Biology Commons^™

Streamlined Preparation Of Genomic Dna In Agarose Plugs For Pulsed-Field Gel Electrophoresis, Linda D. Hicks, Charlotte M. Van Der Graaf, Jacob Childress, Emily Cook, Karen Schmidt, Frank Rosenzweig, Eugene Kroll

Biological Sciences Faculty Publications

Genome analysis using pulsed-field gel electrophoresis (PFGE) has been used in applications ranging from typing bacterial strains to radiobiology to cancer research. While methods for running PFGE have been significantly improved since its invention, the method for preparing chromosomal DNA itself has remained essentially unchanged. This limits the applicability of PFGE, especially when analyses require many samples. We have streamlined sample preparation for routine applications of PFGE through the use of deep-well 48-well plates. Besides saving time, our protocol has the added advantage of reducing the volume of expensive reagents. Our improved protocol enables us to reduce throughput time and …

Planarian Cholinesterase: Molecular And Functional Characterization Of An Evolutionarily Ancient Enzyme To Study Organophosphorus Pesticide Toxicity, D. Hagstrom, S. Zhang, A. Ho, E. S. Tsai, Z. Radić, A. Jahromi, K. J. Kaj, Y. He, P. Taylor, Eva-Maria S. Collins

Biology Faculty Works

The asexual freshwater planarian Dugesia japonica has emerged as a medium-throughput alternative animal model for neurotoxicology. We have previously shown that D. japonica are sensitive to organophosphorus pesticides (OPs) and characterized the in vitro inhibition profile of planarian cholinesterase (DjChE) activity using irreversible and reversible inhibitors. We found that DjChE has intermediate features of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). Here, we identify two candidate genes (Djche1 and Djche2) responsible for DjChE activity. Sequence alignment and structural homology modeling with representative vertebrate AChE and BChE sequences confirmed our structural predictions, and show that both DjChE enzymes have intermediate sized catalytic gorges …

Do Host‐Associated Gut Microbiota Mediate The Effect Of An Herbicide On Disease Risk In Frogs?, Sarah A. Knutie, Caitlin R. Gabor, Kevin D. Kohl, Jason R. Rohr

Integrative Biology Faculty and Staff Publications

1. Environmental stressors, such as pollutants, can increase disease risk in wildlife. For example, the herbicide atrazine affects host defences (e.g. resistance and tolerance) of the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), but the mechanisms for these associations are not entirely clear. Given that pollutants can alter the gut microbiota of hosts, which in turn can affect their health and immune systems, one potential mechanism by which pollutants could increase infection risk is by influencing host‐associated microbiota.
2. Here, we test whether early‐life exposure to the estimated environmental concentration (EEC; 200 μg/L) of atrazine affects the gut bacterial composition of …

Taxonomy Based On Science Is Necessary For Global Conservation, David Campbell

Department of Natural Sciences Faculty Publications

Taxonomy is a scientific discipline that has provided the universal naming and classification system of biodiversity for centuries and continues effectively to accommodate new knowledge. A recent publication by Garnett and Christidis [1] expressed concerns regarding the difficulty that taxonomic changes represent for conservation efforts and proposed the establishment of a system to govern taxonomic changes. Their proposal to “restrict the freedom of taxonomic action” through governing subcommittees that would “review taxonomic papers for compliance” and their assertion that “the scientific community’s failure to govern taxonomy threatens the effectiveness of global efforts to halt biodiversity loss, damages the …

Upregulation Of Coilin Mrna Upon Nopp140-/- In Drosophila Melanogaster., Sara Grace Hubacek

Honors Capstones

No abstract provided.

Digital Photography Provides A Fast, Reliable, And Noninvasive Method To Estimate Anthocyanin Pigment Concentration In Reproductive And Vegetative Plant Tissues, José C. Del Valle, Antonio Gallardo-López, Mª Luisa Buide, Justen B. Whittall, Eduardo Narbona

Biology

Anthocyanin pigments have become a model trait for evolutionary ecology as they often provide adaptive benefits for plants. Anthocyanins have been traditionally quantified biochemically or more recently using spectral reflectance. However, both methods require destructive sampling and can be labor intensive and challenging with small samples. Recent advances in digital photography and image processing make it the method of choice for measuring color in the wild. Here, we use digital images as a quick, noninvasive method to estimate relative anthocyanin concentrations in species exhibiting color variation. Using a consumer‐level digital camera and a free image processing toolbox, we extracted RGB …

