Biology Commons^™

Morphological Changes Of The Asian Shore Crab Across Latitudes, Ainslee Mcmullin, Blaine D. Griffen

Library/Life Sciences Undergraduate Poster Competition 2022

The Asian shore crab, Hemigrapsus sanguineus , is an invasive species that has rapidly spread across the Eastern United States coastline. First observed in North America in 1988, its range currently extends from Maine to North Carolina. H. sanguineus has adapted very well to this region and has displaced several native species as the dominant crab in rocky intertidal habitats. Although the Asian shore crab’s biology and interactions with native species has been well studied, larger scale impacts (economic, potential further spread, community ecology, etc.) are under researched. We collected specimen samples of H. sanguineus throughout its entire East coast …

Species Invasion Vs. Abundance In The Northern And Southern Regions Of Lake Powell, Amanda Lebarge, Mark Belk

Library/Life Sciences Undergraduate Poster Competition 2022

Lake Powell is a dynamic system, evidenced by its yearly fluctuations in water level. In the last 20 years, this reservoir has experienced invasions from two different invasive species: the gizzard shard, and quagga mussel. Due to the unique nature of Lake Powell, our research seeks to understand if there were catastrophic effects of these invasions on fish biomass and abundance patterns, and do these impacts vary based on region? We hypothesize that both species will have a major impact in all regions on the native species in Lake Powell; however, the southern region will be more catastrophic.

Ancestral State Reconstruction Of Oviposition Techniques In New World Stick Insects, Ellie Mcgregor, Jackson Linde, Michael F. Whiting

Library/Life Sciences Undergraduate Poster Competition 2022

Phasmids, commonly known as stick bugs, are unique and interesting creatures, both phenotypically and genotypically. Their cryptic abilities are what draws most people to them, but their oviposition techniques, or how they disperse eggs, has become a new source of interest. While most phasmids are known to flick or drop their eggs from the canopy, there are several other techniques including inserting the eggs into the soil or gluing them to a substrate. New world phasmids have not been thoroughly studied, especially in understanding which technique was ancestral. The purpose of this paper was to construct a phylogenetic tree to …

Teach And Question Data, Rachel Tomco Novak

ScholarsArchive Data

Data collected from a Teach-and-Question assignment in 11 sections of an introductory science course, during Winter semester 2021.

Triophaser: Using Mendelian Inheritance Logic To Improve Genomic Phasing Of Trios, Dustin B. Miller, Stephen R. Piccolo

Faculty Publications

Background: When analyzing DNA sequence data of an individual, knowing which nucleotide was inherited from each parent can be benefcial when trying to identify certain types of DNA variants. Mendelian inheritance logic can be used to accurately phase (haplotype) the majority (67–83%) of an individual’s heterozygous nucleotide positions when genotypes are available for both parents (trio). However, when all members of a trio are heterozygous at a position, Mendelian inheritance logic cannot be used to phase. For such positions, a computational phasing algorithm can be used. Existing phasing algorithms use a haplotype reference panel, sequencing reads, and/or parental genotypes …

Simplifying The Development Of Portable, Scalable, And Reproducible Workflows, Stephen Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang, Andrea H. Bild

Faculty Publications

Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution details. CWL documents can include instructions for executing tools inside software containers. Accordingly, CWL tools are portable—they can be executed on diverse computers—including personal workstations, high-performance clusters, or the cloud. CWL also supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used …

Predicting Drug Sensitivity Of Cancer Cells Based On Dna Methylation Levels, Sofia P. Miranda, Fernanda A. Baião, Julia L. Fleck, Stephen R. Piccolo

Faculty Publications

Cancer cell lines, which are cell cultures derived from tumor samples, represent one of the least expensive and most studied preclinical models for drug development. Accurately predicting drug responses for a given cell line based on molecular features may help to optimize drug-development pipelines and explain mechanisms behind treatment responses. In this study, we focus on DNA methylation profiles as one type of molecular feature that is known to drive tumorigenesis and modulate treatment responses. Using genome-wide, DNA methylation profiles from 987 cell lines in the Genomics of Drug Sensitivity in Cancer database, we used machine-learning algorithms to evaluate the …

