Genomics Commons^™

Investigating The Role Of Cd109 In Pancreatic Ductal Adenocarcinoma, Mennatallah Shaheen

Dissertations & Theses (Open Access)

Pancreatic Ductal Adenocarcinoma (PDAC) is the 3rd leading cause of cancer death in the US. We performed loss of function genomic screening on a cohort of four patient derived PDAC cell populations and our data shows a cell surface receptor CD109 to be a common vulnerability, the biologic role of which in PDAC is yet unstudied and largely unknown. We hypothesized that CD109 expression provides PDAC cells with a survival advantage, and promotes cancer progression through activation of downstream signaling. We believe therefore that targeting CD109 could improve PDAC patients’ survival. Here we report that CD109 plays a role in …

Response Of Early Life Stage Homarus Americanus To Ocean Warming And Acidification: An Interpopulation Comparison, Maura K. Niemisto

Electronic Theses and Dissertations

Anthropogenic carbon released into the atmosphere is driving rapid, concurrent increases in temperature and acidity across the world’s oceans, most prominently in northern latitudes. The geographic range of the iconic American lobster (Homarus americanus) spans a steep thermal gradient and one of the most rapidly warming oceanic environments. Understanding the interactive effects of ocean warming and acidification on this species’ most vulnerable early life stages is important to predict its response to climate change on a stage-specific and population level. This study compares the responses of lobster larvae from two sub-populations spanning New England’s north-south temperature gradient (southern …

Modeling Cancer Using Li-Fraumeni Syndrome Patient-Derived Induced Pluripotent Stem Cells, Ruoji Zhou

Dissertations & Theses (Open Access)

Li-Fraumeni syndrome (LFS) is an autosomal dominant disease caused by germline mutations in the gene TP53, which predispose individuals to a wide range of malignancies, including osteosarcoma and breast cancer. In the previous study, our group developed a novel disease model platform by reprograming LFS patients' fibroblasts to induced pluripotent stem cells (iPSCs), and further differentiate these iPSCs into mesenchymal stem cells (MSCs) then to osteoblasts (OBs), the cells from which osteosarcomas originate. Interestingly, LFS iPSC-derived osteoblasts recapitulated the osteosarcoma phenotype, creating “a bone tumor in a dish”. This “tumor in a dish” platform proved that LFS is an …

Temporal Gene Expression Of Mesenchymal Cells In The Pediatric Lung, Quinlen F. Marshall, Soumyaroop Bhattacharya, Gautam Bandyopadhyay, Ravi Misra, Thomas Mariani, Gloria Pryhuber

Chemistry Student Work

INTRODUCTION: The newborn lung undergoes vast biochemical and physiological changes during adaptation from the intrauterine to the extrauterine environment. Lung morphogenesis continues from birth into early childhood, mediated by dynamic gene expression and a diversity of pulmonary cell types (Whitsett, JA. et al. Physiol. Rev, 2019). Murine models demonstrate that pulmonary mesenchymal cells exhibit remarkable heterogeneity in function and morphology during development, however, confirmation of their role is lacking in human neonates and early childhood (Guo, M. et al. Nat. Comm, 2019). In addition, many current human genomic studies of lung maturation suffer from limited sample size, limiting …

Association Of Copy Number Variations With Chronic Hepatitis B In Chinese Population, Fang Niu

Capstone Experience

With one third of the Hepatitis B virus (HBV) infection population of the world, chronic Hepatitis B (CHB) has become a top burden in China. CHB is a lifelong infection with HBV which can cause serious health problems, like cirrhosis, liver cancer or even death. HBV infection is known to result in various clinical conditions, including asymptomatic HBV carriers to chronic hepatitis and primary hepatocellular carcinoma. Several studies have shown that host genetic susceptibility could be an important factor that determines these various outcomes of HBV infection. Many Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs) have been associated …

Mixing It Up: The Impact Of Episodic Introgression On The Evolution Of High-Latitude Mesocarnivores, Jocelyn P. Colella