Allele Frequencies Of 15 Str Loci (Identifiler™ Kit) In Basque-Americans, Jason Besecker, Gianluca Peri, Michael Davis, Josu Zubizarreta, Greg Hampikian

Biology Faculty Publications and Presentations

Individuals with Basque ancestry form a historically and culturally important minority of the population of the western United States. Allele frequencies for the 15 autosomal STRs in the AmpFlSTR^® Identifiler^® PCR Amplification Kit (Applied Biosystems) from 156 unrelated self-identified Basque individuals born in the United States are presented. Allele frequencies were used to calculate parameters commonly used in genetics and forensics including power of discrimination (PD), power of exclusion (PE), polymorphic information content (PIC), and expected heterozygosity (He). The sample population was also compared with the European Basque population and the major American ethnicities.

Functional Traits Of Tropical Trees And Lianas Explain Spatial Structure Across Multiple Scales, Adam Thomas Clark, Nattei Detto, Helene C. Muller-Laudau, Stefan A. Schnitzer, S. Joseph Wright, Richard Condit, Stephen P. Hubbell

Biological Sciences Faculty Research and Publications

1. Dispersal and density dependence are major determinants of spatial structure, population dynamics and coexistence for tropical forest plants. However, because these two processes can jointly influence spatial structure at similar scales, analysing spatial patterns to separate and quantify them is often difficult.
2. Species functional traits can be useful indicators of dispersal and density dependence. However, few methods exist for linking functional traits to quantitative estimates of these processes that can be compared across multiple species.
3. We analysed static spatial patterns of woody plant populations in the 50 ha Forest Dynamics Plot on Barro Colorado Island, Panama with methods that distinguished …

Lianas Reduce Community-Level Canopy Tree Reproduction In A Panamanian Forest, Maria M. Garcia Leon, Laura Martinez Izquierdo, Filipe Niery Arantes Mello, Jennifer S. Powers, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

1. Lianas are a key component of tropical forests, where they compete intensely with trees, reducing tree recruitment, growth and survival. One of the most important potential outcomes of liana competition is the reduction of tree reproduction; however, no previous study has experimentally determined the effects of lianas on tree reproduction beyond a single tree species.
2. We used a large‐scale liana removal experiment to quantify the effect of lianas on community‐level canopy and understorey tree and palm reproduction. In 2011, we removed lianas from eight 6,400‐m² plots (eight plots served as controls) and surveyed understorey tree reproduction in 2012, canopy …

Tree Species Vary Widely In Their Tolerance For Liana Infestation: A Case Study Of Differential Host Response To Generalist Parasites, Marco D. Visser, Stefan A. Schnitzer, Helene C. Muller-Laudau, Eelke Jongejans, Hans De Kroon, Liza S. Comita, Stephen P. Hubbell, S. Joseph Wright

Biological Sciences Faculty Research and Publications

1. Lianas are structural parasites of trees and reduce individual host tree growth, survival and fecundity. Thus, liana infestation is expected to affect tree population growth rates, with potentially different effects in different species depending on the frequency of liana infestation and the impact of liana infestation on population growth rates. Previous studies have documented the myriad negative effects of lianas on trees and variation in liana infestation among tree species; however, no study has quantified the impact of liana infestation on individual tree species population growth rates. Lianas are increasing in abundance in multiple Neotropical sites, which may have profound …

Does Soil Moisture Availability Explain Liana Seedling Distribution Across A Tropical Rainfall Gradient?, Eric Manzane-Pinzon, Guillermo Goldstein, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Liana density tends to increase with decreasing rainfall and increasing seasonality. However, the pattern of liana distribution may be due to differences in soil water retention capacity, not rainfall and seasonality per se. We tested the effect of rainfall and soil substrate with respect to the distribution of liana seedlings in six sites across a rainfall gradient from the wet Atlantic to the dry Pacific in central Panama. Soils were either limestone, with low water-holding capacity, or laterite, with higher water-holding capacity. We sampled liana seedlings at each site using three 1 × 100 m transect. We found that …

Ten Simple Rules For Collaborative Lesson Development, Gabriel A. Devenyi, Remi Emonet, Rayna M. Harris, Kate L. Hertweck, Damien Irving, Ian Milligan, Greg Wilson

Biology Faculty Publications and Presentations

Lessons take significant effort to build and even more to maintain. Most academics do this work on their own, but leveraging a community approach can make educational resource development more sustainable, robust, and responsive. Treating lessons as a community resource to be updated, adapted, and improved incrementally can free up valuable time while increasing quality.

