Genetics and Genomics Commons^™

Microrna Functions In Uv-Induced Cutaneous Squamous Cell Carcinoma, Tran Nguyen

Dissertations and Theses (Open Access)

Cutaneous squamous cell carcinoma (cuSCC) is the second most common skin cancer, for which long term UV exposure and chronic wounding are the dominant risk factors. Despite these clinically established connections, little is understood about the early molecular response of human skin to UV exposure and its connection to acute wounding and cuSCC. Thus, our goal is to find common and specific signatures driven by UV-exposure and wounding as a means of developing new approaches for treating and preventing cuSCC.

Here, we perform integrated analyses of RNA-seq and miR-seq on 3 datasets: (1) UV-unexposed and acute UV-exposed human skin, (2) …

Genomic And Transcriptomic Landscape Of Colorectal Premalignancy, Kyle Chang

Dissertations and Theses (Open Access)

Colorectal cancer (CRC) is the third most commonly diagnosed cancer among men and women in the United States, with 3 to 5 percent of the cases diagnosed in the background of a hereditary form of the disease. Biologically, CRC is divided into two groups: microsatellite instable (MSI) and chromosomally unstable (CIN). Genomic and transcriptomic characterization of CRC has emerged from large-scale studies in recent years due to the advancement of next-generation sequencing technologies. These studies have identified key genes and pathways altered in CRC and provided insights to the discovery of therapeutic targets. Despite the wealth of knowledge acquired in …

Mechanism Of Incorporation And Repair Of Uracil At Highly Transcribed Genes In Saccharomyces Cerevisiae, Norah Auma Owiti

Dissertations and Theses (Open Access)

Recombination and mutagenesis are elevated by high levels of transcription. The correlation between transcription and genome instability is largely explained by the topological and structural changes in DNA and the associated physical obstacles generated by the transcription machinery. However, such explanation does not directly account for the unique types of mutations originating from the non-canonical residues such as uracil, which are also elevated at highly transcribed regions. Apurinic/Apyrimic or Abasic (AP) sites derived from uracil excision, accumulate at a higher rate in actively transcribed regions of the genome in S. cerevisiae and are primarily repaired by base excision repair (BER) …

Omics Approaches To Uncover Germline And Somatic Variation Underlying Inherited Sarcomagenesis, Justin Wong

Dissertations and Theses (Open Access)

Sarcomas are rare mesenchymal tumors, making up 15% of all childhood and 1% of all adult tumors. They account for a disproportionate share of mortality in young adults, and if left untreated, are highly likely to metastasize. However, sarcoma etiology is poorly understood, and having numerous histological subtypes has complicated elucidation. To better understand factors underlying sarcomagenesis, we leveraged two rare inherited cancer predisposition syndromes, Li-Fraumeni Syndrome (LFS), and LFS-like (LFSL), both with a high incidence of sarcomas. LFS is caused by mutations in the tumor suppressor gene TP53 (p53), but has variable and incomplete penetrance, suggesting additional acquired …

Quantitative Studies Of Amyloidogenic Protein Residue Interaction Networks And Abnormal Ammonia Metabolism In Neurotoxicity And Disease, Jeddidiah Griffin

Electronic Theses and Dissertations

Investigating similarities among neurological diseases can provide insight into disease processes. Two prominent commonalities of neurological diseases are the formation of amyloid deposits and altered ammonia and glutamate metabolism. Computational techniques were used to explore these processes in several neurological diseases. Residue interaction networks (RINs) abstract protein structure into a series of nodes (representing residues) and edges (representing connections between residues likely to interact). Analyzing the RINs of monomeric forms of amyloidogenic proteins for common network features revealed similarities not previously known. First, amyloidogenic variants of lysozyme were used to demonstrate the usefulness of RINs to the study of amyloidogenic …

Characterization Of Fgf-Mediated Sonic Hedgehog Expression During Limb Development, Billy A. Watson