A Survey Of Compound Heterozygous Variants In Pediatric Cancers And Structural Birth Defects, Dustin B. Miller, Stephen R. Piccolo

Faculty Publications

Compound heterozygous (CH) variants occur when two recessive alleles are inherited and the variants are located at different loci within the same gene in a given individual. CH variants are important contributors to many different types of recessively inherited diseases. However, many studies overlook CH variants because identification of this type of variant requires knowing the parent of origin for each nucleotide. Using computational methods, haplotypes can be inferred using a process called “phasing,” which estimates the chromosomal origin of most nucleotides. In this paper, we used germline, phased, whole-genome sequencing (WGS) data to identify CH variants across seven pediatric …

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 …

Topsentinol L Trisulfate, A Marine Natural Product That Targets Basal-Like And Claudin-Low Breast Cancers, Nader N. El-Chaar, Thomas E. Smith, Gajendra Shrestha, Stephen R. Piccolo, Mary Kay Harper, Ryan M. Van Wagoner, Zhenyu Lu, Ashlee R. Venancio, Chris M. Ireland, Andrea H. Bild, Philip J. Moos

Faculty Publications

Patients diagnosed with basal-like breast cancer suffer from poor prognosis and limited treatment options. There is an urgent need to identify new targets that can benefit patients with basal-like and claudin-low (BL-CL) breast cancers. We screened fractions from our Marine Invertebrate Compound Library (MICL) to identify compounds that specifically target BL-CL breast cancers. We identified a previously unreported trisulfated sterol, i.e., topsentinol L trisulfate (TLT), which exhibited increased efficacy against BL-CL breast cancers relative to luminal/HER2+ breast cancer. Biochemical investigation of the effects of TLT on BL-CL cell lines revealed its ability to inhibit activation of AMP-activated protein kinase (AMPK) …

Testing The Effect Of Aquarium-Based Learning On Patron Acceptance Of Evolutionary Theory, Jamie Jensen, Ethan R. Tolman, Spencer G. Shumway, Liam S. Williams

ScholarsArchive Data

This is data collected prior to and directly following an intervention at a public aquarium in Idaho surrounding the reconciliation of evolution with religious audiences.

Using Structural Equation Modeling To Model Compliance With Covid-19 Related Non-Pharmaceutical Interventions Amongst University Students In The United States, Spencer G. Shumway, Jonas D. Hopper, Ethan R. Tolman, Daniel G. Ferguson, Gabriella Hubble, David Patterson, Jamie Jensen

ScholarsArchive Data

There are two data files. The "General Data" comes from a nationwide poll using Qualtrics polling software. The "Utah Data" comes from undergraduate biology students at UVU and BYU. The survey gathered demographic data and attitudes toward the COVID pandemic.

Classification Of Planetary Craters Using Outline-Based Morphometrics, Thomas J. Slezak, Jani Radebaugh, Eric H. Christiansen, Mark C. Belk

Faculty Publications

The morphologies of craters on planetary surfaces reveal clues about the geologic mechanisms by which they originate and subsequently evolve, as well as the materials and physical variables inherent to the environment in which they formed. We carried out a quantitative multivariate analysis of shape descriptors derived from the outlines of craters formed by volcanic processes on Mars, Io, and Earth and by impact cratering on the Moon using elliptic Fourier analysis (EFA) and the Zahn-Roskies (Z-R) shape function. Canonical variate analysis (CVA) was used to construct a statistical model of differences between the crater groups to classify …

Predators As Agents Of Selection And Diversification, Jerald B. Johnson, Mark C. Belk

Faculty Publications

Predation is ubiquitous in nature and can be an important component of both ecological and evolutionary interactions. One of the most striking features of predators is how often they cause evolutionary diversification in natural systems. Here, we review several ways that this can occur, exploring empirical evidence and suggesting promising areas for future work. We also introduce several papers recently accepted in Diversity that demonstrate just how important and varied predation can be as an agent of natural selection. We conclude that there is still much to be done in this field, especially in areas where multiple predator species prey …

