Life Sciences Commons^™

Recovering Ancient Dna Using The Polymerase Chain Reaction, Rose Jennings

Undergraduate Research Symposium

Investigations into aDNA offer a window into the past that modern DNA and paleontological studies alone cannot provide and help address the evolution and connections between hominids, domestication timelines, the analysis of populations over time, and general diversity. Progress in aDNA research has been inherently technology-driven, with modern molecular biology methods, such as the inventions of Polymerase Chain Reaction (PCR) and Next Generation Sequencing (NGS), substantially increasing the analysis possibilities of aDNA. My research this semester has taken me along two parallel paths of investigation: literary research into aDNA and practical exposure to the laboratory techniques used in its analysis. …

Analysis Of The Population Structure And Migration Habits Of The Northern Leopard Frog (Lithobates Pipiens) At Midewin National Tallgrass Prairie, Gretchen A. Brinkman

Scholar Week 2016 - present

Massive amphibian declines of recent years have pushed researchers to pursue population genetics surveys and to assess the status of these essential components of many ecosystems. The Northern Leopard Frog (Lithobates pipiens) has been continuously experiencing population declines across the continental United States due to a combination of habitat loss and environmental change. Midewin National Tallgrass Prairie houses a considerable portion of Northern Leopard Frog (L. pipiens) in Illinois, and within this location, two creeks provide ideal conditions to support these animals. Because this prairie restoration project is a relatively recent development, further assessments on the …

Functional Analysis Provides Insight Into Missing Heritability, Scott L. Baughan, Michael A. Tainsky, Fatima Darwiche

Medical Student Research Symposium

Accurate ascertainment of genetic risk can be potentially lifesaving for patients who inherit cancer promoting mutations. However, even with the most extensive panel testing clinically available, a large number of patients will test negative despite family history of cancer or test positive for a variant of unknown significance (VUS). For these patients, clinical management is complicated; patients want to know their risk, and may fear disease they are not at great risk for (benign VUS) or they may not be given access to potentially lifesaving early screening procedures (pathogenic VUS). ATM has proven a challenge to clinicians due to its …

The Genetics Of Skin Cancer: What Genes Drive The Development Of Basal Cell Carcinoma, Squamous Cell Carcinoma, And Melanoma?, Cassandra Poole, Abagail Pack, Elizabeth Whitehead, Virginia Marshall

Spring Showcase for Research and Creative Inquiry

Skin cancer is one of the most common forms of cancer worldwide. The American Academy of Dermatology estimates that 9500 people in the United States are diagnosed with skin cancer every day, and that 1 in 5 Americans will be diagnosed with skin cancer by age 70. With such a high prevalence of disease, understanding how skin cancer develops and how it can be treated is extremely important. This project aims to analyze the genes involved in the development of the three most common forms of skin cancer: basal cell carcinoma, squamous cell carcinoma, and melanoma.

Examining The Effect Of Knocking Down Dopamine Receptors In Fruitless Sexually Dimorphic Neurons On Social Spacing, Avneet A. Sahota

Undergraduate Student Research Internships Conference

Social behaviour is an individual's response to others within a group. From humans to mice to even fruit flies, social behaviour involves interactions with others and their ability to exchange information. Social spacing is a type of social behaviour which measures the distance between two organisms. It is a balance of attractive and repulsive cues which are influenced by genetics and by the external environment. However, individuals with disorders such as autism spectrum or Williams syndrome display abnormal social spacing as they are unable to understand social and non-social cues. Also, dopamine is a neurotransmitter that is a contributing factor …

Investigating The Biological Function Of Female-Specific Fruitless Transcripts, Liam Mcfarlane

Undergraduate Student Research Internships Conference

In Drosophila, the fruitless (fru) gene encodes an array of alternatively spliced transcription factors, some of which are sex-specifically spliced. The male-specific transcript (fru^M) has been previously determined to be involved in male courtship behaviours. The female counterpart (fru^F) however, has been assumed to have no function due to the incorporation of a stop codon near the 5' end of the transcript. Interestingly, RNAseq data shows that expression levels of fru^F in females exceeds that of fru^M in males in the brain and thoracoabdominal ganglion, bringing to …

Influence Of Myelin-Associated Glycoprotein On Axon Subtype Specific Sheath Targeting, Nazmus Sakib Khan

Ramaley Celebration

During the development of the Central Nervous System, oligodendrocytes wrap axons with myelin, which is necessary for rapid, efficient nerve impulse propagation. For reasons unknown, oligodendrocytes direct myelin to certain subtypes of axons, leaving others incompletely myelinated, or even totally unmyelinated. Previous studies demonstrated mice harboring Mag mutations showed improper sheath targeting of myelin to axons indicating that MAG is a possible facilitator of axon-glia communication.