Loma Linda University Electronic Theses, Dissertations & Projects

Crosstalk between Fibroblast Growth Factors (FGFs) and Sonic hedgehog (SHH) is essential for proper limb development; however, the molecular mechanisms involved in this process remain unclear. Via comparative transcriptome analysis and gene knockdown and overexpression studies, we identified the transcription factor Lim homeobox 2 (LHX2) as an intermediate in FGF-directed SHH expression. We determined that FGF signaling was necessary for LHX2 expression and demonstrated that LHX2 is a primary transcription target of FGF signaling through the RAS and AKT pathways. Additionally, loss of LHX2 in the distal limb results in decreased SHH expression and a truncated limb within 24 hours …

Empirical Investigations Of Rna Fitness Landscapes: Harnessing The Power Of High-Throughput Sequencing And Evolutionary Simulations, Devin Pratt Bendixsen

Boise State University Theses and Dissertations

Fitness landscapes or adaptive landscapes represent the mapping of genotype (sequence) to phenotype (function or fitness). Originally proposed as a metaphor to envision evolutionary processes and mutational interactions, the fitness landscape has recently transitioned from theoretical to empirical. This is due in part to advances in DNA synthesis and high-throughput sequencing. This allows for the construction and analysis of empirical fitness landscapes that encompass thousands of genotypes. These landscapes provide tractable insight into mutational pathways, the predictability of evolution or even the evolution of life. RNA enzymes (ribozymes) are an attractive model system for the construction of empirical fitness landscapes. …

Investigation Of Bacterial Taxa As Biomarkers Of Fescue Toxicosis And Heat Stress In Grazing Beef Cows, Sarah Katherine Chewning

Graduate Theses and Dissertations

Fescue toxicosis in grazing beef cattle is caused by consumption of Ergot alkaloids associated with tall fescue (toxic fescue) and is responsible for substantial economic loss to the U.S. beef industry. Cattle consuming toxic fescue suffer adverse physiological responses, such as: hyperthermia, increased respiration rate (RR), poor reproduction and growth performance. Other adverse responses to fescue toxins include the retention of a winter hair coat and vasoconstriction in the extremities, which can lead to tissue necrosis. Identifying cattle with reduced susceptibility to fescue toxins would allow for efficient use of fescue pastures; thus, the objectives of this thesis was to: …

Computational Analysis Of Genomic Variants Affecting Predicted Microrna:Target Interactions In Prostate Cancer., Angélica Paola Hernández Pérez

KGI Theses and Dissertations

Prostate cancer (PCa) is the most common cancer of men in the United States and is third only to lung and colon as a cause of cancer death. Clinical behavior of the disease is variable and the combination of prostate-specific antigen (PSA) screening and Gleason score staging are currently the best available molecular and pathology tools to predict outcomes. Cancer biology research establishes microRNAs (miRNAs) as key molecular components in both normal and pathological states. Thus, elucidating miRNAs perturbed by genomic alterations will expand our understanding of the molecular taxonomy of PCa with the aim to complement current practices in …

Molecular Adaptations For Sensing And Securing Prey And Insight Into Amniote Genome Diversity From The Garter Snake Genome, Blair W. Perry, Daren C. Card, Joel W. Mcglothlin, Giulia I.M. Pasquesi, Richard H. Adams, Drew R. Schield, Nicole R. Hales, Andrew B. Corbin, Jeffery P. Demuth, Federico G. Hoffmann, Michael W. Vandewege, Ryan K. Schott, Nihar Bhattacharyya, Belinda S.W. Chang, Nicholas R. Casewell, Gareth Whiteley, Jacobo Reyes-Velasco, Stephen P. Mackessy, Tony Gamble, Kenneth B. Storey, Kyle K. Biggar, Courtney N. Passow, Chih-Horng Kuo, Suzanne E. Mcgaugh, Anne M. Bronikowski, A.P. Jason De Koning, Scott V. Edwards, Michael E. Pfrender, Patrick Minx, Edmund D. Brodie Jr., Edmund D. Brodie Jr., Wesley C. Warren, Todd A. Castoe

