Digital Commons Network^™

White Shark Genome Reveals Ancient Elasmobranch Adaptations Associated With Wound Healing And The Maintenance Of Genome Stability, Nicholas J. Marra, Michael J. Stanhope, Nathaniel K. Jue, Minghui Wang, Qi Sun, Paulina D. Pavinski Bitar, Vincent P. Richards, Aleksey S. Komissarov, Mike Rayko, Sergey Kliver, Bryce J. Stanhope, Chuck Winkler, Stephen James O'Brien, Agostinho Antunes, Salvador Jorgensen, Mahmood S. Shivji

Biology Faculty Articles

The white shark (Carcharodon carcharias; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding important genome stability-related genes and functional categories, particularly so for the two elasmobranchs. We hypothesize that the molecular adaptive emphasis on genome stability …

Illumination Pattern Design With Deep Learning For Single-Shot Fourier Ptychographic Microscopy, Yi Fei Cheng , '21, Megan Strachan , '21, Zachary Weiss , '20, Moniher Deb , '19, Dawn M. Carone, Vidya Ganapati

Biology Faculty Works

Fourier ptychographic microscopy allows for the collection of images with a high space-bandwidth product at the cost of temporal resolution. In Fourier ptychographic microscopy, the light source of a conventional widefield microscope is replaced with a light-emitting diode (LED) matrix, and multiple images are collected with different LED illumination patterns. From these images, a higher-resolution image can be computationally reconstructed without sacrificing field-of-view. We use deep learning to achieve single-shot imaging without sacrificing the space-bandwidth product, reducing the acquisition time in Fourier ptychographic microscopy by a factor of 69. In our deep learning approach, a training dataset of high-resolution images …

Mrub_3020, A Paralog Of Mrub_1489, Is Orthologous To E. Coli Casc (Locus Tag B2761), Alfred Dei-Ampeh, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological functions of two genes: mrub_3020 and mrub_1489. We make two hypotheses in this investigation: a) mrub_3020 is orthologous to the gene b2761 in E. coli K12 MG1655 (a.k.a. casC); b) mrub_1489 is a paralog of mrub_3020. We also predict that the two genes encode unique proteins: mrub_3020 with DNA coordinates 3060491…3063190 encodes a CRISPR – associated helicase (Cas3) that supports the Cascade complex of the CRISPR – Cas adaptive immune system …

Comparative Analysis Of Four Dna Preparation Kits For Quercus Falcata, Palustris, And Rubra Dna Extractions And Subsequent Dna Sequencing, Devin Cummins, Timothy D. Trott

Research in Biology

In 2011, of the 8.7 million species of lif suspected to populate the globe only 1.2 million had been catalogued and it was estimated that 1,200 years would pass before the remainder were processed, allowing the possibility that some species would go extinct before they were even discovered (Mora, Tittensor, Adl, Simpson, & Worm, 2011). DNA barcoding may provide an answer to this problem. According to Hebert and Gregory, “DNA barcoding will accelerate the pace of species discovery by allowing taxonomists to rapidly sort specimens... by highlighting divergent taxa that may represent new species… and by making species identifications more …

The Effect Of Anthropogenic Environmental Modifications On Malaria Vectors In Amazonian Peru And Brazil, Catharine Prussing

Legacy Theses & Dissertations (2009 - 2024)

Malaria is the most deadly vector borne disease, causing substantial morbidity and hundreds of thousands of deaths worldwide each year. In the Americas, the incidence of malaria has increased steadily since 2014. The factors driving continued malaria transmission are complex and highly variable across endemic areas. These factors include inadequate access and financial commitment to prevention, diagnosis, and treatment, and a failure to target interventions to heterogeneous malaria transmission patterns and vector populations. Nyssorhynchus darlingi (formerly Anopheles darlingi), the predominant malaria vector in Latin America, is known for behavioral, phenotypic, and genetic variability across its range, which allow it to …

Role Of Daxx As A Predictive Biomarker In Breast Cancer, Michelle Lucia Fernandez

Master's Theses

Breast cancer is the most commonly diagnosed form of cancer in women, besides skin cancer, and second only to lung cancer for cause of mortality. It is divided into three subtypes, depending on different molecular or pathologic characteristics, including estrogen or progesterone receptor-positive (ER/PR+), human epidermal growth factor receptor-2-positive (HER2+) and triple negative breast cancer (TNBC). There are several therapies used to target these subtypes, but there is still a chance that the cancer will recur into a more aggressive, resistant form even if the therapies were successful before. This recurrence is believed to be due to the Cancer Stem …