Genetic Diversity And Distinctness Of Wild Nebraska Hops And Hop Cultivars (Humulus Lupulus L.), Megan Franklin

Honors Program: Senior Projects (Public)

Background Commercial hop (Humulus lupulus) cultivars that are being grown in the Midwest are not performing as successfully as when they are grown in the Pacific Northwest, the region to which they are adapted. To increase adaptation to the Midwest environment, one strategy is to draw from the genetic pool of wild native Midwest hops, which have developed genes that allow them to grow successfully in this environment. Wild hop plants that are genetically distinct from commercial cultivars are likely to have more adaptations, such as pest/disease resistance and drought tolerance, which can be bred into commercial lines. The …

Life Line March 2018, Otterbein Biology And Earth Science Department

Life Line - The Biology Department Newsletter

Welcome Andrew Calinger-Yoak - Outdoor Laboratory - Conservation Biology - Safari in South Africa - Chengdu Panda Base - Mussells

Molecular Evolution Of Odonata Opsins, Odonata Phylogenomics And Detection Of False Positive Sequence Homology Using Machine Learning, Anton Suvorov

Theses and Dissertations

My dissertation comprises three related topics of evolutionary and computational biology, which correspond to the three Chapters. Chapter 1 focuses on tempo and mode of evolution in visual genes, namely opsins, via duplication events and subsequent molecular adaptation in Odonata (dragonflies and damselflies). Gene duplication plays a central role in adaptation to novel environments by providing new genetic material for functional divergence and evolution of biological complexity. Odonata have the largest opsin repertoire of any insect currently known. In particular our results suggest that both the blue sensitive (BS) and long-wave sensitive (LWS) opsin classes were subjected to strong positive …

Communicating Discovery-Based Research Results To The News: A Real-World Lesson In Science Communication For Undergraduate Students, Julie Torruellas Garcia

Biology Faculty Articles

Communicating science effectively to the general public is a necessary skill that takes practice. Generally, undergraduate science majors are taught to communicate to other scientists but are not given formal training on how to communicate with a nonscientist. An opportunity to appear on a news segment can be used as a real-world lesson on science communication for your students. This article will describe how to contact a producer to get your class on a news segment, ideas for types of research that may be of interest to the media, and how to practice communicating the results effectively.

Group B Streptococcus Activates Transcriptomic Pathways Related To Premature Birth In Human Extraplacental Membranes In Vitro, Hae Ryung Park, Sean M. Harris, Erica Boldenow, Richard C. Mceachin

University Faculty Publications and Creative Works

Streptococcus agalactiae (group B streptococcus [GBS]) infection in pregnant women is the leading cause of infectious neonatal morbidity and mortality in the United States. Although inflammation during infection has been associated with preterm birth, the contribution of GBS to preterm birth is less certain. Moreover, the early mechanisms by which GBS interacts with the gestational tissue to affect adverse pregnancy outcomes are poorly understood. We hypothesized that short-term GBS inoculation activates pathways related to inflammation and premature birth in human extraplacental membranes. We tested this hypothesis using GBS-inoculated human extraplacental membranes in vitro. In agreement with our hypothesis, a microarray-based …

Monitoring Of Dung Beetle (Scarabaeidae And Geotrupidae) Activity Along Maryland's Coastal Plain, Patrick Simons, Michael Molina, Mallory A. Hagadorn, Dana L. Price

Biology Faculty Publications

Our understanding of how human activities impact insect communities is limited. Dung beetles, well known for the ecosystem services they provide, are faced with many conservation threats, particularly from deforestation and agriculture. Here we used 200-m transects and human-dung—baited pitfall traps to examine dung beetle populations in 7 forests of Maryland's Coastal Plain. We set traps once a month, from May 2014 to April 2015, to determine species presence, abundance, range, and seasonality. We collected 6463 individuals representing 22 species; Janes Island State Park (JISP) had the highest abundance (2705 individuals) and Martinak State Park (MSP) had the highest species …

Unintended Consequences For Tanf: An Incubator For Domestic Violence?, Kathryn Rose Deleo

Honors Capstones

No abstract provided.