Biology Faculty Publications

Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile …

Multiethnic Meta-Analysis Identifies Ancestry-Specific And Cross-Ancestry Loci For Pulmonary Function, Annah B. Wyss, Tamar Sofer, Mi Kyeong Lee, Natalie Terzikhan, Jennifer N. Nguyen, Lies Lahousse, Jeanne C. Latourelle, Albert Vernon Smith, Traci M. Bartz, Mary F. Feitosa, Wei Gao, Tarunveer S. Ahluwalia, Wenbo Tang, Christopher Oldmeadow, Qing Duan, Kim De Jong, Mary K. Wojczynski, Xin-Qun Wang, Raymond Noordam, Fernando Pires Hartwig, Victoria E. Jackson, Tianyuan Wang, Ma'en Obeidat, Brain D. Hobbs, Tianxiao Huan, Hongsheng Gui, Margaret M. Parker, Donglei Hu, Lauren S. Mogil, Gleb Kichaev, Jianping Jin, Mariaelisa Graff, Tamara B. Harris, Ravi Kalhan, Susan R. Heckbert, Lavinia Paternoster, Kristin M. Burkart, Yongmei Liu, Elizabeth G. Holliday, James G. Wilson, Judith M. Vonk, Jason L. Sanders, R. Graham Barr, Renee De Mutsert, Ana Maria Baptista Menezes, Hieab H. H. Adams, Maarten Van Den Berge, Roby Joehanes, Albert M. Levin, Jennifer Liberto, Lenore J. Launer, Alanna C. Morrison, Colleen M. Sitlani, Juan C. Celedon, Stephen B. Kritchevsky, Rodney J. Scott, Kaare Christensen, Jerome I. Rotter, Tobias N. Bonten, Fernando Cesar Wehrmeister, Yohan Bossé, Shujie Xio, Sam Oh, Nora Franceschini, Jennifer A. Brody, Robert C. Kaplan, Kurt Lohman, Mark Mcevoy, Michael A. Province, Frits R. Rosendaal, Kent D. Taylor, David C. Nickle, L. Keoki Williams, Esteban G. Burchard, Heather E. Wheeler, Don D. Sin, Wilmundur Gudnason, Kari E. North, Myriam Fornage, Bruce M. Psaty, Richard H. Myers, George O'Connor, Torben Hansen, Cathy C. Laurie, Patricia A. Cassano, Joohon Sung, Woo Jin Kim, John R. Attia, Leslie Lange, H. Marike Boezen, Bharat Thyagarajan, Stephen S. Rich, Dennis O. Mook-Kanamori, Bernardo Lessa Horta, André G. Uitterlinden, Hae Kyung Im, Michael H. Cho, Guy G. Brusselle, Sina A. Gharib, Josée Dupuis, Ani Manichaikul, Stephanie J. London

Biology: Faculty Publications and Other Works

Nearly 100 loci have been identified for pulmonary function, almost exclusively in studies of European ancestry populations. We extend previous research by meta-analyzing genome-wide association studies of 1000 Genomes imputed variants in relation to pulmonary function in a multiethnic population of 90,715 individuals of European (N = 60,552), African (N = 8429), Asian (N = 9959), and Hispanic/Latino (N = 11,775) ethnicities. We identify over 50 additional loci at genome-wide significance in ancestry-specific or multiethnic meta-analyses. Using recent fine-mapping methods incorporating functional annotation, gene expression, and differences in linkage disequilibrium between ethnicities, we further shed light …