Despite Similar Perceptions And Attitudes, Postbaccalaureate Students Outperform In Introductory Biology And Chemistry Courses, Erin E. Shortlidge, Liz Rain-Griffith, Chloe Shelby, Gwen Shusterman, Jack Barbera

Biology Faculty Publications and Presentations

Embedding active learning is a common mechanism for meeting science, technology, engineering, and mathematics (STEM) education reform goals. Researchers have identified student benefits from such strategies, yet these benefits may not be universal for all students. We sought to identify how students at a nontraditional university perceive introductory biology and chemistry courses, and whether perceptions relate to course type, performance, or student status. We surveyed students (n = 601) using open-ended prompts regarding their perceptions of factors that impact their learning and interest, and about specific learning strategies. Generally, students did not differ in what influenced their learning or …

Distinct Proteostasis Circuits Cooperate In Nuclear And Cytoplasmic Protein Quality Control, Rahul S. Samant, Christine M. Livingston, Emily M. Sontag, Judith Frydman

Biological Sciences Faculty Research and Publications

Protein misfolding is linked to a wide array of human disorders, including Alzheimer’s disease, Parkinson’s disease and type II diabetes^1,2. Protective cellular protein quality control (PQC) mechanisms have evolved to selectively recognize misfolded proteins and limit their toxic effects^{3,4,5,6,7,8,9}, thus contributing to the maintenance of the proteome (proteostasis). Here we examine how molecular chaperones and the ubiquitin–proteasome system cooperate to recognize and promote the clearance of soluble misfolded proteins. Using a panel of PQC substrates with distinct characteristics and localizations, we define distinct chaperone and ubiquitination circuitries that execute quality control in the cytoplasm and nucleus. …

Interferon Priming Is Essential For Human Cd34+ Cell-Derived Plasmacytoid Dendritic Cell Maturation And Function, A. Lausten, R. O. Bak, C. Krapp, L. Kjær, J. H. Egedahl, C. C. Petersen, S. Pillai, H. Q. Tang, N. Uldbjerg, M. Porteus, N. R. Roan, M. Nyegaard, Paul W. Denton, M. R. Jakobsen

Biology Faculty Publications

Plasmacytoid dendritic cells (pDC) are essential for immune competence. Here we show that pDC precursor differentiated from human CD34+ hematopoietic stem and progenitor cells (HSPC) has low surface expression of pDC markers, and has limited induction of type I interferon (IFN) and IL-6 upon TLR7 and TLR9 agonists treatment; by contrast, cGAS or RIG-I agonists-mediated activation is not altered. Importantly, after priming with type I and II IFN, these precursor pDCs attain a phenotype and functional activity similar to that of peripheral blood-derived pDCs. Data from CRISPR/Cas9-mediated genome editing of HSPCs further show that HSPC-pDCs with genetic modifications can be …

Environmental Factors Influencing Amphibian Community Assemblage In Dune Wetlands On The Lake Michigan Coast, Alex H. Jouney

Masters Theses

Wetlands in dune landscapes provide important breeding habitat for amphibians along the Lake Michigan Coast. Unfortunately, these unique habitats and the corresponding amphibian metapopulations are understudied and threatened. We assessed amphibian species richness and terrestrial habitat type in 16 permanent and ephemeral wetlands along the coast of Lake Michigan in Grand Haven, MI. Wetland area, terrestrial habitat type, depth, hydroperiod, shade, and degree of isolation were measured from April to September of 2017. Nine species of amphibian were found; Green Frog (Rana clamitans melanota) and Spring Peepers (Pseudacris crucifer crucifer) were most abundant and Fowlers Toad …

Directly Light-Regulated Binding Of Rgs-Lov Photoreceptors To Anionic Membrane Phospholipids, Spencer T. Glantz, Erin E. Berlew, Zaynab Jaber, Benjamin S. Schuster, Kevin H. Gardner, Brian Y. Chow

Publications and Research

We report natural light–oxygen–voltage (LOV) photoreceptors with a blue light-switched, high-affinity (KD ∼ 10−7 M), and direct electrostatic interaction with anionic phospholipids. Membrane localization of one such photoreceptor, BcLOV4 from Botrytis cinerea, is directly coupled to its flavin photocycle, and is mediated by a polybasic amphipathic helixinthelinker regionbetween the LOV sensor and its C-terminal domain of unknown function (DUF), as revealed through a combination of bioinformatics, computational protein modeling, structure–function studies, and optogenetic assays in yeast and mammalian cell line expression systems. In model systems, BcLOV4 rapidly translocates from the cytosol to plasma membrane (∼1 second). The reversible electrostatic interaction …