Biology ETDs

At high latitudes, climatic oscillations have triggered repeated episodes of organismal divergence by geographically isolating populations. For terrestrial species, extended isolation in glacial refugia – ice-free regions that enable terrestrial species persistence through glacial maxima – is hypothesized to stimulate allopatric divergence. Alternatively, upon glacial recession, divergent populations expanded from independent glacial refugia and often contacted other diverging populations. In the absence of reproductive isolating mechanisms, this biogeographic process may trigger hybridization and ultimately, gene flow between divergent taxa. My dissertation research aims to understand how these episodic periods of isolation and contact have impacted the evolution of high latitude …

Paired-End Mappability Of Transposable Elements In The Human Genome, Corinne E. Sexton, Mira V. Han

Life Sciences Faculty Research

Though transposable elements make up around half of the human genome, the repetitive nature of their sequences makes it difficult to accurately align conventional sequencing reads. However, in light of new advances in sequencing technology, such as increased read length and paired-end libraries, these repetitive regions are now becoming easier to align to. This study investigates the mappability of transposable elements with 50 bp, 76 bp and 100 bp paired-end read libraries. With respect to those read lengths and allowing for 3 mismatches during alignment, over 68, 85, and 88% of all transposable elements in the RepeatMasker database are uniquely …

A Method For Improving The Accuracy And Efficiency Of Bacteriophage Genome Annotation, Alicia Salisbury, Philippos K. Tsourkas

Life Sciences Faculty Research

Bacteriophages are the most numerous entities on Earth. The number of sequenced phage genomes is approximately 8000 and increasing rapidly. Sequencing of a genome is followed by annotation, where genes, start codons, and functions are putatively identified. The mainstays of phage genome annotation are auto-annotation programs such as Glimmer and GeneMark. Due to the relatively small size of phage genomes, many groups choose to manually curate auto-annotation results to increase accuracy. An additional benefit of manual curation of auto-annotated phage genomes is that the process is amenable to be performed by students, and has been shown to improve student recruitment …

Position-Specific Metabolic Probing And Metagenomics Of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities At High Temperatures, Scott C. Thomas, Kevin O. Tamadonfar, Cale O. Seymour, Dengxun Lai, Jeremy A. Dodsworth, Senthil K. Murugapiran, Emiley A. Eloe-Fadrosh, Paul Dijkstra, Brian P. Hedlund

Life Sciences Faculty Research

Temperature is a primary driver of microbial community composition and taxonomic diversity; however, it is unclear to what extent temperature affects characteristics of central carbon metabolic pathways (CCMPs) at the community level. In this study, 16S rRNA gene amplicon and metagenome sequencing were combined with 13C-labeled metabolite probing of the CCMPs to assess community carbon metabolism along a temperature gradient (60–95°C) in Great Boiling Spring, NV. 16S rRNA gene amplicon diversity was inversely proportional to temperature, and Archaea were dominant at higher temperatures. KO richness and diversity were also inversely proportional to temperature, yet CCMP genes were similarly represented across …

Extreme‐Phenotype Genome‐Wide Association Study (Xp‐Gwas): A Method For Identifying Trait‐Associated Variants By Sequencing Pools Of Individuals Selected From A Diversity Panel, Jinliang Yang, Haiying Jiang, Cheng-Ting Yeh, Jianming Yu, Jeffrey A. Jeddeloh, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Although approaches for performing genome‐wide association studies (GWAS) are well developed, conventional GWAS requires high‐density genotyping of large numbers of individuals from a diversity panel. Here we report a method for performing GWAS that does not require genotyping of large numbers of individuals. Instead XP‐GWAS (extreme‐phenotype GWAS) relies on genotyping pools of individuals from a diversity panel that have extreme phenotypes. This analysis measures allele frequencies in the extreme pools, enabling discovery of associations between genetic variants and traits of interest. This method was evaluated in maize (Zea mays) using the well‐characterized kernel row number trait, which was …

Beef Production Systems In The Nebraska Sandhills, Mckay Erickson

Department of Animal Science: Dissertations, Theses, and Student Research

Four studies were conducted to determine the effectiveness of improving production systems of beef cattle in the Sandhills region of Nebraska. These studies were to determine impacts of modified estrus synchronization protocols, genomic testing heifer calves for longevity, and evaluation of 2 differing calving systems (March or May) for improving biological outcome and improved production. Experiment 1 utilized 180 yearling heifers to determine the effectiveness of a second dose of prostaglandin F_2α(PGF) with those females not expressing estrus after an initial 14 d MGA-PG estrus synchronization protocol. The treatment of PGF did increase estrus expression, but did not …