Effects Of Germline And Somatic Events In Candidate Brca-Like Genes On Breast-Tumor Signatures, Weston R. Bodily, Brian H. Shirts, Tom Walsh, Suleyman Gulsuner, Mary-Claire King, Alyssa Parker, Moom Roosan, Stephen R. Piccolo

Faculty Publications

Mutations in BRCA1 and BRCA2 cause deficiencies in homologous recombination repair (HR), resulting in repair of DNA double-strand breaks by the alternative non-homologous end-joining pathway, which is more error prone. HR deficiency of breast tumors is important because it is associated with better responses to platinum salt therapies and PARP inhibitors. Among other consequences of HR deficiency are characteristic somatic-mutation signatures and gene-expression patterns. The term “BRCA-like” (or “BRCAness”) describes tumors that harbor an HR defect but have no detectable germline mutation in BRCA1 or BRCA2. A better understanding of the genes and molecular events associated with tumors being …

Predictors Of Psychosocial And Physiological Distress In Colorectal Cancer Patients, Hyrum Eddington

Undergraduate Honors Theses

Distress among cancer patients has been broadly accepted as an important indicator of patient well-being. However, questions remain such as what patient characteristics are associated with high distress and whether patient-reported distress is correlated with distress biomarkers. To answer these questions, we performed a survey study of 238 colorectal patients in which we assessed patient-reported distress, possible contributors to that distress, and patient anxiety and depression. We also abstracted demographic and clinical information from patient charts and collected measures for salivary cortisol and sarcopenia. We conducted bivariate statistical analyses between patient demographics, clinical factors, and psychosocial measures with our three …

Morphometric Response Of Galaxias Maculatus (Jenyns) To Lake Colonization In Chile, Margaret Mercer, Peter C. Searle, Roberto Cifuentes, Evelyn Habit, Mark C. Belk

Faculty Publications

Body and head shape in fish responds to environmental factors such as water flow rate, food sources, and niche availability. However, the way in which fish respond to these environmental factors varies. In Central Chile, multiple river and lake systems along the coast provide an ideal study site to investigate these types of shape changes. We use geometric morphometrics to characterize shape differences in Galaxias maculatus (Jenyns) between river and lake populations. Lake fish converge on a shape with a more fusiform body, narrower head, and larger eyes, while river fish have a more robust body, rounder head, and smaller …

Compound Heterozygous Variants In Pediatric Cancers: A Systematic Review, Dustin B. Miller, Stephen R. Piccolo

Faculty Publications

A compound heterozygous (CH) variant is a type of germline variant that occurs when each parent donates one alternate allele and these alleles are located at different loci within the same gene. Pathogenic germline variants have been identified for some pediatric cancer types but in most studies, CH variants are overlooked. Thus, the prevalence of pathogenic CH variants in most pediatric cancer types is unknown. We identified 26 studies (published between 1999 and 2019) that identified a CH variant in at least one pediatric cancer patient. These studies encompass 21 cancer types and have collectively identified 25 different …

Life History Divergence In Livebearing Fishes In Response To Predation: Is There A Microevolution To Macroevolution Barrier?, Mark C. Belk, Spencer J. Ingley, Jerald B. Johnson

Faculty Publications

A central problem in evolutionary biology is to determine whether adaptive phenotypic variation within species (microevolution) ultimately gives rise to new species (macroevolution). Predation environment can select for trait divergence among populations within species. The implied hypothesis is that the selection resulting from predation environment that creates population divergence within species would continue across the speciation boundary such that patterns of divergence after speciation would be a magnified accumulation of the trait variation observed before speciation. In this paper, we test for congruence in the mechanisms of microevolution and macroevolution by comparing the patterns of life history divergence among three …