Biosemiotics As An Argument For The Recontextualization Of Biological Discoveries: A Critical Analysis Of The Biosemiotic Model Of Marcello Barbieri., Augustus Morrissey Snyder

Senior Honors Projects, 2010-2019

The primary purpose of this project was to investigate and explain the philosophical approach of biosemiotics to understanding living systems in contrast to the current scientific paradigm. Secondary goals were to evaluate the potential merits and relevance of this approach to biology and to introduce such a topic for discussion to biologists in a formal academic setting. My method consisted of critical textual analysis supplemented by analogy and biological examples where appropriate. In general, contemporary biosemiotics argues for a teleologic recontextualization of biological discoveries in practice and education. This is accomplished in a sophisticated fashion through the application and modification …

3d Bioprinting Systems For The Study Of Mammary Development And Tumorigenesis, John Reid

Electrical & Computer Engineering Theses & Dissertations

Understanding the microenvironmental factors that control cell function, differentiation, and stem cell renewal represent the forefront of developmental and cancer biology. To accurately recreate and model these dynamic interactions in vitro requires both precision-controlled deposition of multiple cell types and well-defined three-dimensional (3D) extracellular matrix (ECM). To achieve this goal, we hypothesized that accessible bioprinting technology would eliminate the experimental inconsistency and random cell-organoid formation associated with manual cell-matrix embedding techniques commonly used for 3D, in vitro cell cultures. The first objective of this study was to adapt a commercially-available, 3D printer into a 3D bioprinter. Goal-based computer simulations were …

Identification Of Qtl Modifying The Activity Of The Tcb1-S Locus And Characterization And Sequencing Of Two Plutonium-Beryllium Induced Reduced Gametophyte Transmission Mutants In Maize, Merritt Bryer Burch

Electronic Theses and Dissertations

This thesis is split into two independent projects both involving the male gametophyte generation of maize. The first project looks at how pollen interacts with the female gametophyte to reduce its transmission in cross-incompatible reactions controlled by the unilateral cross-incompatibility system, teosinte crossing barrier 1. The second project explores two plutonium-beryllium induced male gametophyte mutants and attempts to uncover their genetic basis.

Identification of QTL Modifying the Activity of the Tcb1-s Locus
Teosinte crossing barrier 1 (Tcb1) is a unilateral cross-incompatibility system present in maize that provides a pre-zygotic pistil barrier to plants carrying Tcb1-s (strong allele) from pollen …

Community Structure And Epizootic Infection Prevalence Of Northern Wisconsin Anurans, Kayla Christine Watters

Browse all Theses and Dissertations

Amphibian populations are declining globally at historically rapid rates, and while a multitude of factors have contributed to amphibian population declines, emerging infectious diseases, such as chytridiomycosis and ranavirus have been linked to a large proportion of the reported amphibian mass mortality events. Distribution and infection prevalence data for chytridiomycosis and ranavirus are lacking, and effective surveillance is crucial. This project aims to describe anuran richness, relative abundance, habitat occupancy, and community structure and to identify the chytridiomycosis and ranavirus infection prevalence rates of the anuran population at Dairymen's Inc. Wood frogs, spring peepers, boreal chorus frogs, northern leopard frogs, …

The Effects Of Temperature On Batrachochytrium Dendrobatidis Resistance And Heart Rate In The Polymorphic Eastern Red-Backed Salamanders, Plethodon Cinereus, Joseph Alan Demarchi

Masters Theses

No abstract provided.

Cytoprotective Effect Of A Functional Antipollutant Blend Through Reducing B[A] P-Induced Intracellular Oxidative Stress And Uva Exposure, Gi̇zem Örs, Sultan Gülçe İz

Turkish Journal of Biology

Benzo[a]pyrene (B[a]P) is a ubiquitous environmental pollutant that reacts with skin and induces intracellular oxidative stress through reactive oxygen species (ROS) accumulation. The antipollution properties of natural extracts, especially including antioxidants, for inhibiting ROS in cells are gaining importance, in addition to the anticancer effects attributed to them. In this study, a commercial functional antipollutant blend of plant extracts consisting of ellagic acid standardized Punica granatum peel extract, Sambucus nigra fruit extract, Prunus cerasus seed extract, and hydrolyzed wheat protein with high antioxidant properties and UV damage-protective properties attributed to each one was investigated. The cytoprotective effect of this functional …

