University of Tennessee, Knoxville

Optimization Of Rt-Qpcr Protocols To Quantify Chua Gene Expression In Campylobacter Jejuni Mutants Under Iron-Limited Conditions, Jacob D. Wilbert

Chancellor’s Honors Program Projects

No abstract provided.


Liver Transcriptomic Analysis After Short- And Long-Term Feeding Of Soy Protein Isolate And Its Ability To Reduce Liver Steatosis In Obese Zucker Rats, Melisa Kozaczek 2020 University of Arkansas, Fayetteville

Liver Transcriptomic Analysis After Short- And Long-Term Feeding Of Soy Protein Isolate And Its Ability To Reduce Liver Steatosis In Obese Zucker Rats, Melisa Kozaczek

Theses and Dissertations

According to the Centers for Disease Control and Prevention (CDC) the prevalence of obesity in adults in the United States during 2017-2018 was a 42.4%, a high number considering all the risks factors associated with this disorder, such as cardiovascular disease, insulin resistance, diabetes type 2, and fatty liver disease, among others. Fatty liver disease is the accumulation of lipids in the liver that can account for more than 5 to 10% of the liver’s weight. There are two types of fatty liver disease, alcoholic fatty liver disease (AFLD), and non-alcoholic fatty liver disease (NAFLD). AFLD is the ...


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 ...


Genetic Variance In Flocculin Protein Family, Sarah Dooley, Dale Beach 2020 Longwood University

Genetic Variance In Flocculin Protein Family, Sarah Dooley, Dale Beach

Student Showcase for Research and Creative Inquiry

Yeast fermentation produces a number of commercially important products, most typically represented by alcoholic beverages. In craft breweries that do not use expensive filtration systems, selecting a yeast variety for fermentation can determine the clarity of the product from hazy Belgian pilsner to a crisp, clear American lager. Flocculation refers to a stress response behavior in yeast to group together (flocculate) in conditions like low sugar or high alcohol content as experienced at the end of fermentation. Higher levels of flocculation increase the clarity. The process of flocculation is genetically controlled through a series of complicated interactions and depends on ...


Using Crispr/Cas9 Gene Editing To Remove Twist2 To Determine Its Role During Somite Development In Zebrafish, Caleb Holdener 2020 Belmont University

Using Crispr/Cas9 Gene Editing To Remove Twist2 To Determine Its Role During Somite Development In Zebrafish, Caleb Holdener

Belmont Undergraduate Research Symposium (BURS)

Embryonic Mesoderm is a precursor to various types of tissues, such as the somatic mesoderm. Somites are a segmented tissue that gives rise to the sclerotome in vertebrates. This sclerotome further develops into the axial skeleton (Stickney, Barresi, and Devoto 2000). Somites are easily observable under low power microscopy during fish development. In fish, great strides have been made in studying the developmental fate of somites (Stoiber, Haslett, and Sänger 1999; Stickney, Barresi, and Devoto 2000). Zebrafish have been studied in many labs due to their similarities with higher vertebrates. These advantages include their inexpensive cost of care, external fertilization ...


Utilizing Crispr/Cas9 Gene Editing Determine The Role Of Cnr1 During Zebrafish Development, Ellis Chase 2020 Belmont University

Utilizing Crispr/Cas9 Gene Editing Determine The Role Of Cnr1 During Zebrafish Development, Ellis Chase

Belmont Undergraduate Research Symposium (BURS)

The CRISPR-Cas 9 system is a process used to create mutations, insertions, or deletions within a desired gene. It can be used to create mutant organisms necessary to study the function and impact of a particular gene1. Cannabinoids are active chemicals found in cannabis, the most common of which being cannabinol (CBD)2. Cannabinoid receptors are an integral part of the endocannabinoid system, recognizing cannabinoid signals to promote physiological processes like pain sensation, memory, mood, and appetite3. Studying these cannabinoid receptors can provide insight into how cannabis can affect bodily processes.