Genomic Signatures Of Adaptive Evolution, Jessica A. Weber

Biology ETDs

Comparative genomics has revolutionized virtually all fields of biology including the study of evolution. In this dissertation, I used next-generation sequencing to explore the evolutionary histories and adaptive evolution of a diverse set of taxa. Comparisons ranged across time scales, from population-level genetic diversity studies to questions spanning the deepest branches of the metazoan lineage. Whole genome sequencing of 50 unrelated Korean individuals revealed that Koreans have a distinct genetic history from the Chinese and Japanese populations. Our Korean-specific variome database was used to identify novel disease-causing variants in the Korean population, highlighting the value of high-quality ethnic variation databases …

Genome-Wide Atlas Of Alternative Polyadenylation In The Forage Legume Red Clover, Manohar Chakrabarti, Randy D. Dinkins, Arthur G. Hunt

Plant and Soil Sciences Faculty Publications

Studies on prevalence and significance of alternative polyadenylation (APA) in plants have been so far limited mostly to the model plants. Here, a genome-wide analysis of APA was carried out in different tissue types in the non-model forage legume red clover (Trifolium pratense L). A profile of poly(A) sites in different tissue types was generated using so-called ‘poly(A)-tag sequencing’ (PATseq) approach. Our analysis revealed tissue-wise dynamics of usage of poly(A) sites located at different genomic locations. We also identified poly(A) sites and underlying genes displaying APA in different tissues. Functional categories enriched in groups of genes manifesting APA between …

Horse Y Chromosome Assembly Displays Unique Evolutionary Features And Putative Stallion Fertility Genes, Jan E. Janečka, Brian W. Davis, Sharmila Ghosh, Nandina Paria, Pranab J. Das, Ludovic Orlando, Mikkel Schubert, Martin K. Nielsen, Tom A. E. Stout, Wesley Brashear, Gang Li, Charles D. Johnson, Richard P. Metz, Al Muatasim Al Zadjali, Charles C. Love, Dickson D. Varner, Daniel W. Bellott, William J. Murphy, Bhanu P. Chowdhary, Terje Raudsepp

Veterinary Science Faculty Publications

Dynamic evolutionary processes and complex structure make the Y chromosome among the most diverse and least understood regions in mammalian genomes. Here, we present an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates. The eMSY comprises single-copy, equine specific multi-copy, PAR transposed, and novel ampliconic sequence classes. The eMSY gene density approaches that of autosomes with the highest number of retained X–Y gametologs recorded in eutherians, in addition to novel Y-born and transposed genes. Horse, donkey and mule testis RNAseq reveals several candidate genes for stallion …

Dual Graph Partitioning Highlights A Small Group Of Pseudoknot-Containing Rna Submotifs, Swati Jain, Cigdem S. Bayrak, Louis Petingi, Tamar Schlick

Publications and Research

RNA molecules are composed of modular architectural units that define their unique structural and functional properties. Characterization of these building blocks can help interpret RNA structure/function relationships. We present an RNA secondary structure motif and submotif library using dual graph representation and partitioning. Dual graphs represent RNA helices as vertices and loops as edges. Unlike tree graphs, dual graphs can represent RNA pseudoknots (intertwined base pairs). For a representative set of RNA structures, we construct dual graphs from their secondary structures, and apply our partitioning algorithm to identify non-separable subgraphs (or blocks) without breaking pseudoknots. We report 56 subgraph blocks …

The Iceman's Last Meal Consisted Of Fat, Wild Meat, And Cereals., Frank Maixner, Dmitrij Turaev, Amaury Cazenave-Gassiot, Marek Janko, Ben Krause-Kyora, Michael R Hoopmann, Ulrike Kusebauch, Mark Sartain, Gea Guerriero, Niall O'Sullivan, Matthew Teasdale, Giovanna Cipollini, Alice Paladin, Valeria Mattiangeli, Marco Samadelli, Umberto Tecchiati, Andreas Putzer, Mine Palazoglu, John Meissen, Sandra Lösch, Philipp Rausch, John F Baines, Bum Jin Kim, Hyun-Joo An, Paul Gostner, Eduard Egarter-Vigl, Peter Malfertheiner, Andreas Keller, Robert W Stark, Markus Wenk, David Bishop, Daniel G Bradley, Oliver Fiehn, Lars Engstrand, Robert L Moritz, Philip Doble, Andre Franke, Almut Nebel, Klaus Oeggl, Thomas Rattei, Rudolf Grimm, Albert Zink