Hidden Diversity In Aquatic Habitats: Lessons From Cryptic Species In Microscopic Invertebrates (Rotifera), Azar Kordbacheh

Open Access Theses & Dissertations

Speciation is a continuous and adaptive process by which lineages are diverged into multiple groups, and species are the product of this process. Taxonomy is the study of relationship between organisms, classifying and naming them, and one of the taxonomical challenges is delimiting species boundaries. Species delimitation can be controversial because biologists do not agree on species concepts and approaches for defining species boundaries. One of the well-known species concepts is the Biological Species Concept that requires studying reproductive barriers among populations. Investigating strength of reproductive isolation among populations is not always practical in the wild. Therefore, many biologists have …

Many Paths Toward Discovery: A Module For Teaching How Science Works, Rebecca M. Price, Kathryn E. Perez

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Improving students' understanding of how science works requires explicit instruction. Here, we test the efficacy of a module based on two previously published activities (the "Cube Puzzle" and the case study "Asteroids and Dinosaurs") that teach how science works to college science majors. Students also use the How Science Works Flowchart from Understanding Science (http://undsci.berkeley. edu/) to reflect on these activities. To assess the efficacy of this module, we asked students to illustrate the process of science before and after the intervention. After the intervention, students' diagrams were significantly more complex and nonlinear. Students also incorporated more social aspects of …

Gene Coexpression Network Analysis Of Fruit Transcriptomes Uncovers A Possible Mechanistically Distinct Class Of Sugar/Acid Ratio-Associated Genes In Sweet Orange, Liang Qiao, Minghao Cao, Jian Zheng, Yihong Zhao, Zhi-Liang Zheng

Publications and Research

Background: The ratio of sugars to organic acids, two of the major metabolites in fleshy fruits, has been considered the most important contributor to fruit sweetness. Although accumulation of sugars and acids have been extensively studied, whether plants evolve a mechanism to maintain, sense or respond to the fruit sugar/acid ratio remains a mystery. In a prior study, we used an integrated systems biology tool to identify a group of 39 acid-associated genes from the fruit transcriptomes in four sweet orange varieties (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal …

Specificity Determination By Paralogous Winged Helix-Turn-Helix Transcription Factors, Adam Joyce

Arts & Sciences Graduate Student Theses and Dissertations

Transcription factors (TFs) localize to regulatory regions throughout the genome, where they exert physical or enzymatic control over the transcriptional machinery and regulate expression of target genes. Despite the substantial diversity of TFs found across all kingdoms of life, most belong to a relatively small number of structural families characterized by homologous DNA-binding domains (DBDs). In homologous DBDs, highly-conserved DNA-contacting residues define a characteristic ‘recognition potential’, or the limited sequence space containing high-affinity binding sites. Specificity-determining residues (SDRs) alter DNA binding preferences to further delineate this sequence space between homologous TFs, enabling functional divergence through the recognition of distinct genomic …

How Do Former Undergraduate Mentors Evaluate Their Mentoring Experience 3-Years Post-Mentoring: A Phenomenological Study, Kari L. Nelson, Christine E. Cutucache

The Qualitative Report

This phenomenological study involves a unique, longitudinal assessment of the lived experiences of former undergraduate mentors (n=7) in light of their current experiences (i.e., career or advanced schooling). The objective of a phenomenological study is to engage in in-depth probing of a representative number of participants. Specifically, we followed up with graduates of the Nebraska STEM 4U (NE STEM 4U) intervention 3 years post-program, with the overall goal of describing the mentors’ experiences using the lens of their current experiences. This type of longitudinal perspective of mentoring is greatly lacking in the current literature. At the time of the interviews, …

A Global Community Effort To Decipher The Unique Biology Of Annual Killifish, Nibia Berois, Graciela Garcia, Rafael O. De Sá

Biology Faculty Publications

Over the past 50 years, annual killifishes arose as alternative model organisms for studies of vertebrate biology. The annual fish offers exceptional advantages for studies of genetics, genomics, developmental biology, population dynamics, ecology, biogeography, and evolution. They inhabit extremely variable freshwater environments in Africa and South America, have a short lifespan and a set of unique and fascinating developmental characteristics. Embryos survive within the dry substrate during the dry season, whereas the adult population dies. Thus, the survival of the populations is entirely dependent on the buried embryos that hatch the next rainy season. Although Old and New World species …