Zebrafish are small translucent freshwater fish residing ...


Utilizing Crispr/Cas9 Gene Editing Determine The Role Of Cnr1 During Zebrafish Development, Camme Sells 2020 Belmont University

Utilizing Crispr/Cas9 Gene Editing Determine The Role Of Cnr1 During Zebrafish Development, Camme Sells

Belmont Undergraduate Research Symposium (BURS)

In a world where cannabinoids are being used more frequently as for medicinal purposes, the importance for research on cannabinoid biology is steadily increasing. The goal of this study was to gain a greater understanding of the effect cannabinoids have on developing zebrafish embryos. Work in this area of developmental biology could give way to an understanding of the safety of a human fetus during pregnancy with a mother who uses cannabis medicinal therapy. The CRISPR/Cas 9 system was utilized in this study to genetically edit the zebrafish embryo genome to remove the function of the Cannabinoid Receptor 1 ...


Expression Of Tgf-Beta Ligands During Sclerotome Development, Estela Williams 2020 Belmont University

Expression Of Tgf-Beta Ligands During Sclerotome Development, Estela Williams

Belmont Undergraduate Research Symposium (BURS)

During early embryogenesis in vertebrates, somites are formed by the segmentation of the presomitic mesoderm (Gomez, Ozbudak, Wunderlich, Baumann. Lewis and Pourquie 2008). The somite possesses several domains within it and the ventral part of the somite is called the sclerotome. The sclerotome gives rise to the axial skeleton and tendons. Twist 1b and Twist 2 are genes that are expressed in the sclerotome during axial skeletal development. Our experiments were developed to help understand the roles of Twist1b and Twist2 in tendon development. By utilizing microinjection to alter gene expression, the Twist 1b and Twist 2 genes can be ...


Scleraxis Expression Within The Axial Tendon Population In Zebrafish, Jessica Bernaba 2020 Belmont University

Scleraxis Expression Within The Axial Tendon Population In Zebrafish, Jessica Bernaba

Belmont Undergraduate Research Symposium (BURS)

Zebrafish are a well-established model organism for vertebrate development. During embryonic development, a pattern of segmentation of mesoderm yields somites, which give rise to specific cell fates. Somites, bilateral blocks of mesoderm along the neural tube in developing vertebrate embryos, subdivide into sclerotome as the vertebrate matures. Depending on migratory position, sclerotome cells give rise to various components of the axial skeletal system, including bone, cartilage, and tendon. Each fate is determined by gene expressions within the sclerotome and occupy distinct domains of the body plan. By method of in situ hybridization, we studied the expression of the scleraxis (scxa ...


Exploring The Role Of Tgfbr2 During Zebrafish Sclerotome Development, Nooralhuda Feron 2020 Belmont University

Exploring The Role Of Tgfbr2 During Zebrafish Sclerotome Development, Nooralhuda Feron

Belmont Undergraduate Research Symposium (BURS)

Zebrafish, Danio rerio, are used as a source model organism for human development of the tendons, bones, and ligaments. The sclerotome is an embryonic structure known as the somite. The sclerotome gives rise to axial bones and tendons. During development, different genes are involved and affect how these skeletal tissues develop. Specifically, within this project, the effects of Twist1b and Twist2 were studied to see their effects on tendon formation, as they are expressed within the developing sclerotome tissue. Transforming growth factor beta receptor type-2 (Tgfbr2) has been shown to be involved in tendon formation (Subramanian, Kanzaki, Galloway and Schilling ...