In the present study, we tested the hypothesis that loss of mag decreases the proportion of myelin directed towards specific axon subtypes. To test this, we perturbed Mag function in zebrafish embryos using knockdown …

Comparison Of Gray Squirrel (Sciurus Carolinensis) And Fox Squirrel (Sciurus Niger) In Order To Explore Genes That Confer A Fitness Advantage, Joshua Franzen

UNO Student Research and Creative Activity Fair

Mutations in the MC1R gene is associated with melanism, or black fur, and the presence of a 24 base pair deletion in the MC1R gene of fox and gray squirrels suggests a shared ancestry between the two species. This could be due to a mutation in a common ancestor or previous mating between species. Evidence has shown that the most likely cause for the presence of MC1R in both species is previous mating between species. If this did occur, then it is possible that other genes traveled between species along with the mutated MC1R gene. Conserved genes shared between species …

Variation In Genes Responsible For Melanism In Sciurus Carolinensis And Sciurus Niger, Ibrahim Hussain

UNO Student Research and Creative Activity Fair

During the past few years, the population of melanistic squirrels in Nebraska has increased. These color variations have been associated with variation in the Melanocortin 1 Receptor (MC1R) and Agouti Signaling Protein (ASIP) genes, which are responsible for pigment production. DNA was isolated from 3 grey and 46 fox squirrels collected from Eastern Nebraska; 8 of the fox squirrels were melanistic in color. Primers were designed to amplify and sequence MC1R and three portions of ASIP to examine the extent of variation in these genes in local squirrels. The sequences were aligned to the grey squirrel reference …

The Nature Of Genes Expressed Differently After Environmental Drug Exposure, Nicci Siffel

Scholars Week

The Nature of Genes Expressed Differently after Environmental Drug Exposure

N. Siffel, S. Anderson, B. Subedi, D.R. Hammond-Weinberger

Drug use, of prescription or illicit varieties, alter bodily functions in different ways, especially in the nervous system. These drugs are found in sources of drinking water because they are not removed by wastewater treatment facilities. To investigate the effects of these drugs as they appear in mixtures, we exposed groups of zebrafish embryos to cocktails of drugs and screened for genes that were differentially expressed between the experimental and control groups and could thus give more insight into their biological functions. …

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

2020 Virtual Spring 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 …

Biol 250: Curly Hair Trait: Homozygous Or Heterozygous, Kaysi Bing

2020 Virtual Spring Student Showcase for Research and Creative Inquiry

Research Aim: To connect the SNP rs17646946 AG genotype and curly hair

Hypothesis: People expressing a GG genotype at the SNP rs17646946 are most likely to have the curly hair trait

The Ethical Implications Of Bioengineering Advancements, Mainstream Media Coverage Of Those Developments, And The Future Of Motherhood, Aliff Abad, Katherine Gregory

Publications and Research

How do the media interpret reproductive interventions that involve genetic testing? When a scientist performed the first known genetic editing on twins, Lulu and Nana, he ignored ethical considerations of CRISPR use. This project provides a content analysis based on a review of popular science and newspaper articles. Our interpretation of these articles suggest that there is a lack of critical understanding of this unethical procedure and a similar attitude towards future genetic developments. While the public is curious about the repercussions of genetic editing, not enough focus is applied to the ethics of conducting such a procedure.

Exploring Secondary Structure In Bacteriophage Programmed Frameshift Elements, Samuel Okabayashi, Sean Mcclory

HON499 projects

Bacteriophages are viruses that infect bacteria and reproduce using host bacterial components. Part of the bacteriophage reproduction is assembly of the tail complex, which requires two assembly chaperone (TAC) proteins. In many phages the TAC’s are produced from a single gene through a non-canonical process called programmed translational frameshifting (PTF). The SEA-PHAGES program has produced hundreds of TAC genes that are accessible through phagesdb, a database of sequenced and annotated phage genomes. The sequences for the TAC gene were gathered from phagesdb and analyzed using ClustalOmega; a multiple sequence alignment (MSA) tool which revealed several positions where total conservation was …

Determining The Functions Of Novel Genes Required For Photosynthesis, Gillian Gomer, Moshe Kafri, Martin Jonikas