Biophysical Studies Of The Intracellular Domains Of The Egfr Family Of Receptor Tyrosine Kinases, Kwabena A N Sarpong

Arts & Sciences Graduate Student Theses and Dissertations

The epidermal growth factor receptor and its three orthologues, HER2, HER3 and HER4 have been the subject of intensive basic, clinical and translational research due to their involvement in cancers. These proteins are part of elaborate networks that interact with a myriad of other molecules to effect diverse signaling pathways and affect cellular processes such as migration, apoptosis, cell differentiation and so on. In addition to the formation of preformed dimers, it is well established that ligand engagement leads to receptor dimerization in all family members, except HER2. In the past decade, it has been shown that their intracellular domains …

The Role Of The Diras Family Members In Regulating Ras Function, Cancer Growth And Autophagy, Margie Nicole Sutton

Dissertations and Theses (Open Access)

DIRAS3 is a maternally imprinted tumor suppressor gene that is downregulated by multiple mechanisms across several tumor types. When re-expressed, DIRAS3 decreases proliferation, inhibits motility, and induces autophagy and tumor dormancy. DIRAS3 encodes a 26 kDa small GTPase with 60% homology to Ras and Rap, differing from oncogenic Ras family members by a 34-amino acid N-terminal extension that is required for its tumor suppressive function in ovarian cancer. By assessing the structure-function relationship, I found that DIRAS3 inhibits Ras-induced transformation and is a natural antagonist of Ras/MAPK signaling. DIRAS3 binds directly to Ras and disrupts cluster formation inhibiting the activation …

Pore Water Salinity Drives Brackish Vegetation Change In Salt Marsh Tidal Restoration, Shri Andrea L. Verrill Ms

All Student Scholarship

Salt marsh vegetation plays an important role in building and maintaining elevation on the marsh surface. For marshes to persist as sea-level-rise (SLR) occurs, the marsh accretion process must increase elevation at a rate greater than or equal to the rate of SLR. If salt marshes do not maintain elevation above sea level, salt marshes will drown, and associated benefits to humans, fish, and wildlife, and their contribution to the health of estuarine and marine ecosystems will be lost. Salt tolerant plant species are adapted to frequent and prolonged periods of inundation with seawater and typically maintain elevation where they …

Bio Buzz Newsletter, Issue 5.2, May 2012, Department Of Biology

Biology Buzz Newsletter

Denison University, Department of Biology newsletter for Spring 2012.

The Hidden History Of Humming Frogs, Rafael O. De Sá

Biology Faculty Publications

In the depths of Brazil’s Atlantic Forest, researchers are battling to identify species before they are lost for good. Dr Rafael O de Sá, Professor of Biology at the University of Richmond, Virginia, USA, specialises in a group known as the ‘narrow-mouthed frogs’ and has already found four species new to science.

How Do Former Undergraduate Mentors Evaluate Their Mentoring Experience 3-Years Post-Mentoring: A Phenomenological Study, Kari L. Nelson, Christine E. Cutucache

Biology Faculty Publications

This phenomenological study involves a unique, longitudinal assessment of the lived experiences of former undergraduate mentors (n=7) in light of their current experiences (i.e., career or advanced schooling). The objective of a phenomenological study is to engage in in-depth probing of a representative number of participants. Specifically, we followed up with graduates of the Nebraska STEM 4U (NE STEM 4U) intervention 3 years post-program, with the overall goal of describing the mentors’ experiences using the lens of their current experiences. This type of longitudinal perspective of mentoring is greatly lacking in the current literature. At the time of the interviews, …

Expression Of Fam171b Protein In Mouse Brain Tissue, Quan Tran

All Graduate Theses, Dissertations, and Other Capstone Projects

Polyglutamine (polyQ) diseases are inherited fatal neurodegenerative disorders caused by expansion of trinucleotide cytosine-adenine-guanine (CAG) repeats, encoding abnormally long glutamine tracts in respective disease proteins. Currently, there are nine polyQ diseases- including Huntington’s disease and a number of Spinocerebellar ataxias. Interestingly, expanded polyQ proteins are prone to aggregate, and this aggregation may underlie neurodegeneration. In this study, we investigate the expression and localization of FAM171B (a novel polyQ protein) in the brain. Western blotting reveals that FAM171B protein is indeed expressed in the developing and adult mouse brain. Furthermore, immunohistochemical analyses suggests widespread localization of FAM171B to many brain regions …