Enhancement Of Nkx3.2 Expression After Twist1b And Twist2 Knockdown In Zebrafish, Peyton Yearick 2020 Belmont University

Enhancement Of Nkx3.2 Expression After Twist1b And Twist2 Knockdown In Zebrafish, Peyton Yearick

Belmont Undergraduate Research Symposium (BURS)

Somitogenesis is a developmental event patterned by cellular signaling during gastrulation, ending around 30-hours post fertilization. Somites are segmented regions of mesoderm along the dorsal side of the body which form paraxial mesoderm in Danio rerio, zebrafish. Somite development results in the formation of the subcompartment called sclerotome, which differentiates to form the axial skeleton and associated tendons (Stickney et al., 2000). Further differentiation allows for sclerotome progenitor cell to develop into bone, muscle, tendon, and cartilage through sclerotome migration along the mesoderm. A portion of sclerotome cells migrate anterior towards the neural tube, where they will form the vertebral ...


Twist1b Knockout Generation In Zebrafish Using Crispr-Cas9, Grace Hurley 2020 Belmont University

Twist1b Knockout Generation In Zebrafish Using Crispr-Cas9, Grace Hurley

Belmont Undergraduate Research Symposium (BURS)

The Twist gene is found in numerous organisms, including humans, mice and zebrafish (Yeo et al., 2009). It is a vital gene in development and is needed for the organism to survive (Yeo et al., 2009). Specifically, the Twist gene family aids in specialization and differentiation of mesodermal cells, telling somites, segmented blocks of mesoderm, what to become (Germanguz et al., 2007). Over time, the Twist gene has duplicated into paralogs, each having differences in their functions (Germanguz et al., 2007). Twist1b is a protein coding gene that is a paralog to the human Twist1 gene (ZFIN, 2020). In zebrafish ...


Chemical Communication In Songbirds, Leanne A. Grieves 2020 The University of Western Ontario

Chemical Communication In Songbirds, Leanne A. Grieves

Electronic Thesis and Dissertation Repository

Avian chemical communication has been understudied due to the misconception that olfaction is unimportant or even lacking in birds. Early work focused on the olfactory foraging capabilities of seabirds because of their ecology (open ocean foraging) and large olfactory bulbs. In contrast, olfaction in passerine birds, comprising over half of all extant avian taxa, was long overlooked due to their relatively small olfactory bulbs. It is now well established that passerines can smell, and their olfactory acuity is comparable to that of macrosmatic mammals such as rats. Much of our theory on communication and mate choice has involved studying visual ...


Environmental Dna Metabarcoding Detects Mammal Use Of Stock Tanks And Natural Springs On The Prescott National Forest, K. A. Smith, Berenice Carreras Mendiolea, C. E. Benson, F. B. Anaya 2020 Montana State University - Billings

Environmental Dna Metabarcoding Detects Mammal Use Of Stock Tanks And Natural Springs On The Prescott National Forest, K. A. Smith, Berenice Carreras Mendiolea, C. E. Benson, F. B. Anaya

Discovery Day - Prescott

Recent research has shown the viability of environmental DNA (eDNA) analysis as a tool for identifying species presence in aquatic ecosystems. However, there is limited research indicating the feasibility of eDNA as a survey tool in water sources such as springs and stock tanks. Because of the scarcity of water in the high desert landscape of Arizona, natural springs and stock tanks are an important water resource. In this study, we examined whether 16S rRNA metabarcoding could detect mammal eDNA in springs and stock tanks in the Prescott National Forest. During summer 2019, we collected and analyzed water samples at ...


Relative Model Fit Does Not Predict Topological Accuracy In Single-Gene Protein Phylogenetics, Stephanie J. Spielman 2020 Rowan University

Relative Model Fit Does Not Predict Topological Accuracy In Single-Gene Protein Phylogenetics, Stephanie J. Spielman

Faculty Scholarship for the College of Science & Mathematics

It is regarded as best practice in phylogenetic reconstruction to perform relative model selection to determine an appropriate evolutionary model for the data. This procedure ranks a set of candidate models according to their goodness of fit to the data, commonly using an information theoretic criterion. Users then specify the best-ranking model for inference. Although it is often assumed that better-fitting models translate to increase accuracy, recent studies have shown that the specific model employed may not substantially affect inferences. We examine whether there is a systematic relationship between relative model fit and topological inference accuracy in protein phylogenetics, using ...


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