Novel Algorithms For Ldd Motif Search, Peng Xiao, Martin Schiller, Sanguthevar Rajasekaran

Life Sciences Faculty Research

Background: Motifs are crucial patterns that have numerous applications including the identification of transcription factors and their binding sites, composite regulatory patterns, similarity between families of proteins, etc. Several motif models have been proposed in the literature. The (l,d)-motif model is one of these that has been studied widely. However, this model will sometimes report too many spurious motifs than expected. We interpret a motif as a biologically significant entity that is evolutionarily preserved within some distance. It may be highly improbable that the motif undergoes the same number of changes in each of the species. To address this issue, …

High-Performance Computing Frameworks For Large-Scale Genome Assembly, Sayan Goswami

LSU Doctoral Dissertations

Genome sequencing technology has witnessed tremendous progress in terms of throughput and cost per base pair, resulting in an explosion in the size of data. Typical de Bruijn graph-based assembly tools demand a lot of processing power and memory and cannot assemble big datasets unless running on a scaled-up server with terabytes of RAMs or scaled-out cluster with several dozens of nodes. In the first part of this work, we present a distributed next-generation sequence (NGS) assembler called Lazer, that achieves both scalability and memory efficiency by using partitioned de Bruijn graphs. By enhancing the memory-to-disk swapping and reducing the …

Mapping A New Disease Resistance Locus In An F1 Progeny Derived From Two Grape Wild Relatives, Gaurab Bhattarai

MSU Graduate Theses

Linkage maps and quantitative trait loci (QTL) analysis have become essential tools for the positional cloning of agronomically important genes and for marker-assisted breeding. In this study, two North American grape species, Vitis rupestris and Vitis riparia, and their 294 F₁ progeny were used to construct parental linkage maps and to perform QTL analysis for downy mildew resistance. Single nucleotide polymorphism (SNP) discovery was accomplished using genotyping-by-sequencing (GBS) and resulted in 348,888 SNPs. Of these, 11,063 informative SNP markers (3.17% of the original SNP dataset) were derived after filtering for various quality parameters and missing data. A two-way …

Clinical Utility Of Exon Deletion/Duplication Microarray Testing - A Children’S Mercy Kansas City Two-Year Experience, Binu Porath

Research Days

No abstract provided.

Simplicity Diffexpress: A Bespoke Cloud-Based Interface For Rna-Seq Differential Expression Modeling And Analysis, Cintia C. Palu, Marcelo Ribeiro-Alves, Yanxin Wu, Brendan Lawlor, Pavel V. Baranov, Brian Kelly, Paul Walsh

Department of Computer Science Publications

One of the key challenges for transcriptomics-based research is not only the processing of large data but also modeling the complexity of features that are sources of variation across samples, which is required for an accurate statistical analysis. Therefore, our goal is to foster access for wet lab researchers to bioinformatics tools, in order to enhance their ability to explore biological aspects and validate hypotheses with robust analysis. In this context, user-friendly interfaces can enable researchers to apply computational biology methods without requiring bioinformatics expertise. Such bespoke platforms can improve the quality of the findings by allowing the researcher to …

A Discrepancy Between The Human Reference Genome (Grch37) And Transcriptome (Refseq) Results In The Incorrect Annotation Of A Clinically-Relevant Sequence Variant In Recql4, Lisa A. Lansdon

Research Days

No abstract provided.