Shinylearner: A Containerized Benchmarking Tool For Machine-Learning Classification Of Tabular Data, Stephen Piccolo, Terry J. Lee, Erica Suh, Kimball Hill

Faculty Publications

Background: Classification algorithms assign observations to groups based on patterns in data. The machine-learning community have developed myriad classification algorithms, which are used in diverse life science research domains. Algorithm choice can affect classification accuracy dramatically, so it is crucial that researchers optimize the choice of which algorithm(s) to apply in a given research domain on the basis of empirical evidence. In benchmark studies, multiple algorithms are applied to multiple datasets, and the researcher examines overall trends. In addition, the researcher may evaluate multiple hyperparameter combinations for each algorithm and use feature selection to reduce data dimensionality. Although software implementations …

A Brief Overview Of Burst Suppression: Causes And Effects On Mortality In Critical Illness, Jake Hogan, Haoqi Sun, Hassan Aboul Nour, Stephen Piccolo, Jacob Crandall, Steven Peck, M Brandon Westover

Undergraduate Honors Theses

This thesis examines the effects of brain inactivation (burst suppression) on mortality in mechanically ventilated ICU patients. Past research has associated burst suppression with increased mortality. However, the effects of burst suppression on ICU patients while taking into account the relative contributions of propofol (a sedative), and critical illness to mortality, and whether preventing burst suppression might reduce mortality, has not yet been quantified. This thesis explores this relationship, and the effect of critical illness and propofol infusion on burst suppression to understand what drives burst suppression.

To measure the relationship between burst suppression, critical illness, propofol infusion, and mortality, …

Does Negative Frequency-Dependent Selection Maintain Gonopodial Asymmetry In A Livebearing Fish?, Mary-Elise Johnson

Undergraduate Honors Theses

How genetic variation is maintained in the face of strong natural selection is an important problem in evolutionary biology. Selection should erode genetic diversity, leading to more and more homogeneous populations. Yet in nature, we commonly see high degrees of genetic variation, even for traits that are important to fitness. Negative frequency-dependent selection, a balancing selective force that favors traits when they are rare but not when they are common, is a mechanism proposed to maintain polymorphisms in a population. However, there is little empirical data to demonstrate how negative frequency-dependent selection sustains variation. Xenophallus umbratilis is a bilaterally symmetrical …

Functional And Transcriptomic Characterization Of Cisplatin-Resistant Ags And Mkn-28 Gastric Cancer Cell Lines, Barbara Mora-Lagos, Irene Cartas-Espinel, Ismael Riquelme, Alyssa C. Parker, Stephen R. Piccolo, Tamara Viscarra, Maria Elena Reyes, Louise Zanella, Kurt Buchegger, Carmen Ili, Priscilla Brebi

Faculty Publications

Gastric cancer (GC) is a significant cancer-related cause of death worldwide. The most used chemotherapeutic regimen in GC is based on platinum drugs such as cisplatin (CDDP). However, CDDP resistance reduces advanced GC survival. In vitro drug-resistant cell model would help in the understanding of molecular mechanisms underlying this drug-resistance phenomenon. The aim of this study was to characterize new models of CDDP-resistant GC cell lines (AGS R-CDDP and MKN-28 R-CDDP) obtained through a stepwise increasing drug doses method, in order to understand the molecular mechanisms underlying chemoresistance as well as identify new therapeutic targets for the treatment of GC. …

Diverse Approaches To Predicting Drug-Induced Liver Injury Using Gene-Expression Profiles, G. Rex Sumsion, Michael S. Bradshaw Iii, Jeremy T. Beales, Emi Ford, Griffin R. G. Caryotakis, Daniel J. Garrett, Emily D. Lebaron, Ifeanyichukwu O. Nwosu, Stephen R. Piccolo

Faculty Publications

Background

Drug-induced liver injury (DILI) is a serious concern during drug development and the treatment of human disease. The ability to accurately predict DILI risk could yield significant improvements in drug attrition rates during drug development, in drug withdrawal rates, and in treatment outcomes. In this paper, we outline our approach to predicting DILI risk using gene-expression data from Build 02 of the Connectivity Map (CMap) as part of the 2018 Critical Assessment of Massive Data Analysis CMap Drug Safety Challenge.