Articles, Abstracts, and Reports

The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary -omics approach combined with microscopy, we analyzed the stomach content of the Iceman, a 5,300-year-old European glacier mummy [2, 3]. He seems to have had a remarkably high proportion of fat in his diet, supplemented with fresh or dried wild meat, cereals, and …

Fitness Consequences Of Interspecific Nesting Associations Among Cavity-Nesting Birds, James C. Mouton, Thomas E. Martin

Aspen Bibliography

Interspecific aggregations of prey may provide benefits by mitigating predation risk, but they can also create costs if they increase competition for resources or are more easily detectable by predators. Variation in predation risk and resource availability may influence the occurrence and fitness effects of aggregating in nature. Yet tests of such possibilities are lacking. Cavity-nesting birds provide an interesting test case. They compete aggressively for resources and experience low nest predation rates, which might predict dispersion, but across 19 years of study we found that they commonly aggregate by sharing nest trees. Tree sharing was more common when aspen …

Removal Of Invasive Plants From Pando Exclosure 2018, Marc Coles-Ritchie

Aspen Bibliography

On July 10-11, 2018 volunteers and staff from Great Old Broads for Wilderness and Grand Canyon Trust removed invasive plants from the Pando exclosure, a fenced portion of the Pando Clone aspen forest adjacent to Fish Lake, in Central Utah. This area has been fenced to restore a portion of the Pando Clone that has been lacking recruitment for decades, by protecting young aspen from browsing by deer and cattle. We have been removing invasive species for five years from this exclosure.

The 2018 trip included 10 women and one staffer of Great Old Broads for Wilderness, from the states …

Genomic Analysis Of 48 Paenibacillus Larvae Bacteriophages, Casey Stamereilers, Christopher P. Fajardo, Jamison K. Walker, Katterinne N. Mendez, Eduardo Castro-Nallar, Julianne H. Grose, Sandra Hope, Philippos K. Tsourkas

Life Sciences Faculty Research

The antibiotic-resistant bacterium Paenibacillus larvae is the causative agent of American foulbrood (AFB), currently the most destructive bacterial disease in honeybees. Phages that infect P. larvae were isolated as early as the 1950s, but it is only in recent years that P. larvae phage genomes have been sequenced and annotated. In this study we analyze the genomes of all 48 currently sequenced P. larvae phage genomes and classify them into four clusters and a singleton. The majority of P. larvaephage genomes are in the 38–45 kbp range and use the cohesive ends (cos) DNA-packaging strategy, while a minority have genomes …

Drosophila Species Learn Dialects Through Communal Living, Balint Z. Kacsoh, Julianna Bozler, Giovanni Bosco

Dartmouth Scholarship

Many species are able to share information about their environment by communicating through auditory, visual, and olfactory cues. In Drosophila melanogaster, exposure to para- sitoid wasps leads to a decline in egg laying, and exposed females communicate this threat to naïve flies, which also depress egg laying. We find that species across the genus Drosophila respond to wasps by egg laying reduction, activate cleaved caspase in oocytes, and communicate the presence of wasps to naïve individuals. Communication within a species and between closely related species is efficient, while more distantly related species exhibit partial communication. Remarkably, partial communication between …

The Hero Organism And Heroism Science: A New Frontier Of Human Consciousness, Olivia Efthimiou

Heroism Science

In the context of a new science of heroism this article presents a brief history of the presence and study of heroism, and an outline of the key characteristics of the modern-day movement of heroism. The potentially wide-reaching impacts of the science of heroism are briefly discussed. The hypothesis of human beings as “hero organisms” is presented, before embarking on a discussion on what it means for each of us to be on our own hero’s journey.