Gillian Gomer

Genetic Diversity Of Local Canines Assessed By Derived Cleaved Amplified Polymorphic Sequences, Nicole Benmoshe, Jeremy Seto

Publications and Research

Breeding of the dog, Canis Iupus familiaris, over centuries has given rise to the selection of certain traits including size, shape, coat length, color and many behavioral traits. Inbreeding within dog breeds has resulted in the increase of genetic diseases, many of which are similar to human diseases making the dog an exemplary model organism to study. Using dCAPS (Derived Cleaved Amplified Polymorphic Sequences) we can identify SNPs (Single Nucleotide Polymorphisms) in the dog genome using buccal samples collected from four local dogs of different breeds, both large and small. After performing DNA extractions, PCR (Polymerase Chain Reaction), restriction enzyme …

Co-Occurrence Of Manganese Oxidase Genes Indicates Lateral Transfer Between Classes Of Proteobacteria, Jacob Olichney

Student Scholar Showcase

Pseudomonas putida GB-1 is a model organism for the study of manganese oxidation in bacteria, however, the frequency of co-localization of multiple known and suspected manganese oxidizing proteins, as well as their occurrence between species, is unknown. Eight different genes isolated from known manganese oxidizing bacteria (MnxG, MopA, McoA, PputGB1_2552, PputGB1_2553, MoxA, MofA, and Bacillus MnxG) were tested individually using BioPython and BLAST (Basic Local Alignment Search Tool) on multiple genomic databases. BLAST searches had an expect value cutoff of 1e-50, limiting gene homologs to those with high sequence similarity. The abundance of homologous genes across classes of proteobacteria point …

Meta-Analysis Of Characteristics In Upper Missouri River Fishes: Prediction Of Invasiveness, Steph Purcell

UNO Student Research and Creative Activity Fair

Invasive species are often considered a global threat due to their association with biodiversity loss and novel diseases. The Missouri-Mississippi River Watershed, including the Missouri River Basin, is particularly vulnerable to invasive species because of low species diversity following historic glaciation events. Management of invasive species is imperative in this watershed but continues to be challenging in that there are over 100 invasive species currently present in this region. The goal of this project is to identify characteristics associated with successful invasions that may assist in developing management strategies to reduce the negative outcomes caused by the establishment of invasive …

Gene Co-Expression Networks Analysis Reveal Novel Molecular Endotypes In Alpha-1 Antitrypsin Deficiency, Jen-Hwa Chu, Wenlan Zang

Yale Day of Data

Rationale:Alpha-1 antitrypsin deficiency (AATD) is a genetic condition that predisposes to early onset pulmonary emphysema and airways obstruction. The exact mechanism through which AATD leads to lung disease is incompletely understood.

Objectives: To investigate the effect of AAT genotype and augmentation therapy on bronchoalveolar lavage (BAL) and peripheral blood mononuclear cells (PBMC) transcriptome, while examining the link between gene expression profiles, and clinical features of AATD.

Methods: We performed RNA-Seq on RNA extracted from BAL and PBMC on samples obtained from 89 AATD patients enrolled in the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Differential …

Exploring The Ipf Lung Through The Lens Of Single Cell Rna Sequencing, Taylor Adams, Jonas Schupp

Yale Day of Data

This poster illustrates the differences between the IPF disease-specific variety of lung macrophages and the two varieties of macrophages known to reside in the normal human lung.

Intro To Rna-Sequencing Lecture Slides, Ray A. Enke

Ray Enke Ph.D.

Rna-Seq Bioinformatics Analysis Using Cyverse Discovery Environment, Ray A. Enke

Ray Enke Ph.D.

Association Of Vasp Polymorphisms And Infectious Disease Burden In Global Populations And Identification Of Candidate Resistance Haplotypes In Sub-Saharan Africa, Melinda Phun, Blake Rosenn, Danny Glenn, Dhanushi Rupasinghe, James Church, David Zuzga, Shaohua Fan, Sarah Tishkoff

HON499 projects

Enteric pathogens employ numerous strategies to breach the intestinal epithelial barrier. One critical target of these pathogens is the host cell cytoskeleton. Pathogens may induce cytoskeletal remodeling to disrupt tight junctions and increase the permeability of the epithelium to gain access to underlying tissue. Alternatively, the cytoskeletal machinery may be directly co-opted to facilitate the attachment, invasion, or intracellular motility of these pathogens. The vasodilator-stimulated phosphoprotein (VASP) is a processive actin polymerase that induces membrane remodeling through the polymerization of actin cytoskeletal filaments. Interestingly, VASP is regulated by a variety of pathogens to induce cytoskeletal remodeling in host cells. If …