Introducing The Jmbe Themed Issue On Science Communication, Dennis F. Mangan, Emily T. Cloyd, Jesus A. Romo, David R. Wessner, David J. Westenberg, For Full List Of Authors, See Publisher's Website.

Biological Sciences Faculty Research & Creative Works

No abstract provided.

A Protocol For Custom Crispr Cas9 Donor Vector Construction To Truncate Genes In Mammalian Cells Using Pcdna3 Backbone, Neftali Vasquez, Lilia Sanchez, Rebecca Marks, Eduardo Martinez, Victor Fanniel, Alma Lopez, Andrea Salinas, Itzel Flores, Jesse Hirshmann, Robert Gilkerson, Erin Schuenzel, Robert Dearth, Wendy Innis-Whitehouse, Megan Keniry

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

Background: Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided adaptive immune systems are found in prokaryotes to defend cells from foreign DNA. CRISPR Cas9 systems have been modified and employed as genome editing tools in wide ranging organisms. Here, we provide a detailed protocol to truncate genes in mammalian cells using CRISPR Cas9 editing. We describe custom donor vector construction using Gibson assembly with the commonly utilized pcDNA3 vector as the backbone.

Results: We describe a step-by-step method to truncate genes of interest in mammalian cell lines using custom-made donor vectors. Our method employs 2 guide RNAs, mutant Cas9D10A nickase …

Population Dynamics Of Off-Host Rhipicephalus (Boophilus) Microplus (Acari: Ixodidae) Larvae In Response To Habitat And Seasonality In South Texas, Brenda Leal, Donald B. Thomas, Robert K. Dearth

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

The cattle tick, Rhipicephalus microplus (Canestrini), is an economically destructive arthropod because of its ability to vector bovine babesiosis. It is known that cattle ticks can spend 80–90% of their lifecycle as questing larvae, yet the effect of climatic factors on their off-host behavior and survival is unclear. The goal of this study was to measure the effects of specific ecological factors on off-host questing larvae in nature. The study was conducted in a south Texas pasture over a two-year period, during which time larval populations were surveyed. Simultaneously, weather variables—precipitation, relative humidity, and ambient temperatures—were recorded. Larval survival rates …

Winter Site Fidelity Of Orange-Crowned Warblers (Oreothlypis Celata) In The Lower Rio Grande Valley Of Texas, Mark H. Conway, Timothy Brush

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

Abstract—We documented between-winter site fidelity of orange-crowned warblers (Oreothlypis celata) in the Lower Rio Grande Valley of Texas, between 2004 and 2017. Overall, we recaptured 13.9% of the 201 banded birds in ‡1 subsequent winter season: 20.8% of the 101 birds banded in urban natural areas, and 7.0% of the 100 banded in rural areas. We recaptured 8 birds ‡3 winters after their initial capture, indicating extended winter site fidelity.

Resumen—Documentamos la fidelidad al sitio invernal de los chipes olivaceos (Oreothlypis celata) en el Valle del R´ıo Grande Baja de Texas entre 2004 y 2017. En general, se …

Efficacy Evaluation Of Six Entomopathogenic Nematode Species Against Engorged Females Of Southern Cattle Fever Tick, Rhipicephalus (=Boophilus) Microplus, N. K. Singh, John A. Goolsby, David I. Shapiro-Ilan, R. J. Miller, D. B. Thomas, Guilherme M. Klafke, Jason Tidwell, Alexis Racelis, Parwinder Grewal, Adalberto A. Perez De Leon

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

The southern cattle fever tick, Rhipicephalus microplus Canestrini, is widely distributed in tropical and subtropical regions, causing huge economic losses to milk and meat production. Application of acaricides is the most widely used control strategy, but because of increasing evidence of resistance to acaricide and environmental concerns, novel strategies are needed. Use of entomopathogenic nematodes is a promising alternative for tick control. Six species of nematodes, Steinernema riobrave Cabanillas, Poinar, and Raulston (355 strain), S. carpocapsae (Weiser) (All strain), S. feltiae Filipjev (SN strain), Heterorhabditis bacteriophora Poinar (VS strain), H. indica Poinar, Karunakar, and David (HOM1 strain), and H. floridensis …