Menthol, A Unique Urinary Volatile Compound, Is Associated With Chronic Inflammation In Interstitial Cystitis., Muhammad Shahid, Min Young Lee, Austin Yeon, Eunho Cho, Vikram Sairam, Luis Valdiviez, Sungyong You, Jayoung Kim

Articles, Abstracts, and Reports

Chronic inflammation is a potential systemic risk factor for many bladder dysfunctions, including interstitial cystitis (IC). However, the underlying mechanism through which a healthy bladder protects itself from inflammatory triggers remains unknown. In this study, we identified odor compounds in urine obtained from IC patients and healthy controls. Using comprehensive solid-phase microextraction-gas chromatography-time-of-flight-mass spectrometry (SPME-GC-TOF-MS) profiling and bioinformatics, we found that levels of urinary volatile metabolites, such as menthol, were significantly reduced in IC patients, compared to healthy controls. In an attempt to understand the mechanistic meaning of our volatile metabolites data and the role of menthol in the immune …

The Search For A Hero Gene: Fact Or Fiction?, Olivia Efthimiou

Heroism Science

The radical entry of heroism research into scientific inquiry presents interesting challenges and possibilities for the study of heroism and the human condition more broadly. This ‘final frontier’ of the enduring phenomenon of heroism stands to offer remarkable, unprecedented, and controversial advances in our understanding of heroic and human behaviour. Is a genetic basis for heroism a real possibility? If so, what would its impacts be? Advances in genomics and increased interest in the fields of epigenetics and neuroplasticity might hold the key to its discovery. This article considers some of the leading emerging research in global health genomics and …

Phytochemical Screening Of Quaking Aspen (Populus Tremuloides) Extracts By Uplc-Qtof-Ms And Evaluation Of Their Antimicrobial Activity, Annabelle St-Pierre, Dorian Blondeau, André Lajeunesse, Julien Bley, Nathalie Bourdeau, Isabel Desgagné-Penix

Aspen Bibliography

The continual emergence of pathogen resistance is a recurring challenge and pushes for the development of antimicrobial compounds. Here, we investigated compounds from quaking aspen trees (Populus tremuloides) as potential antimicrobial agents. Several extractions using different solvents were realized, and corresponding antimicrobial activity was tested against eight microorganisms. Results revealed that polar extraction solvents including water, ethanol and methanol gave the best extraction yields (>15.07%). Minimal inhibition concentration (MIC) and minimal bactericidal/fungicidal concentration (MBC/MFC) demonstrated that water extracts had the best antimicrobial activity by a weak to moderate inhibition of growth of all eight tested microorganisms in addition to …

Impact Of Suburban Landscape Features On Gene Flow Of The Model Invasive Grass, Brachypodium Sylvaticum, Tina Marie Arredondo

Dissertations and Theses

Rapid range expansion of newly invasive species provides a unique opportunity for studying patterns of dispersal and gene flow. In this thesis, I examined the effect of landscape features on gene flow in the invasive grass Brachypodium sylvaticum at the edge of its expanding range. I used genome-wide Single Nucleotide Polymorphism (SNP) surveys of individuals from 22 locations in the Clackamas Watershed in the Portland, Oregon metropolitan region to assess genetic diversity and structure, to identify putative source populations, and to conduct landscape genetic analyses. Resistance surfaces were created for each landscape feature, using ResistanceGA to optimize resistance parameters. My …

Lineage Marker Synchrony In Hematopoietic Genealogies Refutes The Pu.1/Gata1 Toggle Switch Paradigm., Michael K Strasser, Philipp S Hoppe, Dirk Loeffler, Konstantinos D Kokkaliaris, Timm Schroeder, Fabian J Theis, Carsten Marr