Changes In The Proliferation And Gene Expression Of Huvecs In Response To Treatment With Plant Secondary Metabolites, Caleigh Howard

Seaver College Research And Scholarly Achievement Symposium

Medicinal plants have historically been a valuable source of new drugs, and Southern California possesses a rich collection of native plants which have been used as medicines by native people groups for thousands of years. Angiogenesis is the biological process of new blood-vessel growth from endothelial cells. It is an essential part of the wound-healing process, and increased angiogenesis has also been implicated in the growth of some types of cancerous tumors. In this study, extracts of the Southern Californian native plants Red shanks (Adenostoma sparsifolium) and the alkaloid extract of Jimson weed (Datura wrightii) were …

Transcripity Split: Course-Based Rna-Seq Analysis Using The Ultrafast Kallisto-Sleuth Pipeline, Ray A. Enke

Ray Enke Ph.D.

No abstract provided.

A Behavioral Prerequisite For The Genetic Analysis Of Auditory Feature Detection Mechanisms In Female Crickets, Rebecca L. Blisko

Senior Honors Projects

Sexual dimorphism is exhibited across all cricket species and is a central aspect of the mating processes of these insects. Only male crickets possess wing structures and pattern generators in the central nervous system that allow them to produce a mating call that is unique to their species in order to attract conspecific females. Conspecific females possess an auditory feature detection circuit in the central nervous system that is capable of detecting the species-specific frequency and temporal pattern of sound pulses within a male call. In order for dimorphic differences in mating behavior to result in successful continuation of a …

C-Myc’S Role On Methylation Of The Gata-2 Gene In Non-Small Cell Lung Carcinoma, Jonathan D. Hajduk

Student Scholar Showcase

Lung cancer accounts for more deaths per year than any other form of cancer, resulting in a total of 158,000 deaths per year in the U.S. Non-small cell lung cancer (NSCLC) is diagnosed in greater than 224,000 Americans every year. Methylation and subsequent downregulation of certain genes has been directly linked to the uncontrolled growth of NSCLC cells. Natural killer (NK) cells are key innate immune cells responsible for apoptosis of cells with incorrect genetic code. It is believed that one component of uncontrolled NSCLC growth is due to the NK cells’ inability to detect errors within NSCLC cells. Perhaps …

Genetic Effect Of Drought On The California Newt, Taricha Torosa, Madeleine M. Perrault, Samantha Fiallo, Alero Arueyingho, Cindy Kim, Laiken Ritchie

Seaver College Research And Scholarly Achievement Symposium

Droughts are now a common occurrence in Southern California and are known to cause population declines in many species, and such bottlenecks can cause a loss of genetic variation. Genetic variation was examined in a population of the California newt located in Arroyo Sequit Creek in the Santa Monica Mountains. Genetic data from animals examined prior to the current drought were compared to similar data collected from the population after it experienced several years of severe drought. We hypothesized that the drought impacted population should show less genetic variation in comparison to the pre-drought population. Nevertheless, there were no genetic …

Taxonomic Placement Of The Nidulariaceae Of Nebraska And Iowa Based On Molecular And Morphological Data, Goodmond H. Danielsen Iv

UNO Student Research and Creative Activity Fair

Proper taxonomic and molecular study is necessary to better organize closely related species that may not only be used for human needs, but also in the quest for knowledge of how the world around us works. Though important, the taxonomic placement of Nebraskan and Iowan bird’s nest fungi (Nidulariaceae) is not well documented. Here, phylogenetic analysis is used to place the Nidulariaceae of Nebraska and Iowa in the tree of life using molecular and morphological techniques. Based on these results and results of further work done on these specimens, it will be possible to better place the Nidulariaceae of Nebraska …

The Effects Of Chronic Partial Sleep Deprivation On Alcohol Consumption And Delta Fos B Accumulation, Kristian Ponder

Showcase of Graduate Student Scholarship and Creative Activities

The present study explores the relation between sleep restriction and alcohol use and the neural substrates that result from chronic behaviors, such as transcription factors. Transcription factor activity is suggested as a possible outcome of chronic behaviors, such as addiction. Sleep is discussed as possible mediating factor in the relationship between specific transcription factors and alcohol. Analysis will focus on brain areas related to both sleep and reward.