Draft Genome Sequence Of A Dictyoglomus Sp. From An Enrichment Culture Of A New Zealand Geothermal Spring, Anna-Louise Reysenbach, John A. Donaho, John F. Kelley, Emily St. John, Christina Turner, Mircea Podar, Matthew B. Stott

Biology Faculty Publications and Presentations

A draft genome of a novel Dictyoglomus sp., NZ13-RE01, was obtained from a New Zealand hot spring enrichment culture. The 1,927,012-bp genome is similar in both size and G+C content to other Dictyoglomus spp. Like its relatives, Dictyoglomus sp. NZ13-RE01 encodes many genes involved in complex carbohydrate metabolism.

Graduate Certificate In Aquaculture And Fisheries, Joanna Burkhardt

Library Impact Statements

No abstract provided.

Combinations Of Plant Water-Stress And Neonicotinoids Can Lead To Secondary Outbreaks Of Banks Grass Mite (Oligonychus Pratensis Banks), Alice Ruckert, L. Niel Allen, Ricardo A. Ramirez

Civil and Environmental Engineering Faculty Publications

Spider mites, a cosmopolitan pest of agricultural and landscape plants, thrive under hot and dry conditions, which could become more frequent and extreme due to climate change. Recent work has shown that neonicotinoids, a widely used class of systemic insecticides that have come under scrutiny for non-target effects, can elevate spider mite populations. Both water-stress and neonicotinoids independently alter plant resistance against herbivores. Yet, the interaction between these two factors on spider mites is unclear, particularly for Banks grass mite (Oligonychus pratensis; BGM). We conducted a field study to examine the effects of water-stress (optimal irrigation = 100% …

Market Integration Predicts Human Gut Microbiome Attributes Across A Gradient Of Economic Development, Keaton Stagaman, Tara J. Cepon-Robins, Melissa A. Liebert, Theresa E. Gildner, Samuel S. Urlacher, Felicia C. Madimenos, Karen Guillemin, J. Josh Snodgrass, Lawrence S. Sugiyama, Brendan J. M. Bohannan

Publications and Research

Economic development is marked by dramatic increases in the incidence of microbiome-associated diseases, such as autoimmune diseases and metabolic syndromes, but the lifestyle changes that drive alterations in the human microbiome are not known. We measured market integration as a proxy for economically related lifestyle attributes, such as ownership of specific market goods that index degree of market integration and components of traditional and nontraditional (more modern) house structure and infrastructure, and profiled the fecal microbiomes of 213 participants from a contiguous, indigenous Ecuadorian population. Despite relatively modest differences in lifestyle across the population, greater economic development correlated with significantly …

Learning And Behavior In Hatchling Trachemys Scripta Exposed To Bisphenol-A During Embryonic Development, Justin E. Dillard

Theses and Dissertations

Steroids play an integral role in orchestrating embryonic development, and can affect a suite of phenotypic traits, including learning and memory. Endocrine disrupting compounds (EDCs) can mimic the effects of steroids and can affect the same suites of phenotypic traits during embryonic development. Bisphenol-A (BPA) is an EDC that mimics the action of estrogen, and recent work is beginning to implicate BPA in effects on learning and behavior similar to those caused by estrogen treatment studies. Red-eared slider turtles (Trachemys scripta) are a good system to investigate the effects of BPA on learning and behavior, both because the molecular underpinnings …

Skin Gland Concentrations Adapted To Different Evolutionary Pressures In The Head And Posterior Regions Of The Caecilian Siphonops Annulatus, Carlos Jared, Pedro Luiz Mailho-Fontana, Rafael Marques-Porto, Juliana Mozer Sciani, Daniel Carvalho Pimenta, Edmund D. Brodie Jr., Marta Maria Antoniazzi

Biology Faculty Publications

Amphibian skin is rich in mucous glands and poison glands, secreting substances important for gas exchange and playing a fundamental role in chemical defense against predators and microorganisms. In the caecilian Siphonops annulatus (Mikan, 1920) we observed a concentration of enlarged mucous glands in the head region. In the posterior region of the body a similar concentration is made up of enlarged poison glands. These accumulations of glands structurally resemble the macroglands previously reported in anurans and salamanders. The skin glands in these regions are each surrounded by collagen walls forming a honeycomb-like structure. The collagen network in the head …