Articles, Abstracts, and Reports

Molecular regulation of cell fate decisions underlies health and disease. To identify molecules that are active or regulated during a decision, and not before or after, the decision time point is crucial. However, cell fate markers are usually delayed and the time of decision therefore unknown. Fortunately, dividing cells induce temporal correlations in their progeny, which allow for retrospective inference of the decision time point. We present a computational method to infer decision time points from correlated marker signals in genealogies and apply it to differentiating hematopoietic stem cells. We find that myeloid lineage decisions happen generations before lineage marker …

Novel Metrics For Quantifying Bacterial Genome Composition Skews., Lena M Joesch-Cohen, Max Robinson, Neda Jabbari, Christopher G Lausted, Gustavo Glusman

Articles, Abstracts, and Reports

BACKGROUND: Bacterial genomes have characteristic compositional skews, which are differences in nucleotide frequency between the leading and lagging DNA strands across a segment of a genome. It is thought that these strand asymmetries arise as a result of mutational biases and selective constraints, particularly for energy efficiency. Analysis of compositional skews in a diverse set of bacteria provides a comparative context in which mutational and selective environmental constraints can be studied. These analyses typically require finished and well-annotated genomic sequences.

RESULTS: We present three novel metrics for examining genome composition skews; all three metrics can be computed for unfinished or …

Analytical “Bake-Off” Of Whole Genome Sequencing Quality For The Genome Russia Project Using A Small Cohort For Autoimmune Hepatitis, Daria V. Zhernakova, Sergei Kliver, Nikolay Cherkasov, Gaik Tamazian, Mikhail Rotkevich, Ksenia Krasheninnikova, Igor Evsyukov, Sviatoslav Sidorov, Pavel Dobrynin, Andrey A. Yurchenko, Valentin Shimansky, Irina V. Shcherbakova, Andrey S. Glotov, David L. Valle, Minzhong Tang, Emilia Shin, Kathleen B. Schwarz, Stephen James O'Brien

Biology Faculty Articles

A comparative analysis of whole genome sequencing (WGS) and genotype calling was initiated for ten human genome samples sequenced by St. Petersburg State University Peterhof Sequencing Center and by three commercial sequencing centers outside of Russia. The sequence quality, efficiency of DNA variant and genotype calling were compared with each other and with DNA microarrays for each of ten study subjects. We assessed calling of SNPs, indels, copy number variation, and the speed of WGS throughput promised. Twenty separate QC analyses showed high similarities among the sequence quality and called genotypes. The ten genomes tested by the centers included eight …

Tk1; Journey From The Cytoplasm To The Cell Membrane, Weston Burrup, Kim O'Neill

Journal of Undergraduate Research

Thymidine Kinase 1 is an enzyme involved in the synthesis of thymidine triphosphate, an essential DNA building block needed for cell replication. Previous research has shown an upregulated level of TK1 in the serum levels of cancer patients as well as on the cancer cell surface. Due to its’ abnormal presence on the surface of various cancer cells, it is being researched as a potential biomarker for future immunotherapies. In order to be a more reliable biomarker, we need a more in depth understanding of the mechanism of how this protein travels through the cell cytoplasm and eventually attaches on …

Comparative Genetic And Genomic Analysis Of The Novel Fusellovirus Sulfolobus Spindle-Shaped Virus 10, David Andrew Goodman

Dissertations and Theses

Viruses that infect thermophilic Archaea are unique in both their structure and genetic makeup. The lemon-shaped fuselloviruses - which infect members of the order Sulfolobales, growing optimally at 80º C and pH 3 - are some of the most ubiquitous and best studied viruses of the thermoacidophilic Archaea. They provide a malleable and useful genetic tool for probing into the functions of their host, as well as the host responses to infection. Nonetheless, much about these viruses remains to be learned to further understand their morphological, genetic, and life cycle characteristics.

In order to investigate these aspects of these …