Root Hair Single Cell Type Specific Profiles Of Gene Expression And Alternative Polyadenylation Under Cadmium Stress, Jingyi Cao, Congting Ye, Guijie Hao, Carole Dabney-Smith, Arthur G. Hunt, Qingshun Q. Li

Plant and Soil Sciences Faculty Publications

Transcriptional networks are tightly controlled in plant development and stress responses. Alternative polyadenylation (APA) has been found to regulate gene expression under abiotic stress by increasing the heterogeneity at mRNA 3′-ends. Heavy metals like cadmium pollute water and soil due to mining and industry applications. Understanding how plants cope with heavy metal stress remains an interesting question. The Arabidopsis root hair was chosen as a single cell model to investigate the functional role of APA in cadmium stress response. Primary root growth inhibition and defective root hair morphotypes were observed. Poly(A) tag (PAT) libraries from single cell types, i.e., root …

Crispr/Cas9 Driven Eradication Of Hiv-1 In Infected Human Genome, Sydney Loechler

Senior Seminars and Capstones

Once infected with HIV-1, the host immune system is incapable of ridding itself of the virus. HIV-1 uses latent viral reservoirs (LR) within CD4+ T cells to replicate. Within these reservoirs, HIV-1 is able to go into a latent state where it cannot be detected by the host's immune system or current HIV-1 treatments. By utilizing viewing assays and CRISPR-Cas9, there may be a possibility to identify, isolate, and then cut out HIV-1 from an infected cell. Two possible viewing assays have been proposed and studied in recent research. PCR assays are quicker and easier to administer while viral outgrowth …

Physician-Patient Communication About Genomic Tumor Testing: Perceptions Of Oncology Providers, Hayley Mandeville, Eric Anderson, Kimberly Murray, Caitlin Gutheil, Leo Waterston, Lee Lucas, Christine Duarte, Christian Thomas, Susan Miesfeldt, Petra Helbig, Andrey Antov, Jens Rueter, Paul Han

Maine Medical Center

Background:

• Genomic tumor testing (GTT) is a new technology and a cornerstone of the “precision medicine” movement in cancer care.

• GTT uses next-generation genome sequencing technology to identify somatic variants in tumor cells.

• By identifying somatic variants that predict responses to cancer therapies, GTT can help tailor therapy to individual patients, making them more effective.

• However, due to the fact that GTT also detects many variants of uncertain significance, its clinical value is currently unproven.

• When using GTT, physicians counsel patients about both its benefits and its limitations, but the ideal goals and content of …

Identification Of Genes Involved In Iron Metabolism In Rhizobium Leguminosarum Atcc 14479 Genome Through The Use Of In-Silico Analysis, Shuaib A. Siddiqui

Undergraduate Honors Theses

The complete genomic sequence of Rhizobium leguminosarum ATCC 14479 has been determined. Its genome size is 7,935,223 base-pairs of DNA (bp). This multipartite genome contains 5 distinct replicons: a chromosome of 4,883,137 bp and four mega-plasmids of size 1,234,209 bp, 415,988 bp, 771,583 bp, and 630,306 bp. In silico (literally: on computer) analysis was done on the complete genome to detect genes relating to iron metabolism by bacteria. Seven iron-related operons and genes were found: nodulation genes, the Tol operon, the hmuPSTUV operon, iron response regulator genes, the cycHJKL operon, genes for bacterial cyclic glucans, and vicibactin genes.

The Relationship Between Uncertainty Tolerance And Oncologists’ Perceptions Of Large-Panel Genomic Tumor Testing, Eric Anderson, Alexandra Hinton, Christine Lary, Kimberly Murray, Leo Waterson, Paul Han, Maine Cancer Genomics Initiative

Maine Medical Center

Introduction:

Large-panel genomic tumor testing (GTT) is a new technology that promises to make cancer treatment more precise, but that currently poses many uncertainties regarding its clinical value and appropriate use. Uncertainty Tolerance (UT), a psychological construct that describes trait-level differences in individuals’ responses to uncertainty, may influence oncologists’ perceptions and attitudes regarding GTT.

Community Oncology Clinicians’ Knowledge, Beliefs, And Attitudes Regarding Genomic Tumor Testing, Eric Anderson, Alexandra Hinton, Kimberly Murray, Hayley Mandeville, Caitlin Gutheil, Leo Waterston, Lee Lucas, Christine Duarte, Christian Thomas, Susan Miesfeldt, Petra Helbig, Andrey Antov, Jens Rueter, Paul Han

Maine Medical Center

Introduction: Genomic tumor testing (GTT) is a new technology that promises to make cancer treatment more precise. However, little is known about clinicians’ knowledge, beliefs, and attitudes regarding GTT, particularly in community oncology settings.