Results

First, we used seven classification algorithms independently to predict DILI based on gene-expression values for two cell lines. …

Transformation Of The Dental Faculty To Promote Changes In Dental Educaiton, Clark A. Dana

Theses and Dissertations

This work introduces a series of papers developed to explore the case for change in dental education. Three issues facing dental education are (a) the challenging financial environment of higher education, making dental schools very expensive and tuition-intensive for universities to operate and producing high debt levels for students, which limits access to education and restricts career choices; (b) the profession's apparent loss of vision for taking care of the oral health needs of all components of society and the resultant potential for marginalization of dentistry as a specialized health care service available only to the affluent; and (c) the …

Mechanism Of Positive, Non-Additive Litter Decomposition, Na Yin

Theses and Dissertations

Litter decomposition is a fundamental ecosystem process. It is responsible for nutrient cycling and influences carbon (C) sequestration, and soil physical and chemical properties. In nature, litter is usually heterogeneous and may not decompose the way homogeneous litter does. For example, heterogeneous litter decomposition is frequently non-additive. This makes the rate of nutrient cycling as well as fluxes of C into and out of soil C pools impossible to predict. The most frequently proposed mechanisms for positive, non-additive decomposition include the supply of limiting mineral nutrients, the supply of available C (priming), and the improvement of micro-environmental conditions. However, all …

Adversarial Deep Neural Networks Effectively Remove Nonlinear Batch Effects From Gene-Expression Data, Jonathan Bryan Dayton

Theses and Dissertations

Gene-expression profiling enables researchers to quantify transcription levels in cells, thus providing insight into functional mechanisms of diseases and other biological processes. However, because of the high dimensionality of these data and the sensitivity of measuring equipment, expression data often contains unwanted confounding effects that can skew analysis. For example, collecting data in multiple runs causes nontrivial differences in the data (known as batch effects), known covariates that are not of interest to the study may have strong effects, and there may be large systemic effects when integrating multiple expression datasets. Additionally, many of these confounding effects represent higher-order interactions …

Development Of Real-Time Polymerase Chain Reaction (Q-Pcr) Assays For The Detection And Identification Of Drug-Resistance Genes In Carbapenem-Resistant Enterobacteriaceae (Cre), Richard A. Robison, Ph.D.

Journal of Undergraduate Research

I. The Specific aims for the project were as follows:

1. Develop q-PCR assays for the various carbapenem-resistance genes, such as KPC, IMP, VIM, and NDM-1, and then multiplex them into single assays that can be used to quickly characterize an isolate.

A Race Against Time: Deciphering Evolution And Describing New Species Of Threatened Tropical Stick Insects (Phasmatodea), Michael F. Whiting

Journal of Undergraduate Research

Funding was received in 2016 to support mentored research into the phylogeny and evolution of stick insects. Specific goals include providing students with scientific design experience, field-based research experience, collections-based experience, molecular lab experience, bioinformatics experience, and experience in presentation at national meetings and publication in peer reviewed journals. One particular focus was to describe new stick insect species, but it became clear very quickly that the phylogeny portion of this work was essential before any new species could be described, so we concentrated our efforts on stick insect phylogeny. The following is a brief summary of accomplishments.

Byu Undergraduates Solving The Genetic Causes Of Alzheimer’S Disease, John Kauwe

Journal of Undergraduate Research

Successful enrollment in and completion of graduate programs requires a constellation of skills. Students must be prepared to plan and execute experiments, present their findings both verbally and in manuscript form and interact effectively with senior scientists in the field of their choice. In this MEG I will mentor three undergraduate students (Sheradyn Hamilton, Kristen Cockriel, and Moroni Chalita) as they develop skills in study design, data analysis, manuscript preparation, presentation and networking while identifying genetic factors that protect individuals from Alzheimer’s disease.