Developing Technologically Advanced Research In Low- And Middle-Income Countries, Isa Abdulkadir, Tina Slusher, Fidelia Bode-Thomas, Sean Riordan, Jean-Baptiste Lepichon, Laila Hassan, Shehu Abdullahi, Akinyemi Ofakunrin, Stephen Oguche, Steven Shapiro, William Ogala

Posters

This poster presents a collaboration between a group of scientists in Nigeria and the USA in developing a genomic research project and the solutions adopted in tackling the ethical implications and partnership equity and ownership of such a project.

The Full Genome Sequence Of An Antarctic Microbe Constructed Using A Rapid, Portable Sequencer And A Hybrid Assembly, Bruce Wyatt Boles

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Microbial genomes contain combinations of nucleotides that code for genes which subsequently determines the function of the cell. This information provides significant insight into the unique niche of microbes from extreme environments. Here we use two sequencing technologies, the Oxford Nanopore MinION with accompanying software and Illumina HiSeq, to generate a hybrid genome for a Shewanella strain isolated from an Antarctic glacier. Bioinformatic programs, Albacore and SPAdes, allowed us to decrease the time of genome assembly while also obtaining a large quantity of information related to the Shewanella sp. Our combined approach yielded a high quality genome assembly 5.3 …

Ultramicrobacteria Genome Database Project, Abdullah A. Salim, Tien Tran, Andrew Putt, Terry C. Hazen

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Ultramicrobacteria (UMB) are a largely uncultured, globally abundant, and metabolically active group of bacteria. UMB have cell diameters ≤0.3μm, cell volumes ≤0.1 μm3, and small streamlined genomes. Recent findings indicate that UMB aid in bioremediation and nutrient cycling, but future investigations and comprehension of current findings are skewed by highly variable nomenclature and a lack of databases for functional, genomic, geochemical, or spatial data specific to candidate UMB. We aim to develop a user-friendly open-access database of various UMB candidates linked to an open-access online map where researchers can gather genomic, spatial, and geochemical data. Our comprehensive review of literature …

Improved Draft Genome Sequence Of Bacillus Sp. Strain Yf23, Which Has Plant Growth-Promoting Activity, Ye Xia, Seth Debolt, Qin Ma, Adam Mcdermaid, Cankun Wang, Nicole Shapiro, Tanja Woyke, Nikos C. Kyrpides

Horticulture Faculty Publications

We report here the improved draft genome sequence of Bacillus sp. strain YF23, a bacterium originally isolated from switchgrass (Panicum virgatum) plants and shown to exhibit plant growth-promoting activity. The genome comprised 5.82 Mbp, containing 5,933 genes, with 193 as RNA genes, and a GC content of 35.10%.

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 …

Plant Mitochondrial Genome Evolution And Structure Has Been Shaped By Double-Strand Break Repair And Recombination, Emily Wynn

School of Biological Sciences: Dissertations, Theses, and Student Research

Plant mitochondrial genomes are large but contain a small number of genes. These genes have very low mutation rates, but genomes rearrange and expand at significant rates. We propose that much of the apparent complexity of plant mitochondrial genomes can be explained by the interactions of double-strand break repair, recombination, and selection. One possible explanation for the disparity between the low mutation rates of genes and the high divergence of non-genes is that synonymous mutations in genes are not truly neutral. In some species, rps14 has been duplicated in the nucleus, allowing the mitochondrial copy to become a pseudogene. By …

Computational Analysis Of Large-Scale Trends And Dynamics In Eukaryotic Protein Family Evolution, Joseph Boehm Ahrens

FIU Electronic Theses and Dissertations

The myriad protein-coding genes found in present-day eukaryotes arose from a combination of speciation and gene duplication events, spanning more than one billion years of evolution. Notably, as these proteins evolved, the individual residues at each site in their amino acid sequences were replaced at markedly different rates. The relationship between protein structure, protein function, and site-specific rates of amino acid replacement is a topic of ongoing research. Additionally, there is much interest in the different evolutionary constraints imposed on sequences related by speciation (orthologs) versus sequences related by gene duplication (paralogs). A principal aim of this dissertation is to …